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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/hyphy">Debian Med / hyphy</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/d8a6fecc5558ddf14f61e62f2bf14fe1a9ea9fff">d8a6fecc</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-22T20:14:27+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.5.20+dfsg</pre>
</li>
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<h4>25 changed files:</h4>
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<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
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<li class="file-stats">
<a href="#817efc81f1180519a6136b50a447433f20cf679d">
res/TemplateBatchFiles/SelectionAnalyses/FEL.bf
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<li class="file-stats">
<a href="#bc98d7300147ce39ef8ee0f9b35f3252bebd01d2">
res/TemplateBatchFiles/SelectionAnalyses/MEME.bf
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<li class="file-stats">
<a href="#13df3044c13d443b9b6ad8712b47d3bc84725272">
res/TemplateBatchFiles/SelectionAnalyses/SLAC.bf
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<li class="file-stats">
<a href="#48abec8e0d198814ad3898dd7c82ef8b52eef776">
res/TemplateBatchFiles/SelectionAnalyses/contrast-fel.bf
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<li class="file-stats">
<a href="#6912998957054caec329b3714223c03f20dbbd3e">
res/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf
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<li class="file-stats">
<a href="#c50a9ebb34fca832759d3d11698588f8851c99cb">
res/TemplateBatchFiles/libv3/UtilityFunctions.bf
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<li class="file-stats">
<a href="#5dfec713e3892a936e8b5a63db56c03bee3ec252">
res/TemplateBatchFiles/libv3/all-terms.bf
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<li class="file-stats">
<a href="#e7b72a8f9f424fe1e9e9e76f25522816189c14c9">
res/TemplateBatchFiles/libv3/tasks/alignments.bf
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<li class="file-stats">
<a href="#5c5226a707906d461dd112286b111fe4809fac66">
res/TemplateBatchFiles/libv3/tasks/ancestral.bf
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<li class="file-stats">
<a href="#5e59fe71518e21f42170943e14bd565a8f5e0144">
src/core/alignment.cpp
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<li class="file-stats">
<a href="#cbedcf5fec686e5f563504b995c5d7d07fd8c6b2">
src/core/batchlanruntime.cpp
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<li class="file-stats">
<a href="#d09b45303442d6299978fa8d0c8f3338d6a17886">
src/core/formula.cpp
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<li class="file-stats">
<a href="#07aceb8d215a75908cea626d9c80bc2a7c06639c">
src/core/global_things.cpp
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<li class="file-stats">
<a href="#0aac57334e127d66d9818be138193215c7262bbe">
src/core/include/matrix.h
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<li class="file-stats">
<a href="#2a8dd324ded753b0b3c559ac3950a2881ccd7a93">
src/core/likefunc.cpp
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<li class="file-stats">
<a href="#81843dd3cf849d08e0f197d837dd373534c7c756">
src/core/matrix.cpp
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<li class="file-stats">
<a href="#795bd9642f0c76f4bba4eaba7f491566cf16e788">
src/core/operation.cpp
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<li class="file-stats">
<a href="#da5a89d08e8ba5fdabf6bc90c935e625a50f5007">
src/core/tree.cpp
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<li class="file-stats">
<a href="#9f127084157a2a4e11faf03320db0541dbae15dc">
src/core/tree_evaluator.cpp
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<li class="file-stats">
<a href="#adf5ba83265c3f16b63f5fab29404568aa294038">
tests/hbltests/Results/HIVSweden.out
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<li class="file-stats">
<a href="#3bbc19efb5ab1243a9d0c4627a24ef88cf1f3ca0">
tests/hbltests/Results/HIVSweden.out_MODEL_-1.nex
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<li class="file-stats">
<a href="#96e4cef3847de919b0f245e8443e6befe26c217b">
tests/hbltests/Results/HIVSweden.out_MODEL_0.nex
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<li class="file-stats">
<a href="#dc4367ca74d002d80f8b7061c05e7d0232904a74">
tests/hbltests/Results/HIVSweden.out_MODEL_1.nex
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<li class="file-stats">
<a href="#1dea2190f9519da2b039674a61e37385e9584c01">
tests/hbltests/libv3/MEME-partitioned.wbf
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<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d8a6fecc5558ddf14f61e62f2bf14fe1a9ea9fff#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="579" style="width: 35px; color: rgba(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="579" style="width: 35px; color: rgba(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">@@ -579,7 +579,7 @@ add_test (NAME SLAC COMMAND HYPHYMP tests/hbltests/libv3/SLAC.wbf)</td>
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<td class="diff-line-num old_line" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
579
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579
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>NAME SLAC-PARTITIONED COMMAND HYPHYMP tests/hbltests/libv3/SLAC-partitioned.wbf<span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
580
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<td class="diff-line-num new_line" data-linenumber="580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
580
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>NAME FEL COMMAND HYPHYMP tests/hbltests/libv3/FEL.wbf<span class="p">)</span></span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
581
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<td class="diff-line-num new_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
581
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>MEME HYPHYMP tests/hbltests/libv3/MEME.wbf<span class="p">)</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="582" 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">
582
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<td class="diff-line-num new_line old" data-linenumber="582" 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="LC582" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>MEME-PARTITIONED HYPHYMP tests/hbltests/libv3/MEME.wbf<span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="582" 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">
582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>MEME-PARTITIONED HYPHYMP tests/hbltests/libv3/MEME<span class="idiff left right">-partitioned</span>.wbf<span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
583
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<td class="diff-line-num new_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
583
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>BUSTED HYPHYMP tests/hbltests/libv3/BUSTED.wbf<span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
584
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<td class="diff-line-num new_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
584
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>BUSTED-SRV HYPHYMP tests/hbltests/libv3/BUSTED-SRV.wbf<span class="p">)</span></span>
</pre>
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585
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<td class="diff-line-num new_line" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
585
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<pre style="margin: 0;"> <span id="LC585" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span> <span class="p">(</span>RELAX HYPHYMP tests/hbltests/libv3/RELAX.wbf<span class="p">)</span></span>
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</li>
<li id="817efc81f1180519a6136b50a447433f20cf679d">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d8a6fecc5558ddf14f61e62f2bf14fe1a9ea9fff#817efc81f1180519a6136b50a447433f20cf679d"><strong>res/TemplateBatchFiles/SelectionAnalyses/FEL.bf</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="339" style="width: 35px; color: rgba(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">@@ -339,7 +339,7 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod</td>
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339
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339
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha_scaler" = (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha_scaler" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> 3*^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta_scaler_test")/4;</span></span>
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340
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340
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetConstraint ("fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta_scaler_test"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha_scaler"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "");</span></span>
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341
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341
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="brainfuck"></span>
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342
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //Optimize (results</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {"OPTIMIZATION_METHOD" : "nedler</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">mead"</span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left">,</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff"> OPTIMIZATION_PRECISION: 1e</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">-</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">5</span>});</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //Optimize (results</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {"OPTIMIZATION_METHOD" : "nedler</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">mead"});</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Optimize (results</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^lf);</span></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Null = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ExtractMLEs (lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping);</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d8a6fecc5558ddf14f61e62f2bf14fe1a9ea9fff#bc98d7300147ce39ef8ee0f9b35f3252bebd01d2"><strong>res/TemplateBatchFiles/SelectionAnalyses/MEME.bf</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">@@ -118,7 +118,7 @@ This table is meant for HTML rendering in the results web-app; can use HTML char</td>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">is 'pop</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">over' explanation of terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> This is ONLY saved to the JSON file</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> For Markdown screen output see</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">the next set of variables</span><span class="nf" style="color: #900; font-weight: 600;">.</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_screen_output = {{"Codon"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Partition"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "alpha"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "beta</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "p</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "LRT"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Episodic selection detected?"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "# branches"}};</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_screen_output = {{"Codon"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Partition"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "alpha"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "beta</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "p</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "LRT"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Episodic selection detected?"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "# branches"</span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left">,</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"> "Most common codon substitutions at this site"</span>}};</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_output_options = {terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_options</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">header : TRUE</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_options</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">minimum_column_width: 12</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_options</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">align : "center"};</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="brainfuck"></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">@@ -279,6 +279,8 @@ parameters.SetRange ("meme.site_mixture_weight", terms.range_almost_01);</td>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">count = {{0}};</span></span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">composition</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">string = "";</span></span>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">positive_site = {{"" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> (1</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">((meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">filter_specification</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">coverage</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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285
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> 1</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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284
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">7</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="288" style="width: 35px; color: rgba(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">@@ -286,7 +288,8 @@ meme.report.positive_site = {{"" + (1+((meme.filter_specification[meme.report.pa</td>
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286
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288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">4</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">7</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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287
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289
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">5</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">7</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "Yes</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> p = " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> Format(meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">6</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">7</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">4)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">7</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">0)</span></span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Format(meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">7</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">0)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">composition</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">string</span></span>
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290
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293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}};</span></span>
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291
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294
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="brainfuck"></span>
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295
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_results = {};</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="575" style="width: 35px; color: rgba(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="578" style="width: 35px; color: rgba(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">@@ -575,13 +578,8 @@ lfunction meme.handle_a_site (lf_fel, lf_bsrel, filter_data, partition_index, pa</td>
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575
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578
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<pre style="margin: 0;"> <span id="LC578" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ancestral_info = ancestral</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">build (lf_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">FALSE);</span></span>
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576
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579
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="brainfuck"></span>
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577
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580
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //TODO</span></span>
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> branch_substitution_information = selection</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">substitution_mapper (ancestral_info </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"MATRIX"</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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579
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ancestral_info </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"TREE_AVL"</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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580
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<pre style="margin: 0;">-<span id="LC580" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ancestral_info </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"AMBIGS"</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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581
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<pre style="margin: 0;">-<span id="LC581" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">pairwise_counts"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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582
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<td class="diff-line-num new_line old" data-linenumber="581" 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="LC582" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ancestral_info </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"MAPPING"</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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583
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<pre style="margin: 0;">-<span id="LC583" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon_data_info")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">code")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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<pre style="margin: 0;">-<span id="LC584" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> branch_substitution_information = (ancestral</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ComputeSubstitutionBySite (ancestral_info</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">None))</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">substitutions"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> DeleteObject (ancestral_info);</span></span>
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<pre style="margin: 0;"> <span id="LC585" class="line" lang="brainfuck"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="607" style="width: 35px; color: rgba(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">@@ -607,7 +605,7 @@ lfunction meme.handle_a_site (lf_fel, lf_bsrel, filter_data, partition_index, pa</td>
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607
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> LFCompute (^lf_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">LF_DONE_COMPUTE);</span></span>
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608
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606
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<pre style="margin: 0;"> <span id="LC606" class="line" lang="brainfuck"></span>
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609
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607
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<pre style="margin: 0;"> <span id="LC607" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_beta_plus" := ^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_alpha";</span></span>
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610
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<pre style="margin: 0;">-<span id="LC610" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Optimize (results</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^lf_bsrel);</span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Optimize (results</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^lf_bsrel</span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left">,</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff"> {"OPTIMIZATION_METHOD" : "nedler</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">-</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">mead"}</span>);</span></span>
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609
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SpoolLF (lf_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "/tmp/meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">debug"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "MEME</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">null");</span></span>
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<pre style="margin: 0;"> <span id="LC610" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Null = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ExtractMLEs (lf_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping);</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">@@ -666,6 +664,60 @@ function meme.report.echo (meme.report.site, meme.report.partition, meme.report.</td>
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">lfunction meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">store_results (node</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> result</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> arguments) {</span></span>
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> sub_profile = result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_selection_attributes")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">{</span></span>
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "AGA":{</span></span>
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "AGG":{</span></span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "0":"Node1"</span></span>
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "AGG":{</span></span>
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "AAA":{</span></span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "0":"Node3"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "1":"HORSE"</span></span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "ACG":{</span></span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "0":"Node12"</span></span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "GCA":{</span></span>
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "0":"CAT"</span></span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="brainfuck"></span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">**/</span></span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="brainfuck"></span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (None != sub_profile) {</span></span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> total_sub_count = 0;</span></span>
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> sub_by_count = {};</span></span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (i</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> v; in; sub_profile) {</span></span>
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (j</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> b; in; v) {</span></span>
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> c = Abs (b);</span></span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> total_sub_count </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= c;</span></span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if ((sub_by_count/c)==0) {</span></span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> sub_by_count </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">c</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = {};</span></span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> sub_by_count</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">c</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> (i </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> j);</span></span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> sorted_subs = {Abs (sub_by_count)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 1};</span></span>
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> j = 0;</span></span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (i</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> v; in; sub_by_count) {</span></span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> sorted_subs</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">j</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">(</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">i);</span></span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> j </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1; </span></span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> sub_profile = {};</span></span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (i; in; sorted_subs % 0) {</span></span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> sub_profile </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> ("</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> (</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">i) </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> Join ("</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">sub_by_count </span><span class="p">[</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">));</span></span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">composition</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">string" = Join ("|"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> sub_profile);</span></span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="brainfuck"></span>
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721
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<pre style="margin: 0;"> <span id="LC721" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> partition_index = arguments </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">3</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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670
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> pattern_info = arguments </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">4</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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723
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="brainfuck"></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">@@ -730,6 +782,7 @@ lfunction meme.store_results (node, result, arguments) {</td>
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730
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782
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<pre style="margin: 0;"> <span id="LC782" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> sites_mapping_to_pattern = pattern_info</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sites")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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783
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<pre style="margin: 0;"> <span id="LC783" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> sites_mapping_to_pattern</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">count = utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Array1D (sites_mapping_to_pattern);</span></span>
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784
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<pre style="margin: 0;"> <span id="LC784" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC786" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (i = 0; i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> sites_mapping_to_pattern</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">count; i</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">=1) {</span></span>
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<pre style="margin: 0;"> <span id="LC787" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> site_index = sites_mapping_to_pattern</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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788
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<pre style="margin: 0;"> <span id="LC788" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ((^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_results")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">site_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = result_row;</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">@@ -752,3 +805,4 @@ lfunction meme.store_results (node, result, arguments) {</td>
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<pre style="margin: 0;"> <span id="LC805" class="line" lang="brainfuck"></span>
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806
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<pre style="margin: 0;"> <span id="LC806" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //assert (0);</span></span>
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<pre style="margin: 0;"> <span id="LC807" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="brainfuck"></span></pre>
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<li id="13df3044c13d443b9b6ad8712b47d3bc84725272">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d8a6fecc5558ddf14f61e62f2bf14fe1a9ea9fff#13df3044c13d443b9b6ad8712b47d3bc84725272"><strong>res/TemplateBatchFiles/SelectionAnalyses/SLAC.bf</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="246" style="width: 35px; color: rgba(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">@@ -246,6 +246,7 @@ for (slac.i = 0; slac.i < Abs (slac.filter_specification); slac.i += 1) {</td>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> slac</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_output_options</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_options</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">header</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = TRUE;</span></span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> slac</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ancestors = ancestral</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">build (slac</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partitioned_mg_results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">likelihood_function</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> slac</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> None);</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> slac</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">results </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">slac</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = slac</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">compute_the_counts (slac</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ancestors</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"MATRIX"</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> slac</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ancestors</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"TREE_AVL"</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> slac</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ancestors</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"AMBIGS"</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> slac</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">selected_branches</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">slac</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> slac</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">counts);</span></span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> slac</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_sites = utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Array1D ((slac</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">filter_specification</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">slac</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">coverage</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="576" style="width: 35px; color: rgba(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">@@ -575,11 +576,11 @@ lfunction slac.compute_the_counts (matrix, tree, lookup, selected_branches, coun</td>
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relative_branch_length = selected_branches_lengths</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> / selected_branch_total_length;</span></span>
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577
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC578" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> parent_branch = selected_branches_parents</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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580
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (s = 0; s </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> site_count; s </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1) {</span></span>
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581
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> this_state = matrix</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">this_branch</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">s</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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581
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582
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> parent_state = matrix</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">parent_branch</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">s</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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582
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<pre style="margin: 0;">-<span id="LC582" class="line" lang="brainfuck"></span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> // parent state can only be resolved or </span><span class="nf" style="color: #900; font-weight: 600;">---</span><span class="c1" style="color: #998; font-style: italic;"> (</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1)</span></span>
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585
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<pre style="margin: 0;"> <span id="LC585" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (this_state </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;">= 0) { // child fully resolved (this means that the parent is fully resolved as well)</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d8a6fecc5558ddf14f61e62f2bf14fe1a9ea9fff#48abec8e0d198814ad3898dd7c82ef8b52eef776"><strong>res/TemplateBatchFiles/SelectionAnalyses/contrast-fel.bf</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">@@ -748,7 +748,7 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod</td>
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<pre style="margin: 0;"> <span id="LC748" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> );</span></span>
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<pre style="margin: 0;"> <span id="LC749" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC750" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC751" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Optimize (results</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^lf);</span></span>
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Optimize (results</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^lf</span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left">,</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff"> {"OPTIMIZATION_METHOD" : "nedler</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">-</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">mead"}</span>);</span></span>
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<pre style="margin: 0;"> <span id="LC752" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Null = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ExtractMLEs (lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping);</span></span>
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<pre style="margin: 0;"> <span id="LC753" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Null </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log_likelihood")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;"> <span id="LC754" class="line" lang="brainfuck"></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">@@ -761,7 +761,7 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod</td>
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC762" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">RestoreLFStateFromSnapshot (lf_id</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> snapshot);</span></span>
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<pre style="margin: 0;"> <span id="LC763" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetConstraint ((^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler_parameter_names")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">v1n</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">(^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler_parameter_names")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">v2n</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "");</span></span>
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<pre style="margin: 0;">-<span id="LC764" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Optimize (results</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^lf);</span></span>
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Optimize (results</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^lf</span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left">,</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff"> {"OPTIMIZATION_METHOD" : "nedler</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">-</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">mead"}</span>);</span></span>
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> pairwise</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">v1n </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "|" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> v2n</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ExtractMLEs (lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping);</span></span>
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (pairwise</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">v1n </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "|" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> v2n</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log_likelihood")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;"> <span id="LC767" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d8a6fecc5558ddf14f61e62f2bf14fe1a9ea9fff#6912998957054caec329b3714223c03f20dbbd3e"><strong>res/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf</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">@@ -97,7 +97,7 @@ lfunction selection.substitution_mapper (matrix, tree, ambig_lookup, pairwise_co</td>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext"> for (key, value; in; branch_info) {</span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="plaintext"> <span class="idiff left right">result[key]</span>[bname] = value;</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> <span class="idiff left right">(result[key])</span>[bname] = value;</span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext"> }</span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext"> //utility.ForEach (utility.Keys (branch_info), "slac.substituton_mapper.key",</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">@@ -1054,26 +1054,27 @@ function utility.sortStrings (_theList) {</td>
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<pre style="margin: 0;"> <span id="LC1054" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return _gb_sortedStrings;</span></span>
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1055
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1055
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<pre style="margin: 0;"> <span id="LC1055" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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1056
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1056
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<pre style="margin: 0;"> <span id="LC1056" class="line" lang="brainfuck"></span>
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1057
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<td class="diff-line-num new_line old" data-linenumber="1057" 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="LC1057" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">/*</span></span></span>
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1057
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<pre style="margin: 0;">+<span id="LC1057" class="line" lang="brainfuck"></span>
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1058
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1058
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<pre style="margin: 0;"> <span id="LC1058" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">function utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">FinishAndPrintProfile () {</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1059" 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">
1059
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<td class="diff-line-num new_line old" data-linenumber="1059" 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="LC1059" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">#profile _hyphy_profile_dump;</span></span>
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1059
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<pre style="margin: 0;">+<span id="LC1059" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ExecuteCommands ('</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1060" 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">
1060
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<pre style="margin: 0;">+<span id="LC1060" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> #profile _hyphy_profile_dump;</span></span>
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1060
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<td class="diff-line-num new_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1061
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<pre style="margin: 0;"> <span id="LC1061" class="line" lang="brainfuck"></span>
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1061
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<td class="diff-line-num new_line old" data-linenumber="1062" 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="LC1061" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> stats = _hyphy_profile_dump</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"STATS"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1062" 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">
1062
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<td class="diff-line-num new_line old" data-linenumber="1062" 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="LC1062" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _profile_summer = ({1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">Rows(stats)}</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"1"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) * stats;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1063" 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">
1063
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<td class="diff-line-num new_line old" data-linenumber="1062" 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="LC1063" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _instructions = _hyphy_profile_dump</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"INSTRUCTION"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1064" 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">
1064
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<td class="diff-line-num new_line old" data-linenumber="1062" 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="LC1064" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _indices = _hyphy_profile_dump</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"INSTRUCTION INDEX"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1062" 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">
1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>stats = _hyphy_profile_dump</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"STATS"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1063" 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">
1063
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<pre style="margin: 0;">+<span id="LC1063" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>_profile_summer = ({1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">Rows(stats)}</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"1"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) * stats;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1064" 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">
1064
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<pre style="margin: 0;">+<span id="LC1064" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>_instructions = _hyphy_profile_dump</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"INSTRUCTION"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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1065
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<pre style="margin: 0;">+<span id="LC1065" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>_indices = _hyphy_profile_dump</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"INSTRUCTION INDEX"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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1065
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1066
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<pre style="margin: 0;"> <span id="LC1066" class="line" lang="brainfuck"></span>
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1066
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<td class="diff-line-num new_line old" data-linenumber="1067" 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="LC1066" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (stdout</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\nTotal run time (seconds) : "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Format(_profile_summer</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">15</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">6)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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1067
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<td class="diff-line-num new_line old" data-linenumber="1067" 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="LC1067" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "\nTotal number of steps : "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Format(_profile_summer</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">15</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">0)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\n\n");</span></span>
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1067
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<pre style="margin: 0;">+<span id="LC1067" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>fprintf (stdout</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\nTotal run time (seconds) : "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Format(_profile_summer</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">15</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">6)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1068" 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">
1068
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<pre style="margin: 0;">+<span id="LC1068" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>"\nTotal number of steps : "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Format(_profile_summer</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">15</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">0)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\n\n");</span></span>
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1068
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1069
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<pre style="margin: 0;"> <span id="LC1069" class="line" lang="brainfuck"></span>
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1069
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<pre style="margin: 0;">-<span id="LC1069" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> to_sort = stats</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">_MATRIX_ELEMENT_VALUE_*_MATRIX_ELEMENT_COLUMN_</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">(_MATRIX_ELEMENT_COLUMN_==0)*_MATRIX_ELEMENT_ROW_"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> % 1;</span></span>
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1070
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<pre style="margin: 0;">+<span id="LC1070" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>to_sort = stats</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">_MATRIX_ELEMENT_VALUE_*_MATRIX_ELEMENT_COLUMN_</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">(_MATRIX_ELEMENT_COLUMN_==0)*_MATRIX_ELEMENT_ROW_"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> % 1;</span></span>
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1070
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1071
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<pre style="margin: 0;"> <span id="LC1071" class="line" lang="brainfuck"></span>
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1071
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<td class="diff-line-num new_line old" data-linenumber="1072" 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="LC1071" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (k=0; k</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">Columns(_instructions); k=k</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1)</span></span>
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1072
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<td class="diff-line-num new_line old" data-linenumber="1072" 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="LC1072" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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1073
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<pre style="margin: 0;">-<span id="LC1073" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> k2 = to_sort</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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1074
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<td class="diff-line-num new_line old" data-linenumber="1072" 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="LC1074" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf (stdout</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Format (_indices</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k2</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">6</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">0)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> " : "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _instructions</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k2</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\n\tCall count: "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> stats</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k2</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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1075
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<td class="diff-line-num new_line old" data-linenumber="1072" 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="LC1075" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "\n\tTime (seconds): "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> stats</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k2</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\n");</span></span>
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1076
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<pre style="margin: 0;">-<span id="LC1076" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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1077
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<td class="diff-line-num new_line old" data-linenumber="1072" 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="LC1077" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right">return 0</span>;</span></span>
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1072
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<pre style="margin: 0;">+<span id="LC1072" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>for (k=0; k</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">Columns(_instructions); k=k</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1)</span></span>
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1073
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<pre style="margin: 0;">+<span id="LC1073" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>{</span></span>
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1074
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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>k2 = to_sort</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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1075
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<pre style="margin: 0;">+<span id="LC1075" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>fprintf (stdout</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Format (_indices</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k2</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">6</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">0)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> " : "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _instructions</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k2</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\n\tCall count: "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> stats</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k2</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC1076" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>"\n\tTime (seconds): "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> stats</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k2</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\n");</span></span>
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<pre style="margin: 0;">+<span id="LC1077" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>}</span></span>
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<pre style="margin: 0;">+<span id="LC1078" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right">')</span>;</span></span>
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1079
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<pre style="margin: 0;"> <span id="LC1079" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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<pre style="margin: 0;">-<span id="LC1079" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">*/</span></span></span></pre>
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<pre style="margin: 0;">+<span id="LC1080" class="line" lang="brainfuck"></span></pre>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d8a6fecc5558ddf14f61e62f2bf14fe1a9ea9fff#5dfec713e3892a936e8b5a63db56c03bee3ec252"><strong>res/TemplateBatchFiles/libv3/all-terms.bf</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="179" style="width: 35px; color: rgba(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">@@ -179,6 +179,7 @@ namespace terms{</td>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> coverage = "coverage";</span></span>
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180
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> filter_string = "filter</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">string";</span></span>
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181
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> is_constant = "is_constant";</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> characters = "characters";</span></span>
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182
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> pattern_id = "pattern id";</span></span>
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> filename_to_index = "filename</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">to</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">index";</span></span>
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d8a6fecc5558ddf14f61e62f2bf14fe1a9ea9fff#e7b72a8f9f424fe1e9e9e76f25522816189c14c9"><strong>res/TemplateBatchFiles/libv3/tasks/alignments.bf</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">@@ -453,6 +453,8 @@ lfunction alignments.CompressDuplicateSequences (filter_in, filter_out, rename)</td>
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //DataSetFilter ^filter_out = CreateFilter (filter_in);</span></span>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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455
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="brainfuck"></span>
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456
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458
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/**</span></span>
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457
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459
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * Defines filters for multiple partitions</span></span>
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458
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @name alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">DefineFiltersForPartitions</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">@@ -796,6 +798,8 @@ lfunction alignments.Extract_site_patterns (data_filter) {</td>
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<pre style="margin: 0;"> <span id="LC798" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> site_characters = {};</span></span>
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<pre style="margin: 0;"> <span id="LC799" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> sequence_count = ^(data_filter </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">species");</span></span>
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800
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<pre style="margin: 0;"> <span id="LC800" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> GetDataInfo (filter_characters</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^data_filter</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "CHARACTERS");</span></span>
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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803
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<pre style="margin: 0;"> <span id="LC803" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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804
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<pre style="margin: 0;"> <span id="LC804" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (_site_index_</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _pattern_; in; pattern_list) {</span></span>
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805
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<pre style="margin: 0;"> <span id="LC805" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">EnsureKey (site_info</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _pattern_);</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">@@ -810,6 +814,10 @@ lfunction alignments.Extract_site_patterns (data_filter) {</td>
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<pre style="margin: 0;"> <span id="LC814" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC815" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC816" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> site_characters = sc;</span></span>
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (site_info</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_pattern_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">characters"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = {};</span></span>
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (i</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">v; in; site_characters) {</span></span>
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ((site_info</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_pattern_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">characters"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">filter_characters</span><span class="p">[</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;"> = v;</span></span>
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC821" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (site_info</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_pattern_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">is_constant"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = Abs (site_characters) </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">= 1;</span></span>
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<pre style="margin: 0;"> <span id="LC822" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC823" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </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">@@ -267,7 +267,7 @@ lfunction ancestral._buildAncestralCacheInternal(_lfID, _lfComponentID, doSample</td>
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267
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> GetDataInfo(_bacCharState</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _bacAF</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _bacRowIndex </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> _bacFilterSequenceCount</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _bacAncestralPatternMap</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_bacSiteCounter</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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268
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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269
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _bacResolutionCount = </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">_bacCharState;</span></span>
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270
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (_bacResolutionCount == Columns(_bacCharHandles)) {</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (_bacResolutionCount == Columns(_bacCharHandles)<span class="idiff left right"> || _bacResolutionCount == 0</span>) {</span></span>
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271
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /* gap/full ambig */</span></span>
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272
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if ( (reverse_mapping/(</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1)) == FALSE) {</span></span>
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273
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273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _bacHandledResolutions</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_bacCurrentState</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="538" style="width: 35px; color: rgba(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">@@ -538,10 +538,11 @@ lfunction ancestral.ComputeSubstitutionBySite (ancestral_data, site, branch_filt</td>
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538
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538
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> parent = (selected_branches</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">b</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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539
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539
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> own_state = (ancestral_data</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"MATRIX"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">self</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">site</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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540
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540
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> parent_state = (ancestral_data</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"MATRIX"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">parent</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">site</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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541
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="brainfuck"></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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542
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543
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if ((own_state != parent_state) && (own_state != </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1) && (parent_state != </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1)) {</span></span>
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543
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<pre style="margin: 0;">-<span id="LC543" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> own_state = (ancestral_data</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"<span class="idiff left right">CHARS</span>"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">own_state</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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544
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> parent_state = (ancestral_data</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"<span class="idiff left right">CHARS</span>"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">parent_state</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> own_state = (ancestral_data</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"<span class="idiff left right">MAPPING</span>"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">own_state</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> parent_state = (ancestral_data</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"<span class="idiff left right">MAPPING</span>"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">parent_state</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">EnsureKey (result</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> parent_state);</span></span>
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547
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">EnsureKey (result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">parent_state</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> own_state);</span></span>
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548
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ((result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">parent_state</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">own_state</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> selected_branch_names</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">b</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d8a6fecc5558ddf14f61e62f2bf14fe1a9ea9fff#5e59fe71518e21f42170943e14bd565a8f5e0144"><strong>src/core/alignment.cpp</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">@@ -994,6 +994,7 @@ double AlignStrings( char const * r_str</td>
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<pre style="margin: 0;"> <span id="LC994" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC995" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// if anything drops below 0, something bad happened</span></span>
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<pre style="margin: 0;"> <span id="LC996" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</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;">0</span> <span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC997" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="p">[]</span> <span class="n" style="color: #333;">edit_ops</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC998" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INFINITY</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC999" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1000" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d8a6fecc5558ddf14f61e62f2bf14fe1a9ea9fff#cbedcf5fec686e5f563504b995c5d7d07fd8c6b2"><strong>src/core/batchlanruntime.cpp</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">@@ -541,13 +541,16 @@ bool _ElementaryCommand::HandleGetDataInfo (_ExecutionList& current_program</td>
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">site</span> <span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">site</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">filter_source</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetPatternCount</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">filter_source</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">NumberSpecies</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">count_gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hy_env</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EnvVariableTrue</span><span class="p">(</span><span class="n" style="color: #333;">hy_env</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">harvest_frequencies_gap_options</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="cpp"> <span class="n" style="color: #333;">_Matrix</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">_Matrix</span> <span class="p">(</span><span class="n" style="color: #333;">filter_source</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetDimension</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">only_the_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hy_env</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EnvVariableTrue</span><span class="p">(</span><span class="n" style="color: #333;">hy_env</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">get_data_info_returns_only_the_index</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC549" class="line" lang="cpp"> <span class="n" style="color: #333;">_String</span> <span class="n" style="color: #333;">character</span> <span class="p">(</span><span class="n" style="color: #333;">filter_source</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">RetrieveState</span><span class="p">(</span><span class="n" style="color: #333;">site</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">theValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter_source</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Translate2Frequencies</span> <span class="p">(</span><span class="n" style="color: #333;">character</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;">theData</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC550" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">theValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter_source</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Translate2Frequencies</span> <span class="p">(</span><span class="n" style="color: #333;">character</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;">theData</span><span class="p">,</span> <span class="n" style="color: #333;">count_gaps</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">only_the_index</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="cpp"> <span class="n" style="color: #333;">receptacle</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">SetValue</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">_Constant</span> <span class="p">(</span><span class="n" style="color: #333;">theValue</span><span class="p">),</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</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="LC556" class="line" lang="cpp"> <span class="n" style="color: #333;">DeleteObject</span> <span class="p">(</span><span class="n" style="color: #333;">res</span><span class="p">);</span></span>
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<li id="d09b45303442d6299978fa8d0c8f3338d6a17886">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d8a6fecc5558ddf14f61e62f2bf14fe1a9ea9fff#d09b45303442d6299978fa8d0c8f3338d6a17886"><strong>src/core/formula.cpp</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">@@ -2057,7 +2057,7 @@ bool _Formula::CheckSimpleTerm (HBLObjectRef thisObj) {</td>
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2057
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<pre style="margin: 0;"> <span id="LC2057" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">oc</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">NUMBER</span><span class="p">)</span> <span class="p">{</span></span>
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2058
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2058
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<pre style="margin: 0;"> <span id="LC2058" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">oc</span> <span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">MATRIX</span><span class="p">)</span> <span class="p">{</span></span>
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2059
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2059
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<pre style="margin: 0;"> <span id="LC2059" class="line" lang="cpp"> <span class="n" style="color: #333;">_Matrix</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mv</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">_Matrix</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">thisObj</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Compute</span><span class="p">();</span></span>
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2060
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<pre style="margin: 0;">-<span id="LC2060" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">mv</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">SparseDataStructur</span>e</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mv</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">IsIndependent</span> <span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC2060" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">mv</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">is_dens</span>e</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mv</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">IsIndependent</span> <span class="p">())</span> <span class="p">{</span></span>
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2061
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2061
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<pre style="margin: 0;"> <span id="LC2061" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2062" class="line" lang="cpp"> <span class="p">}</span></span>
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2063
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2063
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<pre style="margin: 0;"> <span id="LC2063" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d8a6fecc5558ddf14f61e62f2bf14fe1a9ea9fff#07aceb8d215a75908cea626d9c80bc2a7c06639c"><strong>src/core/global_things.cpp</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">@@ -120,7 +120,7 @@ namespace hy_global {</td>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> <span class="n" style="color: #333;">kErrorStringDatasetRefIndexError</span> <span class="p">(</span><span class="s" style="color: #d14;">"Dataset index reference out of range"</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">kErrorStringMatrixExportError</span> <span class="p">(</span><span class="s" style="color: #d14;">"Export matrix called with a non-polynomial matrix argument"</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">kErrorStringNullOperand</span> <span class="p">(</span><span class="s" style="color: #d14;">"Attempting to operate on an undefined value; this is probably the result of an earlier 'soft' error condition"</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">kHyPhyVersion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"2.5.<span class="idiff left right">19</span>"</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">kHyPhyVersion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"2.5.<span class="idiff left right">20</span>"</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">kNoneToken</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"None"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"> <span class="n" style="color: #333;">kNullToken</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"null"</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d8a6fecc5558ddf14f61e62f2bf14fe1a9ea9fff#0aac57334e127d66d9818be138193215c7262bbe"><strong>src/core/include/matrix.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -142,7 +142,7 @@ private:</td>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// matrix exp truncation precision</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"> <span class="idiff left"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_validateCompressedStorage</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">void</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"><span class="nl">public:</span></span>
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<pre style="margin: 0;"> <span id="LC148" 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">@@ -518,9 +518,6 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">MatrixType</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC519" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">storageType</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">SparseDataStructure</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">theIndex</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC522" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">CALLBACK</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">EXTRACTOR</span><span class="p">></span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ForEach</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;">cbv</span><span class="p">,</span> <span class="n" style="color: #333;">EXTRACTOR</span><span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">accessor</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC523" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">theIndex</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d8a6fecc5558ddf14f61e62f2bf14fe1a9ea9fff#2a8dd324ded753b0b3c559ac3950a2881ccd7a93"><strong>src/core/likefunc.cpp</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">@@ -5288,6 +5288,10 @@ long _LikelihoodFunction::Bracket (long index, hyFloat& left, hyFloat& middle</td>
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<pre style="margin: 0;"> <span id="LC5288" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC5289" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">index</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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5290
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<pre style="margin: 0;"> <span id="LC5290" class="line" lang="cpp"> <span class="n" style="color: #333;">leftStep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">middle</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC5291" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC5292" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">middle</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">leftStep</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">lowerBound</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC5293" class="line" lang="cpp"> <span class="n" style="color: #333;">leftStep</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;">middle</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">lowerBound</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #099;">0.9</span><span class="p">,</span> <span class="mf" style="color: #099;">1e-8</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC5294" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC5295" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC5296" class="line" lang="cpp"></span>
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5297
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<pre style="margin: 0;"> <span id="LC5297" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">saveM</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">middle</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5334" style="width: 35px; color: rgba(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">@@ -5330,7 +5334,7 @@ long _LikelihoodFunction::Bracket (long index, hyFloat& left, hyFloat& middle</td>
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5330
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5334
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<pre style="margin: 0;"> <span id="LC5334" class="line" lang="cpp"> <span class="n" style="color: #333;">leftStep</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;">leftStep</span><span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #099;">0.125</span><span class="p">,</span> <span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">lowerBound</span><span class="p">);</span></span>
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5335
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<pre style="margin: 0;"> <span id="LC5335" class="line" lang="cpp"> </span>
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5336
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<pre style="margin: 0;"> <span id="LC5336" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">leftStep</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">initialStep</span><span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #099;">.1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">leftStep</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">STD_GRAD_STEP</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC5333" class="line" lang="cpp"> <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;">first</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;"><span class="idiff left">index</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">0</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">current_log_l</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 right">INFINITY</span></span><span class="p">)</span> <span class="p">{</span></span>
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5337
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<pre style="margin: 0;">+<span id="LC5337" class="line" lang="cpp"> <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;">first</span> <span class="o" style="font-weight: 600;">||</span> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">index</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">0</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">current_log_l</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">INFINITY</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">leftStep</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><=</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff right">1e-8</span></span><span class="p">)</span> <span class="p">{</span></span>
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5334
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5338
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<pre style="margin: 0;"> <span id="LC5338" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">go2Bound</span><span class="p">)</span> <span class="p">{</span></span>
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5339
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<pre style="margin: 0;"> <span id="LC5339" class="line" lang="cpp"> <span class="n" style="color: #333;">middle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lowerBound</span><span class="p">;</span></span>
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5340
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<pre style="margin: 0;"> <span id="LC5340" class="line" lang="cpp"> </span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d8a6fecc5558ddf14f61e62f2bf14fe1a9ea9fff#81843dd3cf849d08e0f197d837dd373534c7c756"><strong>src/core/matrix.cpp</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">@@ -550,7 +550,7 @@ void DuplicateMatrix (_Matrix* targetMatrix, _Matrix const* sourceMatrix) {</td>
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="cpp"> <span class="n" style="color: #333;">targetMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressedIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nil</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC553" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">sourceMatrix</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">theIndex</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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">sourceMatrix</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">is_dense</span></span><span class="p"><span class="idiff right">()</span>)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">targetMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">MatrixMemAllocate</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;">long</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sourceMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lDim</span><span class="p">)))</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// allocate element index storage</span></span>
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="cpp"> <span class="n" style="color: #333;">HandleApplicationError</span> <span class="p">(</span> <span class="n" style="color: #333;">kErrorStringMemoryFail</span> <span class="p">);</span></span>
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556
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</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">@@ -568,7 +568,7 @@ void DuplicateMatrix (_Matrix* targetMatrix, _Matrix const* sourceMatrix) {</td>
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568
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="cpp"> <span class="n" style="color: #333;">targetMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nil</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="cpp"> </span>
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570
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sourceMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lDim</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sourceMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left">storageType</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></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="LC571" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sourceMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left">is_polynomial</span></span><span class="p"><span class="idiff right">()</span>)</span></span>
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572
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// matrix will store pointers to elements</span></span>
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573
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="cpp"> <span class="p">{</span></span>
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574
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<pre style="margin: 0;"> <span id="LC574" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">targetMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lDim</span><span class="p">)</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">@@ -576,7 +576,7 @@ void DuplicateMatrix (_Matrix* targetMatrix, _Matrix const* sourceMatrix) {</td>
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576
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="cpp"> <span class="n" style="color: #333;">HandleApplicationError</span> <span class="p">(</span> <span class="n" style="color: #333;">kErrorStringMemoryFail</span> <span class="p">);</span></span>
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577
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577
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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578
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578
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<pre style="margin: 0;"> <span id="LC578" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">targetMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span><span class="p">,(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">sourceMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span><span class="p">,</span><span class="n" style="color: #333;">sourceMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lDim</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;">void</span><span class="o" style="font-weight: 600;">*</span><span class="p">));</span></span>
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579
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">sourceMatrix</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">theIndex</span></span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// non-sparse matrix</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">sourceMatrix</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">is_dense</span></span><span class="p"><span class="idiff right">()</span>)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// non-sparse matrix</span></span>
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580
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580
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<pre style="margin: 0;"> <span id="LC580" 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;">long</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;">sourceMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lDim</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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581
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581
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sourceMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetMatrixObject</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="LC582" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">sourceMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetMatrixObject</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;">AddAReference</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">@@ -591,12 +591,12 @@ void DuplicateMatrix (_Matrix* targetMatrix, _Matrix const* sourceMatrix) {</td>
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591
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<pre style="margin: 0;"> <span id="LC591" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC594" class="line" lang="cpp"> <span class="p">}</span> <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;">sourceMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left">storageType</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="cpp"> <span class="p">}</span> <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;">sourceMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left">is_expression_based</span></span><span class="p"><span class="idiff right">()</span>)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">targetMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lDim</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="cpp"> <span class="n" style="color: #333;">targetMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">MatrixMemAllocate</span><span class="p">(</span><span class="n" style="color: #333;">sourceMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lDim</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;">void</span><span class="o" style="font-weight: 600;">*</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="cpp"> <span class="n" style="color: #333;">_Formula</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">theFormulas</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">_Formula</span><span class="o" style="font-weight: 600;">**</span><span class="p">)(</span><span class="n" style="color: #333;">sourceMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span><span class="p">),</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">newFormulas</span> <span class="o" style="font-weight: 600;">=</span></span>
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598
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">_Formula</span><span class="o" style="font-weight: 600;">**</span><span class="p">)(</span><span class="n" style="color: #333;">targetMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC599" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sourceMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left right">theIndex</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sourceMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left">is_dense</span></span><span class="p"><span class="idiff">()</span></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">false</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC600" 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;">long</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;">sourceMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lDim</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="LC601" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sourceMatrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">IsNonEmpty</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="LC602" class="line" lang="cpp"> <span class="n" style="color: #333;">newFormulas</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="p">(</span><span class="n" style="color: #333;">_Formula</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">theFormulas</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;">makeDynamic</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">@@ -653,10 +653,10 @@ _Matrix::_Matrix (long theHDim, long theVDim, bool sparse, bool allocateStorage)</td>
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<pre style="margin: 0;"> <span id="LC653" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_____________________________________________________________________________________________</span></span>
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<pre style="margin: 0;"> <span id="LC654" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC655" class="line" lang="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">_Matrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IsNonEmpty</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">logicalIndex</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC656" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">theIndex</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC657" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">theIndex</span><span class="p">[</span><span class="n" style="color: #333;">logicalIndex</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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<pre style="margin: 0;">+<span id="LC656" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">is_dense</span></span><span class="p"><span class="idiff">()</span></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">false</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">theIndex</span><span class="idiff left right"> </span><span class="p">[</span><span class="n" style="color: #333;">logicalIndex</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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<pre style="margin: 0;"> <span id="LC658" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC659" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">storageType</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">_NUMERICAL_TYPE</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">is_numeric</span></span><span class="p"><span class="idiff right">()</span>)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC660" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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661
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661
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="cpp"> <span class="p">}</span></span>
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662
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">GetMatrixObject</span><span class="p">(</span><span class="n" style="color: #333;">logicalIndex</span><span class="p">)</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">ZEROPOINTER</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="707" style="width: 35px; color: rgba(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="707" style="width: 35px; color: rgba(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">@@ -707,7 +707,7 @@ bool _Matrix::is_square_numeric(bool dense) const {</td>
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707
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707
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<pre style="margin: 0;"> <span id="LC707" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">storageType</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">_NUMERICAL_TYPE</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">hDim</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">vDim</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">hDim</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0L</span><span class="p">){</span></span>
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708
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708
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<pre style="margin: 0;"> <span id="LC708" class="line" lang="cpp"> <span class="n" style="color: #333;">HandleApplicationError</span> <span class="p">(</span><span class="s" style="color: #d14;">"Square numerical matrix required"</span><span class="p">);</span></span>
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709
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709
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<pre style="margin: 0;"> <span id="LC709" class="line" lang="cpp"> <span class="p">}</span></span>
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710
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<pre style="margin: 0;">-<span id="LC710" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dense</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;"><span class="idiff left right">theIndex</span></span><span class="p">)</span> <span class="p">{</span></span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dense</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">is_dense</span></span><span class="p"><span class="idiff right">()</span>)</span> <span class="p">{</span></span>
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711
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711
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<pre style="margin: 0;"> <span id="LC711" class="line" lang="cpp"> <span class="n" style="color: #333;">HandleApplicationError</span> <span class="p">(</span><span class="s" style="color: #d14;">"Square dense numerical matrix required"</span><span class="p">);</span></span>
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712
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<pre style="margin: 0;"> <span id="LC712" class="line" lang="cpp"> <span class="p">}</span></span>
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713
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713
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<pre style="margin: 0;"> <span id="LC713" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1228" style="width: 35px; color: rgba(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">@@ -1228,9 +1228,10 @@ HBLObjectRef _Matrix::LUDecompose (void) const {</td>
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1228
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1228
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<pre style="margin: 0;"> <span id="LC1228" class="line" lang="cpp"> <span class="p">}</span></span>
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1229
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1229
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<pre style="margin: 0;"> <span id="LC1229" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1230
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1230
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<pre style="margin: 0;"> <span id="LC1230" 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;">long</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;">lDim</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="p">{</span></span>
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1231
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<pre style="margin: 0;">-<span id="LC1231" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">IsNonEmpty</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="p">{</span></span>
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1231
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<pre style="margin: 0;">+<span id="LC1231" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">theIndex</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">]</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="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">)</span> <span class="p">{</span></span>
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1232
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1232
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<pre style="margin: 0;"> <span id="LC1232" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">cell_coord</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theIndex</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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1233
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<pre style="margin: 0;">-<span id="LC1233" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Store</span><span class="p">(</span><span class="n" style="color: #333;">cell_coord</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">vDim</span><span class="p">,</span><span class="n" style="color: #333;">cell_coord</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">vDim</span><span class="p">,</span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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1233
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<pre style="margin: 0;">+<span id="LC1233" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cell_coord</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">hDim</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1234" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Store</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span><span class="n" style="color: #333;">cell_coord</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">vDim</span><span class="p">,</span><span class="n" style="color: #333;">theData</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="LC1235" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1236" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1237" class="line" lang="cpp"> <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">@@ -1491,37 +1492,77 @@ HBLObjectRef _Matrix::MultByFreqs (long freqID, bool reuse_value_object) {</td>
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<pre style="margin: 0;"> <span id="LC1492" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1493" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">theIndex</span><span class="p">)</span> <span class="p">{</span></span>
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1493
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1494
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<pre style="margin: 0;"> <span id="LC1494" class="line" lang="cpp"> <span class="n" style="color: #333;">_Matrix</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">vm</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">_Matrix</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">value</span><span class="p">;</span></span>
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1494
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<pre style="margin: 0;">-<span id="LC1494" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vm</span> <span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span><span class="p">;</span></span>
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1495
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<pre style="margin: 0;">-<span id="LC1495" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tempDiags</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">alloca</span> <span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hDim</span><span class="p">);</span></span>
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1496
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<pre style="margin: 0;">-<span id="LC1496" class="line" lang="cpp"> <span class="n" style="color: #333;">InitializeArray</span><span class="p">(</span><span class="n" style="color: #333;">tempDiags</span><span class="p">,</span> <span class="n" style="color: #333;">hDim</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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1497
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<pre style="margin: 0;">-<span id="LC1497" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1498" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">freq_matrix</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1499" 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;">long</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;">lDim</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="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1500" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theIndex</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="LC1501" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">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 class="p">{</span></span>
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1502
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<pre style="margin: 0;">-<span id="LC1502" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">vDim</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1503" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">vDim</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1504" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1505" class="line" lang="cpp"> <span class="n" style="color: #333;">tempDiags</span><span class="p">[</span><span class="n" style="color: #333;">h</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">dp</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;">freq_matrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</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="LC1495" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">dp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vm</span> <span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span><span class="p">;</span></span>
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1496
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<pre style="margin: 0;">+<span id="LC1496" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1497" 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">
1497
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<pre style="margin: 0;">+<span id="LC1497" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vm</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressedIndex</span><span class="p">)</span> <span class="p">{</span></span>
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1498
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<pre style="margin: 0;">+<span id="LC1498" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//vm->_validateCompressedStorage();</span></span>
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1499
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<pre style="margin: 0;">+<span id="LC1499" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1500" 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">
1500
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<pre style="margin: 0;">+<span id="LC1500" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">freq_matrix</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1501" 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">
1501
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<pre style="margin: 0;">+<span id="LC1501" 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;">long</span> <span class="n" style="color: #333;">r</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;">r</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hDim</span><span class="p">;</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1502
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<pre style="margin: 0;">+<span id="LC1502" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">diagEntry</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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<td class="diff-line-num new new_line" data-linenumber="1503" 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">
1503
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<pre style="margin: 0;">+<span id="LC1503" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">diagAccumulator</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1504" 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">
1504
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<pre style="margin: 0;">+<span id="LC1504" 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;">long</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">from</span><span class="p">;</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">vm</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">];</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1505
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<pre style="margin: 0;">+<span id="LC1505" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">col_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vm</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">hDim</span><span class="p">];</span></span>
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1506
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<pre style="margin: 0;">+<span id="LC1506" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">col_index</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">r</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1507" 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">
1507
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<pre style="margin: 0;">+<span id="LC1507" class="line" lang="cpp"> <span class="n" style="color: #333;">dp</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">freq_matrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">col_index</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1508" 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">
1508
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<pre style="margin: 0;">+<span id="LC1508" class="line" lang="cpp"> <span class="n" style="color: #333;">diagAccumulator</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">dp</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1509" 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">
1509
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<pre style="margin: 0;">+<span id="LC1509" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</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="cpp"> <span class="n" style="color: #333;">diagEntry</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1511" 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">
1511
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<pre style="margin: 0;">+<span id="LC1511" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1512" 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">
1512
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<pre style="margin: 0;">+<span id="LC1512" class="line" lang="cpp"> <span class="p">}</span></span>
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1513
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<pre style="margin: 0;">+<span id="LC1513" class="line" lang="cpp"> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vm</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1514" 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">
1514
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<pre style="margin: 0;">+<span id="LC1514" class="line" lang="cpp"> <span class="n" style="color: #333;">dp</span><span class="p">[</span><span class="n" style="color: #333;">diagEntry</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">diagAccumulator</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="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" 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="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1517" 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">
1517
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<pre style="margin: 0;">+<span id="LC1517" 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;">long</span> <span class="n" style="color: #333;">r</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;">r</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hDim</span><span class="p">;</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1518" 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">
1518
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<pre style="margin: 0;">+<span id="LC1518" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">diagEntry</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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<td class="diff-line-num new new_line" data-linenumber="1519" 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">
1519
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<pre style="margin: 0;">+<span id="LC1519" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">diagAccumulator</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1520" 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">
1520
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<pre style="margin: 0;">+<span id="LC1520" 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;">long</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">from</span><span class="p">;</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">vm</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">];</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1521" 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">
1521
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<pre style="margin: 0;">+<span id="LC1521" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printf ("%ld\n", vm->theIndex[c]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1522" 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">
1522
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<pre style="margin: 0;">+<span id="LC1522" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vm</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">hDim</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">r</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1523" 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">
1523
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<pre style="margin: 0;">+<span id="LC1523" class="line" lang="cpp"> <span class="n" style="color: #333;">diagAccumulator</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">dp</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1524" 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">
1524
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<pre style="margin: 0;">+<span id="LC1524" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1525" 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">
1525
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<pre style="margin: 0;">+<span id="LC1525" class="line" lang="cpp"> <span class="n" style="color: #333;">diagEntry</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1526" 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">
1526
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<pre style="margin: 0;">+<span id="LC1526" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1527" 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">
1527
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<pre style="margin: 0;">+<span id="LC1527" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1528" 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">
1528
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<pre style="margin: 0;">+<span id="LC1528" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printf ("%ld %ld %g\n", r, diagEntry, diagAccumulator);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1529" 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">
1529
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<pre style="margin: 0;">+<span id="LC1529" class="line" lang="cpp"> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vm</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1530" 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">
1530
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<pre style="margin: 0;">+<span id="LC1530" class="line" lang="cpp"> <span class="n" style="color: #333;">dp</span><span class="p">[</span><span class="n" style="color: #333;">diagEntry</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">diagAccumulator</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1531" 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">
1531
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<pre style="margin: 0;">+<span id="LC1531" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1532" 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">
1532
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<pre style="margin: 0;">+<span id="LC1532" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1533" 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">
1533
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<pre style="margin: 0;">+<span id="LC1533" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//vm->_validateCompressedStorage();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1534" 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">
1534
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<pre style="margin: 0;">+<span id="LC1534" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1535" 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">
1535
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<pre style="margin: 0;">+<span id="LC1535" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tempDiags</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">alloca</span> <span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hDim</span><span class="p">);</span></span>
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1536
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<pre style="margin: 0;">+<span id="LC1536" class="line" lang="cpp"> <span class="n" style="color: #333;">InitializeArray</span><span class="p">(</span><span class="n" style="color: #333;">tempDiags</span><span class="p">,</span> <span class="n" style="color: #333;">hDim</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</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="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1538" 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">
1538
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<pre style="margin: 0;">+<span id="LC1538" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">freq_matrix</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" 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">
1539
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<pre style="margin: 0;">+<span id="LC1539" 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;">long</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;">lDim</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="p">{</span></span>
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1540
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<pre style="margin: 0;">+<span id="LC1540" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theIndex</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 new new_line" 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">
1541
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<pre style="margin: 0;">+<span id="LC1541" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">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 class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1542" 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">
1542
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<pre style="margin: 0;">+<span id="LC1542" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">vDim</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1543" 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">
1543
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<pre style="margin: 0;">+<span id="LC1543" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">vDim</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1544" 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">
1544
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<pre style="margin: 0;">+<span id="LC1544" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1545" 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">
1545
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<pre style="margin: 0;">+<span id="LC1545" class="line" lang="cpp"> <span class="n" style="color: #333;">tempDiags</span><span class="p">[</span><span class="n" style="color: #333;">h</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">dp</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;">freq_matrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]);</span></span>
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1546
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<pre style="margin: 0;">+<span id="LC1546" class="line" lang="cpp"> <span class="p">}</span></span>
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1506
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1547
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<pre style="margin: 0;"> <span id="LC1547" class="line" lang="cpp"> <span class="p">}</span></span>
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1507
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1548
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<pre style="margin: 0;"> <span id="LC1548" class="line" lang="cpp"> <span class="p">}</span></span>
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1508
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<td class="diff-line-num new_line old" data-linenumber="1549" 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="LC1508" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="p">}</span></span>
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1509
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<td class="diff-line-num new_line old" data-linenumber="1549" 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="LC1509" class="line" lang="cpp"> <span class="p"><span class="idiff left right">}</span></span></span>
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1510
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<td class="diff-line-num new_line old" data-linenumber="1549" 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="LC1510" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left right">else</span></span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1511" 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">
1511
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<pre style="margin: 0;">-<span id="LC1511" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">for</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">lDim</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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1512
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<td class="diff-line-num new_line old" data-linenumber="1549" 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="LC1512" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">p</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">theIndex</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">];</span></span></span>
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1513
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<pre style="margin: 0;">-<span id="LC1513" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">p</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="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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1514
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<pre style="margin: 0;">-<span id="LC1514" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">h</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">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">/</span></span><span class="n" style="color: #333;">vDim</span><span class="p">;</span></span>
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1515
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<td class="diff-line-num new_line old" data-linenumber="1549" 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="LC1515" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">p</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">h</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">vDim</span></span><span class="p"><span class="idiff right">;</span></span></span>
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1516
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<pre style="margin: 0;">-<span id="LC1516" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">h</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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1517
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<pre style="margin: 0;">-<span id="LC1517" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">tempDiags</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">h</span></span><span class="p"><span class="idiff">]</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">dp</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">];</span></span></span>
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1549
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<pre style="margin: 0;">+<span id="LC1549" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1550" 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">
1550
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<pre style="margin: 0;">+<span id="LC1550" class="line" lang="cpp"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1551" 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">
1551
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<pre style="margin: 0;">+<span id="LC1551" class="line" lang="cpp"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">lDim</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="p"><span class="idiff right">)</span></span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1552" 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">
1552
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<pre style="margin: 0;">+<span id="LC1552" class="line" lang="cpp"> <span class="idiff left"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">p</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">theIndex</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">];</span></span></span>
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1553
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<pre style="margin: 0;">+<span id="LC1553" class="line" lang="cpp"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">p</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="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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1554
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<pre style="margin: 0;">+<span id="LC1554" class="line" lang="cpp"> <span class="idiff left"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">h</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">p</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">vDim</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1555" 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">
1555
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<pre style="margin: 0;">+<span id="LC1555" class="line" lang="cpp"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">p</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">p</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">h</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">*</span></span><span class="n" style="color: #333;">vDim</span><span class="p">;</span></span>
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1556
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<pre style="margin: 0;">+<span id="LC1556" class="line" lang="cpp"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">h</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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1557
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<pre style="margin: 0;">+<span id="LC1557" class="line" lang="cpp"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">tempDiags</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">h</span></span><span class="p"><span class="idiff">]</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">dp</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">];</span></span></span>
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1558
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<pre style="margin: 0;">+<span id="LC1558" class="line" lang="cpp"> <span class="p"><span class="idiff left right">}</span></span></span>
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1518
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1559
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<pre style="margin: 0;"> <span id="LC1559" class="line" lang="cpp"> <span class="p">}</span></span>
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1519
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1560
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<pre style="margin: 0;"> <span id="LC1560" class="line" lang="cpp"> <span class="p">}</span></span>
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1520
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<pre style="margin: 0;">-<span id="LC1520" class="line" lang="cpp"> <span class="p">}</span></span>
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1521
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<pre style="margin: 0;">-<span id="LC1521" class="line" lang="cpp"> <span class="p">}</span></span>
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1561
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<pre style="margin: 0;">+<span id="LC1561" class="line" lang="cpp"> <span class="p">}</span></span>
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1522
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1562
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<pre style="margin: 0;"> <span id="LC1562" class="line" lang="cpp"> </span>
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1523
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<td class="diff-line-num new_line old" data-linenumber="1563" 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="LC1523" 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;">long</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0L</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;">hDim</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="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1524" 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">
1524
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<td class="diff-line-num new_line old" data-linenumber="1563" 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="LC1524" class="line" lang="cpp"> <span class="n" style="color: #333;">vm</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Store</span> <span class="p">(</span><span class="n" style="color: #333;">j</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;">tempDiags</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1525" 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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1563
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<pre style="margin: 0;">+<span id="LC1563" 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;">long</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0L</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;">hDim</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="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1564" 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">
1564
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<pre style="margin: 0;">+<span id="LC1564" class="line" lang="cpp"> <span class="n" style="color: #333;">vm</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Store</span> <span class="p">(</span><span class="n" style="color: #333;">j</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;">tempDiags</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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1565
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<pre style="margin: 0;">+<span id="LC1565" class="line" lang="cpp"> <span class="p">}</span></span>
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1525
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1566
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<pre style="margin: 0;"> <span id="LC1566" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1526
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1567
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<pre style="margin: 0;"> <span id="LC1567" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="1527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1527
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1568
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<pre style="margin: 0;"> <span id="LC1568" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1529" style="width: 35px; color: rgba(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="1570" style="width: 35px; color: rgba(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">@@ -1529,9 +1570,7 @@ HBLObjectRef _Matrix::MultByFreqs (long freqID, bool reuse_value_object) {</td>
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1529
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1570
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<pre style="margin: 0;"> <span id="LC1570" class="line" lang="cpp"></span>
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1530
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1571
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<pre style="margin: 0;"> <span id="LC1571" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">freq_matrix</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1531
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<td class="diff-line-num new_line" data-linenumber="1572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1572
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<pre style="margin: 0;"> <span id="LC1572" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">freq_matrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theIndex</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1532" 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">
1532
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<td class="diff-line-num new_line old" data-linenumber="1573" 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="LC1532" 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;">long</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;">lDim</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="p">{</span></span>
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1533
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<td class="diff-line-num new_line old" data-linenumber="1573" 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="LC1533" class="line" lang="cpp"> <span class="n" style="color: #333;">theMatrix</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="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">freq_matrix</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;">vDim</span><span class="p">];</span></span>
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1534
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<pre style="margin: 0;">-<span id="LC1534" class="line" lang="cpp"> <span class="p">}</span></span>
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1573
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<pre style="margin: 0;">+<span id="LC1573" class="line" lang="cpp"> <span class="n" style="color: #333;">HandleApplicationError</span><span class="p">(</span><span class="n" style="color: #333;">_String</span><span class="p">(</span><span class="s" style="color: #d14;">"Sparse frequency matrices are not supported"</span><span class="p">));</span></span>
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1535
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1574
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<pre style="margin: 0;"> <span id="LC1574" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1536
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<td class="diff-line-num new_line" data-linenumber="1575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1575
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<pre style="margin: 0;"> <span id="LC1575" 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;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">column</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0UL</span><span class="p">;</span> <span class="n" style="color: #333;">column</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">vDim</span><span class="p">;</span> <span class="n" style="color: #333;">column</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1537
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<td class="diff-line-num new_line" data-linenumber="1576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1576
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<pre style="margin: 0;"> <span id="LC1576" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">freq_i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">freq_matrix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">column</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">@@ -1856,14 +1895,40 @@ bool _Matrix::AmISparseFast (_Matrix& whereTo) {</td>
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1856
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1895
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<pre style="margin: 0;"> <span id="LC1895" class="line" lang="cpp"> </span>
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1857
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1896
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<pre style="margin: 0;"> <span id="LC1896" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">non_zero_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">alloca</span> <span class="p">(</span><span class="n" style="color: #333;">threshold</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;">long</span><span class="p">));</span></span>
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1858
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1897
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<pre style="margin: 0;"> <span id="LC1897" class="line" lang="cpp"> </span>
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1859
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<pre style="margin: 0;">-<span id="LC1859" 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;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0UL</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;">lDim</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="p">{</span></span>
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1860
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<pre style="margin: 0;">-<span id="LC1860" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">__builtin_expect</span><span class="p">(</span><span class="n" style="color: #333;">theData</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;">ZEROOBJECT</span><span class="p">,</span> <span class="mi" style="color: #099;">0L</span><span class="p">))</span> <span class="p">{</span></span>
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1861
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<pre style="margin: 0;">-<span id="LC1861" class="line" lang="cpp"> <span class="n" style="color: #333;">non_zero_index</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 class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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1862
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<pre style="margin: 0;">-<span id="LC1862" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">threshold</span><span class="p">)</span> <span class="p">{</span></span>
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1863
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<pre style="margin: 0;">-<span id="LC1863" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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1864
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<pre style="margin: 0;">-<span id="LC1864" class="line" lang="cpp"> <span class="p">}</span></span>
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1865
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<pre style="margin: 0;">-<span id="LC1865" class="line" lang="cpp"> <span class="p">}</span></span>
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1898
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<pre style="margin: 0;">+<span id="LC1898" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_AVX_INTRINSICS</span></span>
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1899
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<pre style="margin: 0;">+<span id="LC1899" class="line" lang="cpp"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">zeros</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_setzero_pd</span><span class="p">();</span></span>
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1900
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<pre style="margin: 0;">+<span id="LC1900" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">lDimMOD4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lDim</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">2</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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1901
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<pre style="margin: 0;">+<span id="LC1901" 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;">long</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;">lDimMOD4</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;">4</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1902" 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">
1902
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<pre style="margin: 0;">+<span id="LC1902" class="line" lang="cpp"> <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;">_mm256_movemask_pd</span><span class="p">(</span><span class="n" style="color: #333;">_mm256_cmp_pd</span> <span class="p">(</span><span class="n" style="color: #333;">_mm256_loadu_pd</span> <span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">),</span> <span class="n" style="color: #333;">zeros</span><span class="p">,</span> <span class="n" style="color: #333;">_CMP_NEQ_OQ</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1903" 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">
1903
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<pre style="margin: 0;">+<span id="LC1903" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">res</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// something is different</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1904" 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">
1904
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<pre style="margin: 0;">+<span id="LC1904" class="line" lang="cpp"> <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="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">non_zero_index</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 class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">threshold</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC1905" class="line" lang="cpp"> <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="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">non_zero_index</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 class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">threshold</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="p">};</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1906" 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">
1906
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<pre style="margin: 0;">+<span id="LC1906" class="line" lang="cpp"> <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="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">non_zero_index</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 class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">threshold</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="p">};</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1907" 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">
1907
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<pre style="margin: 0;">+<span id="LC1907" class="line" lang="cpp"> <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="mi" style="color: #099;">8</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">non_zero_index</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 class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">3</span><span class="p">;</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">threshold</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="p">};</span></span>
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1908
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<pre style="margin: 0;">+<span id="LC1908" class="line" lang="cpp"> <span class="p">}</span></span>
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1866
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1909
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<pre style="margin: 0;"> <span id="LC1909" class="line" lang="cpp"> <span class="p">}</span></span>
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1910
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<pre style="margin: 0;">+<span id="LC1910" class="line" lang="cpp"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1911" 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">
1911
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<pre style="margin: 0;">+<span id="LC1911" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">threshold</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1912" 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">
1912
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<pre style="margin: 0;">+<span id="LC1912" 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;">long</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lDimMOD4</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;">lDim</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="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1913" 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">
1913
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<pre style="margin: 0;">+<span id="LC1913" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">theData</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="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1914" 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">
1914
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<pre style="margin: 0;">+<span id="LC1914" class="line" lang="cpp"> <span class="n" style="color: #333;">non_zero_index</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 class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1915" 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">
1915
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<pre style="margin: 0;">+<span id="LC1915" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">threshold</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1916" 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">
1916
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<pre style="margin: 0;">+<span id="LC1916" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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1917
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<pre style="margin: 0;">+<span id="LC1917" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1918" 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">
1918
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<pre style="margin: 0;">+<span id="LC1918" class="line" lang="cpp"> <span class="p">}</span></span>
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1919
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<pre style="margin: 0;">+<span id="LC1919" class="line" lang="cpp"> <span class="p">}</span></span>
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1920
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<pre style="margin: 0;">+<span id="LC1920" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1921" 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">
1921
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<pre style="margin: 0;">+<span id="LC1921" 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;">long</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;">lDim</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="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1922" 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">
1922
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<pre style="margin: 0;">+<span id="LC1922" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">theData</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="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1923" 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">
1923
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<pre style="margin: 0;">+<span id="LC1923" class="line" lang="cpp"> <span class="n" style="color: #333;">non_zero_index</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 class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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1924
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<pre style="margin: 0;">+<span id="LC1924" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">threshold</span><span class="p">)</span> <span class="p">{</span></span>
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1925
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<pre style="margin: 0;">+<span id="LC1925" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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1926
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<pre style="margin: 0;">+<span id="LC1926" class="line" lang="cpp"> <span class="p">}</span></span>
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1927
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<pre style="margin: 0;">+<span id="LC1927" class="line" lang="cpp"> <span class="p">}</span></span>
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1928
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<pre style="margin: 0;">+<span id="LC1928" class="line" lang="cpp"> <span class="p">}</span></span>
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1929
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<pre style="margin: 0;">+<span id="LC1929" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1930
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<pre style="margin: 0;">+<span id="LC1930" class="line" lang="cpp"> </span>
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1931
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<pre style="margin: 0;">+<span id="LC1931" class="line" lang="cpp"> </span>
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1932
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<pre style="margin: 0;"> <span id="LC1932" class="line" lang="cpp"></span>
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1933
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<pre style="margin: 0;"> <span id="LC1933" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">threshold</span><span class="p">)</span> <span class="p">{</span></span>
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1869
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1934
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<pre style="margin: 0;"> <span id="LC1934" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// we indeed are sparse enough</span></span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1953" style="width: 35px; color: rgba(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">@@ -1888,14 +1953,15 @@ bool _Matrix::AmISparseFast (_Matrix& whereTo) {</td>
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1888
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1953
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<pre style="margin: 0;"> <span id="LC1953" class="line" lang="cpp"> <span class="n" style="color: #333;">whereTo</span><span class="p">.</span><span class="n" style="color: #333;">theIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">MatrixMemAllocate</span> <span class="p">(</span><span class="n" style="color: #333;">whereTo</span><span class="p">.</span><span class="n" style="color: #333;">lDim</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;">long</span><span class="p">));</span></span>
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1889
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1954
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<pre style="margin: 0;"> <span id="LC1954" class="line" lang="cpp"> <span class="p">}</span></span>
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1890
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1955
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<pre style="margin: 0;"> <span id="LC1955" class="line" lang="cpp"> </span>
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1891
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<pre style="margin: 0;">-<span id="LC1891" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;"><span class="idiff left">_hprestrict_</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">*</span></span> <span class="n" style="color: #333;">newData</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">canReuse</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">whereTo</span><span class="p">.</span><span class="n" style="color: #333;">theData</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">MatrixMemAllocate</span> <span class="p">(</span><span class="n" style="color: #333;">whereTo</span><span class="p">.</span><span class="n" style="color: #333;">lDim</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="p">));</span></span>
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1956
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<pre style="margin: 0;">+<span id="LC1956" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</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 right">_hprestrict_</span></span> <span class="n" style="color: #333;">newData</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">canReuse</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">whereTo</span><span class="p">.</span><span class="n" style="color: #333;">theData</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">MatrixMemAllocate</span> <span class="p">(</span><span class="n" style="color: #333;">whereTo</span><span class="p">.</span><span class="n" style="color: #333;">lDim</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="p">));</span></span>
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1892
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1957
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<pre style="margin: 0;"> <span id="LC1957" class="line" lang="cpp"> </span>
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1893
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1958
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<pre style="margin: 0;"> <span id="LC1958" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">whereTo</span><span class="p">.</span><span class="n" style="color: #333;">compressedIndex</span><span class="p">)</span> <span class="p">{</span></span>
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1894
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1959
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<pre style="margin: 0;"> <span id="LC1959" class="line" lang="cpp"> <span class="n" style="color: #333;">MatrixMemFree</span><span class="p">(</span><span class="n" style="color: #333;">whereTo</span><span class="p">.</span><span class="n" style="color: #333;">compressedIndex</span><span class="p">);</span></span>
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1895
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1960
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<pre style="margin: 0;"> <span id="LC1960" class="line" lang="cpp"> <span class="p">}</span></span>
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1896
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1961
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<pre style="margin: 0;"> <span id="LC1961" class="line" lang="cpp"> <span class="n" style="color: #333;">whereTo</span><span class="p">.</span><span class="n" style="color: #333;">compressedIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">MatrixMemAllocate</span><span class="p">((</span><span class="n" style="color: #333;">whereTo</span><span class="p">.</span><span class="n" style="color: #333;">lDim</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">hDim</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;">long</span><span class="p">));</span></span>
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1897
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1962
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<pre style="margin: 0;"> <span id="LC1962" class="line" lang="cpp"> </span>
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1898
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<td class="diff-line-num new_line old" data-linenumber="1963" 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="LC1898" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">currentRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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1963
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<pre style="margin: 0;">+<span id="LC1963" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">currentRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1964" 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">
1964
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<pre style="margin: 0;">+<span id="LC1964" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">wci</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">whereTo</span><span class="p">.</span><span class="n" style="color: #333;">compressedIndex</span><span class="p">;</span></span>
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1899
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1965
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<pre style="margin: 0;"> <span id="LC1965" class="line" lang="cpp"></span>
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1900
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1966
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<pre style="margin: 0;"> <span id="LC1966" 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;">long</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0L</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;">k</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="p">{</span></span>
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1901
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1967
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<pre style="margin: 0;"> <span id="LC1967" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printf ("%ld %ld", i, theIndex[i]);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1905" style="width: 35px; color: rgba(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="1971" style="width: 35px; color: rgba(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">@@ -1905,10 +1971,10 @@ bool _Matrix::AmISparseFast (_Matrix& whereTo) {</td>
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1905
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1971
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<pre style="margin: 0;"> <span id="LC1971" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">indexRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">entryIndex</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">vDim</span><span class="p">,</span></span>
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1906
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1972
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<pre style="margin: 0;"> <span id="LC1972" class="line" lang="cpp"> <span class="n" style="color: #333;">indexColumn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">entryIndex</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">indexRow</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">vDim</span><span class="p">;</span></span>
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1907
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1973
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<pre style="margin: 0;"> <span id="LC1973" class="line" lang="cpp"> </span>
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1908
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<td class="diff-line-num new_line old" data-linenumber="1974" 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="LC1908" class="line" lang="cpp"> <span class="n" style="color: #333;">w<span class="idiff left">hereTo</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">compressedIndex</span></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;">hDim</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexColumn</span><span class="p">;</span></span>
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1974
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<pre style="margin: 0;">+<span id="LC1974" class="line" lang="cpp"> <span class="n" style="color: #333;">w<span class="idiff left right">ci</span></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;">hDim</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexColumn</span><span class="p">;</span></span>
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1909
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1975
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<pre style="margin: 0;"> <span id="LC1975" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">indexRow</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">currentRow</span><span class="p">)</span> <span class="p">{</span></span>
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1910
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1976
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<pre style="margin: 0;"> <span id="LC1976" 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;">long</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">currentRow</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;">indexRow</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="p">{</span></span>
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1911
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<pre style="margin: 0;">-<span id="LC1911" class="line" lang="cpp"> <span class="n" style="color: #333;">w<span class="idiff left">hereTo</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">compressedIndex</span></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;">i</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1977" 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">
1977
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<pre style="margin: 0;">+<span id="LC1977" class="line" lang="cpp"> <span class="n" style="color: #333;">w<span class="idiff left right">ci</span></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;">i</span><span class="p">;</span></span>
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1912
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1978
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<pre style="margin: 0;"> <span id="LC1978" class="line" lang="cpp"> <span class="p">}</span></span>
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1913
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1979
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<pre style="margin: 0;"> <span id="LC1979" class="line" lang="cpp"> <span class="n" style="color: #333;">currentRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexRow</span><span class="p">;</span></span>
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1914
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1980
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<pre style="margin: 0;"> <span id="LC1980" class="line" lang="cpp"> <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">@@ -2151,53 +2217,33 @@ bool _Matrix::CheckIfSparseEnough(bool force, bool copy) {</td>
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2151
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<pre style="margin: 0;"> <span id="LC2217" class="line" lang="cpp"><span class="p">}</span></span>
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2218
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<pre style="margin: 0;"> <span id="LC2218" class="line" lang="cpp"></span>
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2153
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2219
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<pre style="margin: 0;"> <span id="LC2219" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_____________________________________________________________________________________________</span></span>
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2154
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<pre style="margin: 0;">-<span id="LC2154" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">_Matrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IncreaseStorage</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span></span>
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2155
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<pre style="margin: 0;">-<span id="LC2155" class="line" lang="cpp"><span class="p">{</span></span>
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2220
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<pre style="margin: 0;">+<span id="LC2220" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">_Matrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IncreaseStorage</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC2221" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">compressedIndex</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC2222" class="line" lang="cpp"> <span class="n" style="color: #333;">HandleApplicationError</span><span class="p">(</span><span class="s" style="color: #d14;">"Internal error. Called _Matrix::IncreaseStorage on compressed index matrix"</span><span class="p">);</span></span>
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2223
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<pre style="margin: 0;">+<span id="LC2223" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2224" class="line" lang="cpp"> <span class="p">}</span></span>
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2225
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<pre style="margin: 0;"> <span id="LC2225" class="line" lang="cpp"> <span class="n" style="color: #333;">lDim</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">allocationBlock</span><span class="p">;</span></span>
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2157
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<pre style="margin: 0;">-<span id="LC2157" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC2158" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tempIndex</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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2159
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<pre style="margin: 0;">-<span id="LC2159" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC2160" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">tempIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">MatrixMemAllocate</span><span class="p">(</span><span class="n" style="color: #333;">lDim</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;">long</span><span class="p">))))</span> <span class="p">{</span></span>
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2161
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<pre style="margin: 0;">-<span id="LC2161" class="line" lang="cpp"> <span class="n" style="color: #333;">HandleApplicationError</span> <span class="p">(</span> <span class="n" style="color: #333;">kErrorStringMemoryFail</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC2162" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC2163" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span> <span class="p">(</span><span class="n" style="color: #333;">tempIndex</span><span class="p">,</span> <span class="n" style="color: #333;">theIndex</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">lDim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">allocationBlock</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;">long</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC2164" class="line" lang="cpp"> <span class="n" style="color: #333;">MatrixMemFree</span><span class="p">(</span> <span class="n" style="color: #333;">theIndex</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC2165" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC2166" class="line" lang="cpp"> <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;">lDim</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;">lDim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">allocationBlock</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="p">{</span></span>
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2167
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<pre style="margin: 0;">-<span id="LC2167" class="line" lang="cpp"> <span class="n" style="color: #333;">tempIndex</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="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2168
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<pre style="margin: 0;">-<span id="LC2168" class="line" lang="cpp"> <span class="p">}</span></span>
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2169
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<td class="diff-line-num new_line old" data-linenumber="2226" 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="LC2169" class="line" lang="cpp"> <span class="n" style="color: #333;">theIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempIndex</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2170" 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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2226
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<pre style="margin: 0;">+<span id="LC2226" class="line" lang="cpp"> <span class="n" style="color: #333;">theIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">MemReallocate</span><span class="p">(</span><span class="n" style="color: #333;">theIndex</span><span class="p">,</span> <span class="n" style="color: #333;">lDim</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;">long</span><span class="p">));</span></span>
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2227
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<pre style="margin: 0;">+<span id="LC2227" 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;">long</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lDim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">allocationBlock</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;">lDim</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="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2228" 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">
2228
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<pre style="margin: 0;">+<span id="LC2228" class="line" lang="cpp"> <span class="n" style="color: #333;">theIndex</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="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2170
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2229
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<pre style="margin: 0;"> <span id="LC2229" class="line" lang="cpp"> <span class="p">}</span></span>
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2171
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2230
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<pre style="margin: 0;"> <span id="LC2230" class="line" lang="cpp"></span>
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2172
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<pre style="margin: 0;">-<span id="LC2172" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">storageType</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">1</span></span><span class="p"><span class="idiff right">)</span></span></span>
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2231
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<pre style="margin: 0;">+<span id="LC2231" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">is_numeric</span></span><span class="p"><span class="idiff">())</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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2173
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2232
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<pre style="margin: 0;"> <span id="LC2232" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// pointers or formulas</span></span>
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2174
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<pre style="margin: 0;">-<span id="LC2174" class="line" lang="cpp"> <span class="p">{</span></span>
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2175
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2233
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<pre style="margin: 0;"> <span id="LC2233" class="line" lang="cpp"> <span class="n" style="color: #333;">_MathObject</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">tempData</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2176
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<td class="diff-line-num new_line" data-linenumber="2234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2234
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<pre style="margin: 0;"> <span id="LC2234" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">tempData</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">_MathObject</span><span class="o" style="font-weight: 600;">**</span><span class="p">)</span> <span class="n" style="color: #333;">MatrixMemAllocate</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;">char</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lDim</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;">void</span><span class="o" style="font-weight: 600;">*</span><span class="p">))))</span> <span class="p">{</span></span>
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2177
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2235
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<pre style="margin: 0;"> <span id="LC2235" class="line" lang="cpp"> <span class="n" style="color: #333;">HandleApplicationError</span> <span class="p">(</span> <span class="n" style="color: #333;">kErrorStringMemoryFail</span> <span class="p">);</span></span>
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2178
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2236
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<pre style="margin: 0;"> <span id="LC2236" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2179" 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">
2179
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<td class="diff-line-num new_line old" data-linenumber="2237" 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="LC2179" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span> <span class="p">(</span><span class="n" style="color: #333;">tempData</span><span class="p">,</span> <span class="n" style="color: #333;">theData</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">lDim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">allocationBlock</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;">void</span><span class="o" style="font-weight: 600;">*</span><span class="p">));</span></span>
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2180
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<pre style="margin: 0;">-<span id="LC2180" class="line" lang="cpp"> <span class="n" style="color: #333;">MatrixMemFree</span> <span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="p">);</span></span>
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2181
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<pre style="margin: 0;">-<span id="LC2181" class="line" lang="cpp"> <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;">lDim</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;">lDim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">allocationBlock</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="p">{</span></span>
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2182
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<pre style="margin: 0;">-<span id="LC2182" class="line" lang="cpp"> <span class="n" style="color: #333;">tempData</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;">ZEROPOINTER</span><span class="p">;</span></span>
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2237
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<pre style="margin: 0;">+<span id="LC2237" class="line" lang="cpp"> <span class="n" style="color: #333;">theData</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">MemReallocate</span><span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="p">,</span> <span class="n" style="color: #333;">lDim</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;">void</span><span class="o" style="font-weight: 600;">*</span><span class="p">));</span></span>
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2238
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<pre style="margin: 0;">+<span id="LC2238" 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;">long</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lDim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">allocationBlock</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;">lDim</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="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2239" 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">
2239
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<pre style="margin: 0;">+<span id="LC2239" class="line" lang="cpp"> <span class="n" style="color: #333;">theData</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;">ZEROPOINTER</span><span class="p">;</span></span>
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2183
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2240
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<pre style="margin: 0;"> <span id="LC2240" class="line" lang="cpp"> <span class="p">}</span></span>
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2184
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<td class="diff-line-num new_line old" data-linenumber="2241" 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="LC2184" class="line" lang="cpp"> <span class="n" style="color: #333;">theData</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">tempData</span><span class="p">;</span></span>
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2185
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2241
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<pre style="margin: 0;"> <span id="LC2241" class="line" lang="cpp"> <span class="p">}</span></span>
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2186
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<td class="diff-line-num new_line 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="LC2186" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span></span>
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2242
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<pre style="margin: 0;">+<span id="LC2242" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span><span class="idiff left"> </span><span class="p"><span class="idiff right">{</span></span></span>
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2187
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2243
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<pre style="margin: 0;"> <span id="LC2243" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//objects</span></span>
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2188
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<pre style="margin: 0;">-<span id="LC2188" class="line" lang="cpp"> <span class="p">{</span></span>
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2189
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<pre style="margin: 0;">-<span id="LC2189" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tempData</span><span class="p">;</span></span>
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2190
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<pre style="margin: 0;">-<span id="LC2190" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">tempData</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">MatrixMemAllocate</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lDim</span><span class="p">)))</span> <span class="p">{</span></span>
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2191
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<pre style="margin: 0;">-<span id="LC2191" class="line" lang="cpp"> <span class="n" style="color: #333;">HandleApplicationError</span> <span class="p">(</span> <span class="n" style="color: #333;">kErrorStringMemoryFail</span> <span class="p">);</span></span>
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2192
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<pre style="margin: 0;">-<span id="LC2192" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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2193
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<td class="diff-line-num new_line old" data-linenumber="2244" 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="LC2193" class="line" lang="cpp"> <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;">lDim</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;">lDim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">allocationBlock</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="p">{</span></span>
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2194
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<td class="diff-line-num new_line old" data-linenumber="2244" 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="LC2194" class="line" lang="cpp"> <span class="n" style="color: #333;">tempData</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;">ZEROOBJECT</span><span class="p">;</span></span>
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2195
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<pre style="margin: 0;">-<span id="LC2195" class="line" lang="cpp"> <span class="p">}</span></span>
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2196
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<pre style="margin: 0;">-<span id="LC2196" class="line" lang="cpp"> <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="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="cpp"> <span class="n" style="color: #333;">tempData</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="p">((</span><span class="n" style="color: #333;">hyFloat</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">theData</span><span class="p">)</span> <span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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2198
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<pre style="margin: 0;">-<span id="LC2198" class="line" lang="cpp"> <span class="p">}</span></span>
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2199
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<pre style="margin: 0;">-<span id="LC2199" class="line" lang="cpp"> <span class="n" style="color: #333;">MatrixMemFree</span><span class="p">(</span> <span class="n" style="color: #333;">theData</span><span class="p">);</span></span>
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2200
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<pre style="margin: 0;">-<span id="LC2200" class="line" lang="cpp"> <span class="n" style="color: #333;">theData</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempData</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="cpp"> <span class="n" style="color: #333;">theData</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">MemReallocate</span><span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="p">,</span> <span class="n" style="color: #333;">lDim</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="p">));</span></span>
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2245
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<pre style="margin: 0;">+<span id="LC2245" 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;">long</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lDim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">allocationBlock</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;">lDim</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="p">{</span></span>
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2246
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<pre style="margin: 0;">+<span id="LC2246" class="line" lang="cpp"> <span class="n" style="color: #333;">theData</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;">ZEROOBJECT</span><span class="p">;</span></span>
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2201
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2247
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<pre style="margin: 0;"> <span id="LC2247" class="line" lang="cpp"> <span class="p">}</span></span>
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2202
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2248
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<pre style="margin: 0;"> <span id="LC2248" class="line" lang="cpp"> <span class="p">}</span></span>
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2203
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2249
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<pre style="margin: 0;"> <span id="LC2249" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">TRUE</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2209" style="width: 35px; color: rgba(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">@@ -2209,10 +2255,10 @@ bool _Matrix::IncreaseStorage (void)</td>
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2209
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2255
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<pre style="margin: 0;"> <span id="LC2255" class="line" lang="cpp"></span>
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2210
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2256
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<pre style="margin: 0;"> <span id="LC2256" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">_Matrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Convert2Formulas</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span></span>
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2211
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2257
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<pre style="margin: 0;"> <span id="LC2257" class="line" lang="cpp"><span class="p">{</span></span>
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2212
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<pre style="margin: 0;">-<span id="LC2212" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">storageType</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">1</span></span><span class="p">)</span> <span class="p">{</span></span>
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2213
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<pre style="margin: 0;">-<span id="LC2213" class="line" lang="cpp"> <span class="n" style="color: #333;">storageType</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">;</span></span>
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2258
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<pre style="margin: 0;">+<span id="LC2258" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">is_numeric</span></span><span class="p"><span class="idiff right">()</span>)</span> <span class="p">{</span></span>
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2259
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<pre style="margin: 0;">+<span id="LC2259" class="line" lang="cpp"> <span class="n" style="color: #333;">storageType</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">_FORMULA_TYPE</span></span><span class="p">;</span></span>
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2214
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2260
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<pre style="margin: 0;"> <span id="LC2260" class="line" lang="cpp"> <span class="n" style="color: #333;">_Formula</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">tempData</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">_Formula</span><span class="o" style="font-weight: 600;">**</span><span class="p">)</span><span class="n" style="color: #333;">MatrixMemAllocate</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;">void</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;">lDim</span><span class="p">);</span></span>
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2215
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<pre style="margin: 0;">-<span id="LC2215" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff right">theIndex</span></span><span class="p">)</span> <span class="p">{</span></span>
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2261
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<pre style="margin: 0;">+<span id="LC2261" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">is_dense</span></span><span class="p"><span class="idiff right">()</span>)</span> <span class="p">{</span></span>
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2216
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2262
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<pre style="margin: 0;"> <span id="LC2262" 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;">long</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;">lDim</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="p">{</span></span>
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2217
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2263
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<pre style="margin: 0;"> <span id="LC2263" class="line" lang="cpp"> <span class="n" style="color: #333;">tempData</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="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">_Formula</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">_Constant</span> <span class="p">(((</span><span class="n" style="color: #333;">hyFloat</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">theData</span><span class="p">)[</span><span class="n" style="color: #333;">i</span><span class="p">]));</span></span>
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2218
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2264
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<pre style="margin: 0;"> <span id="LC2264" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2575" style="width: 35px; color: rgba(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="2621" style="width: 35px; color: rgba(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">@@ -2575,7 +2621,7 @@ _String* _Matrix::BranchLengthExpression (_Matrix* baseFreqs, bool mbf) {</td>
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2575
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2621
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<pre style="margin: 0;"> <span id="LC2621" class="line" lang="cpp"></span>
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2576
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2622
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<pre style="margin: 0;"> <span id="LC2622" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_____________________________________________________________________________________________</span></span>
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2577
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2623
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<pre style="margin: 0;"> <span id="LC2623" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">_Matrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">MakeMeSimple</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="p">{</span></span>
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2578
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<pre style="margin: 0;">-<span id="LC2578" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">storageType</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">_FORMULA_TYPE</span></span><span class="p">)</span> <span class="p">{</span></span>
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2624
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<pre style="margin: 0;">+<span id="LC2624" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">is_expression_based</span></span><span class="p"><span class="idiff right">()</span>)</span> <span class="p">{</span></span>
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2579
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2625
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<pre style="margin: 0;"> <span id="LC2625" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">stackLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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2580
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2626
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<pre style="margin: 0;"> <span id="LC2626" class="line" lang="cpp"></span>
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2581
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2627
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<pre style="margin: 0;"> <span id="LC2627" class="line" lang="cpp"> <span class="n" style="color: #333;">_SimpleList</span> <span class="n" style="color: #333;">newFormulas</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2588" style="width: 35px; color: rgba(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="2634" style="width: 35px; color: rgba(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">@@ -2588,6 +2634,10 @@ void _Matrix::MakeMeSimple (void) {</td>
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2588
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2634
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<pre style="margin: 0;"> <span id="LC2634" class="line" lang="cpp"> <span class="n" style="color: #333;">_SimpleList</span> <span class="n" style="color: #333;">varListAux</span><span class="p">;</span></span>
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2589
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2635
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<pre style="margin: 0;"> <span id="LC2635" class="line" lang="cpp"> <span class="n" style="color: #333;">_AVLList</span> <span class="n" style="color: #333;">varList</span> <span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">varListAux</span><span class="p">);</span></span>
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2590
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2636
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<pre style="margin: 0;"> <span id="LC2636" class="line" lang="cpp"> </span>
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2637
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<pre style="margin: 0;">+<span id="LC2637" class="line" lang="cpp"> </span>
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<td class="diff-line-num new new_line" data-linenumber="2638" 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">
2638
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<pre style="margin: 0;">+<span id="LC2638" class="line" lang="cpp"> <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;">is_dense</span><span class="p">())</span> <span class="p">{</span></span>
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2639
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<pre style="margin: 0;">+<span id="LC2639" class="line" lang="cpp"> <span class="n" style="color: #333;">CompressSparseMatrix</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">alloca</span> <span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lDim</span><span class="p">));</span></span>
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2640
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<pre style="margin: 0;">+<span id="LC2640" class="line" lang="cpp"> <span class="p">}</span></span>
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2591
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<td class="diff-line-num new_line" data-linenumber="2641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2641
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<pre style="margin: 0;"> <span id="LC2641" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ProcessFormulas</span> <span class="p">(</span><span class="n" style="color: #333;">stackLength</span><span class="p">,</span><span class="n" style="color: #333;">varList</span><span class="p">,</span><span class="n" style="color: #333;">newFormulas</span><span class="p">,</span><span class="n" style="color: #333;">references</span><span class="p">,</span><span class="n" style="color: #333;">flaStrings</span><span class="p">))</span> <span class="p">{</span></span>
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2592
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2642
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<pre style="margin: 0;"> <span id="LC2642" class="line" lang="cpp"> <span class="n" style="color: #333;">storageType</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_SIMPLE_FORMULA_TYPE</span><span class="p">;</span></span>
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2593
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2643
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<pre style="margin: 0;"> <span id="LC2643" 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">@@ -2816,6 +2866,51 @@ void _Matrix::FillInList (_List& fillMe, bool convert_numbers) const {</td>
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2816
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2866
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<pre style="margin: 0;"> <span id="LC2866" class="line" lang="cpp"> <span class="p">}</span></span>
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2867
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<pre style="margin: 0;"> <span id="LC2867" class="line" lang="cpp"><span class="p">}</span></span>
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2818
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2868
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<pre style="margin: 0;"> <span id="LC2868" class="line" lang="cpp"></span>
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2869
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<pre style="margin: 0;">+<span id="LC2869" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_____________________________________________________________________________________________</span></span>
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2870
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<pre style="margin: 0;">+<span id="LC2870" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">_Matrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_validateCompressedStorage</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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2871
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<pre style="margin: 0;">+<span id="LC2871" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">theIndex</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">compressedIndex</span><span class="p">)</span> <span class="p">{</span></span>
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2872
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<pre style="margin: 0;">+<span id="LC2872" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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2873
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<pre style="margin: 0;">+<span id="LC2873" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">last_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1L</span><span class="p">;</span></span>
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2874
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<pre style="margin: 0;">+<span id="LC2874" 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;">long</span> <span class="n" style="color: #333;">r</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;">r</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hDim</span><span class="p">;</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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2875
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<pre style="margin: 0;">+<span id="LC2875" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lDim</span> <span class="p">)</span> <span class="p">{</span></span>
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2876
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<pre style="margin: 0;">+<span id="LC2876" class="line" lang="cpp"> <span class="n" style="color: #333;">HandleApplicationError</span><span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"Inconsistent compressedIndex row element count at "</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">r</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;">from</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">" vs "</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">]);</span></span>
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2877
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<pre style="margin: 0;">+<span id="LC2877" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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2878
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<pre style="margin: 0;">+<span id="LC2878" class="line" lang="cpp"> <span class="p">}</span></span>
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2879
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<pre style="margin: 0;">+<span id="LC2879" 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;">long</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">from</span><span class="p">;</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">];</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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2880
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<pre style="margin: 0;">+<span id="LC2880" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">myIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theIndex</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">];</span></span>
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2881
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<pre style="margin: 0;">+<span id="LC2881" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">myIndex</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">last_index</span><span class="p">)</span> <span class="p">{</span></span>
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2882
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<pre style="margin: 0;">+<span id="LC2882" class="line" lang="cpp"> <span class="n" style="color: #333;">HandleApplicationError</span><span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"Lack of sortedness in theIndex at "</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">c</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;">myIndex</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">" vs "</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">last_index</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2883" 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">
2883
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<pre style="margin: 0;">+<span id="LC2883" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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2884
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<pre style="margin: 0;">+<span id="LC2884" class="line" lang="cpp"> <span class="p">}</span></span>
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2885
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<pre style="margin: 0;">+<span id="LC2885" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">myIndex</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">myIndex</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">hDim</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">vDim</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2886" 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">
2886
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<pre style="margin: 0;">+<span id="LC2886" class="line" lang="cpp"> <span class="n" style="color: #333;">HandleApplicationError</span><span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"Out of bounds in theIndex at "</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">c</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;">myIndex</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">", lDim = "</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">lDim</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2887" 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">
2887
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<pre style="margin: 0;">+<span id="LC2887" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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2888
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<pre style="margin: 0;">+<span id="LC2888" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2889" 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">
2889
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<pre style="margin: 0;">+<span id="LC2889" class="line" lang="cpp"> <span class="n" style="color: #333;">last_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">myIndex</span><span class="p">;</span></span>
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2890
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<pre style="margin: 0;">+<span id="LC2890" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">from</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2891" 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">
2891
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<pre style="margin: 0;">+<span id="LC2891" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">hDim</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">compressedIndex</span> <span class="p">[</span><span class="n" style="color: #333;">c</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;">hDim</span><span class="p">])</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2892" 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">
2892
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<pre style="margin: 0;">+<span id="LC2892" class="line" lang="cpp"> <span class="n" style="color: #333;">HandleApplicationError</span><span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"Lack of sortedness in columns at "</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">c</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;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">hDim</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">" vs "</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">hDim</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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2893
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<pre style="margin: 0;">+<span id="LC2893" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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2894
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<pre style="margin: 0;">+<span id="LC2894" class="line" lang="cpp"> <span class="p">}</span></span>
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2895
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<pre style="margin: 0;">+<span id="LC2895" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2896" 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">
2896
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<pre style="margin: 0;">+<span id="LC2896" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">myIndex</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">vDim</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">myIndex</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">hDim</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">vDim</span><span class="p">])</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2897" 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">
2897
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<pre style="margin: 0;">+<span id="LC2897" class="line" lang="cpp"> <span class="n" style="color: #333;">HandleApplicationError</span><span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"Stored index does match row/column "</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">myIndex</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;">c</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;">r</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;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">hDim</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2898" 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">
2898
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<pre style="margin: 0;">+<span id="LC2898" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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2899
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<pre style="margin: 0;">+<span id="LC2899" class="line" lang="cpp"> <span class="p">}</span></span>
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2900
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<pre style="margin: 0;">+<span id="LC2900" class="line" lang="cpp"> <span class="p">}</span></span>
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2901
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<pre style="margin: 0;">+<span id="LC2901" class="line" lang="cpp"> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">];</span></span>
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2902
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<pre style="margin: 0;">+<span id="LC2902" class="line" lang="cpp"> <span class="p">}</span></span>
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2903
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<pre style="margin: 0;">+<span id="LC2903" class="line" lang="cpp"> </span>
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2904
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<pre style="margin: 0;">+<span id="LC2904" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">hDim</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;">lDim</span><span class="p">)</span> <span class="p">{</span></span>
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2905
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<pre style="margin: 0;">+<span id="LC2905" class="line" lang="cpp"> <span class="n" style="color: #333;">HandleApplicationError</span><span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"Incompatible compressedIndex[hDim-1] and lDim: "</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">hDim</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="s" style="color: #d14;">" : "</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">lDim</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2906" 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">
2906
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<pre style="margin: 0;">+<span id="LC2906" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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2907
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<pre style="margin: 0;">+<span id="LC2907" class="line" lang="cpp"> <span class="p">}</span></span>
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2908
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<pre style="margin: 0;">+<span id="LC2908" class="line" lang="cpp"> </span>
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2909
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<pre style="margin: 0;">+<span id="LC2909" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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2910
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<pre style="margin: 0;">+<span id="LC2910" class="line" lang="cpp"> <span class="p">}</span></span>
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2911
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<pre style="margin: 0;">+<span id="LC2911" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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2912
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<pre style="margin: 0;">+<span id="LC2912" class="line" lang="cpp"><span class="p">}</span></span>
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2913
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<pre style="margin: 0;">+<span id="LC2913" class="line" lang="cpp"></span>
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2819
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2914
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<pre style="margin: 0;"> <span id="LC2914" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_____________________________________________________________________________________________</span></span>
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2820
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2915
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<pre style="margin: 0;"> <span id="LC2915" class="line" lang="cpp"><span class="n" style="color: #333;">HBLObjectRef</span> <span class="n" style="color: #333;">_Matrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EvaluateSimple</span> <span class="p">(</span><span class="n" style="color: #333;">_Matrix</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">existing_storage</span><span class="p">)</span> <span class="p">{</span></span>
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2821
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2916
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<pre style="margin: 0;"> <span id="LC2916" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// evaluate the matrix overwriting the old one</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2848" style="width: 35px; color: rgba(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="2943" style="width: 35px; color: rgba(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">@@ -2848,46 +2943,152 @@ HBLObjectRef _Matrix::EvaluateSimple (_Matrix* existing_storage) {</td>
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2848
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2943
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<pre style="margin: 0;"> <span id="LC2943" class="line" lang="cpp"> <span class="p">}</span></span>
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2849
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2944
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<pre style="margin: 0;"> <span id="LC2944" class="line" lang="cpp"></span>
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2850
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2945
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<pre style="margin: 0;"> <span id="LC2945" class="line" lang="cpp"></span>
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2851
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<pre style="margin: 0;">-<span id="LC2851" 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;">long</span> <span class="n" style="color: #333;">f</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;">f</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">formulasToEval</span><span class="p">.</span><span class="n" style="color: #333;">lLength</span><span class="p">;</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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2946
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<pre style="margin: 0;">+<span id="LC2946" 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;">long</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0<span class="idiff left right">L</span></span><span class="p">;</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">formulasToEval</span><span class="p">.</span><span class="n" style="color: #333;">lLength</span><span class="p">;</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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2852
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<pre style="margin: 0;"> <span id="LC2947" class="line" lang="cpp"> <span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">formulaValues</span> <span class="p">[</span><span class="n" style="color: #333;">f</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">_Formula</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">formulasToEval</span><span class="p">.</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">f</span><span class="p">])</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ComputeSimple</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theStack</span><span class="p">,</span> <span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">varValues</span><span class="p">);</span></span>
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2948
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<pre style="margin: 0;"> <span id="LC2948" class="line" lang="cpp"> <span class="p">}</span></span>
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2949
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<pre style="margin: 0;"> <span id="LC2949" class="line" lang="cpp"></span>
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2855
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2950
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<pre style="margin: 0;"> <span id="LC2950" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">formulaRefs</span><span class="p">;</span></span>
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2856
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2951
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<pre style="margin: 0;"> <span id="LC2951" class="line" lang="cpp"></span>
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2857
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2952
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<pre style="margin: 0;"> <span id="LC2952" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">theIndex</span><span class="p">)</span> <span class="p">{</span></span>
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2858
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<pre style="margin: 0;">-<span id="LC2858" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lDim</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">lDim</span><span class="p">)</span> <span class="p">{</span></span>
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2859
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<td class="diff-line-num new_line old" data-linenumber="2953" 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="LC2859" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lDim</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lDim</span><span class="p">;</span></span>
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2860
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<pre style="margin: 0;">-<span id="LC2860" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">MemReallocate</span><span class="p">((</span><span class="n" style="color: #333;">hyPointer</span><span class="p">)</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theIndex</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;">long</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lDim</span><span class="p">);</span></span>
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2861
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<pre style="margin: 0;">-<span id="LC2861" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">MemReallocate</span> <span class="p">((</span><span class="n" style="color: #333;">hyPointer</span><span class="p">)</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span><span class="p">,</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lDim</span><span class="p">);</span></span>
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2862
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<pre style="margin: 0;">-<span id="LC2862" class="line" lang="cpp"> <span class="p">}</span></span>
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2953
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<pre style="margin: 0;">+<span id="LC2953" class="line" lang="cpp"> </span>
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2863
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2954
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<pre style="margin: 0;"> <span id="LC2954" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bufferPerRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bufferPerRow</span><span class="p">;</span></span>
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2864
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2955
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<pre style="margin: 0;"> <span id="LC2955" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overflowBuffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">overflowBuffer</span><span class="p">;</span></span>
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2865
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2956
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<pre style="margin: 0;"> <span id="LC2956" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">allocationBlock</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allocationBlock</span><span class="p">;</span></span>
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2957
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<pre style="margin: 0;">+<span id="LC2957" class="line" lang="cpp"> </span>
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2958
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<pre style="margin: 0;">+<span id="LC2958" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">diagIndices</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nil</span><span class="p">;</span></span>
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2866
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2959
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<pre style="margin: 0;"> <span id="LC2959" class="line" lang="cpp"></span>
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2960
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<pre style="margin: 0;">+<span id="LC2960" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">compressedIndex</span><span class="p">)</span> <span class="p">{</span></span>
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2961
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<pre style="margin: 0;">+<span id="LC2961" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lDim</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">lDim</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">hDim</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2962" 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">
2962
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<pre style="margin: 0;">+<span id="LC2962" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">MemReallocate</span><span class="p">((</span><span class="n" style="color: #333;">hyPointer</span><span class="p">)</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theIndex</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;">long</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">lDim</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">hDim</span><span class="p">));</span></span>
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2963
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<pre style="margin: 0;">+<span id="LC2963" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">MemReallocate</span> <span class="p">((</span><span class="n" style="color: #333;">hyPointer</span><span class="p">)</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span><span class="p">,</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">lDim</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">hDim</span><span class="p">));</span></span>
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2964
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<pre style="margin: 0;">+<span id="LC2964" class="line" lang="cpp"> </span>
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2965
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<pre style="margin: 0;">+<span id="LC2965" class="line" lang="cpp"> <span class="p">}</span></span>
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2966
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<pre style="margin: 0;">+<span id="LC2966" class="line" lang="cpp"> </span>
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2967
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<pre style="margin: 0;">+<span id="LC2967" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lDim</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lDim</span><span class="p">;</span></span>
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2968
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<pre style="margin: 0;">+<span id="LC2968" class="line" lang="cpp"> </span>
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<td class="diff-line-num new new_line" data-linenumber="2969" 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">
2969
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<pre style="margin: 0;">+<span id="LC2969" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressedIndex</span><span class="p">)</span> <span class="p">{</span></span>
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2970
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<pre style="margin: 0;">+<span id="LC2970" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressedIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">MemReallocate</span> <span class="p">((</span><span class="n" style="color: #333;">hyPointer</span><span class="p">)</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressedIndex</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;">long</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">lDim</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">hDim</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">hDim</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2971" 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">
2971
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<pre style="margin: 0;">+<span id="LC2971" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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2972
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<pre style="margin: 0;">+<span id="LC2972" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressedIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">MemAllocate</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;">long</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">lDim</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">hDim</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">hDim</span><span class="p">));</span></span>
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2973
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<pre style="margin: 0;">+<span id="LC2973" class="line" lang="cpp"> <span class="p">}</span></span>
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2974
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<pre style="margin: 0;">+<span id="LC2974" class="line" lang="cpp"> </span>
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2975
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<pre style="margin: 0;">+<span id="LC2975" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hDim</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">vDim</span><span class="p">)</span> <span class="p">{</span></span>
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2976
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<pre style="margin: 0;">+<span id="LC2976" class="line" lang="cpp"> </span>
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<td class="diff-line-num new new_line" data-linenumber="2977" 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">
2977
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<pre style="margin: 0;">+<span id="LC2977" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">elements_added</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2978" 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">
2978
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<pre style="margin: 0;">+<span id="LC2978" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">current_element_index_old_matrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2979" 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">
2979
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<pre style="margin: 0;">+<span id="LC2979" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">current_element_index_new_matrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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2980
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<pre style="margin: 0;">+<span id="LC2980" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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2981
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<pre style="margin: 0;">+<span id="LC2981" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">copy_indices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="o" style="font-weight: 600;">&</span><span class="p">]</span> <span class="p">()</span> <span class="o" style="font-weight: 600;">-></span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="p">{</span></span>
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2982
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<pre style="margin: 0;">+<span id="LC2982" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theIndex</span><span class="p">[</span><span class="n" style="color: #333;">current_element_index_new_matrix</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theIndex</span><span class="p">[</span><span class="n" style="color: #333;">current_element_index_old_matrix</span><span class="p">];</span></span>
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2983
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<pre style="margin: 0;">+<span id="LC2983" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">current_element_index_new_matrix</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">hDim</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">hDim</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">current_element_index_old_matrix</span><span class="p">];</span></span>
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2984
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<pre style="margin: 0;">+<span id="LC2984" class="line" lang="cpp"> <span class="p">};</span></span>
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2985
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<pre style="margin: 0;">+<span id="LC2985" class="line" lang="cpp"> <span class="n" style="color: #333;">diagIndices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">alloca</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;">long</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hDim</span><span class="p">);</span></span>
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2986
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<pre style="margin: 0;">+<span id="LC2986" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">inject_diagonal</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="o" style="font-weight: 600;">&</span><span class="p">]</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">r</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="p">{</span></span>
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2987
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<pre style="margin: 0;">+<span id="LC2987" class="line" lang="cpp"> <span class="n" style="color: #333;">elements_added</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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2988
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<pre style="margin: 0;">+<span id="LC2988" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lDim</span> <span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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2989
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<pre style="margin: 0;">+<span id="LC2989" class="line" lang="cpp"> <span class="n" style="color: #333;">diagIndices</span> <span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_element_index_new_matrix</span><span class="p">;</span></span>
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2990
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<pre style="margin: 0;">+<span id="LC2990" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theIndex</span><span class="p">[</span><span class="n" style="color: #333;">current_element_index_new_matrix</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">vDim</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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2991
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<pre style="margin: 0;">+<span id="LC2991" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">current_element_index_new_matrix</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.</span><span class="p">;</span></span>
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2992
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<pre style="margin: 0;">+<span id="LC2992" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">current_element_index_new_matrix</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">hDim</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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2993
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<pre style="margin: 0;">+<span id="LC2993" class="line" lang="cpp"> <span class="n" style="color: #333;">current_element_index_new_matrix</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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2994
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<pre style="margin: 0;">+<span id="LC2994" class="line" lang="cpp"> <span class="p">};</span></span>
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2995
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<pre style="margin: 0;">+<span id="LC2995" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*if (!_validateCompressedStorage()) {</span></span>
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2996
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<pre style="margin: 0;">+<span id="LC2996" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> HandleApplicationError("Error in compressed storage [before]");</span></span>
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2997
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<pre style="margin: 0;">+<span id="LC2997" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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2998
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<pre style="margin: 0;">+<span id="LC2998" 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;">long</span> <span class="n" style="color: #333;">r</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;">r</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hDim</span><span class="p">;</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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2999
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<pre style="margin: 0;">+<span id="LC2999" class="line" lang="cpp"> <span class="n" style="color: #333;">diagIndices</span><span class="p">[</span><span class="n" style="color: #333;">r</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;">1L</span><span class="p">;</span></span>
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3000
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<pre style="margin: 0;">+<span id="LC3000" 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;">long</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">from</span><span class="p">;</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">];</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">current_element_index_old_matrix</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">current_element_index_new_matrix</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3001" 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">
3001
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<pre style="margin: 0;">+<span id="LC3001" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">hDim</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">r</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// column before diagonal; copy data</span></span>
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3002
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<pre style="margin: 0;">+<span id="LC3002" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">current_element_index_new_matrix</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">formulaValues</span><span class="p">[</span><span class="n" style="color: #333;">fidx</span><span class="p">[</span><span class="n" style="color: #333;">current_element_index_old_matrix</span><span class="p">]];</span></span>
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3003
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<pre style="margin: 0;">+<span id="LC3003" class="line" lang="cpp"> <span class="n" style="color: #333;">copy_indices</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3004" 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">
3004
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<pre style="margin: 0;">+<span id="LC3004" class="line" lang="cpp"> <span class="p">}</span> <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;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">hDim</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">r</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3005" 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">
3005
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<pre style="margin: 0;">+<span id="LC3005" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">diagIndices</span><span class="p">[</span><span class="n" style="color: #333;">r</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 class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// no diagonal entry</span></span>
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3006
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<pre style="margin: 0;">+<span id="LC3006" class="line" lang="cpp"> <span class="n" style="color: #333;">inject_diagonal</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">);</span></span>
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3007
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<pre style="margin: 0;">+<span id="LC3007" class="line" lang="cpp"> <span class="p">}</span></span>
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3008
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<pre style="margin: 0;">+<span id="LC3008" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">current_element_index_new_matrix</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">formulaValues</span><span class="p">[</span><span class="n" style="color: #333;">fidx</span><span class="p">[</span><span class="n" style="color: #333;">current_element_index_old_matrix</span><span class="p">]];</span></span>
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3009
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<pre style="margin: 0;">+<span id="LC3009" class="line" lang="cpp"> <span class="n" style="color: #333;">copy_indices</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3010" 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">
3010
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<pre style="margin: 0;">+<span id="LC3010" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// diagnoal entry</span></span>
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3011
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<pre style="margin: 0;">+<span id="LC3011" class="line" lang="cpp"> <span class="n" style="color: #333;">copy_indices</span><span class="p">();</span></span>
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3012
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<pre style="margin: 0;">+<span id="LC3012" class="line" lang="cpp"> <span class="n" style="color: #333;">diagIndices</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_element_index_new_matrix</span><span class="p">;</span></span>
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3013
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<pre style="margin: 0;">+<span id="LC3013" class="line" lang="cpp"> <span class="p">}</span></span>
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3014
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<pre style="margin: 0;">+<span id="LC3014" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3015" 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">
3015
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<pre style="margin: 0;">+<span id="LC3015" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">diagIndices</span><span class="p">[</span><span class="n" style="color: #333;">r</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 class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// no diagonal entry</span></span>
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3016
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<pre style="margin: 0;">+<span id="LC3016" class="line" lang="cpp"> <span class="n" style="color: #333;">inject_diagonal</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">);</span></span>
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3017
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<pre style="margin: 0;">+<span id="LC3017" class="line" lang="cpp"> <span class="p">}</span></span>
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3018
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<pre style="margin: 0;">+<span id="LC3018" class="line" lang="cpp"> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">];</span></span>
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3019
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<pre style="margin: 0;">+<span id="LC3019" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">from</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">elements_added</span><span class="p">;</span></span>
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3020
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<pre style="margin: 0;">+<span id="LC3020" class="line" lang="cpp"> </span>
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3021
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<pre style="margin: 0;">+<span id="LC3021" class="line" lang="cpp"> <span class="p">}</span></span>
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3022
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<pre style="margin: 0;">+<span id="LC3022" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*if (!result->_validateCompressedStorage()) {</span></span>
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3023
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<pre style="margin: 0;">+<span id="LC3023" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> HandleApplicationError("Error in compressed storage");</span></span>
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3024
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<pre style="margin: 0;">+<span id="LC3024" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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3025
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<pre style="margin: 0;">+<span id="LC3025" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3026" 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">
3026
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<pre style="margin: 0;">+<span id="LC3026" 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;">long</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;">lDim</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="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3027" 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">
3027
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<pre style="margin: 0;">+<span id="LC3027" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theIndex</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 new new_line" data-linenumber="3028" 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">
3028
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<pre style="margin: 0;">+<span id="LC3028" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</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;">cmd</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">formulaValues</span><span class="p">[</span><span class="n" style="color: #333;">fidx</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]];</span></span>
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3029
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<pre style="margin: 0;">+<span id="LC3029" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theIndex</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;">idx</span><span class="p">;</span></span>
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3030
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<pre style="margin: 0;">+<span id="LC3030" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressedIndex</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;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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3031
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<pre style="margin: 0;">+<span id="LC3031" class="line" lang="cpp"> <span class="p">}</span></span>
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3032
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<pre style="margin: 0;">+<span id="LC3032" 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;">long</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lDim</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;">lDim</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">hDim</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="p">{</span></span>
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3033
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<pre style="margin: 0;">+<span id="LC3033" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressedIndex</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;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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3034
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<pre style="margin: 0;">+<span id="LC3034" class="line" lang="cpp"> <span class="p">}</span></span>
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3035
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<pre style="margin: 0;">+<span id="LC3035" class="line" lang="cpp"> <span class="p">}</span></span>
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2867
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3036
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<pre style="margin: 0;"> <span id="LC3036" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="2868" 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">
2868
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<td class="diff-line-num new_line old" data-linenumber="3037" 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="LC2868" 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;">long</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;">lDim</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="p">{</span></span>
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2869
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<pre style="margin: 0;">-<span id="LC2869" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theIndex</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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2870
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<pre style="margin: 0;">-<span id="LC2870" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC2871" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">idx</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="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC2872" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</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;">cmd</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">formulaValues</span><span class="p">[</span><span class="n" style="color: #333;">fidx</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="LC3037" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC3038" class="line" lang="cpp"> </span>
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3039
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<pre style="margin: 0;">+<span id="LC3039" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lDim</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">lDim</span><span class="p">)</span> <span class="p">{</span></span>
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3040
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<pre style="margin: 0;">+<span id="LC3040" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lDim</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lDim</span><span class="p">;</span></span>
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3041
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<pre style="margin: 0;">+<span id="LC3041" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">MemReallocate</span><span class="p">((</span><span class="n" style="color: #333;">hyPointer</span><span class="p">)</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theIndex</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;">long</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lDim</span><span class="p">);</span></span>
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3042
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<pre style="margin: 0;">+<span id="LC3042" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">MemReallocate</span> <span class="p">((</span><span class="n" style="color: #333;">hyPointer</span><span class="p">)</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span><span class="p">,</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lDim</span><span class="p">);</span></span>
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3043
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<pre style="margin: 0;"> <span id="LC3043" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC3044" class="line" lang="cpp"> </span>
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3045
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<pre style="margin: 0;">+<span id="LC3045" 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;">long</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;">lDim</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="p">{</span></span>
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3046
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<pre style="margin: 0;">+<span id="LC3046" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theIndex</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="LC3047" class="line" lang="cpp"></span>
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3048
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<pre style="margin: 0;">+<span id="LC3048" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">idx</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="p">{</span></span>
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3049
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<pre style="margin: 0;">+<span id="LC3049" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</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;">cmd</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">formulaValues</span><span class="p">[</span><span class="n" style="color: #333;">fidx</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="LC3050" class="line" lang="cpp"> <span class="p">}</span></span>
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2874
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3051
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<pre style="margin: 0;"> <span id="LC3051" class="line" lang="cpp"></span>
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2875
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<pre style="margin: 0;">-<span id="LC2875" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theIndex</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;">idx</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC3052" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theIndex</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;">idx</span><span class="p">;</span></span>
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3053
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<pre style="margin: 0;">+<span id="LC3053" class="line" lang="cpp"> <span class="p">}</span></span>
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2876
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3054
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<pre style="margin: 0;"> <span id="LC3054" class="line" lang="cpp"> <span class="p">}</span></span>
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2877
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3055
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<pre style="margin: 0;"> <span id="LC3055" class="line" lang="cpp"></span>
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2878
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3056
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<pre style="margin: 0;"> <span id="LC3056" class="line" lang="cpp"></span>
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2879
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<td class="diff-line-num new_line" data-linenumber="3057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3057
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<pre style="margin: 0;"> <span id="LC3057" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hDim</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">vDim</span><span class="p">)</span> <span class="p">{</span></span>
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2880
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<td class="diff-line-num new_line old" data-linenumber="3058" 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="LC2880" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">diagStorage</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">alloca</span> <span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hDim</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2881" 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">
2881
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<td class="diff-line-num new_line old" data-linenumber="3058" 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="LC2881" class="line" lang="cpp"> <span class="n" style="color: #333;">InitializeArray</span><span class="p">(</span><span class="n" style="color: #333;">diagStorage</span><span class="p">,</span> <span class="n" style="color: #333;">hDim</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2882" 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">
2882
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<td class="diff-line-num new_line old" data-linenumber="3058" 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="LC2882" 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;">long</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;">lDim</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="p">{</span></span>
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2883
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<td class="diff-line-num new_line old" data-linenumber="3058" 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="LC2883" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theIndex</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 old old_line" data-linenumber="2884" 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">
2884
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<td class="diff-line-num new_line old" data-linenumber="3058" 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="LC2884" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2885" 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">
2885
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<td class="diff-line-num new_line old" data-linenumber="3058" 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="LC2885" class="line" lang="cpp"> <span class="n" style="color: #333;">diagStorage</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">hDim</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</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 new old_line" data-linenumber="2886" 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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3058
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<pre style="margin: 0;">+<span id="LC3058" class="line" lang="cpp"> </span>
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<td class="diff-line-num new new_line" data-linenumber="3059" 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">
3059
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<pre style="margin: 0;">+<span id="LC3059" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressedIndex</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3060" 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">
3060
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<pre style="margin: 0;">+<span id="LC3060" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3061" 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">
3061
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<pre style="margin: 0;">+<span id="LC3061" 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;">long</span> <span class="n" style="color: #333;">r</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;">r</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hDim</span><span class="p">;</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3062" 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">
3062
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<pre style="margin: 0;">+<span id="LC3062" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printf ("%ld\n", diagIndices[r]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3063" 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">
3063
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<pre style="margin: 0;">+<span id="LC3063" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">di</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">diagIndices</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3064" 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">
3064
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<pre style="margin: 0;">+<span id="LC3064" 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;">long</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">from</span><span class="p">;</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">];</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3065" 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">
3065
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<pre style="margin: 0;">+<span id="LC3065" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printf ("%ld %g\n", c, result->theData[c]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3066" 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">
3066
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<pre style="margin: 0;">+<span id="LC3066" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">di</span><span class="p">)</span> <span class="p">{</span></span>
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3067
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<pre style="margin: 0;">+<span id="LC3067" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">di</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">];</span></span>
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3068
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<pre style="margin: 0;">+<span id="LC3068" class="line" lang="cpp"> <span class="p">}</span></span>
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3069
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<pre style="margin: 0;">+<span id="LC3069" class="line" lang="cpp"> <span class="p">}</span></span>
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3070
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<pre style="margin: 0;">+<span id="LC3070" class="line" lang="cpp"> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">];</span></span>
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2886
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3071
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<pre style="margin: 0;"> <span id="LC3071" class="line" lang="cpp"> <span class="p">}</span></span>
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3072
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<pre style="margin: 0;">+<span id="LC3072" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*for (long r = 0; r < hDim; r++) {</span></span>
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3073
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<pre style="margin: 0;">+<span id="LC3073" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> printf ("%ld %g\n", diagIndices[r], result->theData[diagIndices[r]]);</span></span>
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3074
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<pre style="margin: 0;">+<span id="LC3074" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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3075
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<pre style="margin: 0;">+<span id="LC3075" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> exit (0);*/</span></span>
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2887
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3076
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<pre style="margin: 0;"> <span id="LC3076" class="line" lang="cpp"> <span class="p">}</span></span>
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2888
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<pre style="margin: 0;">-<span id="LC2888" 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;">long</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;">hDim</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="p">{</span></span>
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2889
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<pre style="margin: 0;">-<span id="LC2889" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">result</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;">hDim</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">diagStorage</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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2890
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<pre style="margin: 0;">-<span id="LC2890" class="line" lang="cpp"> <span class="p">}</span></span>
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3077
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<pre style="margin: 0;">+<span id="LC3077" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</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="cpp"> <span class="n" style="color: #333;">hyFloat</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">diagStorage</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">alloca</span> <span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hDim</span><span class="p">);</span></span>
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3079
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<pre style="margin: 0;">+<span id="LC3079" class="line" lang="cpp"> <span class="n" style="color: #333;">memset</span> <span class="p">(</span><span class="n" style="color: #333;">diagStorage</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hDim</span><span class="p">);</span></span>
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3080
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<pre style="margin: 0;">+<span id="LC3080" 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;">long</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;">lDim</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="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3081" 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">
3081
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<pre style="margin: 0;">+<span id="LC3081" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theIndex</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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3082
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<pre style="margin: 0;">+<span id="LC3082" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">1</span><span class="p">)</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="cpp"> <span class="n" style="color: #333;">diagStorage</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">hDim</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">i</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="cpp"> <span class="p">}</span></span>
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3085
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<pre style="margin: 0;">+<span id="LC3085" class="line" lang="cpp"> <span class="p">}</span></span>
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3086
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<pre style="margin: 0;">+<span id="LC3086" 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;">long</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;">hDim</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="p">{</span></span>
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3087
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<pre style="margin: 0;">+<span id="LC3087" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">result</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;">hDim</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">diagStorage</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="LC3088" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC3089" class="line" lang="cpp"> <span class="p">}</span></span>
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3090
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<pre style="margin: 0;">+<span id="LC3090" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC3091" class="line" lang="cpp"> </span>
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3092
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<pre style="margin: 0;"> <span id="LC3092" class="line" lang="cpp"> <span class="p">}</span></span>
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3093
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<pre style="margin: 0;"> <span id="LC3093" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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3094
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<pre style="margin: 0;"> <span id="LC3094" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2997" style="width: 35px; color: rgba(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="3198" style="width: 35px; color: rgba(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">@@ -2997,7 +3198,7 @@ void _Matrix::Clear (bool complete) {</td>
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3198
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<pre style="margin: 0;"> <span id="LC3198" class="line" lang="cpp"></span>
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3199
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<pre style="margin: 0;"> <span id="LC3199" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">_Matrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ZeroNumericMatrix</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="p">{</span></span>
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2999
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3200
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<pre style="margin: 0;"> <span id="LC3200" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_numeric</span><span class="p">())</span> <span class="p">{</span></span>
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3000
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<pre style="margin: 0;">-<span id="LC3000" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">InitializeArray</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">theData</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">lDim</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff right">0.0</span></span><span class="p">);</span></span>
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3201
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<pre style="margin: 0;">+<span id="LC3201" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">memset</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">theData</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">sizeof</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">hyFloat</span></span><span class="p"><span class="idiff">)</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">lDim</span></span><span class="p">);</span></span>
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3001
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3202
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<pre style="margin: 0;"> <span id="LC3202" class="line" lang="cpp"> <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;">is_dense</span><span class="p">())</span> <span class="p">{</span></span>
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3002
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3203
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<pre style="margin: 0;"> <span id="LC3203" class="line" lang="cpp"> <span class="n" style="color: #333;">InitializeArray</span> <span class="p">(</span><span class="n" style="color: #333;">theIndex</span><span class="p">,</span> <span class="n" style="color: #333;">lDim</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1L</span><span class="p">);</span></span>
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3003
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3204
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<pre style="margin: 0;"> <span id="LC3204" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3006" style="width: 35px; color: rgba(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="3207" style="width: 35px; color: rgba(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">@@ -3006,9 +3207,8 @@ void _Matrix::ZeroNumericMatrix (void) {</td>
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3006
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3207
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<pre style="margin: 0;"> <span id="LC3207" class="line" lang="cpp"></span>
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3007
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3208
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<pre style="margin: 0;"> <span id="LC3208" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_____________________________________________________________________________________________</span></span>
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3008
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3209
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<pre style="margin: 0;"> <span id="LC3209" class="line" lang="cpp"></span>
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3009
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<pre style="margin: 0;">-<span id="LC3009" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">_Matrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Resize</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">newH</span><span class="p">)</span></span>
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3010
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<pre style="margin: 0;">-<span id="LC3010" class="line" lang="cpp"><span class="p">{</span></span>
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3011
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<pre style="margin: 0;">-<span id="LC3011" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">newH</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">newH</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">hDim</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">storageType</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;">theIndex</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">nil</span><span class="p">)</span> <span class="p">{</span></span>
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3210
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<pre style="margin: 0;">+<span id="LC3210" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">_Matrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Resize</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">newH</span><span class="p">)</span> <span class="p">{</span></span>
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3211
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<pre style="margin: 0;">+<span id="LC3211" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">newH</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">newH</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">hDim</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_numeric</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_dense</span><span class="p">())</span> <span class="p">{</span></span>
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3012
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3212
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<pre style="margin: 0;"> <span id="LC3212" class="line" lang="cpp"> <span class="n" style="color: #333;">hDim</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newH</span><span class="p">;</span></span>
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3013
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3213
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<pre style="margin: 0;"> <span id="LC3213" class="line" lang="cpp"> <span class="n" style="color: #333;">lDim</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newH</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">vDim</span><span class="p">;</span></span>
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3014
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3214
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<pre style="margin: 0;"> <span id="LC3214" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3151" style="width: 35px; color: rgba(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">@@ -3151,13 +3351,24 @@ void _Matrix::AddMatrix (_Matrix& storage, _Matrix& secondArg, bool subtract</td>
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3351
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<pre style="margin: 0;"> <span id="LC3351" class="line" lang="cpp"> </span>
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3152
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3352
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<pre style="margin: 0;"> <span id="LC3352" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">subtract</span><span class="p">)</span> <span class="p">{</span></span>
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3153
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3353
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<pre style="margin: 0;"> <span id="LC3353" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_AVX_INTRINSICS</span></span>
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3154
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<pre style="margin: 0;">-<span id="LC3154" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define CELL_OP(x) _mm256_storeu_pd (stData+x, _mm256_sub_pd (_mm256_loadu_pd (stData+x), _mm256_loadu_pd (argData+x)))</span></span>
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3354
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<pre style="margin: 0;">+<span id="LC3354" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define CELL_OP1(x,y) __m256d y = _mm256_sub_pd (_mm256_loadu_pd (stData+x), _mm256_loadu_pd (argData+x))</span></span>
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3355
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<pre style="margin: 0;">+<span id="LC3355" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define CELL_OP2(x,y) _mm256_storeu_pd (stData+x,y)</span></span>
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3155
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3356
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<pre style="margin: 0;"> <span id="LC3356" class="line" lang="cpp"> </span>
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3156
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<pre style="margin: 0;">-<span id="LC3156" 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;">long</span> <span class="n" style="color: #333;">idx</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;">idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">upto</span><span class="p">;</span> <span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">16</span><span class="p">)</span> <span class="p">{</span></span>
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3157
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<pre style="margin: 0;">-<span id="LC3157" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">);</span></span>
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3158
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<pre style="margin: 0;">-<span id="LC3158" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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3159
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<pre style="margin: 0;">-<span id="LC3159" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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3160
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<pre style="margin: 0;">-<span id="LC3160" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">12</span><span class="p">);</span></span>
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3357
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<pre style="margin: 0;">+<span id="LC3357" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>
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3358
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<pre style="margin: 0;">+<span id="LC3358" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop vectorize(enable)</span></span>
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3359
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<pre style="margin: 0;">+<span id="LC3359" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop interleave(enable)</span></span>
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3360
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<pre style="margin: 0;">+<span id="LC3360" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop unroll(enable)</span></span>
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3361
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<pre style="margin: 0;">+<span id="LC3361" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC ivdep</span></span>
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3362
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<pre style="margin: 0;">+<span id="LC3362" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma ivdep</span></span>
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3363
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<pre style="margin: 0;">+<span id="LC3363" 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;">long</span> <span class="n" style="color: #333;">idx</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;">idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">upto</span><span class="p">;</span> <span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">16</span><span class="p">)</span> <span class="p">{</span></span>
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3364
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<pre style="margin: 0;">+<span id="LC3364" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">,</span><span class="n" style="color: #333;">r1</span><span class="p">);</span></span>
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3365
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<pre style="margin: 0;">+<span id="LC3365" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">4</span><span class="p">,</span><span class="n" style="color: #333;">r2</span><span class="p">);</span></span>
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3366
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<pre style="margin: 0;">+<span id="LC3366" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">8</span><span class="p">,</span><span class="n" style="color: #333;">r3</span><span class="p">);</span></span>
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3367
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<pre style="margin: 0;">+<span id="LC3367" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">12</span><span class="p">,</span><span class="n" style="color: #333;">r4</span><span class="p">);</span></span>
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3368
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<pre style="margin: 0;">+<span id="LC3368" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">,</span><span class="n" style="color: #333;">r1</span><span class="p">);</span></span>
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3369
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<pre style="margin: 0;">+<span id="LC3369" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">4</span><span class="p">,</span><span class="n" style="color: #333;">r2</span><span class="p">);</span></span>
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3370
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<pre style="margin: 0;">+<span id="LC3370" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">8</span><span class="p">,</span><span class="n" style="color: #333;">r3</span><span class="p">);</span></span>
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3371
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<pre style="margin: 0;">+<span id="LC3371" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">12</span><span class="p">,</span><span class="n" style="color: #333;">r4</span><span class="p">);</span></span>
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3161
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3372
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<pre style="margin: 0;"> <span id="LC3372" class="line" lang="cpp"> <span class="p">}</span></span>
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3162
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3373
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<pre style="margin: 0;"> <span id="LC3373" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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3163
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3374
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<pre style="margin: 0;"> <span id="LC3374" 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;">long</span> <span class="n" style="color: #333;">idx</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;">idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">upto</span><span class="p">;</span> <span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3170" style="width: 35px; color: rgba(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="3381" style="width: 35px; color: rgba(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">@@ -3170,14 +3381,19 @@ void _Matrix::AddMatrix (_Matrix& storage, _Matrix& secondArg, bool subtract</td>
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3170
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3381
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<pre style="margin: 0;"> <span id="LC3381" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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3171
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3382
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<pre style="margin: 0;"> <span id="LC3382" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_AVX_INTRINSICS</span></span>
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3172
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3383
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<pre style="margin: 0;"> <span id="LC3383" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define CELL_OP(x) _mm256_storeu_pd (stData+x, _mm256_add_pd (_mm256_loadu_pd (stData+x), _mm256_loadu_pd (argData+x)))</span></span>
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3173
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<pre style="margin: 0;">-<span id="LC3173" class="line" lang="cpp"> </span>
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3384
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<pre style="margin: 0;">+<span id="LC3384" class="line" lang="cpp"></span>
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3385
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<pre style="margin: 0;">+<span id="LC3385" class="line" lang="cpp"></span>
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3386
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<pre style="margin: 0;">+<span id="LC3386" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>
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3387
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<pre style="margin: 0;">+<span id="LC3387" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop vectorize(enable)</span></span>
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3388
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<pre style="margin: 0;">+<span id="LC3388" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop interleave(enable)</span></span>
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3389
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<pre style="margin: 0;">+<span id="LC3389" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop unroll(enable)</span></span>
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3174
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3390
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<pre style="margin: 0;"> <span id="LC3390" 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;">long</span> <span class="n" style="color: #333;">idx</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;">idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">upto</span><span class="p">;</span> <span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">16</span><span class="p">)</span> <span class="p">{</span></span>
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3175
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3391
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<pre style="margin: 0;"> <span id="LC3391" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">);</span></span>
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3176
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3392
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<pre style="margin: 0;"> <span id="LC3392" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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3177
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3393
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<pre style="margin: 0;"> <span id="LC3393" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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3178
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3394
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<pre style="margin: 0;"> <span id="LC3394" class="line" lang="cpp"> <span class="n" style="color: #333;">CELL_OP</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">12</span><span class="p">);</span></span>
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3179
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3395
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<pre style="margin: 0;"> <span id="LC3395" class="line" lang="cpp"> <span class="p">}</span></span>
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3180
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<pre style="margin: 0;">-<span id="LC3180" class="line" lang="cpp"></span>
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3396
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<pre style="margin: 0;">+<span id="LC3396" class="line" lang="cpp"> </span>
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3181
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3397
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<pre style="margin: 0;"> <span id="LC3397" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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3182
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3398
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<pre style="margin: 0;"> <span id="LC3398" 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;">long</span> <span class="n" style="color: #333;">idx</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;">idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">upto</span><span class="p">;</span> <span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>
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3183
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3399
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<pre style="margin: 0;"> <span id="LC3399" class="line" lang="cpp"> <span class="n" style="color: #333;">stData</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">]</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">argData</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3493" style="width: 35px; color: rgba(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="3709" style="width: 35px; color: rgba(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">@@ -3493,12 +3709,14 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix const& secondArg) const</td>
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3493
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3709
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<pre style="margin: 0;"> <span id="LC3709" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">storage</span><span class="p">.</span><span class="n" style="color: #333;">theData</span><span class="p">;</span></span>
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3494
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3710
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<pre style="margin: 0;"> <span id="LC3710" class="line" lang="cpp"> </span>
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3495
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<td class="diff-line-num new_line" data-linenumber="3711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3711
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<pre style="margin: 0;"> <span id="LC3711" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3712" 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">
3712
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<pre style="margin: 0;">+<span id="LC3712" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define DO_GROUP_OP0(X,Y,k) Y = _mm256_loadu_pd(secondArg.theData + col_offset + k); X = _mm256_mul_pd (A4,Y);</span></span>
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3496
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<td class="diff-line-num new_line" data-linenumber="3713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3713
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<pre style="margin: 0;"> <span id="LC3713" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_FMA3_INTRINSICS</span></span>
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3497
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3714
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<pre style="margin: 0;"> <span id="LC3714" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define DO_GROUP_OP(X,Y,k) X = _mm256_loadu_pd(dest + row_offset + k); Y = _mm256_loadu_pd(secondArg.theData + col_offset + k); _mm256_storeu_pd (dest + row_offset + k, _mm256_fmadd_pd (A4,Y,X));</span></span>
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3498
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3715
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<pre style="margin: 0;"> <span id="LC3715" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define DO_GROUP_OP1(X,Y,k) X = _mm256_loadu_pd(dest + row_offset + k); Y = _mm256_loadu_pd(secondArg.theData + col_offset + k); X = _mm256_fmadd_pd (A4,Y,X);</span></span>
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3499
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3716
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<pre style="margin: 0;"> <span id="LC3716" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define DO_GROUP_OP2(X,k) _mm256_storeu_pd (dest + row_offset + k,X);</span></span>
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3500
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3717
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<pre style="margin: 0;"> <span id="LC3717" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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3501
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<td class="diff-line-num new_line" data-linenumber="3718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3718
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<pre style="margin: 0;"> <span id="LC3718" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define DO_GROUP_OP(X,Y,k) X = _mm256_loadu_pd(dest + row_offset + k); Y = _mm256_loadu_pd(secondArg.theData + col_offset + k); _mm256_storeu_pd (dest + row_offset + k, _mm256_add_pd (X, _mm256_mul_pd(A4, Y)));</span></span>
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3719
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<pre style="margin: 0;">+<span id="LC3719" class="line" lang="cpp"></span>
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3502
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<td class="diff-line-num new_line" data-linenumber="3720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3720
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<pre style="margin: 0;"> <span id="LC3720" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define DO_GROUP_OP1(X,Y,k) X = _mm256_loadu_pd(dest + row_offset + k); Y = _mm256_loadu_pd(secondArg.theData + col_offset + k); X = _mm256_add_pd (X, _mm256_mul_pd(A4, Y));</span></span>
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3503
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<td class="diff-line-num new_line" data-linenumber="3721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3721
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<pre style="margin: 0;"> <span id="LC3721" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define DO_GROUP_OP2(X,k) _mm256_storeu_pd (dest + row_offset + k,X);</span></span>
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3504
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3722
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<pre style="margin: 0;"> <span id="LC3722" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3513" style="width: 35px; color: rgba(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="3731" style="width: 35px; color: rgba(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">@@ -3513,7 +3731,6 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix const& secondArg) const</td>
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3513
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3731
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<pre style="margin: 0;"> <span id="LC3731" class="line" lang="cpp"> </span>
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3514
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3732
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<pre style="margin: 0;"> <span id="LC3732" class="line" lang="cpp"> </span>
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3515
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<td class="diff-line-num new_line" data-linenumber="3733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3733
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<pre style="margin: 0;"> <span id="LC3733" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dimm4</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">vDim</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3516" 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">
3516
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<td class="diff-line-num new_line old" data-linenumber="3734" 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="LC3516" class="line" lang="cpp"> <span class="n" style="color: #333;">memset</span> <span class="p">(</span><span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">lDim</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="p">));</span></span>
</pre>
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3517
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<td class="diff-line-num new_line" data-linenumber="3734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3734
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<pre style="margin: 0;"> <span id="LC3734" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS</span></span>
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<td class="diff-line-num old_line" data-linenumber="3518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3518
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<td class="diff-line-num new_line" data-linenumber="3735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3735
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<pre style="margin: 0;"> <span id="LC3735" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">ti</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="3519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3519
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<td class="diff-line-num new_line" data-linenumber="3736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3736
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<pre style="margin: 0;"> <span id="LC3736" class="line" lang="cpp"> <span class="n" style="color: #333;">row_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3521" style="width: 35px; color: rgba(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="3738" style="width: 35px; color: rgba(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">@@ -3521,10 +3738,23 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix const& secondArg) const</td>
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3521
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3738
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<pre style="margin: 0;"> <span id="LC3738" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vDim</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">20UL</span><span class="p">)</span> <span class="p">{</span></span>
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3522
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<td class="diff-line-num new_line" data-linenumber="3739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3739
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<pre style="margin: 0;"> <span id="LC3739" 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;">long</span> <span class="n" style="color: #333;">r</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;">r</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">20</span><span class="p">;</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">row_offset</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">20</span><span class="p">)</span> <span class="p">{</span></span>
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3523
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3740
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<pre style="margin: 0;"> <span id="LC3740" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">col_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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3524
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<td class="diff-line-num new_line old" data-linenumber="3741" 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="LC3524" 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;">long</span> <span class="n" style="color: #333;">c</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;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">20L</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">col_offset</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">20L</span><span class="p">)</span> <span class="p">{</span></span>
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3525
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<td class="diff-line-num new_line old" data-linenumber="3741" 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="LC3525" class="line" lang="cpp"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">A4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_set1_pd</span><span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]);</span></span>
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3741
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<pre style="margin: 0;">+<span id="LC3741" class="line" lang="cpp"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">A4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_set1_pd</span><span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]);</span></span>
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3742
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<pre style="margin: 0;">+<span id="LC3742" class="line" lang="cpp"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">D4</span><span class="p">,</span> <span class="n" style="color: #333;">B4</span><span class="p">,</span> <span class="n" style="color: #333;">D4_1</span><span class="p">,</span> <span class="n" style="color: #333;">B4_1</span><span class="p">,</span> <span class="n" style="color: #333;">D4_2</span><span class="p">,</span> <span class="n" style="color: #333;">B4_2</span><span class="p">,</span> <span class="n" style="color: #333;">D4_3</span><span class="p">,</span> <span class="n" style="color: #333;">B4_3</span><span class="p">,</span> <span class="n" style="color: #333;">D4_4</span><span class="p">,</span> <span class="n" style="color: #333;">B4_4</span><span class="p">;</span></span>
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3743
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<pre style="margin: 0;">+<span id="LC3743" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">D4</span><span class="p">,</span> <span class="n" style="color: #333;">B4</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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3744
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<pre style="margin: 0;">+<span id="LC3744" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">D4_1</span><span class="p">,</span> <span class="n" style="color: #333;">B4_1</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3745" 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">
3745
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<pre style="margin: 0;">+<span id="LC3745" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">D4_2</span><span class="p">,</span> <span class="n" style="color: #333;">B4_2</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3746" 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">
3746
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<pre style="margin: 0;">+<span id="LC3746" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">D4_3</span><span class="p">,</span> <span class="n" style="color: #333;">B4_3</span><span class="p">,</span> <span class="mi" style="color: #099;">12</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3747" 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">
3747
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<pre style="margin: 0;">+<span id="LC3747" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">D4_4</span><span class="p">,</span> <span class="n" style="color: #333;">B4_4</span><span class="p">,</span> <span class="mi" style="color: #099;">16</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3748" 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">
3748
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<pre style="margin: 0;">+<span id="LC3748" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3749" 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">
3749
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<pre style="margin: 0;">+<span id="LC3749" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_1</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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3750
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<pre style="margin: 0;">+<span id="LC3750" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_2</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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3751
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<pre style="margin: 0;">+<span id="LC3751" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_3</span><span class="p">,</span> <span class="mi" style="color: #099;">12</span><span class="p">);</span></span>
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3752
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<pre style="margin: 0;">+<span id="LC3752" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4_4</span><span class="p">,</span> <span class="mi" style="color: #099;">16</span><span class="p">);</span></span>
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3753
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<pre style="margin: 0;">+<span id="LC3753" class="line" lang="cpp"> <span class="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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3754
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<pre style="margin: 0;">+<span id="LC3754" class="line" lang="cpp"> <span class="n" style="color: #333;">col_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">20L</span><span class="p">;</span></span>
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3755
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<pre style="margin: 0;">+<span id="LC3755" 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;">long</span> <span class="n" style="color: #333;">c</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;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">20L</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">col_offset</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">20L</span><span class="p">)</span> <span class="p">{</span></span>
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3756
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<pre style="margin: 0;">+<span id="LC3756" class="line" lang="cpp"> <span class="n" style="color: #333;">A4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_set1_pd</span><span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]);</span></span>
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3526
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3757
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<pre style="margin: 0;"> <span id="LC3757" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//for (long k = 0; k < 20L; k+=4) {</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3527" 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">
3527
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<pre style="margin: 0;">-<span id="LC3527" class="line" lang="cpp"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">D4</span><span class="p">,</span> <span class="n" style="color: #333;">B4</span><span class="p">,</span> <span class="n" style="color: #333;">D4_1</span><span class="p">,</span> <span class="n" style="color: #333;">B4_1</span><span class="p">,</span> <span class="n" style="color: #333;">D4_2</span><span class="p">,</span> <span class="n" style="color: #333;">B4_2</span><span class="p">,</span> <span class="n" style="color: #333;">D4_3</span><span class="p">,</span> <span class="n" style="color: #333;">B4_3</span><span class="p">,</span> <span class="n" style="color: #333;">D4_4</span><span class="p">,</span> <span class="n" style="color: #333;">B4_4</span><span class="p">;</span></span>
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3528
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3758
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<pre style="margin: 0;"> <span id="LC3758" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">D4</span><span class="p">,</span> <span class="n" style="color: #333;">B4</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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3529
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3759
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<pre style="margin: 0;"> <span id="LC3759" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">D4_1</span><span class="p">,</span> <span class="n" style="color: #333;">B4_1</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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3530
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3760
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<pre style="margin: 0;"> <span id="LC3760" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">D4_2</span><span class="p">,</span> <span class="n" style="color: #333;">B4_2</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3541" style="width: 35px; color: rgba(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="3771" style="width: 35px; color: rgba(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">@@ -3541,8 +3771,16 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix const& secondArg) const</td>
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3541
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3771
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<pre style="margin: 0;"> <span id="LC3771" class="line" lang="cpp"> <span class="p">}</span> <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;">vDim</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">60UL</span><span class="p">)</span> <span class="p">{</span></span>
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3542
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3772
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<pre style="margin: 0;"> <span id="LC3772" 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;">long</span> <span class="n" style="color: #333;">r</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;">r</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">60</span><span class="p">;</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">row_offset</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">60</span><span class="p">)</span> <span class="p">{</span></span>
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3543
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3773
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<pre style="margin: 0;"> <span id="LC3773" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">col_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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3544
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<td class="diff-line-num new_line old" data-linenumber="3774" 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="LC3544" 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;">long</span> <span class="n" style="color: #333;">c</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;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">60L</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">col_offset</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">60L</span><span class="p">)</span> <span class="p">{</span></span>
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3545
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<td class="diff-line-num new_line old" data-linenumber="3774" 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="LC3545" class="line" lang="cpp"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">A4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_set1_pd</span><span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]);</span></span>
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3774
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<pre style="margin: 0;">+<span id="LC3774" class="line" lang="cpp"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">A4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_set1_pd</span><span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]);</span></span>
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3775
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<pre style="margin: 0;">+<span id="LC3775" 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;">long</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;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">60L</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;">4</span><span class="p">)</span> <span class="p">{</span></span>
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3776
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<pre style="margin: 0;">+<span id="LC3776" class="line" lang="cpp"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">D4</span><span class="p">,</span> <span class="n" style="color: #333;">B4</span><span class="p">;</span></span>
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3777
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<pre style="margin: 0;">+<span id="LC3777" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">D4</span><span class="p">,</span> <span class="n" style="color: #333;">B4</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>
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3778
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<pre style="margin: 0;">+<span id="LC3778" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>
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3779
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<pre style="margin: 0;">+<span id="LC3779" class="line" lang="cpp"> <span class="p">}</span></span>
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3780
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<pre style="margin: 0;">+<span id="LC3780" class="line" lang="cpp"> <span class="n" style="color: #333;">col_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">60L</span><span class="p">;</span></span>
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3781
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<pre style="margin: 0;">+<span id="LC3781" class="line" lang="cpp"> <span class="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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3782
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<pre style="margin: 0;">+<span id="LC3782" 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;">long</span> <span class="n" style="color: #333;">c</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;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">60L</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">col_offset</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">60L</span><span class="p">)</span> <span class="p">{</span></span>
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3783
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<pre style="margin: 0;">+<span id="LC3783" class="line" lang="cpp"> <span class="n" style="color: #333;">A4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_set1_pd</span><span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]);</span></span>
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3546
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3784
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<pre style="margin: 0;"> <span id="LC3784" 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;">long</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;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">60L</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;">4</span><span class="p">)</span> <span class="p">{</span></span>
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3547
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3785
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<pre style="margin: 0;"> <span id="LC3785" class="line" lang="cpp"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">D4</span><span class="p">,</span> <span class="n" style="color: #333;">B4</span><span class="p">;</span></span>
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3548
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3786
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<pre style="margin: 0;"> <span id="LC3786" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP</span> <span class="p">(</span><span class="n" style="color: #333;">D4</span><span class="p">,</span> <span class="n" style="color: #333;">B4</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3552" style="width: 35px; color: rgba(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">@@ -3552,8 +3790,16 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix const& secondArg) const</td>
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3552
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3790
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<pre style="margin: 0;"> <span id="LC3790" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span></span>
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3553
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3791
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<pre style="margin: 0;"> <span id="LC3791" 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;">long</span> <span class="n" style="color: #333;">r</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;">r</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">vDim</span><span class="p">;</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">row_offset</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">vDim</span><span class="p">)</span> <span class="p">{</span></span>
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3554
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3792
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<pre style="margin: 0;"> <span id="LC3792" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">col_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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3555
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<pre style="margin: 0;">-<span id="LC3555" 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;">long</span> <span class="n" style="color: #333;">c</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;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">vDim</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">col_offset</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">vDim</span><span class="p">)</span> <span class="p">{</span></span>
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3556
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<pre style="margin: 0;">-<span id="LC3556" class="line" lang="cpp"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">A4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_set1_pd</span><span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]);</span></span>
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3793
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<pre style="margin: 0;">+<span id="LC3793" class="line" lang="cpp"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">A4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_set1_pd</span><span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]);</span></span>
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3794
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<pre style="margin: 0;">+<span id="LC3794" 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;">long</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;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">vDim</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;">4</span><span class="p">)</span> <span class="p">{</span></span>
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3795
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<pre style="margin: 0;">+<span id="LC3795" class="line" lang="cpp"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">D4</span><span class="p">,</span> <span class="n" style="color: #333;">B4</span><span class="p">;</span></span>
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3796
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<pre style="margin: 0;">+<span id="LC3796" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP0</span> <span class="p">(</span><span class="n" style="color: #333;">D4</span><span class="p">,</span> <span class="n" style="color: #333;">B4</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>
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3797
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<pre style="margin: 0;">+<span id="LC3797" class="line" lang="cpp"> <span class="n" style="color: #333;">DO_GROUP_OP2</span> <span class="p">(</span><span class="n" style="color: #333;">D4</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3798" 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">
3798
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<pre style="margin: 0;">+<span id="LC3798" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3799" 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">
3799
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<pre style="margin: 0;">+<span id="LC3799" class="line" lang="cpp"> <span class="n" style="color: #333;">col_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vDim</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3800" 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">
3800
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<pre style="margin: 0;">+<span id="LC3800" class="line" lang="cpp"> <span class="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3801" 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">
3801
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<pre style="margin: 0;">+<span id="LC3801" 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;">long</span> <span class="n" style="color: #333;">c</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;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">vDim</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">col_offset</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">vDim</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3802" 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">
3802
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<pre style="margin: 0;">+<span id="LC3802" class="line" lang="cpp"> <span class="n" style="color: #333;">A4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm256_set1_pd</span><span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]);</span></span>
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3557
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<td class="diff-line-num new_line" data-linenumber="3803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3803
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<pre style="margin: 0;"> <span id="LC3803" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>
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<td class="diff-line-num old_line" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3558
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3804
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<pre style="margin: 0;"> <span id="LC3804" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop vectorize(enable)</span></span>
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<td class="diff-line-num old_line" data-linenumber="3559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3559
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3805
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<pre style="margin: 0;"> <span id="LC3805" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop interleave(enable)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3566" style="width: 35px; color: rgba(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="3812" style="width: 35px; color: rgba(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">@@ -3566,7 +3812,8 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix const& secondArg) const</td>
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3566
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3812
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<pre style="margin: 0;"> <span id="LC3812" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="3567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3567
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<td class="diff-line-num new_line" data-linenumber="3813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3813
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<pre style="margin: 0;"> <span id="LC3813" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="3568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3568
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<td class="diff-line-num new_line" data-linenumber="3814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3814
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<pre style="margin: 0;"> <span id="LC3814" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#elif _SLKP_USE_SSE_INTRINSICS</span></span>
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3569
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<td class="diff-line-num new_line old" data-linenumber="3815" 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="LC3569" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">ti</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3570" 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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3815
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<pre style="margin: 0;">+<span id="LC3815" class="line" lang="cpp"> <span class="n" style="color: #333;">memset</span> <span class="p">(</span><span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">lDim</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3816" 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">
3816
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<pre style="margin: 0;">+<span id="LC3816" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">ti</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">,</span></span>
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3570
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<td class="diff-line-num new_line" data-linenumber="3817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3817
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<pre style="margin: 0;"> <span id="LC3817" class="line" lang="cpp"> <span class="n" style="color: #333;">row_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="3571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3571
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<td class="diff-line-num new_line" data-linenumber="3818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3818
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<pre style="margin: 0;"> <span id="LC3818" class="line" lang="cpp"> </span>
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<td class="diff-line-num old_line" data-linenumber="3572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3572
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<td class="diff-line-num new_line" data-linenumber="3819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3819
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<pre style="margin: 0;"> <span id="LC3819" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vDim</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">20UL</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3617" style="width: 35px; color: rgba(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="3864" style="width: 35px; color: rgba(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">@@ -3617,7 +3864,8 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix const& secondArg) const</td>
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3617
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3864
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<pre style="margin: 0;"> <span id="LC3864" class="line" lang="cpp"> <span class="p">}</span></span>
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3618
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<td class="diff-line-num new_line" data-linenumber="3865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3865
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<pre style="margin: 0;"> <span id="LC3865" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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3619
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<td class="diff-line-num new_line" data-linenumber="3866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3866
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<pre style="margin: 0;"> <span id="LC3866" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC3620" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC3867" class="line" lang="cpp"> <span class="n" style="color: #333;">memset</span> <span class="p">(</span><span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">lDim</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC3868" class="line" lang="cpp"></span>
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3869
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<pre style="margin: 0;"> <span id="LC3869" 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;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0UL</span><span class="p">;</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">secondArg</span><span class="p">.</span><span class="n" style="color: #333;">vDim</span><span class="p">;</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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3870
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<pre style="margin: 0;"> <span id="LC3870" class="line" lang="cpp"></span>
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3871
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<pre style="margin: 0;"> <span id="LC3871" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4481" style="width: 35px; color: rgba(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">@@ -4481,7 +4729,42 @@ hyFloat _Matrix::MaxElement (char runMode, long* indexStore) const {</td>
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4481
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4729
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<pre style="margin: 0;"> <span id="LC4729" class="line" lang="cpp"> <span class="p">}</span></span>
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4482
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4730
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<pre style="margin: 0;"> <span id="LC4730" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">max</span><span class="p">;</span></span>
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4483
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4731
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<pre style="margin: 0;"> <span id="LC4731" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4484
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<pre style="margin: 0;">-<span id="LC4484" 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;">long</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;">lDim</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="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC4732" class="line" lang="cpp"> </span>
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4733
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<pre style="margin: 0;">+<span id="LC4733" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">doAbsValue</span><span class="p">)</span> <span class="p">{</span></span>
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4734
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<pre style="margin: 0;">+<span id="LC4734" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">doMaxElement</span><span class="p">)</span> <span class="p">{</span></span>
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4735
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<pre style="margin: 0;">+<span id="LC4735" 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;">long</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;">lDim</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="p">{</span></span>
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4736
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<pre style="margin: 0;">+<span id="LC4736" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fabs</span><span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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4737
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<pre style="margin: 0;">+<span id="LC4737" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max</span><span class="p">)</span> <span class="p">{</span></span>
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4738
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<pre style="margin: 0;">+<span id="LC4738" class="line" lang="cpp"> <span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t</span><span class="p">;</span></span>
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4739
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<pre style="margin: 0;">+<span id="LC4739" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">indexStore</span><span class="p">)</span> <span class="p">{</span></span>
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4740
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<pre style="margin: 0;">+<span id="LC4740" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">indexStore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC4741" class="line" lang="cpp"> <span class="p">}</span></span>
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4742
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<pre style="margin: 0;">+<span id="LC4742" class="line" lang="cpp"> <span class="p">}</span></span>
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4743
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<pre style="margin: 0;">+<span id="LC4743" class="line" lang="cpp"> <span class="p">}</span></span>
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4744
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<pre style="margin: 0;">+<span id="LC4744" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4745" 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">
4745
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<pre style="margin: 0;">+<span id="LC4745" 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;">long</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;">lDim</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="p">{</span></span>
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4746
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<pre style="margin: 0;">+<span id="LC4746" class="line" lang="cpp"> <span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">fabs</span> <span class="p">(</span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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4747
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<pre style="margin: 0;">+<span id="LC4747" class="line" lang="cpp"> <span class="p">}</span></span>
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4748
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<pre style="margin: 0;">+<span id="LC4748" class="line" lang="cpp"> <span class="p">}</span></span>
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4749
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<pre style="margin: 0;">+<span id="LC4749" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4750
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<pre style="margin: 0;">+<span id="LC4750" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">doMaxElement</span><span class="p">)</span> <span class="p">{</span></span>
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4751
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<pre style="margin: 0;">+<span id="LC4751" 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;">long</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;">lDim</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="p">{</span></span>
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4752
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<pre style="margin: 0;">+<span id="LC4752" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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4753
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<pre style="margin: 0;">+<span id="LC4753" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max</span><span class="p">)</span> <span class="p">{</span></span>
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4754
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<pre style="margin: 0;">+<span id="LC4754" class="line" lang="cpp"> <span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t</span><span class="p">;</span></span>
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4755
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<pre style="margin: 0;">+<span id="LC4755" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">indexStore</span><span class="p">)</span> <span class="p">{</span></span>
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4756
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<pre style="margin: 0;">+<span id="LC4756" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">indexStore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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4757
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<pre style="margin: 0;">+<span id="LC4757" class="line" lang="cpp"> <span class="p">}</span></span>
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4758
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<pre style="margin: 0;">+<span id="LC4758" class="line" lang="cpp"> <span class="p">}</span></span>
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4759
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<pre style="margin: 0;">+<span id="LC4759" class="line" lang="cpp"> <span class="p">}</span></span>
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4760
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<pre style="margin: 0;">+<span id="LC4760" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4761
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<pre style="margin: 0;">+<span id="LC4761" 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;">long</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;">lDim</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="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4762" 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">
4762
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<pre style="margin: 0;">+<span id="LC4762" class="line" lang="cpp"> <span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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4763
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<pre style="margin: 0;">+<span id="LC4763" class="line" lang="cpp"> <span class="p">}</span></span>
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4764
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<pre style="margin: 0;">+<span id="LC4764" class="line" lang="cpp"> <span class="p">}</span></span>
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4765
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<pre style="margin: 0;">+<span id="LC4765" class="line" lang="cpp"> <span class="p">}</span></span>
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4766
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<pre style="margin: 0;">+<span id="LC4766" class="line" lang="cpp"> </span>
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4767
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<pre style="margin: 0;">+<span id="LC4767" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*for (long i = 0; i<lDim; i++) {</span></span>
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4485
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4768
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<pre style="margin: 0;"> <span id="LC4768" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> temp = theData[i];</span></span>
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4486
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4769
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<pre style="margin: 0;"> <span id="LC4769" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (doAbsValue && temp<0.0) {</span></span>
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4487
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4770
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<pre style="margin: 0;"> <span id="LC4770" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> temp = -temp;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4497" style="width: 35px; color: rgba(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="4780" style="width: 35px; color: rgba(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">@@ -4497,7 +4780,7 @@ hyFloat _Matrix::MaxElement (char runMode, long* indexStore) const {</td>
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4497
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4780
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<pre style="margin: 0;"> <span id="LC4780" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> } else {</span></span>
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4498
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4781
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<pre style="margin: 0;"> <span id="LC4781" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> max += temp;</span></span>
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4782
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<pre style="margin: 0;"> <span id="LC4782" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC4500" class="line" lang="cpp"> <span class="p">}</span></span>
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4783
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<pre style="margin: 0;">+<span id="LC4783" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }<span class="idiff left right">*/</span></span></span>
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4501
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4784
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<pre style="margin: 0;"> <span id="LC4784" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">max</span><span class="p">;</span></span>
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4785
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<pre style="margin: 0;"> <span id="LC4785" class="line" lang="cpp"> <span class="p">}</span></span>
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4503
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4786
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<pre style="margin: 0;"> <span id="LC4786" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4510" style="width: 35px; color: rgba(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="4793" style="width: 35px; color: rgba(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">@@ -4510,13 +4793,11 @@ hyFloat _Matrix::MaxElement (char runMode, long* indexStore) const {</td>
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4510
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4793
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<pre style="margin: 0;"> <span id="LC4793" class="line" lang="cpp"></span>
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4511
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4794
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<pre style="margin: 0;"> <span id="LC4794" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_____________________________________________________________________________________________</span></span>
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4795
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<pre style="margin: 0;"> <span id="LC4795" class="line" lang="cpp"></span>
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4513
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<pre style="margin: 0;">-<span id="LC4513" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">_Matrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">RowAndColumnMax</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">hyFloat</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">hyFloat</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cache</span><span class="p">)</span></span>
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4796
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<pre style="margin: 0;">+<span id="LC4796" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">_Matrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">RowAndColumnMax</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">hyFloat</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">hyFloat</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cache</span><span class="p">)</span><span class="idiff left"> </span><span class="p"><span class="idiff right">{</span></span></span>
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4514
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4797
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<pre style="margin: 0;"> <span id="LC4797" class="line" lang="cpp"></span>
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4515
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4798
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<pre style="margin: 0;"> <span id="LC4798" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// returns the maximum row sum / column sum</span></span>
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4516
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4799
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<pre style="margin: 0;"> <span id="LC4799" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// the cache must be big enough to hold hDim + vDim</span></span>
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4517
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4800
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<pre style="margin: 0;"> <span id="LC4800" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// leave as nil to allocate cache run time</span></span>
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4518
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<pre style="margin: 0;">-<span id="LC4518" class="line" lang="cpp"></span>
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4519
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<pre style="margin: 0;">-<span id="LC4519" class="line" lang="cpp"><span class="p">{</span></span>
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4520
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4801
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<pre style="margin: 0;"> <span id="LC4801" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">10.</span><span class="p">;</span></span>
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4521
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4802
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<pre style="margin: 0;"> <span id="LC4802" class="line" lang="cpp"></span>
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4522
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4803
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<pre style="margin: 0;"> <span id="LC4803" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_numeric</span><span class="p">())</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// numeric matrix</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4531" style="width: 35px; color: rgba(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">@@ -4531,23 +4812,39 @@ void _Matrix::RowAndColumnMax (hyFloat& r, hyFloat &c, hyFloat * cache)</td>
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4531
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4812
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<pre style="margin: 0;"> <span id="LC4812" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rowMax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxScratch</span><span class="p">,</span></span>
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4532
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4813
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<pre style="margin: 0;"> <span id="LC4813" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">colMax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxScratch</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">hDim</span><span class="p">;</span></span>
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4533
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4814
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<pre style="margin: 0;"> <span id="LC4814" class="line" lang="cpp"></span>
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4534
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<pre style="margin: 0;">-<span id="LC4534" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">theIndex</span><span class="p">)</span></span>
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4535
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<pre style="margin: 0;">-<span id="LC4535" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// sparse matrix</span></span>
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4536
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<pre style="margin: 0;">-<span id="LC4536" 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;">long</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;">lDim</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="p">{</span></span>
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4537
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<pre style="margin: 0;">-<span id="LC4537" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theIndex</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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4538
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<pre style="margin: 0;">-<span id="LC4538" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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4539
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<pre style="margin: 0;">-<span id="LC4539" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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4815
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<pre style="margin: 0;">+<span id="LC4815" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">theIndex</span><span class="p">)</span> <span class="p">{</span></span>
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4816
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<pre style="margin: 0;">+<span id="LC4816" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">compressedIndex</span><span class="p">)</span> <span class="p">{</span></span>
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4817
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<pre style="margin: 0;">+<span id="LC4817" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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4818
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<pre style="margin: 0;">+<span id="LC4818" 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;">long</span> <span class="n" style="color: #333;">r</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;">r</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hDim</span><span class="p">;</span> <span class="n" style="color: #333;">r</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="LC4819" 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;">long</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">from</span><span class="p">;</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">];</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4820" 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">
4820
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<pre style="margin: 0;">+<span id="LC4820" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4821" 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">
4821
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<pre style="margin: 0;">+<span id="LC4821" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4822" 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">
4822
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<pre style="margin: 0;">+<span id="LC4822" class="line" lang="cpp"> <span class="n" style="color: #333;">rowMax</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">temp</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4823" 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">
4823
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<pre style="margin: 0;">+<span id="LC4823" class="line" lang="cpp"> <span class="n" style="color: #333;">colMax</span><span class="p">[</span><span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">hDim</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">temp</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4824" 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">
4824
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<pre style="margin: 0;">+<span id="LC4824" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4825" 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">
4825
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<pre style="margin: 0;">+<span id="LC4825" class="line" lang="cpp"> <span class="n" style="color: #333;">rowMax</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">temp</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4826" 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">
4826
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<pre style="margin: 0;">+<span id="LC4826" class="line" lang="cpp"> <span class="n" style="color: #333;">colMax</span><span class="p">[</span><span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">hDim</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">temp</span><span class="p">;</span></span>
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4827
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<pre style="margin: 0;">+<span id="LC4827" class="line" lang="cpp"> <span class="p">}</span></span>
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4828
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<pre style="margin: 0;">+<span id="LC4828" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4829" 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">
4829
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<pre style="margin: 0;">+<span id="LC4829" class="line" lang="cpp"> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">];</span></span>
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4830
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<pre style="margin: 0;">+<span id="LC4830" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4831" 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">
4831
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<pre style="margin: 0;">+<span id="LC4831" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4832
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<pre style="margin: 0;">+<span id="LC4832" 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;">long</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;">lDim</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="p">{</span></span>
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4833
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<pre style="margin: 0;">+<span id="LC4833" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theIndex</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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4834
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<pre style="margin: 0;">+<span id="LC4834" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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4835
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<pre style="margin: 0;">+<span id="LC4835" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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4540
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4836
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<pre style="margin: 0;"> <span id="LC4836" class="line" lang="cpp"></span>
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4541
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<pre style="margin: 0;">-<span id="LC4541" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="o" style="font-weight: 600;"><</span><span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="p">{</span></span>
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4542
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<pre style="margin: 0;">-<span id="LC4542" class="line" lang="cpp"> <span class="n" style="color: #333;">rowMax</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">vDim</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">temp</span><span class="p">;</span></span>
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4543
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<pre style="margin: 0;">-<span id="LC4543" class="line" lang="cpp"> <span class="n" style="color: #333;">colMax</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">vDim</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">temp</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC4544" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC4545" class="line" lang="cpp"> <span class="n" style="color: #333;">rowMax</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">vDim</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">temp</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC4546" class="line" lang="cpp"> <span class="n" style="color: #333;">colMax</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">vDim</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">temp</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC4837" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="o" style="font-weight: 600;">></span><span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC4838" class="line" lang="cpp"> <span class="n" style="color: #333;">rowMax</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">vDim</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">temp</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC4839" class="line" lang="cpp"> <span class="n" style="color: #333;">colMax</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">vDim</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">temp</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC4840" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC4841" class="line" lang="cpp"> <span class="n" style="color: #333;">rowMax</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">vDim</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">temp</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC4842" class="line" lang="cpp"> <span class="n" style="color: #333;">colMax</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">vDim</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">temp</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC4843" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC4844" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC4845" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC4846" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC4550" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC4847" class="line" lang="cpp"> <span class="p"><span class="idiff left">}</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;"> <span id="LC4848" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// dense matrix</span></span>
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<pre style="margin: 0;"> <span id="LC4849" 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;">long</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;">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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">hDim</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="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC4850" 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;">long</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;">vDim</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="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</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">@@ -4585,7 +4882,7 @@ bool _Matrix::IsMaxElement (hyFloat bench) {</td>
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4882
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<pre style="margin: 0;"> <span id="LC4882" class="line" lang="cpp"> <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;">theIndex</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">compressedIndex</span><span class="p">)</span> <span class="p">{</span></span>
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4586
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4883
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<pre style="margin: 0;"> <span id="LC4883" 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;">long</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;">lDim</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="p">{</span></span>
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4587
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4884
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<pre style="margin: 0;"> <span id="LC4884" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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4588
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<pre style="margin: 0;">-<span id="LC4588" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;"><span class="idiff left"><</span></span><span class="n" style="color: #333;"><span class="idiff">mBench</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">t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="n" style="color: #333;"><span class="idiff right">b</span>ench</span> <span class="p">)</span> <span class="p">{</span></span>
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4885
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<pre style="margin: 0;">+<span id="LC4885" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;"><span class="idiff left">></span></span><span class="n" style="color: #333;"><span class="idiff">bench</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">t</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff right">mB</span>ench</span> <span class="p">)</span> <span class="p">{</span></span>
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4589
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4886
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<pre style="margin: 0;"> <span id="LC4886" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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4590
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4887
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<pre style="margin: 0;"> <span id="LC4887" class="line" lang="cpp"> <span class="p">}</span></span>
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4591
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4888
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<pre style="margin: 0;"> <span id="LC4888" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4593" style="width: 35px; color: rgba(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="4890" style="width: 35px; color: rgba(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">@@ -4593,7 +4890,7 @@ bool _Matrix::IsMaxElement (hyFloat bench) {</td>
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4593
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4890
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<pre style="margin: 0;"> <span id="LC4890" 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;">long</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;">lDim</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="p">{</span></span>
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4594
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4891
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<pre style="margin: 0;"> <span id="LC4891" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">theIndex</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 class="p">{</span></span>
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4595
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4892
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<pre style="margin: 0;"> <span id="LC4892" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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4596
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<pre style="margin: 0;">-<span id="LC4596" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;"><span class="idiff left"><</span></span><span class="n" style="color: #333;"><span class="idiff">mBench</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">t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="n" style="color: #333;"><span class="idiff right">b</span>ench</span> <span class="p">)</span> <span class="p">{</span></span>
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4893
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<pre style="margin: 0;">+<span id="LC4893" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;"><span class="idiff left">></span></span><span class="n" style="color: #333;"><span class="idiff">bench</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">t</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff right">mB</span>ench</span> <span class="p">)</span> <span class="p">{</span></span>
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4597
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4894
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<pre style="margin: 0;"> <span id="LC4894" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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4598
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4895
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<pre style="margin: 0;"> <span id="LC4895" class="line" lang="cpp"> <span class="p">}</span></span>
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4599
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4896
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<pre style="margin: 0;"> <span id="LC4896" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4841" style="width: 35px; color: rgba(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="5138" style="width: 35px; color: rgba(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">@@ -4841,6 +5138,73 @@ void _Matrix::CompressSparseMatrix (bool transpose, hyFloat * stash) {</td>
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4841
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5138
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<pre style="margin: 0;"> <span id="LC5138" class="line" lang="cpp"> </span>
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4842
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5139
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<pre style="margin: 0;"> <span id="LC5139" class="line" lang="cpp"> </span>
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4843
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5140
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<pre style="margin: 0;"> <span id="LC5140" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">theIndex</span><span class="p">)</span> <span class="p">{</span></span>
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5141
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<pre style="margin: 0;">+<span id="LC5141" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC5142" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">compressedIndex</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">transpose</span><span class="p">)</span> <span class="p">{</span></span>
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5143
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<pre style="margin: 0;">+<span id="LC5143" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">ai</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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5144
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<pre style="margin: 0;">+<span id="LC5144" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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5145
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<pre style="margin: 0;">+<span id="LC5145" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span> <span class="p">(</span><span class="n" style="color: #333;">stash</span><span class="p">,</span> <span class="n" style="color: #333;">theData</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lDim</span><span class="p">);</span></span>
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5146
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<pre style="margin: 0;">+<span id="LC5146" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">by_column_counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">alloca</span> <span class="p">((</span><span class="n" style="color: #333;">hDim</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">lDim</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;">long</span><span class="p">));</span></span>
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5147
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<pre style="margin: 0;">+<span id="LC5147" class="line" lang="cpp"> </span>
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5148
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<pre style="margin: 0;">+<span id="LC5148" class="line" lang="cpp"> <span class="n" style="color: #333;">memset</span> <span class="p">(</span><span class="n" style="color: #333;">by_column_counts</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">hDim</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;">long</span><span class="p">));</span></span>
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5149
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<pre style="margin: 0;">+<span id="LC5149" class="line" lang="cpp"> </span>
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5150
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<pre style="margin: 0;">+<span id="LC5150" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// pass 1 : count records by column</span></span>
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5151
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<pre style="margin: 0;">+<span id="LC5151" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">stored_by_col</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">alloca</span> <span class="p">(</span><span class="n" style="color: #333;">hDim</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;">long</span><span class="p">));</span></span>
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5152
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<pre style="margin: 0;">+<span id="LC5152" class="line" lang="cpp"> <span class="n" style="color: #333;">memset</span> <span class="p">(</span><span class="n" style="color: #333;">stored_by_col</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">hDim</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;">long</span><span class="p">));</span></span>
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5153
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<pre style="margin: 0;">+<span id="LC5153" class="line" lang="cpp"></span>
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5154
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<pre style="margin: 0;">+<span id="LC5154" 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;">long</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hDim</span><span class="p">;</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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5155
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<pre style="margin: 0;">+<span id="LC5155" 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;">long</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">from</span><span class="p">;</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">];</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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5156
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<pre style="margin: 0;">+<span id="LC5156" class="line" lang="cpp"> <span class="n" style="color: #333;">by_column_counts</span><span class="p">[</span><span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">hDim</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">c</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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5157
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<pre style="margin: 0;">+<span id="LC5157" class="line" lang="cpp"> <span class="p">}</span></span>
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5158
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<pre style="margin: 0;">+<span id="LC5158" class="line" lang="cpp"> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">];</span></span>
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5159
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<pre style="margin: 0;">+<span id="LC5159" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC5160" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC5161" class="line" lang="cpp"> </span>
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5162
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<pre style="margin: 0;">+<span id="LC5162" 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;">long</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1L</span><span class="p">;</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hDim</span><span class="p">;</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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5163
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<pre style="margin: 0;">+<span id="LC5163" class="line" lang="cpp"> <span class="n" style="color: #333;">by_column_counts</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">by_column_counts</span><span class="p">[</span><span class="n" style="color: #333;">r</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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5164
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<pre style="margin: 0;">+<span id="LC5164" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printf ("%ld %ld (%ld)\n", r, by_column_counts[r], compressedIndex[r]);</span></span>
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5165
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<pre style="margin: 0;">+<span id="LC5165" class="line" lang="cpp"> <span class="p">}</span></span>
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5166
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<pre style="margin: 0;">+<span id="LC5166" class="line" lang="cpp"> </span>
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5167
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<pre style="margin: 0;">+<span id="LC5167" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// pass 2 : invert indices</span></span>
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5168
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<pre style="margin: 0;">+<span id="LC5168" class="line" lang="cpp"> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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5169
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<pre style="margin: 0;">+<span id="LC5169" class="line" lang="cpp"> </span>
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5170
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<pre style="margin: 0;">+<span id="LC5170" class="line" lang="cpp"> </span>
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5171
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<pre style="margin: 0;">+<span id="LC5171" 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;">long</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hDim</span><span class="p">;</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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5172
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<pre style="margin: 0;">+<span id="LC5172" 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;">long</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">from</span><span class="p">;</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">];</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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5173
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<pre style="margin: 0;">+<span id="LC5173" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">my_col</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">hDim</span><span class="p">];</span></span>
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5174
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<pre style="margin: 0;">+<span id="LC5174" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// (i,j) => (j,i)</span></span>
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5175
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<pre style="margin: 0;">+<span id="LC5175" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">new_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">my_col</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hDim</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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5176
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<pre style="margin: 0;">+<span id="LC5176" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">col_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">my_col</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">by_column_counts</span><span class="p">[</span><span class="n" style="color: #333;">my_col</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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5177
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<pre style="margin: 0;">+<span id="LC5177" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">new_compressed_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stored_by_col</span><span class="p">[</span><span class="n" style="color: #333;">my_col</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">col_offset</span><span class="p">;</span></span>
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5178
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<pre style="margin: 0;">+<span id="LC5178" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printf ("%ld => %ld (%ld, %ld)\n", c, new_compressed_index,r*hDim + my_col, new_index);</span></span>
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5179
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<pre style="margin: 0;">+<span id="LC5179" class="line" lang="cpp"> <span class="n" style="color: #333;">theIndex</span><span class="p">[</span><span class="n" style="color: #333;">new_compressed_index</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_index</span><span class="p">;</span></span>
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5180
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<pre style="margin: 0;">+<span id="LC5180" class="line" lang="cpp"> <span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">new_compressed_index</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stash</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">];</span></span>
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5181
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<pre style="margin: 0;">+<span id="LC5181" class="line" lang="cpp"> <span class="n" style="color: #333;">by_column_counts</span><span class="p">[</span><span class="n" style="color: #333;">hDim</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">new_compressed_index</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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5182
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<pre style="margin: 0;">+<span id="LC5182" class="line" lang="cpp"> <span class="n" style="color: #333;">stored_by_col</span><span class="p">[</span><span class="n" style="color: #333;">my_col</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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5183
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<pre style="margin: 0;">+<span id="LC5183" class="line" lang="cpp"> <span class="p">}</span></span>
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5184
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<pre style="margin: 0;">+<span id="LC5184" class="line" lang="cpp"> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">];</span></span>
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5185
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<pre style="margin: 0;">+<span id="LC5185" class="line" lang="cpp"> <span class="p">}</span></span>
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5186
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<pre style="margin: 0;">+<span id="LC5186" class="line" lang="cpp"> </span>
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5187
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<pre style="margin: 0;">+<span id="LC5187" class="line" lang="cpp"> </span>
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5188
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<pre style="margin: 0;">+<span id="LC5188" class="line" lang="cpp"> </span>
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5189
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<pre style="margin: 0;">+<span id="LC5189" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span> <span class="p">(</span><span class="n" style="color: #333;">compressedIndex</span><span class="p">,</span> <span class="n" style="color: #333;">by_column_counts</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;">long</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">lDim</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">hDim</span><span class="p">));</span></span>
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5190
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<pre style="margin: 0;">+<span id="LC5190" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//_validateCompressedStorage();</span></span>
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5191
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<pre style="margin: 0;">+<span id="LC5191" class="line" lang="cpp"> </span>
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5192
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<pre style="margin: 0;">+<span id="LC5192" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*for (long r = 0; r < hDim; r++) {</span></span>
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5193
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<pre style="margin: 0;">+<span id="LC5193" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> long trow = r;</span></span>
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5194
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<pre style="margin: 0;">+<span id="LC5194" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> for (long c = from; c < compressedIndex[r]; c++) {</span></span>
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5195
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<pre style="margin: 0;">+<span id="LC5195" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> long tcol = compressedIndex[hDim+c];</span></span>
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5196
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<pre style="margin: 0;">+<span id="LC5196" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> long transposed_index = tcol * vDim + trow;</span></span>
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5197
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<pre style="margin: 0;">+<span id="LC5197" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> stash[ai] = theData[c];</span></span>
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5198
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<pre style="margin: 0;">+<span id="LC5198" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> //sortedIndex.list_data[ai] = transposed_index;</span></span>
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5199
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<pre style="margin: 0;">+<span id="LC5199" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> //sortedIndex3.list_data[ai] = transposed_index;</span></span>
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5200
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<pre style="margin: 0;">+<span id="LC5200" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> ai++;</span></span>
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5201
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<pre style="margin: 0;">+<span id="LC5201" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> //if (max < transposed_index) max = transposed_index;</span></span>
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5202
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<pre style="margin: 0;">+<span id="LC5202" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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5203
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<pre style="margin: 0;">+<span id="LC5203" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> from = compressedIndex[r];</span></span>
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5204
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<pre style="margin: 0;">+<span id="LC5204" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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5205
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<pre style="margin: 0;">+<span id="LC5205" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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5206
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<pre style="margin: 0;">+<span id="LC5206" class="line" lang="cpp"> <span class="p">}</span></span>
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5207
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<pre style="margin: 0;">+<span id="LC5207" class="line" lang="cpp"> </span>
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4844
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5208
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<pre style="margin: 0;"> <span id="LC5208" class="line" lang="cpp"> <span class="n" style="color: #333;">_SimpleList</span> <span class="n" style="color: #333;">sortedIndex</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">lDim</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">alloca</span> <span class="p">(</span><span class="n" style="color: #333;">lDim</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;">long</span><span class="p">))),</span></span>
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4845
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5209
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<pre style="margin: 0;"> <span id="LC5209" class="line" lang="cpp"> <span class="n" style="color: #333;">sortedIndex3</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">lDim</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">alloca</span> <span class="p">(</span><span class="n" style="color: #333;">lDim</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;">long</span><span class="p">))),</span></span>
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4846
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5210
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<pre style="margin: 0;"> <span id="LC5210" class="line" lang="cpp"> <span class="n" style="color: #333;">sortedIndex2</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4855" style="width: 35px; color: rgba(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="5219" style="width: 35px; color: rgba(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">@@ -4855,44 +5219,27 @@ void _Matrix::CompressSparseMatrix (bool transpose, hyFloat * stash) {</td>
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4855
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5219
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<pre style="margin: 0;"> <span id="LC5219" class="line" lang="cpp"></span>
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4856
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5220
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<pre style="margin: 0;"> <span id="LC5220" class="line" lang="cpp"></span>
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4857
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5221
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<pre style="margin: 0;"> <span id="LC5221" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">transpose</span><span class="p">)</span> <span class="p">{</span></span>
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5222
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<pre style="margin: 0;">+<span id="LC5222" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">ai</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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5223
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<pre style="margin: 0;">+<span id="LC5223" class="line" lang="cpp"> </span>
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4858
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5224
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<pre style="margin: 0;"> <span id="LC5224" 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;">long</span> <span class="n" style="color: #333;">i2</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;">i2</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">lDim</span><span class="p">;</span> <span class="n" style="color: #333;">i2</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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4859
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<td class="diff-line-num new_line" data-linenumber="5225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5225
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<pre style="margin: 0;"> <span id="LC5225" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theIndex</span><span class="p">[</span><span class="n" style="color: #333;">i2</span><span class="p">];</span></span>
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4860
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5226
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<pre style="margin: 0;"> <span id="LC5226" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">__builtin_expect</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;">1</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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4861
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<pre style="margin: 0;">-<span id="LC4861" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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4862
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<pre style="margin: 0;">-<span id="LC4862" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> long r = k/vDim,</span></span>
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4863
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<pre style="margin: 0;">-<span id="LC4863" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> c = k%vDim,</span></span>
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4864
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<pre style="margin: 0;">-<span id="LC4864" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> r2 = c / blockChunk * blockShift + r / blockChunk,</span></span>
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4865
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<pre style="margin: 0;">-<span id="LC4865" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> r3 = r2 * lDim + r * vDim + c;</span></span>
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4866
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<pre style="margin: 0;">-<span id="LC4866" class="line" lang="cpp"></span>
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4867
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<pre style="margin: 0;">-<span id="LC4867" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> sortedIndex << (c*vDim + r);</span></span>
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<pre style="margin: 0;">-<span id="LC4868" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> sortedIndex3 << r3;</span></span>
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4869
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<pre style="margin: 0;">-<span id="LC4869" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> stash[sortedIndex.lLength-1] = theData[i2];</span></span>
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4870
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<pre style="margin: 0;">-<span id="LC4870" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (r3 > max) {</span></span>
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4871
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<pre style="margin: 0;">-<span id="LC4871" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> max = r3;</span></span>
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4872
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<pre style="margin: 0;">-<span id="LC4872" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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4873
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<pre style="margin: 0;">-<span id="LC4873" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">transposed_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">vDim</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">vDim</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="n" style="color: #333;">vDim</span><span class="p">;</span></span>
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4874
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<pre style="margin: 0;">-<span id="LC4874" class="line" lang="cpp"> <span class="n" style="color: #333;">stash</span><span class="p">[</span><span class="n" style="color: #333;">sortedIndex</span><span class="p">.</span><span class="n" style="color: #333;">lLength</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">i2</span><span class="p">];</span></span>
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4875
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<pre style="margin: 0;">-<span id="LC4875" class="line" lang="cpp"> <span class="n" style="color: #333;">sortedIndex</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">transposed_index</span><span class="p">;</span></span>
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4876
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<pre style="margin: 0;">-<span id="LC4876" class="line" lang="cpp"> <span class="n" style="color: #333;">sortedIndex3</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">transposed_index</span><span class="p">;</span></span>
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5227
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<pre style="margin: 0;">+<span id="LC5227" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">trow</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="n" style="color: #333;">vDim</span><span class="p">,</span> <span class="n" style="color: #333;">tcol</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="n" style="color: #333;">trow</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">vDim</span><span class="p">;</span></span>
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5228
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<pre style="margin: 0;">+<span id="LC5228" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">transposed_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tcol</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">vDim</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">trow</span><span class="p">;</span></span>
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5229
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<pre style="margin: 0;">+<span id="LC5229" class="line" lang="cpp"> <span class="n" style="color: #333;">stash</span><span class="p">[</span><span class="n" style="color: #333;">ai</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">i2</span><span class="p">];</span></span>
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5230
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<pre style="margin: 0;">+<span id="LC5230" class="line" lang="cpp"> <span class="n" style="color: #333;">sortedIndex</span><span class="p">.</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">ai</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transposed_index</span><span class="p">;</span></span>
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5231
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<pre style="margin: 0;">+<span id="LC5231" class="line" lang="cpp"> <span class="n" style="color: #333;">sortedIndex3</span><span class="p">.</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">ai</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transposed_index</span><span class="p">;</span></span>
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5232
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<pre style="margin: 0;">+<span id="LC5232" class="line" lang="cpp"> <span class="n" style="color: #333;">ai</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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4877
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5233
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<pre style="margin: 0;"> <span id="LC5233" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">transposed_index</span><span class="p">)</span> <span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transposed_index</span><span class="p">;</span></span>
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4878
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<pre style="margin: 0;">-<span id="LC4878" class="line" lang="cpp"> </span>
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4879
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5234
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<pre style="margin: 0;"> <span id="LC5234" class="line" lang="cpp"> <span class="p">}</span></span>
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4880
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5235
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<pre style="margin: 0;"> <span id="LC5235" class="line" lang="cpp"> <span class="p">}</span></span>
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5236
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<pre style="margin: 0;">+<span id="LC5236" class="line" lang="cpp"> </span>
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5237
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<pre style="margin: 0;">+<span id="LC5237" class="line" lang="cpp"> <span class="n" style="color: #333;">sortedIndex3</span><span class="p">.</span><span class="n" style="color: #333;">lLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ai</span><span class="p">;</span></span>
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5238
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<pre style="margin: 0;">+<span id="LC5238" class="line" lang="cpp"> <span class="n" style="color: #333;">sortedIndex</span><span class="p">.</span><span class="n" style="color: #333;">lLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ai</span><span class="p">;</span></span>
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4881
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5239
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<pre style="margin: 0;"> <span id="LC5239" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4882
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5240
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<pre style="margin: 0;"> <span id="LC5240" 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;">long</span> <span class="n" style="color: #333;">i2</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;">i2</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">lDim</span><span class="p">;</span> <span class="n" style="color: #333;">i2</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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4883
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5241
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<pre style="margin: 0;"> <span id="LC5241" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theIndex</span><span class="p">[</span><span class="n" style="color: #333;">i2</span><span class="p">];</span></span>
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4884
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5242
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<pre style="margin: 0;"> <span id="LC5242" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">__builtin_expect</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;">1</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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4885
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<pre style="margin: 0;">-<span id="LC4885" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*long r = k%vDim,</span></span>
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4886
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<pre style="margin: 0;">-<span id="LC4886" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> c = k/vDim,</span></span>
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4887
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<pre style="margin: 0;">-<span id="LC4887" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> r2 = c / blockChunk * blockShift + r / blockChunk,</span></span>
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4888
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<pre style="margin: 0;">-<span id="LC4888" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> r3 = r2 * lDim + r * vDim + c;</span></span>
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4889
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<pre style="margin: 0;">-<span id="LC4889" class="line" lang="cpp"></span>
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4890
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<pre style="margin: 0;">-<span id="LC4890" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> sortedIndex << (c*vDim + r);</span></span>
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4891
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<pre style="margin: 0;">-<span id="LC4891" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> sortedIndex3 << r3;</span></span>
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4892
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<pre style="margin: 0;">-<span id="LC4892" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> stash[sortedIndex.lLength-1] = theData[i2];</span></span>
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4893
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<pre style="margin: 0;">-<span id="LC4893" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (r3 > max) {</span></span>
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4894
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<pre style="margin: 0;">-<span id="LC4894" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> max = r3;</span></span>
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4895
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<pre style="margin: 0;">-<span id="LC4895" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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4896
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5243
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<pre style="margin: 0;"> <span id="LC5243" class="line" lang="cpp"> <span class="n" style="color: #333;">stash</span><span class="p">[</span><span class="n" style="color: #333;">sortedIndex</span><span class="p">.</span><span class="n" style="color: #333;">lLength</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">i2</span><span class="p">];</span></span>
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4897
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5244
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<pre style="margin: 0;"> <span id="LC5244" class="line" lang="cpp"> <span class="n" style="color: #333;">sortedIndex</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">k</span><span class="p">;</span></span>
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4898
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5245
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<pre style="margin: 0;"> <span id="LC5245" class="line" lang="cpp"> <span class="n" style="color: #333;">sortedIndex3</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">k</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">@@ -4957,32 +5304,6 @@ void _Matrix::CompressSparseMatrix (bool transpose, hyFloat * stash) {</td>
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5304
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<pre style="margin: 0;"> <span id="LC5304" class="line" lang="cpp"> </span>
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5305
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<pre style="margin: 0;"> <span id="LC5305" 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;">long</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">currentRow</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;">firstDim</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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4959
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5306
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<pre style="margin: 0;"> <span id="LC5306" class="line" lang="cpp"> <span class="n" style="color: #333;">compressedIndex</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;">lDim</span><span class="p">;</span></span>
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4960
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<pre style="margin: 0;">-<span id="LC4960" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//compressedIndex[firstDim-1] = lDim;</span></span>
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4961
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<td class="diff-line-num new_line old" data-linenumber="5307" 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="LC4961" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printf (">[%ld] %ld\n", firstDim-1, compressedIndex[firstDim-1]);</span></span>
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4962
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<td class="diff-line-num new_line old" data-linenumber="5307" 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="LC4962" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//exit (1);</span></span>
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4963
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<pre style="margin: 0;">-<span id="LC4963" class="line" lang="cpp"> </span>
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4964
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<pre style="margin: 0;">-<span id="LC4964" class="line" lang="cpp"> </span>
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4965
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<td class="diff-line-num new_line old" data-linenumber="5307" 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="LC4965" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// this code checks conversion consistency</span></span>
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4966
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<pre style="margin: 0;">-<span id="LC4966" class="line" lang="cpp"> </span>
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4967
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<pre style="margin: 0;">-<span id="LC4967" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*long ei = 0;</span></span>
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4968
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<pre style="margin: 0;">-<span id="LC4968" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> long from = 0;</span></span>
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4969
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<td class="diff-line-num new_line old" data-linenumber="5307" 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="LC4969" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> for (long i=0; i<hDim; i++) {</span></span>
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4970
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<td class="diff-line-num new_line old" data-linenumber="5307" 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="LC4970" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> for (long k = from; k < compressedIndex[i]; k++, ei++) {</span></span>
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4971
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<pre style="margin: 0;">-<span id="LC4971" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> long my_row = theIndex[ei] / vDim,</span></span>
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4972
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<pre style="margin: 0;">-<span id="LC4972" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> my_column = theIndex[ei] % vDim;</span></span>
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4973
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<pre style="margin: 0;">-<span id="LC4973" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> </span></span>
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4974
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<td class="diff-line-num new_line old" data-linenumber="5307" 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="LC4974" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (my_row != i || my_column != compressedIndex[hDim+k]) {</span></span>
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4975
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<td class="diff-line-num new_line old" data-linenumber="5307" 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="LC4975" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> printf ("BARF\n");</span></span>
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4976
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<pre style="margin: 0;">-<span id="LC4976" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4977
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<pre style="margin: 0;">-<span id="LC4977" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4978
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<pre style="margin: 0;">-<span id="LC4978" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> from = compressedIndex[i];</span></span>
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4979
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<pre style="margin: 0;">-<span id="LC4979" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4980
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<pre style="margin: 0;">-<span id="LC4980" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> </span></span>
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4981
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<pre style="margin: 0;">-<span id="LC4981" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (ei != lDim) {</span></span>
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4982
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<td class="diff-line-num new_line old" data-linenumber="5307" 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="LC4982" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> printf ("BARF\n");</span></span>
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4983
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<pre style="margin: 0;">-<span id="LC4983" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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<pre style="margin: 0;">-<span id="LC4984" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC4985" class="line" lang="cpp"></span>
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4986
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5307
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<pre style="margin: 0;"> <span id="LC5307" class="line" lang="cpp"> <span class="p">}</span></span>
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5308
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<pre style="margin: 0;"> <span id="LC5308" class="line" lang="cpp"><span class="p">}</span></span>
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5309
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<pre style="margin: 0;"> <span id="LC5309" 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">@@ -5202,11 +5523,27 @@ _Matrix* _Matrix::Exponentiate (hyFloat scale_to, bool check_transition, _Mat</td>
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5202
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5523
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<pre style="margin: 0;"> <span id="LC5523" class="line" lang="cpp"> </span>
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5203
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5524
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<pre style="margin: 0;"> <span id="LC5524" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">theIndex</span><span class="p">)</span> <span class="p">{</span></span>
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5204
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5525
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<pre style="margin: 0;"> <span id="LC5525" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// transpose back</span></span>
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5205
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<pre style="margin: 0;">-<span id="LC5205" class="line" lang="cpp"> <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;">lDim</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="p">{</span></span>
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5206
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<pre style="margin: 0;">-<span id="LC5206" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theIndex</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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5207
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<pre style="margin: 0;">-<span id="LC5207" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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5208
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<pre style="margin: 0;">-<span id="LC5208" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">div</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="n" style="color: #333;">vDim</span><span class="p">;</span></span>
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5209
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<pre style="margin: 0;">-<span id="LC5209" class="line" lang="cpp"> <span class="n" style="color: #333;">theIndex</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="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">div</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">vDim</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">vDim</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">div</span><span class="p">;</span></span>
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5526
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<pre style="margin: 0;">+<span id="LC5526" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">compressedIndex</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5527" 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">
5527
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<pre style="margin: 0;">+<span id="LC5527" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</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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<td class="diff-line-num new new_line" data-linenumber="5528" 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">
5528
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<pre style="margin: 0;">+<span id="LC5528" 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;">long</span> <span class="n" style="color: #333;">r</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;">r</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hDim</span><span class="p">;</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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5529
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<pre style="margin: 0;">+<span id="LC5529" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>
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5530
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<pre style="margin: 0;">+<span id="LC5530" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop vectorize(enable)</span></span>
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5531
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<pre style="margin: 0;">+<span id="LC5531" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop interleave(enable)</span></span>
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5532
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<pre style="margin: 0;">+<span id="LC5532" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop unroll(enable)</span></span>
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5533
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<pre style="margin: 0;">+<span id="LC5533" 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;">long</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">from</span><span class="p">;</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">];</span> <span class="n" style="color: #333;">c</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="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5534" 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">
5534
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<pre style="margin: 0;">+<span id="LC5534" class="line" lang="cpp"> <span class="n" style="color: #333;">theIndex</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;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">hDim</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">vDim</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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5535
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<pre style="margin: 0;">+<span id="LC5535" class="line" lang="cpp"> <span class="p">}</span></span>
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5536
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<pre style="margin: 0;">+<span id="LC5536" class="line" lang="cpp"> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">];</span></span>
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5537
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<pre style="margin: 0;">+<span id="LC5537" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5538" 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">
5538
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<pre style="margin: 0;">+<span id="LC5538" class="line" lang="cpp"> <span class="n" style="color: #333;">MatrixMemFree</span><span class="p">(</span><span class="n" style="color: #333;">compressedIndex</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5539" 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">
5539
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<pre style="margin: 0;">+<span id="LC5539" class="line" lang="cpp"> <span class="n" style="color: #333;">compressedIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nil</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5540" 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">
5540
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<pre style="margin: 0;">+<span id="LC5540" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5541" 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">
5541
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<pre style="margin: 0;">+<span id="LC5541" class="line" lang="cpp"> <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;">lDim</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="p">{</span></span>
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5542
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<pre style="margin: 0;">+<span id="LC5542" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theIndex</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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5543
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<pre style="margin: 0;">+<span id="LC5543" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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5544
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<pre style="margin: 0;">+<span id="LC5544" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">div</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="n" style="color: #333;">vDim</span><span class="p">;</span></span>
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5545
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<pre style="margin: 0;">+<span id="LC5545" class="line" lang="cpp"> <span class="n" style="color: #333;">theIndex</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="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">div</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">vDim</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">vDim</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">div</span><span class="p">;</span></span>
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5546
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<pre style="margin: 0;">+<span id="LC5546" class="line" lang="cpp"> <span class="p">}</span></span>
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5210
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5547
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<pre style="margin: 0;"> <span id="LC5547" class="line" lang="cpp"> <span class="p">}</span></span>
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5211
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5548
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<pre style="margin: 0;"> <span id="LC5548" class="line" lang="cpp"> <span class="p">}</span></span>
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5212
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5549
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<pre style="margin: 0;"> <span id="LC5549" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Transpose</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5323" style="width: 35px; color: rgba(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">@@ -5323,12 +5660,41 @@ long _Matrix::Hash (long i, long j) const {</td>
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5323
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5660
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<pre style="margin: 0;"> <span id="LC5660" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">vDim</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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5324
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5661
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<pre style="margin: 0;"> <span id="LC5661" class="line" lang="cpp"> <span class="p">}</span></span>
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5325
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5662
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<pre style="margin: 0;"> <span id="LC5662" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// ordinary matrix</span></span>
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5663
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<pre style="margin: 0;">+<span id="LC5663" class="line" lang="cpp"> </span>
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5664
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<pre style="margin: 0;">+<span id="LC5664" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">compressedIndex</span><span class="p">)</span> <span class="p">{</span></span>
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5665
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<pre style="margin: 0;">+<span id="LC5665" 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;">long</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">compressedIndex</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 class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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5666
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<pre style="margin: 0;">+<span id="LC5666" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">hDim</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">c</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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>
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5667
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<pre style="margin: 0;">+<span id="LC5667" class="line" lang="cpp"> <span class="p">}</span></span>
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5668
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<pre style="margin: 0;">+<span id="LC5668" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</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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5669
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<pre style="margin: 0;">+<span id="LC5669" class="line" lang="cpp"> <span class="p">}</span></span>
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5326
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5670
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<pre style="margin: 0;"> <span id="LC5670" class="line" lang="cpp"></span>
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5327
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<pre style="margin: 0;">-<span id="LC5327" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">elementIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">vDim</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;">k</span><span class="p">,</span> <span class="n" style="color: #333;">l</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;">i</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bufferPerRow</span><span class="p">,</span><span class="n" style="color: #333;">n</span><span class="p">,</span><span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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5671
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<pre style="margin: 0;">+<span id="LC5671" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">elementIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">vDim</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">j</span><span class="p">,</span></span>
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5672
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<pre style="margin: 0;">+<span id="LC5672" class="line" lang="cpp"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bufferPerRow</span><span class="p">;</span></span>
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5673
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<pre style="margin: 0;">+<span id="LC5673" class="line" lang="cpp"> </span>
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5674
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<pre style="margin: 0;">+<span id="LC5674" 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;">long</span> <span class="n" style="color: #333;">allocation_block_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span> <span class="n" style="color: #333;">allocation_block_index</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">lDim</span><span class="p">;</span> <span class="n" style="color: #333;">allocation_block_index</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">allocationBlock</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;">allocationBlock</span><span class="p">)</span> <span class="p">{</span></span>
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5675
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<pre style="margin: 0;">+<span id="LC5675" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// look within the row for this allocation block</span></span>
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5676
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<pre style="margin: 0;">+<span id="LC5676" 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;">long</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m</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;">m</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bufferPerRow</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="p">{</span></span>
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5677
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<pre style="margin: 0;">+<span id="LC5677" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">try_me</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theIndex</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">];</span></span>
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5678
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<pre style="margin: 0;">+<span id="LC5678" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">try_me</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">elementIndex</span><span class="p">)</span> <span class="p">{</span></span>
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5679
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<pre style="margin: 0;">+<span id="LC5679" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">try_me</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</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;">2</span><span class="p">;</span></span>
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5680
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<pre style="margin: 0;">+<span id="LC5680" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">l</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC5681" class="line" lang="cpp"> <span class="p">}</span></span>
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5682
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<pre style="margin: 0;">+<span id="LC5682" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// if not found, look in the overflow are for this block</span></span>
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5683
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<pre style="margin: 0;">+<span id="LC5683" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">upper_bound</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;">lDim</span><span class="p">,</span> <span class="n" style="color: #333;">allocation_block_index</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">allocationBlock</span><span class="p">);</span></span>
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5684
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<pre style="margin: 0;">+<span id="LC5684" 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;">long</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">upper_bound</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">overflowBuffer</span><span class="p">;</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">upper_bound</span><span class="p">;</span> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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5685
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<pre style="margin: 0;">+<span id="LC5685" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">try_me</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theIndex</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">];</span></span>
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5686
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<pre style="margin: 0;">+<span id="LC5686" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">try_me</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">elementIndex</span><span class="p">)</span> <span class="p">{</span></span>
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5687
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<pre style="margin: 0;">+<span id="LC5687" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">try_me</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">n</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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5688
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<pre style="margin: 0;">+<span id="LC5688" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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5689
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<pre style="margin: 0;">+<span id="LC5689" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC5690" class="line" lang="cpp"> <span class="p">}</span></span>
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5691
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<pre style="margin: 0;">+<span id="LC5691" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</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="LC5692" class="line" lang="cpp"> </span>
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5693
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<pre style="margin: 0;"> <span id="LC5693" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC5329" class="line" lang="cpp"> <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;">k</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">lDim</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">allocationBlock</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 class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">allocationBlock</span><span class="p">)</span> <span class="p">{</span></span>
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5330
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<pre style="margin: 0;">-<span id="LC5330" class="line" lang="cpp"> <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="n" style="color: #333;">m</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;">m</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">bufferPerRow</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="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC5331" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theIndex</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC5694" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC5695" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*for (long blockIndex = 0; blockIndex<lDim/allocationBlock; blockIndex++,m+=allocationBlock) {</span></span>
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<pre style="margin: 0;">+<span id="LC5696" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> for (long l=m; l<m+bufferPerRow; l++) {</span></span>
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<pre style="margin: 0;">+<span id="LC5697" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> long p = theIndex[l];</span></span>
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<pre style="margin: 0;"> <span id="LC5698" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (p!=elementIndex) {</span></span>
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5333
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5699
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<pre style="margin: 0;"> <span id="LC5699" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (p==-1) {</span></span>
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5334
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5700
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<pre style="margin: 0;"> <span id="LC5700" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return -l-2;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5337" style="width: 35px; color: rgba(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="5703" style="width: 35px; color: rgba(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">@@ -5337,9 +5703,9 @@ long _Matrix::Hash (long i, long j) const {</td>
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5337
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5703
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<pre style="margin: 0;"> <span id="LC5703" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return l;</span></span>
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5338
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5704
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<pre style="margin: 0;"> <span id="LC5704" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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5339
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5705
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<pre style="margin: 0;"> <span id="LC5705" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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5340
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<td class="diff-line-num new_line old" data-linenumber="5706" 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="LC5340" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">n</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">k</span></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;">allocationBlock</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="diff-line-num old old_line" data-linenumber="5341" 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">
5341
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<td class="diff-line-num new_line old" data-linenumber="5706" 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="LC5341" class="line" lang="cpp"> <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="n" style="color: #333;">n</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;">n</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">overflowBuffer</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="p">{</span></span>
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5342
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<pre style="margin: 0;">-<span id="LC5342" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theIndex</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">];</span></span>
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5706
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<pre style="margin: 0;">+<span id="LC5706" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> <span class="idiff left right">long n = (blockIndex</span>+1)*allocationBlock-1;</span></span>
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5707
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<pre style="margin: 0;">+<span id="LC5707" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> for (l<span class="idiff left right">ong l</span> = n; l>n-overflowBuffer; l--) {</span></span>
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5708
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<pre style="margin: 0;">+<span id="LC5708" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> <span class="idiff left right">long </span>p = theIndex[l];</span></span>
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5343
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5709
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<pre style="margin: 0;"> <span id="LC5709" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (p!=elementIndex) {</span></span>
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5344
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5710
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<pre style="margin: 0;"> <span id="LC5710" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (p==-1) {</span></span>
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5345
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5711
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<pre style="margin: 0;"> <span id="LC5711" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return -l-2;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5348" style="width: 35px; color: rgba(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="5714" style="width: 35px; color: rgba(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">@@ -5348,8 +5714,8 @@ long _Matrix::Hash (long i, long j) const {</td>
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5348
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5714
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<pre style="margin: 0;"> <span id="LC5714" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return l;</span></span>
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5349
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5715
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<pre style="margin: 0;"> <span id="LC5715" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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5350
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5716
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<pre style="margin: 0;"> <span id="LC5716" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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5351
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<pre style="margin: 0;">-<span id="LC5351" class="line" lang="cpp"> <span class="p">}</span></span>
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5352
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<pre style="margin: 0;">-<span id="LC5352" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</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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5717
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<pre style="margin: 0;">+<span id="LC5717" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }<span class="idiff left right">*/</span></span></span>
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5718
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<pre style="margin: 0;">+<span id="LC5718" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>return -1;</span></span>
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<pre style="margin: 0;"> <span id="LC5719" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC5720" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC5721" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_____________________________________________________________________________________________</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d8a6fecc5558ddf14f61e62f2bf14fe1a9ea9fff#795bd9642f0c76f4bba4eaba7f491566cf16e788"><strong>src/core/operation.cpp</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">@@ -662,10 +662,10 @@ bool _Operation::ExecutePolynomial (_Stack& theScrap, _VariableContainer*</td>
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC663" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC665" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC666" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC667" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">theData</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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<pre style="margin: 0;">-<span id="LC668" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_Polynomial</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">LocateVar</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">theData</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="n" style="color: #333;"><span class="idiff">theData</span></span><span class="o" style="font-weight: 600;"><span class="idiff">:-</span></span><span class="n" style="color: #333;"><span class="idiff">theData</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff right">));</span></span></span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="cpp"> <span class="p">}</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">theData</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="LC667" class="line" lang="cpp"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_Polynomial</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">LocateVar</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">theData</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="n" style="color: #333;"><span class="idiff">theData</span></span><span class="o" style="font-weight: 600;"><span class="idiff">:-</span></span><span class="n" style="color: #333;"><span class="idiff">theData</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff right">));</span></span></span>
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="cpp"> <span class="p"><span class="idiff left right">}</span></span></span>
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC671" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d8a6fecc5558ddf14f61e62f2bf14fe1a9ea9fff#da5a89d08e8ba5fdabf6bc90c935e625a50f5007"><strong>src/core/tree.cpp</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">@@ -3050,6 +3050,11 @@ hyFloat _TheTree::ComputeLLWithBranchCache (</td>
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<pre style="margin: 0;"> <span id="LC3050" class="line" lang="cpp"> <span class="n" style="color: #333;">storageVec</span> <span class="p">[</span><span class="n" style="color: #333;">direct_index</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">accumulator</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC3051" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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3052
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3052
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<pre style="margin: 0;"> <span id="LC3052" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">accumulator</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="p">{</span></span>
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3053
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<pre style="margin: 0;">+<span id="LC3053" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//fprintf (stderr, "ZERO TERM AT SITE %ld (direct %ld) EVAL %ld\n",siteID,direct_index, likeFuncEvalCallCount);</span></span>
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3054
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<pre style="margin: 0;">+<span id="LC3054" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*for (long s = 0; s < theFilter->NumberSpecies(); s++) {</span></span>
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3055
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<pre style="margin: 0;">+<span id="LC3055" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf (stderr, "%s", theFilter->RetrieveState(direct_index, s).get_str());</span></span>
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3056
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<pre style="margin: 0;">+<span id="LC3056" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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3057
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<pre style="margin: 0;">+<span id="LC3057" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf (stderr, "\n");*/</span></span>
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3053
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3058
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<pre style="margin: 0;"> <span id="LC3058" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="p">(</span><span class="mi" style="color: #099;">1L</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">direct_index</span><span class="p">);</span></span>
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3054
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3059
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<pre style="margin: 0;"> <span id="LC3059" class="line" lang="cpp"> <span class="p">}</span></span>
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3060
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<pre style="margin: 0;"> <span id="LC3060" class="line" lang="cpp"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3061" style="width: 35px; color: rgba(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="3066" style="width: 35px; color: rgba(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">@@ -3061,7 +3066,7 @@ hyFloat _TheTree::ComputeLLWithBranchCache (</td>
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3061
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3066
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<pre style="margin: 0;"> <span id="LC3066" class="line" lang="cpp"> <span class="n" style="color: #333;">term</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">accumulator</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">correction</span><span class="p">;</span></span>
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3062
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3067
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<pre style="margin: 0;"> <span id="LC3067" class="line" lang="cpp"> <span class="p">}</span></span>
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3063
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3068
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<pre style="margin: 0;"> <span id="LC3068" class="line" lang="cpp"> </span>
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3064
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<pre style="margin: 0;">-<span id="LC3064" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*if (likeFuncEvalCallCount == 1<span class="idiff left right">1035</span>) {</span></span>
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3069
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<pre style="margin: 0;">+<span id="LC3069" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*if (likeFuncEvalCallCount == 1<span class="idiff left right">5098</span>) {</span></span>
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3065
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3070
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<pre style="margin: 0;"> <span id="LC3070" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf (stderr, "CACHE, %ld, %ld, %20.15lg, %20.15lg, %20.15lg\n", likeFuncEvalCallCount, siteID, accumulator, correction, term);</span></span>
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3066
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3071
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<pre style="margin: 0;"> <span id="LC3071" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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3067
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3072
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<pre style="margin: 0;"> <span id="LC3072" class="line" lang="cpp"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3093" style="width: 35px; color: rgba(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="3098" style="width: 35px; color: rgba(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">@@ -3093,6 +3098,12 @@ hyFloat _TheTree::ComputeLLWithBranchCache (</td>
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3093
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3098
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<pre style="margin: 0;"> <span id="LC3098" class="line" lang="cpp"> </span>
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3094
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3099
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<pre style="margin: 0;"> <span id="LC3099" class="line" lang="cpp"> </span>
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3095
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3100
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<pre style="margin: 0;"> <span id="LC3100" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// cases by alphabet dimension</span></span>
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3101
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<pre style="margin: 0;">+<span id="LC3101" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*if (likeFuncEvalCallCount == 15098) {</span></span>
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3102
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<pre style="margin: 0;">+<span id="LC3102" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf (stderr, "\nBRANCH ID %ld (%s)\n", brID, givenTreeNode->GetName()->get_str());</span></span>
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3103
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<pre style="margin: 0;">+<span id="LC3103" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> for (long e = 0; e < 16; e++) {</span></span>
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3104
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<pre style="margin: 0;">+<span id="LC3104" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf (stderr, "%ld => %lg\n", transitionMatrix[e]);</span></span>
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3105
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<pre style="margin: 0;">+<span id="LC3105" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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3106
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<pre style="margin: 0;">+<span id="LC3106" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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3107
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<pre style="margin: 0;"> <span id="LC3107" class="line" lang="cpp"> </span>
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3097
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3108
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<pre style="margin: 0;"> <span id="LC3108" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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3098
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3109
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<pre style="margin: 0;"> <span id="LC3109" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">alphabetDimension</span><span class="p">)</span> <span class="p">{</span></span>
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<li id="9f127084157a2a4e11faf03320db0541dbae15dc">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d8a6fecc5558ddf14f61e62f2bf14fe1a9ea9fff#9f127084157a2a4e11faf03320db0541dbae15dc"><strong>src/core/tree_evaluator.cpp</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">@@ -45,6 +45,8 @@</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "global_things.h"</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "likefunc.h"</span></span>
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">likeFuncEvalCallCount</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">hy_global</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">hy_env</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">@@ -144,11 +146,24 @@ template<long D> inline bool __ll_handle_conditional_array_initialization ( long</td>
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144
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"> <span class="p">}</span></span>
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">__builtin_expect</span><span class="p">(</span><span class="n" style="color: #333;">siteState</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0L</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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146
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// a single character state; sweep down the appropriate column</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*if (likeFuncEvalCallCount == 15098 && nodeCode == 3706 && siteID == 91) {</span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf (stderr, "\nSITE CHECK: ID %ld, STATE %ld\n", nodeCode, siteState);</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> for (long e = 0; e < 4; e++) {</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf (stderr, "%ld => %lg\n", e, parentConditionals[e]);</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"> </span>
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147
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma unroll(4)</span></span>
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148
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>
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149
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158
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<pre style="margin: 0;"> <span id="LC158" 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;">long</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">D</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 class="p">{</span></span>
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150
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="cpp"> <span class="n" style="color: #333;">parentConditionals</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="n" style="color: #333;">tMatrix</span><span class="p">[</span><span class="n" style="color: #333;">siteState</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>
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151
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="cpp"> <span class="p">}</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*if (likeFuncEvalCallCount == 15098 && nodeCode == 3706 && siteID == 91) {</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf (stderr, "\nSITE CHECK: ID %ld, STATE %ld\n", nodeCode, siteState);</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> for (long e = 0; e < 4; e++) {</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf (stderr, "%ld => %lg\n", e, parentConditionals[e]);</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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152
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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153
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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154
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp"> <span class="n" style="color: #333;">childVector</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lNodeResolutions</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</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;">siteState</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;">D</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="471" style="width: 35px; color: rgba(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="486" style="width: 35px; color: rgba(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">@@ -471,11 +486,18 @@ template<long D, bool ADJUST> inline void __ll_loop_handle_scaling (hyFloat& sum</td>
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471
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486
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="cpp"> </span>
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472
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487
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">scaler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_computeBoostScaler</span><span class="p">(</span><span class="n" style="color: #333;">scalingAdjustments</span> <span class="p">[</span><span class="n" style="color: #333;">parentCode</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">siteCount</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">siteID</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_lfScalerUpwards</span><span class="p">,</span> <span class="n" style="color: #333;">sum</span><span class="p">,</span> <span class="n" style="color: #333;">didScale</span><span class="p">);</span></span>
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473
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488
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*if (likeFuncEvalCallCount == 15098 && siteID == 91) {</span></span>
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf (stderr, "UP %ld (%ld) %lg\n", didScale, parentCode, scaler);</span></span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">didScale</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma unroll(4)</span></span>
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>
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<pre style="margin: 0;"> <span id="LC496" 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;">long</span> <span class="n" style="color: #333;">c</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;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">D</span><span class="p">;</span> <span class="n" style="color: #333;">c</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="LC497" class="line" lang="cpp"> <span class="n" style="color: #333;">parentConditionals</span> <span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">scaler</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*if (likeFuncEvalCallCount == 15098 && siteID == 91) {</span></span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf (stderr, "%ld=>%g\n", c, parentConditionals [c]);</span></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">siteFrequency</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1L</span><span class="p">)</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">@@ -492,13 +514,19 @@ template<long D, bool ADJUST> inline void __ll_loop_handle_scaling (hyFloat& sum</td>
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">HUGE_VAL</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// no point scaling an infinity</span></span>
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<pre style="margin: 0;"> <span id="LC515" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC516" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">scaler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_computeReductionScaler</span> <span class="p">(</span><span class="n" style="color: #333;">scalingAdjustments</span> <span class="p">[</span><span class="n" style="color: #333;">parentCode</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">siteCount</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">siteID</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_lfScalingFactorThreshold</span><span class="p">,</span> <span class="n" style="color: #333;">sum</span><span class="p">,</span> <span class="n" style="color: #333;">didScale</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*if (likeFuncEvalCallCount == 15098 && siteID == 91) {</span></span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf (stderr, "DOWN %ld (%ld) %lg\n", didScale, parentCode, scaler);</span></span>
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">didScale</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC522" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma unroll(4)</span></span>
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<pre style="margin: 0;"> <span id="LC523" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>
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<pre style="margin: 0;"> <span id="LC524" 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;">long</span> <span class="n" style="color: #333;">c</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;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">D</span><span class="p">;</span> <span class="n" style="color: #333;">c</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="LC500" class="line" lang="cpp"> <span class="n" style="color: #333;">parentConditionals</span> <span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">scaler</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="cpp"> <span class="n" style="color: #333;">parentConditionals</span> <span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">scaler</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*if (likeFuncEvalCallCount == 15098 && siteID == 91) {</span></span>
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf (stderr, "%ld=>%g\n", c, parentConditionals [c]);</span></span>
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">siteFrequency</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1L</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="cpp"> <span class="n" style="color: #333;">localScalerChange</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">didScale</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">@@ -858,7 +886,16 @@ hyFloat _TheTree::ComputeTreeBlockByBranch ( _SimpleList</td>
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<pre style="margin: 0;"> <span id="LC886" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC887" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_hprestrict_</span> <span class="n" style="color: #333;">transitionMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">currentTreeNode</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetCompExp</span><span class="p">(</span><span class="n" style="color: #333;">catID</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC888" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC861" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (likeFuncEvalCallCount == 15098 && parentCode == 3688) {</span></span>
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> //if (currentTreeNode->GetName()->EndsWith("mt811400_SARS2_orf1ab_usa__4")) {</span></span>
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf (stderr, "\nBRANCH ID %ld (%ld = parent ID, parent name = %s) (%s)\n", nodeCode, parentCode, ((_CalcNode*)flatTree (parentCode))->GetName()->get_str(), currentTreeNode->GetName()->get_str());</span></span>
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> for (long e = 0; e < 16; e++) {</span></span>
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf (stderr, "%ld => %lg\n", transitionMatrix[e]);</span></span>
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895
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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896
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> //}</span></span>
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897
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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899
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<pre style="margin: 0;"> <span id="LC899" class="line" lang="cpp"> </span>
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900
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<pre style="margin: 0;"> <span id="LC900" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">currentTCCIndex</span><span class="p">,</span><span class="n" style="color: #333;">currentTCCBit</span><span class="p">,</span><span class="n" style="color: #333;">parentTCCIIndex</span><span class="p">,</span><span class="n" style="color: #333;">parentTCCIBit</span><span class="p">;</span></span>
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864
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901
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<pre style="margin: 0;"> <span id="LC901" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_tcc_init</span> <span class="p">(</span><span class="n" style="color: #333;">tcc</span><span class="p">,</span> <span class="n" style="color: #333;">isLeaf</span><span class="p">,</span> <span class="n" style="color: #333;">siteCount</span><span class="p">,</span> <span class="n" style="color: #333;">siteFrom</span><span class="p">,</span> <span class="n" style="color: #333;">nodeCode</span><span class="p">,</span> <span class="n" style="color: #333;">parentCode</span><span class="p">,</span> <span class="n" style="color: #333;">parentTCCIBit</span><span class="p">,</span> <span class="n" style="color: #333;">parentTCCIIndex</span><span class="p">,</span> <span class="n" style="color: #333;">currentTCCBit</span><span class="p">,</span> <span class="n" style="color: #333;">currentTCCIndex</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="922" style="width: 35px; color: rgba(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">@@ -885,7 +922,8 @@ hyFloat _TheTree::ComputeTreeBlockByBranch ( _SimpleList</td>
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885
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922
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<pre style="margin: 0;"> <span id="LC922" class="line" lang="cpp"> <span class="n" style="color: #333;">lNodeFlags</span><span class="p">,</span> <span class="n" style="color: #333;">isLeaf</span><span class="p">,</span> <span class="n" style="color: #333;">nodeCode</span><span class="p">,</span> <span class="n" style="color: #333;">setBranch</span><span class="p">,</span> <span class="n" style="color: #333;">flatTree</span><span class="p">.</span><span class="n" style="color: #333;">lLength</span><span class="p">,</span> <span class="n" style="color: #333;">siteID</span><span class="p">,</span> <span class="n" style="color: #333;">siteFrom</span><span class="p">,</span> <span class="n" style="color: #333;">siteCount</span><span class="p">,</span> <span class="n" style="color: #333;">siteOrdering</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">lNodeResolutions</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">tcc</span><span class="p">,</span> <span class="n" style="color: #333;">currentTCCBit</span><span class="p">,</span> <span class="n" style="color: #333;">currentTCCIndex</span><span class="p">,</span> <span class="n" style="color: #333;">lastUpdatedSite</span><span class="p">,</span> <span class="n" style="color: #333;">setBranchTo</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC923" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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887
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924
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<pre style="margin: 0;"> <span id="LC924" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC888" class="line" lang="cpp"></span>
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925
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<pre style="margin: 0;">+<span id="LC925" class="line" lang="cpp"> </span>
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926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="cpp"> </span>
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927
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<pre style="margin: 0;"> <span id="LC927" class="line" lang="cpp"> </span>
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928
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<pre style="margin: 0;"> <span id="LC928" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_AVX_INTRINSICS</span></span>
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929
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<pre style="margin: 0;"> <span id="LC929" class="line" lang="cpp"> <span class="n" style="color: #333;">_handle4x4_pruning_case</span> <span class="p">(</span><span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">tmatrix_transpose</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1245" style="width: 35px; color: rgba(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="1283" style="width: 35px; color: rgba(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">@@ -1245,7 +1283,9 @@ hyFloat _TheTree::ComputeTreeBlockByBranch ( _SimpleList</td>
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1245
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1283
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<pre style="margin: 0;"> <span id="LC1283" class="line" lang="cpp"> <span class="n" style="color: #333;">accumulator</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rootConditionals</span><span class="p">[</span><span class="n" style="color: #333;">rootIndex</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">theProbs</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">];</span></span>
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1246
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1284
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<pre style="margin: 0;"> <span id="LC1284" class="line" lang="cpp"> <span class="p">}</span></span>
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1247
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1285
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<pre style="margin: 0;"> <span id="LC1285" class="line" lang="cpp"> <span class="p">}</span></span>
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1248
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<pre style="margin: 0;">-<span id="LC1248" class="line" lang="cpp"> </span>
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1286
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<pre style="margin: 0;">+<span id="LC1286" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*if (likeFuncEvalCallCount == 15098 && siteID == 91) {</span></span>
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1287
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<pre style="margin: 0;">+<span id="LC1287" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf (stderr, "\nREGULAR COMPUTE %lg (%ld) (%lg %lg %lg %lg)\n", accumulator, setBranch, rootConditionals[rootIndex-4],rootConditionals[rootIndex-3],rootConditionals[rootIndex-2],rootConditionals[rootIndex-1]);</span></span>
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1288
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<pre style="margin: 0;">+<span id="LC1288" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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1249
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1289
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<pre style="margin: 0;"> <span id="LC1289" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">storageVec</span><span class="p">)</span> <span class="p">{</span></span>
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1250
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1290
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<pre style="margin: 0;"> <span id="LC1290" class="line" lang="cpp"> <span class="n" style="color: #333;">storageVec</span> <span class="p">[</span><span class="n" style="color: #333;">siteOrdering</span><span class="p">.</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">siteID</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">accumulator</span><span class="p">;</span></span>
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1251
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1291
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<pre style="margin: 0;"> <span id="LC1291" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1297" style="width: 35px; color: rgba(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="1337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1297,7 +1337,6 @@ template<long D> inline bool __lcache_loop_preface (bool isLeaf, long* __restric</td>
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1297
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1337
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<pre style="margin: 0;"> <span id="LC1337" 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;">long</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">D</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 class="n" style="color: #333;">target_index</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="p">{</span></span>
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1298
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1338
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<pre style="margin: 0;"> <span id="LC1338" class="line" lang="cpp"> <span class="n" style="color: #333;">parentConditionals</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="n" style="color: #333;">tMatrix</span><span class="p">[</span><span class="n" style="color: #333;">target_index</span><span class="p">];</span></span>
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1299
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1339
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<pre style="margin: 0;"> <span id="LC1339" class="line" lang="cpp"> <span class="p">}</span></span>
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1300
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<pre style="margin: 0;">-<span id="LC1300" class="line" lang="cpp"> </span>
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1301
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1340
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<pre style="margin: 0;"> <span id="LC1340" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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1302
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1341
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<pre style="margin: 0;"> <span id="LC1341" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1303
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1342
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<pre style="margin: 0;"> <span id="LC1342" class="line" lang="cpp"> <span class="n" style="color: #333;">childVector</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lNodeResolutions</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</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;">siteState</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;">D</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1563" style="width: 35px; color: rgba(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="1602" style="width: 35px; color: rgba(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">@@ -1563,6 +1602,16 @@ void _TheTree::ComputeBranchCache (</td>
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1563
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1602
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<pre style="margin: 0;"> <span id="LC1602" class="line" lang="cpp"> <span class="n" style="color: #333;">taggedNodes</span><span class="p">.</span><span class="n" style="color: #333;">Populate</span> <span class="p">(</span><span class="n" style="color: #333;">flatTree</span><span class="p">.</span><span class="n" style="color: #333;">lLength</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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1564
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1603
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<pre style="margin: 0;"> <span id="LC1603" class="line" lang="cpp"> <span class="n" style="color: #333;">rootPath</span><span class="p">.</span><span class="n" style="color: #333;">Flip</span> <span class="p">();</span></span>
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1565
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1604
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<pre style="margin: 0;"> <span id="LC1604" class="line" lang="cpp"> </span>
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1605
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<pre style="margin: 0;">+<span id="LC1605" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*if (likeFuncEvalCallCount == 15098) {</span></span>
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1606
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<pre style="margin: 0;">+<span id="LC1606" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf (stderr, "\nCaching branch %ld\n", brID);</span></span>
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1607
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<pre style="margin: 0;">+<span id="LC1607" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> rootPath.Each ([&](long n, unsigned long i) -> void {</span></span>
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1608
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<pre style="margin: 0;">+<span id="LC1608" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> _CalcNode * current_node = (_CalcNode*) (n < flatLeaves.lLength ? flatCLeaves (n):</span></span>
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1609
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<pre style="margin: 0;">+<span id="LC1609" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> flatTree (n-flatLeaves.lLength));</span></span>
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1610
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<pre style="margin: 0;">+<span id="LC1610" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf (stderr, "[%d: %d] %s\n", i, n,current_node->GetName()->get_str());</span></span>
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1611
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<pre style="margin: 0;">+<span id="LC1611" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> });</span></span>
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1612
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<pre style="margin: 0;">+<span id="LC1612" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> ObjectToConsole(&nodesToProcess);NLToConsole();</span></span>
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1613
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<pre style="margin: 0;">+<span id="LC1613" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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1614
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<pre style="margin: 0;">+<span id="LC1614" class="line" lang="cpp"> </span>
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1566
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1615
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<pre style="margin: 0;"> <span id="LC1615" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">node_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nodesToProcess</span><span class="p">.</span><span class="n" style="color: #333;">lLength</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rootPath</span><span class="p">.</span><span class="n" style="color: #333;">lLength</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2L</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1567
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1616
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<pre style="margin: 0;"> <span id="LC1616" class="line" lang="cpp"> </span>
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1568
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1617
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<pre style="margin: 0;"> <span id="LC1617" 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;">long</span> <span class="n" style="color: #333;">nodeID</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;">nodeID</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">node_count</span><span class="p">;</span> <span class="n" style="color: #333;">nodeID</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1585" style="width: 35px; color: rgba(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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1585,9 +1634,8 @@ void _TheTree::ComputeBranchCache (</td>
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1585
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1634
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<pre style="margin: 0;"> <span id="LC1634" class="line" lang="cpp"> <span class="p">}</span></span>
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1586
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<td class="diff-line-num new_line" 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="cpp"> </span>
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1587
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<td class="diff-line-num new_line" 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="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">parentConditionals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">iNodeCache</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">siteFrom</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">parentCode</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">siteCount</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alphabetDimension</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1588" 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">
1588
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<td class="diff-line-num new_line old" data-linenumber="1637" 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="LC1588" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">taggedNodes</span><span class="p">.</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">parentCode</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0L</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1589" 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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1637
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<pre style="margin: 0;">+<span id="LC1637" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">taggedNodes</span><span class="p">.</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">parentCode</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0L</span><span class="p">)</span><span class="idiff left"> </span><span class="p"><span class="idiff right">{</span></span></span>
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1589
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<td class="diff-line-num new_line" data-linenumber="1638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1638
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<pre style="margin: 0;"> <span id="LC1638" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// mark the parent for update and clear its conditionals if needed</span></span>
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1590
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<pre style="margin: 0;">-<span id="LC1590" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1591
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<td class="diff-line-num new_line" data-linenumber="1639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1639
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<pre style="margin: 0;"> <span id="LC1639" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printf ("Resetting parentCode = %ld\n", parentCode);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1592
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<td class="diff-line-num new_line" data-linenumber="1640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1640
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<pre style="margin: 0;"> <span id="LC1640" class="line" lang="cpp"> <span class="n" style="color: #333;">taggedNodes</span><span class="p">.</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">parentCode</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1L</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1593
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<td class="diff-line-num new_line" data-linenumber="1641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1641
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<pre style="margin: 0;"> <span id="LC1641" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">localScalingFactor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scalingAdjustments</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">parentCode</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">siteCount</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">@@ -1616,10 +1664,11 @@ void _TheTree::ComputeBranchCache (</td>
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1616
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1664
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<pre style="margin: 0;"> <span id="LC1664" class="line" lang="cpp"> <span class="n" style="color: #333;">_CalcNode</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">currentTreeNode</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">_CalcNode</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">isLeaf</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">flatCLeaves</span> <span class="p">(</span><span class="n" style="color: #333;">nodeCode</span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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1617
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1665
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<pre style="margin: 0;"> <span id="LC1665" class="line" lang="cpp"> <span class="n" style="color: #333;">flatTree</span> <span class="p">(</span><span class="n" style="color: #333;">notPassedRoot</span><span class="o" style="font-weight: 600;">?</span><span class="n" style="color: #333;">nodeCode</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">parentCode</span><span class="p">));</span></span>
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1618
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1666
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<pre style="margin: 0;"> <span id="LC1666" class="line" lang="cpp"> </span>
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1619
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<pre style="margin: 0;">-<span id="LC1619" class="line" lang="cpp"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">hyFloat</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</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">transitionMatrix</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">currentTreeNode</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">GetCompExp</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">catID</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">theData</span></span><span class="p"><span class="idiff right">;</span></span></span>
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1620
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<pre style="margin: 0;">-<span id="LC1620" class="line" lang="cpp"> </span>
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1621
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<pre style="margin: 0;">-<span id="LC1621" class="line" lang="cpp"></span>
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1667
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<pre style="margin: 0;">+<span id="LC1667" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">/*if (likeFuncEvalCallCount == 15098) {</span></span></span>
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1668
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<pre style="margin: 0;">+<span id="LC1668" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> <span class="idiff left right"> fprintf (stderr, "%ld/%ld (%ld/%ld) => %s\n", nodeID, nodeCode, isLeaf, notPassedRoot, currentTreeNode->GetName()->get_str());</span></span></span>
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1669
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<pre style="margin: 0;">+<span id="LC1669" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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1622
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1670
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<pre style="margin: 0;"> <span id="LC1670" class="line" lang="cpp"> </span>
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1671
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<pre style="margin: 0;">+<span id="LC1671" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">transitionMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">currentTreeNode</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetCompExp</span><span class="p">(</span><span class="n" style="color: #333;">catID</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span><span class="p">;</span></span>
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1623
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1672
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<pre style="margin: 0;"> <span id="LC1672" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lastUpdatedSite</span><span class="p">;</span></span>
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1624
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1673
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<pre style="margin: 0;"> <span id="LC1673" class="line" lang="cpp"> </span>
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1625
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1674
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<pre style="margin: 0;"> <span id="LC1674" class="line" lang="cpp"> <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;">isLeaf</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold new_line" data-linenumber="1679" style="width: 35px; color: rgba(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">@@ -1630,8 +1679,7 @@ void _TheTree::ComputeBranchCache (</td>
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1630
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1679
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<pre style="margin: 0;"> <span id="LC1679" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">currentTCCIndex</span><span class="p">,</span><span class="n" style="color: #333;">currentTCCBit</span><span class="p">,</span><span class="n" style="color: #333;">parentTCCIIndex</span><span class="p">,</span><span class="n" style="color: #333;">parentTCCIBit</span><span class="p">;</span></span>
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1631
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1680
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<pre style="margin: 0;"> <span id="LC1680" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_tcc_init</span> <span class="p">(</span><span class="n" style="color: #333;">tcc</span><span class="p">,</span> <span class="n" style="color: #333;">isLeaf</span><span class="p">,</span> <span class="n" style="color: #333;">siteCount</span><span class="p">,</span> <span class="n" style="color: #333;">siteFrom</span><span class="p">,</span> <span class="n" style="color: #333;">nodeCode</span><span class="p">,</span> <span class="n" style="color: #333;">parentCode</span><span class="p">,</span> <span class="n" style="color: #333;">parentTCCIBit</span><span class="p">,</span> <span class="n" style="color: #333;">parentTCCIIndex</span><span class="p">,</span> <span class="n" style="color: #333;">currentTCCBit</span><span class="p">,</span> <span class="n" style="color: #333;">currentTCCIndex</span><span class="p">);</span></span>
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1632
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1681
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<pre style="margin: 0;"> <span id="LC1681" class="line" lang="cpp"></span>
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1633
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<pre style="margin: 0;">-<span id="LC1633" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">canScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">notPassedRoot</span><span class="p">;</span></span>
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1634
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<pre style="margin: 0;">-<span id="LC1634" class="line" lang="cpp"></span>
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1682
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<pre style="margin: 0;">+<span id="LC1682" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC1683" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alphabetDimension</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4L</span><span class="p">)</span> <span class="p">{</span></span>
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1636
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1684
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<pre style="margin: 0;"> <span id="LC1684" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_USE_AVX_INTRINSICS</span></span>
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1637
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1685
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<pre style="margin: 0;"> <span id="LC1685" class="line" lang="cpp"> <span class="n" style="color: #333;">__m256d</span> <span class="n" style="color: #333;">tmatrix_transpose</span> <span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1642" style="width: 35px; color: rgba(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">@@ -1642,9 +1690,13 @@ void _TheTree::ComputeBranchCache (</td>
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1642
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1690
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<pre style="margin: 0;"> <span id="LC1690" class="line" lang="cpp"> <span class="p">};</span></span>
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1691
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<pre style="margin: 0;"> <span id="LC1691" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1692
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<pre style="margin: 0;"> <span id="LC1692" 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;">long</span> <span class="n" style="color: #333;">siteID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">siteFrom</span><span class="p">;</span> <span class="n" style="color: #333;">siteID</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">siteTo</span><span class="p">;</span> <span class="n" style="color: #333;">siteID</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">4L</span><span class="p">)</span> <span class="p">{</span></span>
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1693
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<pre style="margin: 0;">+<span id="LC1693" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">canScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">notPassedRoot</span><span class="p">;</span></span>
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1645
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1694
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<pre style="margin: 0;"> <span id="LC1694" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transitionMatrix</span><span class="p">;</span></span>
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1646
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1695
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<pre style="margin: 0;"> <span id="LC1695" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">__lcache_loop_preface</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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1647
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1696
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<pre style="margin: 0;"> <span id="LC1696" class="line" lang="cpp"> <span class="n" style="color: #333;">isLeaf</span><span class="p">,</span> <span class="n" style="color: #333;">lNodeFlags</span><span class="p">,</span> <span class="n" style="color: #333;">siteID</span><span class="p">,</span> <span class="n" style="color: #333;">siteOrdering</span><span class="p">,</span> <span class="n" style="color: #333;">nodeCode</span><span class="p">,</span> <span class="n" style="color: #333;">siteCount</span><span class="p">,</span> <span class="n" style="color: #333;">siteFrom</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">canScale</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">lastUpdatedSite</span><span class="p">,</span> <span class="n" style="color: #333;">tcc</span><span class="p">,</span> <span class="n" style="color: #333;">currentTCCBit</span><span class="p">,</span> <span class="n" style="color: #333;">currentTCCIndex</span><span class="p">,</span> <span class="n" style="color: #333;">parentTCCIBit</span><span class="p">,</span> <span class="n" style="color: #333;">parentTCCIIndex</span><span class="p">,</span> <span class="n" style="color: #333;">notPassedRoot</span><span class="p">,</span> <span class="n" style="color: #333;">lNodeResolutions</span><span class="p">))</span> <span class="p">{</span></span>
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1697
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<pre style="margin: 0;">+<span id="LC1697" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*if (likeFuncEvalCallCount == 15098 && siteID == 91) {</span></span>
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1698
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<pre style="margin: 0;">+<span id="LC1698" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf (stderr, "__lcache_loop_preface (%ld) %g %g %g %g\n", nodeCode, parentConditionals[0], parentConditionals[1], parentConditionals[2], parentConditionals[3]);</span></span>
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1699
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<pre style="margin: 0;">+<span id="LC1699" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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1700
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<pre style="margin: 0;"> <span id="LC1700" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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1649
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1701
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<pre style="margin: 0;"> <span id="LC1701" class="line" lang="cpp"> <span class="p">}</span></span>
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1650
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1702
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<pre style="margin: 0;"> <span id="LC1702" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">didScale</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1659,6 +1711,9 @@ void _TheTree::ComputeBranchCache (</td>
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1659
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1711
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<pre style="margin: 0;"> <span id="LC1711" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_loop_handle_scaling</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">4L</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">sum</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">scalingAdjustments</span><span class="p">,</span> <span class="n" style="color: #333;">didScale</span><span class="p">,</span> <span class="n" style="color: #333;">nodeCode</span><span class="p">,</span> <span class="n" style="color: #333;">siteCount</span><span class="p">,</span> <span class="n" style="color: #333;">siteID</span><span class="p">,</span> <span class="n" style="color: #333;">localScalerChange</span><span class="p">,</span> <span class="n" style="color: #333;">theFilter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theFrequencies</span><span class="p">.</span><span class="n" style="color: #333;">get</span> <span class="p">(</span><span class="n" style="color: #333;">siteOrdering</span><span class="p">.</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">siteID</span><span class="p">]));</span></span>
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1660
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<td class="diff-line-num new_line" data-linenumber="1712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1712
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<pre style="margin: 0;"> <span id="LC1712" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="1661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1661
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<td class="diff-line-num new_line" data-linenumber="1713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1713
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<pre style="margin: 0;"> <span id="LC1713" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1714" 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">
1714
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<pre style="margin: 0;">+<span id="LC1714" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*if (likeFuncEvalCallCount == 15098 && siteID == 91) {</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1715" 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">
1715
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<pre style="margin: 0;">+<span id="LC1715" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf (stderr, "NODE = %ld, PARENT = %ld (%ld), P(G) = %lg, P(T) = %lg, scale = %ld\n", nodeCode, parentCode, canScale, parentConditionals[2], parentConditionals[3], didScale);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1716" 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">
1716
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<pre style="margin: 0;">+<span id="LC1716" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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<td class="diff-line-num old_line" data-linenumber="1662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1662
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<td class="diff-line-num new_line" data-linenumber="1717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1717
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<pre style="margin: 0;"> <span id="LC1717" class="line" lang="cpp"> <span class="n" style="color: #333;">childVector</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">4L</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1663
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<td class="diff-line-num new_line" data-linenumber="1718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1718
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<pre style="margin: 0;"> <span id="LC1718" class="line" lang="cpp"> <span class="n" style="color: #333;">__handle_site_corrections</span><span class="p">(</span><span class="n" style="color: #333;">didScale</span><span class="p">,</span> <span class="n" style="color: #333;">siteID</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1664
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<td class="diff-line-num new_line" data-linenumber="1719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1719
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<pre style="margin: 0;"> <span id="LC1719" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1667" style="width: 35px; color: rgba(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="1722" style="width: 35px; color: rgba(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">@@ -1667,6 +1722,7 @@ void _TheTree::ComputeBranchCache (</td>
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<td class="diff-line-num old_line" data-linenumber="1667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1667
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<td class="diff-line-num new_line" data-linenumber="1722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1722
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<pre style="margin: 0;"> <span id="LC1722" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_matrix_transpose</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrixT</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1668
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<td class="diff-line-num new_line" data-linenumber="1723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1723
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<pre style="margin: 0;"> <span id="LC1723" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="diff-line-num old_line" data-linenumber="1669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1669
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<td class="diff-line-num new_line" data-linenumber="1724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1724
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<pre style="margin: 0;"> <span id="LC1724" 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;">long</span> <span class="n" style="color: #333;">siteID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">siteFrom</span><span class="p">;</span> <span class="n" style="color: #333;">siteID</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">siteTo</span><span class="p">;</span> <span class="n" style="color: #333;">siteID</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">20L</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1725" 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">
1725
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<pre style="margin: 0;">+<span id="LC1725" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">canScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">notPassedRoot</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1670
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<td class="diff-line-num new_line" data-linenumber="1726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1726
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<pre style="margin: 0;"> <span id="LC1726" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transitionMatrix</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1671
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<td class="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC1727" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">__lcache_loop_preface</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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<td class="diff-line-num old_line" data-linenumber="1672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1672
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<td class="diff-line-num new_line" data-linenumber="1728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1728
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<pre style="margin: 0;"> <span id="LC1728" class="line" lang="cpp"> <span class="n" style="color: #333;">isLeaf</span><span class="p">,</span> <span class="n" style="color: #333;">lNodeFlags</span><span class="p">,</span> <span class="n" style="color: #333;">siteID</span><span class="p">,</span> <span class="n" style="color: #333;">siteOrdering</span><span class="p">,</span> <span class="n" style="color: #333;">nodeCode</span><span class="p">,</span> <span class="n" style="color: #333;">siteCount</span><span class="p">,</span> <span class="n" style="color: #333;">siteFrom</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">canScale</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">lastUpdatedSite</span><span class="p">,</span> <span class="n" style="color: #333;">tcc</span><span class="p">,</span> <span class="n" style="color: #333;">currentTCCBit</span><span class="p">,</span> <span class="n" style="color: #333;">currentTCCIndex</span><span class="p">,</span> <span class="n" style="color: #333;">parentTCCIBit</span><span class="p">,</span> <span class="n" style="color: #333;">parentTCCIIndex</span><span class="p">,</span> <span class="n" style="color: #333;">notPassedRoot</span><span class="p">,</span> <span class="n" style="color: #333;">lNodeResolutions</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1699" style="width: 35px; color: rgba(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="1755" style="width: 35px; color: rgba(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">@@ -1699,6 +1755,7 @@ void _TheTree::ComputeBranchCache (</td>
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<td class="diff-line-num old_line" data-linenumber="1699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1699
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<td class="diff-line-num new_line" data-linenumber="1755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1755
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1755" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_matrix_transpose</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">60L</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrixT</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1700
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<td class="diff-line-num new_line" data-linenumber="1756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1756
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<pre style="margin: 0;"> <span id="LC1756" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1701
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1757
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<pre style="margin: 0;"> <span id="LC1757" 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;">long</span> <span class="n" style="color: #333;">siteID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">siteFrom</span><span class="p">;</span> <span class="n" style="color: #333;">siteID</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">siteTo</span><span class="p">;</span> <span class="n" style="color: #333;">siteID</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">60L</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1758" 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">
1758
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<pre style="margin: 0;">+<span id="LC1758" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">canScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">notPassedRoot</span><span class="p">;</span></span>
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1702
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1759
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<pre style="margin: 0;"> <span id="LC1759" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transitionMatrix</span><span class="p">;</span></span>
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1703
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<td class="diff-line-num new_line" data-linenumber="1760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1760
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<pre style="margin: 0;"> <span id="LC1760" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">__lcache_loop_preface</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">60</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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<td class="diff-line-num old_line" data-linenumber="1704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1704
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<td class="diff-line-num new_line" data-linenumber="1761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1761
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<pre style="margin: 0;"> <span id="LC1761" class="line" lang="cpp"> <span class="n" style="color: #333;">isLeaf</span><span class="p">,</span> <span class="n" style="color: #333;">lNodeFlags</span><span class="p">,</span> <span class="n" style="color: #333;">siteID</span><span class="p">,</span> <span class="n" style="color: #333;">siteOrdering</span><span class="p">,</span> <span class="n" style="color: #333;">nodeCode</span><span class="p">,</span> <span class="n" style="color: #333;">siteCount</span><span class="p">,</span> <span class="n" style="color: #333;">siteFrom</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">canScale</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">lastUpdatedSite</span><span class="p">,</span> <span class="n" style="color: #333;">tcc</span><span class="p">,</span> <span class="n" style="color: #333;">currentTCCBit</span><span class="p">,</span> <span class="n" style="color: #333;">currentTCCIndex</span><span class="p">,</span> <span class="n" style="color: #333;">parentTCCIBit</span><span class="p">,</span> <span class="n" style="color: #333;">parentTCCIIndex</span><span class="p">,</span> <span class="n" style="color: #333;">notPassedRoot</span><span class="p">,</span> <span class="n" style="color: #333;">lNodeResolutions</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1738" style="width: 35px; color: rgba(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="1795" style="width: 35px; color: rgba(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">@@ -1738,6 +1795,7 @@ void _TheTree::ComputeBranchCache (</td>
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1738
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<td class="diff-line-num new_line" data-linenumber="1795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1795
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<pre style="margin: 0;"> <span id="LC1795" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_matrix_transpose</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61L</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrixT</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" 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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1796
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<pre style="margin: 0;"> <span id="LC1796" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1740
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1797
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<pre style="margin: 0;"> <span id="LC1797" 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;">long</span> <span class="n" style="color: #333;">siteID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">siteFrom</span><span class="p">;</span> <span class="n" style="color: #333;">siteID</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">siteTo</span><span class="p">;</span> <span class="n" style="color: #333;">siteID</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">61L</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1798" 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">
1798
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<pre style="margin: 0;">+<span id="LC1798" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">canScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">notPassedRoot</span><span class="p">;</span></span>
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1741
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1799
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<pre style="margin: 0;"> <span id="LC1799" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transitionMatrix</span><span class="p">;</span></span>
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1742
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<td class="diff-line-num new_line" data-linenumber="1800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1800
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<pre style="margin: 0;"> <span id="LC1800" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">__lcache_loop_preface</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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1743
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<td class="diff-line-num new_line" data-linenumber="1801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1801
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<pre style="margin: 0;"> <span id="LC1801" class="line" lang="cpp"> <span class="n" style="color: #333;">isLeaf</span><span class="p">,</span> <span class="n" style="color: #333;">lNodeFlags</span><span class="p">,</span> <span class="n" style="color: #333;">siteID</span><span class="p">,</span> <span class="n" style="color: #333;">siteOrdering</span><span class="p">,</span> <span class="n" style="color: #333;">nodeCode</span><span class="p">,</span> <span class="n" style="color: #333;">siteCount</span><span class="p">,</span> <span class="n" style="color: #333;">siteFrom</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">canScale</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">lastUpdatedSite</span><span class="p">,</span> <span class="n" style="color: #333;">tcc</span><span class="p">,</span> <span class="n" style="color: #333;">currentTCCBit</span><span class="p">,</span> <span class="n" style="color: #333;">currentTCCIndex</span><span class="p">,</span> <span class="n" style="color: #333;">parentTCCIBit</span><span class="p">,</span> <span class="n" style="color: #333;">parentTCCIIndex</span><span class="p">,</span> <span class="n" style="color: #333;">notPassedRoot</span><span class="p">,</span> <span class="n" style="color: #333;">lNodeResolutions</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1782" style="width: 35px; color: rgba(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="1840" style="width: 35px; color: rgba(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">@@ -1782,6 +1840,7 @@ void _TheTree::ComputeBranchCache (</td>
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1782
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1840
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<pre style="margin: 0;"> <span id="LC1840" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_product_sum_loop</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">61L</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">tMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">sum</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1783
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1841
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<pre style="margin: 0;"> <span id="LC1841" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1784
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1842
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<pre style="margin: 0;"> <span id="LC1842" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">canScale</span><span class="p">)</span> <span class="p">{</span></span>
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1843
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<pre style="margin: 0;">+<span id="LC1843" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">canScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">notPassedRoot</span><span class="p">;</span></span>
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1785
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1844
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<pre style="margin: 0;"> <span id="LC1844" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined _SLKP_USE_AVX_INTRINSICS</span></span>
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1786
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1845
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<pre style="margin: 0;"> <span id="LC1845" class="line" lang="cpp"> <span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_avx_sum_4</span><span class="p">(</span><span class="n" style="color: #333;">grandTotal</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s60</span><span class="p">;</span></span>
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1787
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1846
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<pre style="margin: 0;"> <span id="LC1846" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#elif defined _SLKP_USE_SSE_INTRINSICS</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1856" style="width: 35px; color: rgba(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">@@ -1797,6 +1856,7 @@ void _TheTree::ComputeBranchCache (</td>
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1797
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1856
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<pre style="margin: 0;"> <span id="LC1856" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_matrix_transpose</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62L</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrixT</span><span class="p">);</span></span>
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1798
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1857
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<pre style="margin: 0;"> <span id="LC1857" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1799
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1858
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<pre style="margin: 0;"> <span id="LC1858" 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;">long</span> <span class="n" style="color: #333;">siteID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">siteFrom</span><span class="p">;</span> <span class="n" style="color: #333;">siteID</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">siteTo</span><span class="p">;</span> <span class="n" style="color: #333;">siteID</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">62L</span><span class="p">)</span> <span class="p">{</span></span>
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1859
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<pre style="margin: 0;">+<span id="LC1859" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">canScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">notPassedRoot</span><span class="p">;</span></span>
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1800
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1860
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<pre style="margin: 0;"> <span id="LC1860" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transitionMatrix</span><span class="p">;</span></span>
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1801
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1861
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<pre style="margin: 0;"> <span id="LC1861" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">__lcache_loop_preface</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">62</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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1802
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1862
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<pre style="margin: 0;"> <span id="LC1862" class="line" lang="cpp"> <span class="n" style="color: #333;">isLeaf</span><span class="p">,</span> <span class="n" style="color: #333;">lNodeFlags</span><span class="p">,</span> <span class="n" style="color: #333;">siteID</span><span class="p">,</span> <span class="n" style="color: #333;">siteOrdering</span><span class="p">,</span> <span class="n" style="color: #333;">nodeCode</span><span class="p">,</span> <span class="n" style="color: #333;">siteCount</span><span class="p">,</span> <span class="n" style="color: #333;">siteFrom</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">canScale</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">lastUpdatedSite</span><span class="p">,</span> <span class="n" style="color: #333;">tcc</span><span class="p">,</span> <span class="n" style="color: #333;">currentTCCBit</span><span class="p">,</span> <span class="n" style="color: #333;">currentTCCIndex</span><span class="p">,</span> <span class="n" style="color: #333;">parentTCCIBit</span><span class="p">,</span> <span class="n" style="color: #333;">parentTCCIIndex</span><span class="p">,</span> <span class="n" style="color: #333;">notPassedRoot</span><span class="p">,</span> <span class="n" style="color: #333;">lNodeResolutions</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1876" style="width: 35px; color: rgba(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="1936" style="width: 35px; color: rgba(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">@@ -1876,6 +1936,7 @@ void _TheTree::ComputeBranchCache (</td>
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1876
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1936
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<pre style="margin: 0;"> <span id="LC1936" class="line" lang="cpp"> <span class="n" style="color: #333;">__ll_handle_matrix_transpose</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63L</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">transitionMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrixT</span><span class="p">);</span></span>
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1877
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1937
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<pre style="margin: 0;"> <span id="LC1937" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1878
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1938
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<pre style="margin: 0;"> <span id="LC1938" 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;">long</span> <span class="n" style="color: #333;">siteID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">siteFrom</span><span class="p">;</span> <span class="n" style="color: #333;">siteID</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">siteTo</span><span class="p">;</span> <span class="n" style="color: #333;">siteID</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">63L</span><span class="p">)</span> <span class="p">{</span></span>
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1939
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<pre style="margin: 0;">+<span id="LC1939" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">canScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">notPassedRoot</span><span class="p">;</span></span>
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1879
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1940
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<pre style="margin: 0;"> <span id="LC1940" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transitionMatrix</span><span class="p">;</span></span>
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1880
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1941
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<pre style="margin: 0;"> <span id="LC1941" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">__lcache_loop_preface</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">63</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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1881
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1942
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<pre style="margin: 0;"> <span id="LC1942" class="line" lang="cpp"> <span class="n" style="color: #333;">isLeaf</span><span class="p">,</span> <span class="n" style="color: #333;">lNodeFlags</span><span class="p">,</span> <span class="n" style="color: #333;">siteID</span><span class="p">,</span> <span class="n" style="color: #333;">siteOrdering</span><span class="p">,</span> <span class="n" style="color: #333;">nodeCode</span><span class="p">,</span> <span class="n" style="color: #333;">siteCount</span><span class="p">,</span> <span class="n" style="color: #333;">siteFrom</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">canScale</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">lastUpdatedSite</span><span class="p">,</span> <span class="n" style="color: #333;">tcc</span><span class="p">,</span> <span class="n" style="color: #333;">currentTCCBit</span><span class="p">,</span> <span class="n" style="color: #333;">currentTCCIndex</span><span class="p">,</span> <span class="n" style="color: #333;">parentTCCIBit</span><span class="p">,</span> <span class="n" style="color: #333;">parentTCCIIndex</span><span class="p">,</span> <span class="n" style="color: #333;">notPassedRoot</span><span class="p">,</span> <span class="n" style="color: #333;">lNodeResolutions</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1972" style="width: 35px; color: rgba(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="2033" style="width: 35px; color: rgba(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 +2033,8 @@ void _TheTree::ComputeBranchCache (</td>
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1972
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2033
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<pre style="margin: 0;"> <span id="LC2033" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num 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">
1973
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<td class="diff-line-num new_line" data-linenumber="2034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2034
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<pre style="margin: 0;"> <span id="LC2034" class="line" lang="cpp"> </span>
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<td class="diff-line-num old_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">
1974
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<td class="diff-line-num new_line" data-linenumber="2035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2035
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<pre style="margin: 0;"> <span id="LC2035" 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;">long</span> <span class="n" style="color: #333;">siteID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">siteFrom</span><span class="p">;</span> <span class="n" style="color: #333;">siteID</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">siteTo</span><span class="p">;</span> <span class="n" style="color: #333;">siteID</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">alphabetDimension</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2036" 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">
2036
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<pre style="margin: 0;">+<span id="LC2036" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">canScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">notPassedRoot</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2037" 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">
2037
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<pre style="margin: 0;">+<span id="LC2037" class="line" lang="cpp"></span>
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1975
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<td class="diff-line-num new_line" data-linenumber="2038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2038
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<pre style="margin: 0;"> <span id="LC2038" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transitionMatrix</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1976
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<td class="diff-line-num new_line" data-linenumber="2039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2039
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<pre style="margin: 0;"> <span id="LC2039" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">__lcache_loop_preface_generic</span><span class="p">(</span></span>
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<td class="diff-line-num old_line" data-linenumber="1977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1977
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2040
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<pre style="margin: 0;"> <span id="LC2040" class="line" lang="cpp"> <span class="n" style="color: #333;">isLeaf</span><span class="p">,</span> <span class="n" style="color: #333;">lNodeFlags</span><span class="p">,</span> <span class="n" style="color: #333;">siteID</span><span class="p">,</span> <span class="n" style="color: #333;">siteOrdering</span><span class="p">,</span> <span class="n" style="color: #333;">nodeCode</span><span class="p">,</span> <span class="n" style="color: #333;">siteCount</span><span class="p">,</span> <span class="n" style="color: #333;">siteFrom</span><span class="p">,</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">,</span> <span class="n" style="color: #333;">tMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">canScale</span><span class="p">,</span> <span class="n" style="color: #333;">childVector</span><span class="p">,</span> <span class="n" style="color: #333;">lastUpdatedSite</span><span class="p">,</span> <span class="n" style="color: #333;">tcc</span><span class="p">,</span> <span class="n" style="color: #333;">currentTCCBit</span><span class="p">,</span> <span class="n" style="color: #333;">currentTCCIndex</span><span class="p">,</span> <span class="n" style="color: #333;">parentTCCIBit</span><span class="p">,</span> <span class="n" style="color: #333;">parentTCCIIndex</span><span class="p">,</span> <span class="n" style="color: #333;">notPassedRoot</span><span class="p">,</span> <span class="n" style="color: #333;">lNodeResolutions</span><span class="p">,</span> <span class="n" style="color: #333;">alphabetDimension</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2007" style="width: 35px; color: rgba(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="2070" style="width: 35px; color: rgba(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">@@ -2007,7 +2070,9 @@ void _TheTree::ComputeBranchCache (</td>
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2007
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<td class="diff-line-num new_line" data-linenumber="2070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2070
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<pre style="margin: 0;"> <span id="LC2070" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">site_bound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alphabetDimension</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">siteTo</span><span class="p">;</span></span>
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2008
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<td class="diff-line-num new_line" data-linenumber="2071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2071
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<pre style="margin: 0;"> <span id="LC2071" 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;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">ii</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">siteFrom</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alphabetDimension</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">site_bound</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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2009
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<td class="diff-line-num new_line" data-linenumber="2072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2072
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<pre style="margin: 0;"> <span id="LC2072" class="line" lang="cpp"> <span class="n" style="color: #333;">state</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rootConditionals</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">];</span></span>
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2010
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<td class="diff-line-num new_line old" data-linenumber="2073" 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="LC2010" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//printf ("Root conditional [%ld] = %g, node state [%ld] = %g\n", ii, state[ii], ii, cache[ii]);</span></span>
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2073
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<pre style="margin: 0;">+<span id="LC2073" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*if (likeFuncEvalCallCount == 15098 && ii / alphabetDimension == 91) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2074" 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">
2074
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<pre style="margin: 0;">+<span id="LC2074" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> printf ("Site %ld, Root conditional [%ld] = %g, node state [%ld] = %g\n", ii/alphabetDimension, ii, state[ii], ii, cache[ii]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2075" 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">
2075
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<pre style="margin: 0;">+<span id="LC2075" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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2011
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<td class="diff-line-num new_line" data-linenumber="2076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2076
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<pre style="margin: 0;"> <span id="LC2076" class="line" lang="cpp"> <span class="p">}</span></span>
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2012
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2077
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<pre style="margin: 0;"> <span id="LC2077" class="line" lang="cpp"> </span>
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2013
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2078
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<pre style="margin: 0;"> <span id="LC2078" class="line" lang="cpp"> <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;">siteCorrectionCounts</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">localScalerChange</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d8a6fecc5558ddf14f61e62f2bf14fe1a9ea9fff#adf5ba83265c3f16b63f5fab29404568aa294038"><strong>tests/hbltests/Results/HIVSweden.out</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">@@ -2,27 +2,27 @@</td>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">*** RUNNING SINGLE RATE MODEL ***</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">#################################</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">>Done in <span class="idiff left right">6</span> seconds </span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">>Done in <span class="idiff left right">5</span> seconds </span>
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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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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">-1137.68842968<span class="idiff left right">525</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">-1137.68842968<span class="idiff left right">708</span></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">-----------------------------------</span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">dN/dS = 0.9051395<span class="idiff left right">111492303</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">dN/dS = 0.9051395<span class="idiff left right">450601901</span></span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">*** RUNNING MODEL 1 (Neutral) ***</span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">######################################</span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">>Done in <span class="idiff left right">4</span> seconds </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">>Done in <span class="idiff left right">3</span> seconds </span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">-1114.6419<span class="idiff left right">8020114</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">-1114.6419<span class="idiff left right">7979838</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">------------------------------------------------</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">dN/dS = 0.5549192<span class="idiff left right">853457614 (sample variance = 0.2120268218125002</span>)</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">dN/dS = 0.5549192<span class="idiff left right">972885679 (sample variance = 0.2120268320358276</span>)</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">Rate[1]= 0.0785409<span class="idiff left right">2</span> (weight=0.4830173)</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Rate[1]= 0.0785409<span class="idiff left right">0</span> (weight=0.4830173)</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Rate[2]= 1.00000000 (weight=0.5169827)</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">------------------------------------------------</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">@@ -37,215 +37,215 @@ Import the following part into a data processing program</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">for further analysis</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">Rate/Site Rate=0.078540<span class="idiff left right">92332840576</span> Rate=1</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">1 0.00041548<span class="idiff left right">68030844993 0.9995845131969154</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">2 0.949480<span class="idiff left right">2777599012 0.0505197222400988</span>2</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">3 0.85271<span class="idiff left right">4319138601 0.147285680861399</span>1</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext">4 0.977295<span class="idiff left right">4463652723 0.02270455363472769</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext">5 0.708927<span class="idiff left right">6354636231 0.2910723645363769</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">6 0.970603<span class="idiff left right">5417626925 0.02939645823730756</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">13 0.959299<span class="idiff left right">3214137728 0.0407006785862272</span>1</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext">17 0.949480<span class="idiff left right">2777599012 0.0505197222400988</span>2</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext">20 0.4254<span class="idiff left right">706661865902 0.574529333813409</span>9</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">22 0.0011806<span class="idiff left right">22306850325 0.9988193776931497</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext">23 0.949480<span class="idiff left right">2777599012 0.0505197222400988</span>2</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext">24 7.060<span class="idiff left right">704132933913e-05 0.9999293929586708</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext">25 0.860035<span class="idiff left right">8212119197 0.1399641787880803</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext">26 2.2397<span class="idiff left right">69512514203e-05 0.9999776023048749</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext">27 0.715786<span class="idiff left right">7575924926 0.2842132424075075</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext">28 1.8239<span class="idiff left right">75588109884e-08 0.9999999817602442</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext">29 0.978583<span class="idiff left right">3755496693 0.0214166244503306</span>6</span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext">30 0.58238<span class="idiff left right">51349951137 0.4176148650048864</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext">31 0.0023793<span class="idiff left right">75352658659 0.9976206246473412</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext">32 0.84117<span class="idiff left right">68348369065 0.1588231651630935</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext">33 0.936297<span class="idiff left right">677903 0.06370232209699996</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext">34 0.69798<span class="idiff left right">372452262 0.30201627547738</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext">35 0.77839<span class="idiff left right">34327640782 0.2216065672359217</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext">36 0.014210<span class="idiff left right">65602379084 0.9857893439762092</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext">37 0.06336<span class="idiff left right">725390958133 0.9366327460904187</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext">38 0.69128<span class="idiff left right">45829568349 0.3087154170431651</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext">39 0.0019198<span class="idiff left right">64543239184 0.9980801354567608</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext">40 0.003960<span class="idiff left right">918088554947 0.99603908191144</span>5</span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext">41 0.5294<span class="idiff left right">505098102081 0.4705494901897919</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext">42 0.838379<span class="idiff left right">9272270489 0.161620072772951</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext">43 0.592177<span class="idiff left right">3317964253 0.40782266820357</span>47</span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext">44 0.20819<span class="idiff left right">55268461745 0.791804473153825</span>4</span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext">46 0.018548<span class="idiff left right">63190175804 0.981451368098242</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="plaintext">47 0.763829<span class="idiff left right">7673435148 0.2361702326564851</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="plaintext">48 0.14028<span class="idiff left right">1306330095 0.8597186936699051</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext">49 0.076490<span class="idiff left right">47470366999 0.9235095252963</span>3</span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext">50 0.55655<span class="idiff left right">61271083909 0.4434438728916091</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext">51 4.4014<span class="idiff left right">4046907096e-06 0.9999955985595309</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext">52 0.968685<span class="idiff left right">5178831441 0.03131448211685599</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext">53 0.933799<span class="idiff left right">6664820075 0.06620033351799245</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext">54 0.057131<span class="idiff left right">39133742776 0.9428686086625723</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext">55 0.67339<span class="idiff left right">77936690815 0.3266022063309185</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="plaintext">56 0.978583<span class="idiff left right">3755496693 0.0214166244503306</span>6</span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="plaintext">57 0.0363<span class="idiff left right">9030672341932 0.9636096932765807</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="plaintext">58 0.936600<span class="idiff left right">3459987027 0.06339965400129738</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="plaintext">62 0.17206<span class="idiff left right">33735589035 0.8279366264410964</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="plaintext">66 2.8346<span class="idiff left right">15995562944e-08 0.9999999716538401</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="plaintext">69 2.8734<span class="idiff left right">58507277488e-05 0.9999712654149272</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="plaintext">70 0.32347<span class="idiff left right">42246568454 0.6765257753431545</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="plaintext">72 0.16192<span class="idiff left right">85389636656 0.8380714610363343</span></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="plaintext">73 0.139476<span class="idiff left right">9516923916 0.8605230483076084</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="plaintext">74 0.949480<span class="idiff left right">2777599012 0.0505197222400988</span>2</span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="plaintext">75 0.0245820<span class="idiff left right">8685945937 0.9754179131405406</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="plaintext">76 6.411<span class="idiff left right">330212760092e-05 0.9999358866978725</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="plaintext">77 0.971544<span class="idiff left right">3626189237 0.02845563738107615</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="plaintext">78 0.78627<span class="idiff left right">94565538135 0.2137205434461865</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="plaintext">79 0.73287<span class="idiff left right">51080906223 0.2671248919093778</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="plaintext">80 0.970603<span class="idiff left right">5417626925 0.02939645823730756</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="plaintext">81 0.86117<span class="idiff left right">16902269267 0.1388283097730733</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="plaintext">82 0.76682<span class="idiff left right">32725859022 0.2331767274140977</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="plaintext">83 5.672<span class="idiff left right">72509224703e-05 0.9999432727490775</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="plaintext">84 0.0067417<span class="idiff left right">94211132465 0.9932582057888676</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="plaintext">85 0.968365<span class="idiff left right">4697043729 0.0316345302956271</span>9</span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="plaintext">86 0.968685<span class="idiff left right">5178831441 0.03131448211685599</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="plaintext">87 1.53110<span class="idiff left right">154208541e-05 0.9999846889845792</span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="plaintext">88 0.76682<span class="idiff left right">32725859022 0.2331767274140977</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="plaintext">89 0.93161<span class="idiff left right">22623318611 0.0683877376681389</span>1</span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="plaintext">90 0.038617<span class="idiff left right">91813650284 0.9613820818634972</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="plaintext">91 0.587208<span class="idiff left right">5267662471 0.4127914732337529</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Rate/Site Rate=0.078540<span class="idiff left right">89951899505</span> Rate=1</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">1 0.00041548<span class="idiff left right">41702208897 0.9995845158297791</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">2 0.949480<span class="idiff left right">0946553694 0.0505199053446305</span>2</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">3 0.85271<span class="idiff left right">38076557068 0.147286192344293</span>1</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">4 0.977295<span class="idiff left right">3209605599 0.02270467903944003</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">5 0.708927<span class="idiff left right">0358876215 0.2910729641123785</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">6 0.970603<span class="idiff left right">4286518881 0.02939657134811178</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">7 0.84117<span class="idiff left right">59549187992 0.1588240450812008</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">8 0.64485<span class="idiff left right">0909128687 0.3551490908713131</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">9 0.0090239<span class="idiff left right">03715709264 0.9909760962842907</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">10 0.25159<span class="idiff left right">32185849544 0.7484067814150457</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">11 0.936297<span class="idiff left right">1760831602 0.0637028239168398</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">12 0.803991<span class="idiff left right">1310919982 0.1960088689080018</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">13 0.959299<span class="idiff left right">0339188422 0.0407009660811578</span>1</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">14 0.68312<span class="idiff left right">16537039989 0.3168783462960011</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">15 0.968685<span class="idiff left right">3075822512 0.03131469241774875</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">16 0.968685<span class="idiff left right">3075822512 0.03131469241774875</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">17 0.949480<span class="idiff left right">0946553694 0.0505199053446305</span>2</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">18 0.096277<span class="idiff left right">09694116433 0.9037229030588357</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">19 0.80465<span class="idiff left right">71650681456 0.1953428349318545</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">20 0.4254<span class="idiff left right">688557117581 0.574531144288241</span>9</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">21 0.0011621<span class="idiff left right">13715308391 0.9988378862846916</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">22 0.0011806<span class="idiff left right">17896019509 0.9988193821039805</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">23 0.949480<span class="idiff left right">0946553694 0.0505199053446305</span>2</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">24 7.060<span class="idiff left right">663427640608e-05 0.9999293933657236</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">25 0.860035<span class="idiff left right">3102504529 0.1399646897495471</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">26 2.2397<span class="idiff left right">54017472222e-05 0.9999776024598254</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">27 0.715786<span class="idiff left right">2269098134 0.2842137730901866</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">28 1.8239<span class="idiff left right">68038733901e-08 0.9999999817603197</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">29 0.978583<span class="idiff left right">2556654707 0.0214167443345292</span>6</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">30 0.58238<span class="idiff left right">4830553312 0.417615169446688</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">31 0.0023793<span class="idiff left right">58355164586 0.9976206416448354</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">32 0.84117<span class="idiff left right">59549187992 0.1588240450812008</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">33 0.936297<span class="idiff left right">1760831602 0.0637028239168398</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">34 0.69798<span class="idiff left right">22928927298 0.3020177071072702</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">35 0.77839<span class="idiff left right">2401117516 0.2216075988824839</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">36 0.014210<span class="idiff left right">53968210576 0.9857894603178943</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">37 0.06336<span class="idiff left right">691422415654 0.9366330857758434</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">38 0.69128<span class="idiff left right">31003120626 0.3087168996879373</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">39 0.0019198<span class="idiff left right">52660566921 0.998080147339433</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">40 0.003960<span class="idiff left right">890204721402 0.996039109795278</span>5</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">41 0.5294<span class="idiff left right">498773319029 0.470550122668097</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">42 0.838379<span class="idiff left right">2474897703 0.1616207525102296</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">43 0.592177<span class="idiff left right">1900482152 0.40782280995178</span>47</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">44 0.20819<span class="idiff left right">4488060306 0.79180551193969</span>4</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">45 0.48125<span class="idiff left right">47391790605 0.5187452608209394</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">46 0.018548<span class="idiff left right">54305069108 0.9814514569493089</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">47 0.763829<span class="idiff left right">0038081602 0.2361709961918397</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">48 0.14028<span class="idiff left right">05111076657 0.8597194888923344</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">49 0.076490<span class="idiff left right">19370504373 0.923509806294956</span>3</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">50 0.55655<span class="idiff left right">53788637815 0.4434446211362185</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">51 4.4014<span class="idiff left right">12699981744e-06 0.9999955985873</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">52 0.968685<span class="idiff left right">3075822512 0.03131469241774875</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">53 0.933799<span class="idiff left right">5342113474 0.06620046578865253</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">54 0.057131<span class="idiff left right">11117495385 0.9428688888250462</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">55 0.67339<span class="idiff left right">62368122044 0.3266037631877956</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">56 0.978583<span class="idiff left right">2556654707 0.0214167443345292</span>6</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">57 0.0363<span class="idiff left right">8999158091847 0.9636100084190816</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">58 0.936600<span class="idiff left right">1361131814 0.06339986388681852</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">59 0.023631<span class="idiff left right">53610583355 0.9763684638941664</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">60 0.715786<span class="idiff left right">2269098134 0.2842137730901866</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">61 0.27406<span class="idiff left right">28614189302 0.7259371385810699</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">62 0.17206<span class="idiff left right">28516827533 0.8279371483172466</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">63 0.066960<span class="idiff left right">27896282203 0.933039721037178</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">64 0.15902<span class="idiff left right">55451412893 0.8409744548587106</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">65 0.13715<span class="idiff left right">57240403739 0.8628442759596261</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">66 2.8346<span class="idiff left right">0436728884e-08 0.9999999716539563</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">67 0.539046<span class="idiff left right">0493463879 0.4609539506536121</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">68 0.0006628<span class="idiff left right">127730370201 0.999337187226963</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">69 2.8734<span class="idiff left right">41346176776e-05 0.9999712655865381</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">70 0.32347<span class="idiff left right">33611365553 0.6765266388634448</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">71 0.22492<span class="idiff left right">83193971887 0.7750716806028114</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">72 0.16192<span class="idiff left right">7560424059 0.8380724395759409</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">73 0.139476<span class="idiff left right">4462745381 0.8605235537254619</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">74 0.949480<span class="idiff left right">0946553694 0.0505199053446305</span>2</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">75 0.0245820<span class="idiff left right">2885075857 0.9754179711492413</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">76 6.411<span class="idiff left right">295676480708e-05 0.9999358870432352</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">77 0.971544<span class="idiff left right">1430178714 0.02845585698212867</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">78 0.78627<span class="idiff left right">85460776877 0.2137214539223124</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">79 0.73287<span class="idiff left right">37186780433 0.2671262813219566</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">80 0.970603<span class="idiff left right">4286518881 0.02939657134811178</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">81 0.86117<span class="idiff left right">06364190057 0.1388293635809944</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">82 0.76682<span class="idiff left right">24471831266 0.2331775528168733</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">83 5.672<span class="idiff left right">677285259407e-05 0.9999432732271474</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">84 0.0067417<span class="idiff left right">59929513022 0.993258240070487</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">85 0.968365<span class="idiff left right">26712463 0.0316347328753698</span>9</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">86 0.968685<span class="idiff left right">3075822512 0.03131469241774875</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">87 1.53110<span class="idiff left right">6965534881e-05 0.9999846889303446</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">88 0.76682<span class="idiff left right">24471831266 0.2331775528168733</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">89 0.93161<span class="idiff left right">17506366601 0.0683882493633398</span>1</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">90 0.038617<span class="idiff left right">5672192274 0.9613824327807726</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">91 0.587208<span class="idiff left right">2036930426 0.4127917963069574</span></span>
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132
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="plaintext"></span>
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133
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="plaintext">*** RUNNING MODEL 2 (Selection) ***</span>
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134
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="plaintext">######################################</span>
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135
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="plaintext"></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="plaintext">>Done in <span class="idiff left right">11</span> seconds </span>
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<td class="diff-line-num new old_line" data-linenumber="137" 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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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">>Done in <span class="idiff left right">8</span> seconds </span>
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137
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="plaintext"></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="plaintext">-1106.445<span class="idiff left right">57162008</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">-1106.445<span class="idiff left right">45333916</span></span>
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139
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="plaintext"></span>
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140
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="plaintext">------------------------------------------------</span>
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141
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="plaintext"></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="plaintext">dN/dS = 1.1<span class="idiff left right">30289110692444 (sample variance = 1.591177897940909</span>)</span>
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<td class="diff-line-num new old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">dN/dS = 1.1<span class="idiff left right">29068005488161 (sample variance = 1.588067143267372</span>)</span>
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143
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<td class="diff-line-num new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="plaintext"></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="plaintext">Rate[1]= 0.058<span class="idiff left right">03552 (weight=0.3738941</span>)</span>
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145
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<td class="diff-line-num new_line old" data-linenumber="144" 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="LC145" class="line" lang="plaintext">Rate[2]= 1.00000000 (weight=0.44<span class="idiff left right">37247</span>)</span>
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146
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<td class="diff-line-num new_line old" data-linenumber="144" 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="LC146" class="line" lang="plaintext">Rate[3]= 3.64<span class="idiff left right">547162 (weight=0.182381</span>1)</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">Rate[1]= 0.058<span class="idiff left right">54806 (weight=0.3747723</span>)</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">Rate[2]= 1.00000000 (weight=0.44<span class="idiff left right">27396</span>)</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">Rate[3]= 3.64<span class="idiff left right">070986 (weight=0.182488</span>1)</span>
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147
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="plaintext"></span>
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148
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="plaintext">------------------------------------------------</span>
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149
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="plaintext"></span>
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150
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="plaintext"> Sites with dN/dS>1 (Posterior cutoff = 0.9)</span>
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151
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="plaintext"></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="plaintext">26 (0.907<span class="idiff left right">2435350390498</span>)</span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="plaintext">28 (0.99920<span class="idiff left right">39672038171</span>)</span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="plaintext">66 (0.9984<span class="idiff left right">916647170328</span>)</span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="plaintext">87 (0.9856<span class="idiff left right">690772721554</span>)</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">26 (0.907<span class="idiff left right">1235888236596</span>)</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">28 (0.99920<span class="idiff left right">8561635355</span>)</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">66 (0.9984<span class="idiff left right">823131311625</span>)</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">87 (0.9856<span class="idiff left right">39180825136</span>)</span>
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156
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157
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="plaintext"></span>
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158
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="plaintext">------------------------------------------------</span>
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159
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="plaintext"></span>
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160
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="plaintext"> Sites with dN/dS<=1 (Posterior cutoff = 0.9)</span>
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161
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="plaintext"></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="plaintext">1 (0.505<span class="idiff left right">1655529606731</span>)</span>
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163
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<td class="diff-line-num new_line old" data-linenumber="162" 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="LC163" class="line" lang="plaintext">2 (0.00045<span class="idiff left right">86047622872992</span>)</span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="plaintext">3 (0.00591<span class="idiff left right">0658864265369</span>)</span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="plaintext">4 (9.6<span class="idiff left right">46181948062124</span>e-05)</span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="plaintext">5 (0.0317<span class="idiff left right">0339502414456</span>)</span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="plaintext">6 (0.00015<span class="idiff left right">08897972951693</span>)</span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="plaintext">7 (0.0069<span class="idiff left right">38725368587095</span>)</span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="plaintext">8 (0.0567<span class="idiff left right">0024471475955</span>)</span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="plaintext">9 (0.722<span class="idiff left right">5295530504859</span>)</span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="plaintext">10 (0.096<span class="idiff left right">38049255699262</span>)</span>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="plaintext">11 (0.0009<span class="idiff left right">198237591565945</span>)</span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="plaintext">12 (0.0106<span class="idiff left right">2846379830087</span>)</span>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="plaintext">13 (0.00049<span class="idiff left right">2759842270657</span>)</span>
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="plaintext">14 (0.039<span class="idiff left right">88301095601996</span>)</span>
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="plaintext">15 (0.000222<span class="idiff left right">2234934517179</span>)</span>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="plaintext">16 (0.000222<span class="idiff left right">2234934517179</span>)</span>
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="plaintext">17 (0.00045<span class="idiff left right">86047622872992</span>)</span>
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="plaintext">18 (0.43<span class="idiff left right">27849002774984</span>)</span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="plaintext">19 (0.0116<span class="idiff left right">0494123323598</span>)</span>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="plaintext">20 (0.0336<span class="idiff left right">3712511964109</span>)</span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="plaintext">21 (0.247<span class="idiff left right">0930495779124</span>)</span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="plaintext">22 (0.7984<span class="idiff left right">738153061429</span>)</span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="plaintext">23 (0.00045<span class="idiff left right">86047622872992</span>)</span>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="plaintext">24 (0.5842<span class="idiff left right">524457215786</span>)</span>
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="plaintext">25 (0.0051<span class="idiff left right">67728308291355</span>)</span>
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="plaintext">27 (0.029<span class="idiff left right">38020791912619</span>)</span>
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="plaintext">29 (7.9<span class="idiff left right">37517626711708</span>e-05)</span>
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="plaintext">30 (0.0914<span class="idiff left right">0259016602403</span>)</span>
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="plaintext">31 (0.569<span class="idiff left right">773943770624</span>1)</span>
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="plaintext">32 (0.0069<span class="idiff left right">38725368587095</span>)</span>
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="plaintext">33 (0.0009<span class="idiff left right">198237591565945</span>)</span>
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="plaintext">34 (0.00451<span class="idiff left right">0681205167178</span>)</span>
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="plaintext">35 (0.0020<span class="idiff left right">49191785207676</span>)</span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="plaintext">36 (0.105<span class="idiff left right">0024130149768</span>)</span>
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="plaintext">37 (0.08<span class="idiff left right">580607126297962</span>)</span>
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="plaintext">38 (0.00539<span class="idiff left right">3833634333682</span>)</span>
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="plaintext">39 (0.64<span class="idiff left right">39589837233456</span>)</span>
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="plaintext">40 (0.4558<span class="idiff left right">413160848798</span>)</span>
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="plaintext">41 (0.0118<span class="idiff left right">3180050372747</span>)</span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="plaintext">42 (0.00685<span class="idiff left right">2010985023359</span>)</span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="plaintext">43 (0.0836<span class="idiff left right">1182186992157</span>)</span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="plaintext">44 (0.011<span class="idiff left right">79227732643408</span>)</span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="plaintext">45 (0.017<span class="idiff left right">48204559061378</span>)</span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="plaintext">46 (0.429<span class="idiff left right">0997677225385</span>)</span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="plaintext">47 (0.0183<span class="idiff left right">6409760634284</span>)</span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="plaintext">48 (0.025<span class="idiff left right">26647483127544</span>)</span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="plaintext">49 (0.07<span class="idiff left right">094810710714877</span>)</span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="plaintext">50 (0.0106<span class="idiff left right">1737774286497</span>)</span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="plaintext">51 (0.886<span class="idiff left right">2701608782172</span>)</span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="plaintext">52 (0.000222<span class="idiff left right">2234934517179</span>)</span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="plaintext">53 (0.00076<span class="idiff left right">707720469310</span>27)</span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="plaintext">54 (0.098<span class="idiff left right">12221578787755</span>)</span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="plaintext">55 (0.00633<span class="idiff left right">3685430651</span>68)</span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="plaintext">56 (7.9<span class="idiff left right">37517626711708</span>e-05)</span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="plaintext">57 (0.20<span class="idiff left right">48056654398318</span>)</span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="plaintext">58 (0.00072<span class="idiff left right">6417634129623</span>)</span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="plaintext">59 (0.331<span class="idiff left right">1273587672101</span>)</span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="plaintext">60 (0.029<span class="idiff left right">38020791912619</span>)</span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="plaintext">61 (0.08<span class="idiff left right">189294413402423</span>)</span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="plaintext">62 (0.193<span class="idiff left right">4504467092352</span>)</span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="plaintext">63 (0.077<span class="idiff left right">06489107214247</span>)</span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="plaintext">64 (0.0214<span class="idiff left right">0744778728731</span>)</span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="plaintext">65 (0.027<span class="idiff left right">36638268870059</span>)</span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="plaintext">67 (0.1261<span class="idiff left right">045684713601</span>)</span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="plaintext">68 (0.6055<span class="idiff left right">404804211916</span>)</span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="plaintext">69 (0.833<span class="idiff left right">597533314407</span>)</span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="plaintext">70 (0.055<span class="idiff left right">25842075956964</span>)</span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="plaintext">71 (0.122<span class="idiff left right">6377952204414</span>)</span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="plaintext">72 (0.021<span class="idiff left right">03774540341517</span>)</span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="plaintext">73 (0.277<span class="idiff left right">4126502695526</span>)</span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="plaintext">74 (0.00045<span class="idiff left right">86047622872992</span>)</span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="plaintext">75 (0.30<span class="idiff left right">69616959027847</span>)</span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="plaintext">76 (0.675<span class="idiff left right">7852477037506</span>)</span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="plaintext">77 (0.000230<span class="idiff left right">2410972905876</span>)</span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="plaintext">78 (0.0149<span class="idiff left right">8418396816613</span>)</span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="plaintext">79 (0.00322<span class="idiff left right">3456269673978</span>)</span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="plaintext">80 (0.00015<span class="idiff left right">08897972951693</span>)</span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="plaintext">81 (0.00517<span class="idiff left right">1093611428542</span>)</span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="plaintext">82 (0.0177<span class="idiff left right">5770256526435</span>)</span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="plaintext">83 (0.814<span class="idiff left right">3632663221626</span>)</span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="plaintext">84 (0.27<span class="idiff left right">74516014562403</span>)</span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="plaintext">85 (0.000196<span class="idiff left right">1741149948456</span>)</span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="plaintext">86 (0.000222<span class="idiff left right">2234934517179</span>)</span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="plaintext">88 (0.0177<span class="idiff left right">5770256526435</span>)</span>
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246
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="plaintext">89 (0.00117<span class="idiff left right">235030558950</span>7)</span>
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247
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="plaintext">90 (0.186<span class="idiff left right">17295415604</span>8)</span>
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248
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="plaintext">91 (0.0882<span class="idiff left right">2774719946876</span>)</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext">1 (0.505<span class="idiff left right">2373923971539</span>)</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">2 (0.00045<span class="idiff left right">93492021371499</span>)</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">3 (0.00591<span class="idiff left right">7205452138728</span>)</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">4 (9.6<span class="idiff left right">63607149571083</span>e-05)</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext">5 (0.0317<span class="idiff left right">2842746069128</span>)</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">6 (0.00015<span class="idiff left right">11795330813065</span>)</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">7 (0.0069<span class="idiff left right">43635909993886</span>)</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext">8 (0.0567<span class="idiff left right">3891477006113</span>)</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">9 (0.722<span class="idiff left right">6692280451891</span>)</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext">10 (0.096<span class="idiff left right">51028335914213</span>)</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext">11 (0.0009<span class="idiff left right">207100403048468</span>)</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext">12 (0.0106<span class="idiff left right">4028334210353</span>)</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">13 (0.00049<span class="idiff left right">34182636844576</span>)</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext">14 (0.039<span class="idiff left right">91745163515635</span>)</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext">15 (0.000222<span class="idiff left right">5580972989534</span>)</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext">16 (0.000222<span class="idiff left right">5580972989534</span>)</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext">17 (0.00045<span class="idiff left right">93492021371499</span>)</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext">18 (0.43<span class="idiff left right">30406113257519</span>)</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext">19 (0.0116<span class="idiff left right">121595707726</span>)</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">20 (0.0336<span class="idiff left right">812685288552</span>)</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext">21 (0.247<span class="idiff left right">3118054259542</span>)</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">22 (0.7984<span class="idiff left right">465921549734</span>)</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext">23 (0.00045<span class="idiff left right">93492021371499</span>)</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext">24 (0.5842<span class="idiff left right">280859182822</span>)</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext">25 (0.0051<span class="idiff left right">72980464989402</span>)</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">27 (0.029<span class="idiff left right">40476216359821</span>)</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext">29 (7.9<span class="idiff left right">52947195176931</span>e-05)</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext">30 (0.0914<span class="idiff left right">6670281887008</span>)</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">31 (0.569<span class="idiff left right">903044821400</span>1)</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext">32 (0.0069<span class="idiff left right">43635909993886</span>)</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext">33 (0.0009<span class="idiff left right">207100403048468</span>)</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">34 (0.00451<span class="idiff left right">5364181301996</span>)</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">35 (0.0020<span class="idiff left right">50750658840959</span>)</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext">36 (0.105<span class="idiff left right">2215418403245</span>)</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext">37 (0.08<span class="idiff left right">602792425933428</span>)</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext">38 (0.00539<span class="idiff left right">8479347200226</span>)</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext">39 (0.64<span class="idiff left right">40044083471241</span>)</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext">40 (0.4558<span class="idiff left right">311806110331</span>)</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext">41 (0.0118<span class="idiff left right">5264798035508</span>)</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext">42 (0.00685<span class="idiff left right">7989522987185</span>)</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext">43 (0.0836<span class="idiff left right">7248274274289</span>)</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext">44 (0.011<span class="idiff left right">83660486503293</span>)</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext">45 (0.017<span class="idiff left right">50623812172373</span>)</span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext">46 (0.429<span class="idiff left right">4127609528174</span>)</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext">47 (0.0183<span class="idiff left right">780006215666</span>)</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext">48 (0.025<span class="idiff left right">34884977862542</span>)</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">49 (0.07<span class="idiff left right">112745644118525</span>)</span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext">50 (0.0106<span class="idiff left right">3437293207849</span>)</span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext">51 (0.886<span class="idiff left right">1014582086777</span>)</span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext">52 (0.000222<span class="idiff left right">5580972989534</span>)</span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext">53 (0.00076<span class="idiff left right">836043937605</span>27)</span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext">54 (0.098<span class="idiff left right">35228649247904</span>)</span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext">55 (0.00633<span class="idiff left right">95455648993</span>68)</span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext">56 (7.9<span class="idiff left right">52947195176931</span>e-05)</span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext">57 (0.20<span class="idiff left right">50735349427733</span>)</span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext">58 (0.00072<span class="idiff left right">7531168723411</span>)</span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext">59 (0.331<span class="idiff left right">4435529804894</span>)</span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext">60 (0.029<span class="idiff left right">40476216359821</span>)</span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext">61 (0.08<span class="idiff left right">200111674080049</span>)</span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext">62 (0.193<span class="idiff left right">666026549605</span>)</span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext">63 (0.077<span class="idiff left right">2513986346591</span>)</span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext">64 (0.0214<span class="idiff left right">8421691961612</span>)</span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext">65 (0.027<span class="idiff left right">45286636506417</span>)</span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext">67 (0.1261<span class="idiff left right">823647518457</span>)</span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext">68 (0.6055<span class="idiff left right">55060135807</span>)</span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext">69 (0.833<span class="idiff left right">3573458992974</span>)</span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext">70 (0.055<span class="idiff left right">34546347214257</span>)</span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext">71 (0.122<span class="idiff left right">7852244756305</span>)</span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext">72 (0.021<span class="idiff left right">10507208988902</span>)</span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext">73 (0.277<span class="idiff left right">6010249671293</span>)</span>
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232
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext">75 (0.30<span class="idiff left right">73445506286841</span>)</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext">76 (0.675<span class="idiff left right">9845714674814</span>)</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext">77 (0.000230<span class="idiff left right">5219770671781</span>)</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext">78 (0.0149<span class="idiff left right">9353952539858</span>)</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext">79 (0.00322<span class="idiff left right">5300542333516</span>)</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext">80 (0.00015<span class="idiff left right">11795330813065</span>)</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext">81 (0.00517<span class="idiff left right">3815704594973</span>)</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext">82 (0.0177<span class="idiff left right">7066638393202</span>)</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext">83 (0.814<span class="idiff left right">2466349701873</span>)</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext">84 (0.27<span class="idiff left right">83391381741632</span>)</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext">85 (0.000196<span class="idiff left right">4834081581603</span>)</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext">86 (0.000222<span class="idiff left right">5580972989534</span>)</span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext">88 (0.0177<span class="idiff left right">7066638393202</span>)</span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext">89 (0.00117<span class="idiff left right">339492890614</span>7)</span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext">90 (0.186<span class="idiff left right">417657516345</span>8)</span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext">91 (0.0882<span class="idiff left right">8981163248605</span>)</span>
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="plaintext"></span>
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250
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="plaintext">------------------------------------------------</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">@@ -256,95 +256,95 @@ Import the following part into a data processing program</td>
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="plaintext">for further analysis</span>
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="plaintext"></span>
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258
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258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="plaintext"></span>
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259
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="plaintext">Rate/Site Rate=0.058<span class="idiff left right">03551904096559 Rate=1 Rate=3.64547161773776</span></span>
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260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="plaintext">1 2.<span class="idiff left right">039042780824998e-05 0.4948140566115184 0.5051655529606731</span></span>
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="plaintext">2 0.84<span class="idiff left right">47543711358414 0.1547870241018713 0.0004586047622872992</span></span>
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="plaintext">3 0.71<span class="idiff left right">61602740418139 0.2779290670939206 0.005910658864265369</span></span>
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="plaintext">4 0.90<span class="idiff left right">18001736475444 0.09810336453297497 9.646181948062124</span>e-05</span>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="plaintext">5 0.58<span class="idiff left right">17941052410429 0.3865024997348125 0.03170339502414456</span></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="plaintext">6 0.88<span class="idiff left right">69026108142981 0.1129464993884068 0.0001508897972951693</span></span>
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="plaintext">7 0.70<span class="idiff left right">02133060545321 0.2928479685768806 0.006938725368587095</span></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="plaintext">8 0.52<span class="idiff left right">47416076674776 0.4185581476177629 0.05670024471475955</span></span>
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="plaintext">9 0.0010<span class="idiff left right">30497098954651 0.2764399498505593 0.7225295530504859</span></span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="plaintext">10 0.<span class="idiff left right">09922289423382447 0.804396613209183 0.09638049255699262</span></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="plaintext">11 0.81<span class="idiff left right">85856564565643 0.1804945197842791 0.0009198237591565945</span></span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="plaintext">12 0.67<span class="idiff left right">06899182118367 0.3186816179898624 0.01062846379830087</span></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="plaintext">13 0.86<span class="idiff left right">39581578245099 0.1355490823332193 0.000492759842270657</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="plaintext">14 0.56<span class="idiff left right">13226223127381 0.3987943667312419 0.03988301095601996</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="plaintext">15 0.88<span class="idiff left right">16214532222431 0.1181563232843053 0.0002222234934517179</span></span>
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="plaintext">16 0.88<span class="idiff left right">16214532222431 0.1181563232843053 0.0002222234934517179</span></span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="plaintext">17 0.84<span class="idiff left right">47543711358414 0.1547870241018713 0.0004586047622872992</span></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="plaintext">18 0.032<span class="idiff left right">58041875304914 0.5346346809694525 0.4327849002774984</span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="plaintext">19 0.66<span class="idiff left right">34627593773434 0.3249322993894206 0.01160494123323598</span></span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="plaintext">20 0.15<span class="idiff left right">78423652751871 0.8085205096051719 0.03363712511964109</span></span>
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="plaintext">21 6.<span class="idiff left right">238970153028547e-05 0.7528445607205574 0.2470930495779124</span></span>
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="plaintext">22 <span class="idiff left right">5.957427093987687e-05 0.2014666104229171 0.7984738153061429</span></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="plaintext">23 0.84<span class="idiff left right">47543711358414 0.1547870241018713 0.0004586047622872992</span></span>
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283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="plaintext">24 1.<span class="idiff left right">722473813988775e-06 0.4157458318046073 0.5842524457215786</span></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="plaintext">25 0.72<span class="idiff left right">48831494482354 0.2699491222434732 0.005167728308291355</span></span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="plaintext">26 1.<span class="idiff left right">79098661219942e-07 0.09275628586228903 0.9072435350390498</span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="plaintext">27 0.58<span class="idiff left right">85447664274595 0.3820750256534142 0.02938020791912619</span></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="plaintext">28 7.<span class="idiff left right">739153851019017e-14 0.0007960327961054919 0.9992039672038171</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="plaintext">29 0.905<span class="idiff left right">003826260647 0.09491679856308587 7.937517626711708</span>e-05</span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="plaintext">30 0.47<span class="idiff left right">0463461189876 0.4381339486440999 0.09140259016602403</span></span>
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="plaintext">31 0.00019<span class="idiff left right">18709301161739 0.4300341852992596 0.569773943770624</span>1</span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="plaintext">32 0.70<span class="idiff left right">02133060545321 0.2928479685768806 0.006938725368587095</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="plaintext">33 0.81<span class="idiff left right">85856564565643 0.1804945197842791 0.0009198237591565945</span></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="plaintext">34 0.29<span class="idiff left right">30556524542092 0.7024336663406237 0.004510681205167178</span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="plaintext">35 0.35<span class="idiff left right">26141222772732 0.6453366859375191 0.002049191785207676</span></span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="plaintext">36 0.001<span class="idiff left right">268385541760359 0.8937292014432627 0.1050024130149768</span></span>
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="plaintext">37 0.011<span class="idiff left right">54829414988456 0.9026456345871359 0.08580607126297962</span></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="plaintext">38 0.29<span class="idiff left right">11048433357678 0.7035013230298984 0.005393833634333682</span></span>
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="plaintext">39 0.0001<span class="idiff left right">396861588575296 0.355901330117797 0.6439589837233456</span></span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="plaintext">40 0.0002<span class="idiff left right">448465541435865 0.5439138373609765 0.4558413160848798</span></span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="plaintext">41 0.2<span class="idiff left right">097066876421463 0.7784615118541262 0.01183180050372747</span></span>
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="plaintext">42 0.<span class="idiff left right">6996255088940389 0.2935224801209377 0.006852010985023359</span></span>
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="plaintext">43 0.48<span class="idiff left right">30787052206162 0.4333094729094621 0.08361182186992157</span></span>
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="plaintext">44 0.0<span class="idiff left right">2944754568248423 0.9587601769910816 0.01179227732643408</span></span>
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="plaintext">45 0.18<span class="idiff left right">71451780503118 0.7953727763590743 0.01748204559061378</span></span>
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="plaintext">46 0.003<span class="idiff left right">286918686078104 0.5676133135913832 0.4290997677225385</span></span>
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="plaintext">47 0.6<span class="idiff left right">289631399679325 0.3526727624257246 0.01836409760634284</span></span>
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="plaintext">48 0.02<span class="idiff left right">157260676327798 0.9531609184054467 0.02526647483127544</span></span>
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="plaintext">49 0.013<span class="idiff left right">26287909287238 0.9157890137999789 0.07094810710714877</span></span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="plaintext">50 0.22<span class="idiff left right">16072057730993 0.7677754164840356 0.01061737774286497</span></span>
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="plaintext">51 2.<span class="idiff left right">348084455917174e-08 0.1137298156409383 0.8862701608782172</span></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="plaintext">52 0.88<span class="idiff left right">16214532222431 0.1181563232843053 0.0002222234934517179</span></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="plaintext">53 0.82<span class="idiff left right">03687814430313 0.1788641413522757 0.00076707720469310</span>27</span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="plaintext">54 0.01<span class="idiff left right">075878173450459 0.891119002477618 0.09812221578787755</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="plaintext">55 0.28<span class="idiff left right">04057512651671 0.7132605633041813 0.006333685430651</span>68</span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="plaintext">56 0.905<span class="idiff left right">003826260647 0.09491679856308587 7.937517626711708</span>e-05</span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="plaintext">57 0.00<span class="idiff left right">6889612047585912 0.7883047225125823 0.2048056654398318</span></span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="plaintext">58 0.82<span class="idiff left right">32664662614319 0.1760071161044386 0.000726417634129623</span></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="plaintext">59 0.004<span class="idiff left right">480976740308936 0.664391664492481 0.3311273587672101</span></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="plaintext">60 0.58<span class="idiff left right">85447664274595 0.3820750256534142 0.02938020791912619</span></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="plaintext">61 0.10<span class="idiff left right">64914550524415 0.8116156008135343 0.08189294413402423</span></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="plaintext">62 0.06<span class="idiff left right">777171429588846 0.7387778389948764 0.1934504467092352</span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="plaintext">63 0.012<span class="idiff left right">14975847301941 0.9107853504548381 0.07706489107214247</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="plaintext">64 0.023<span class="idiff left right">37288930759019 0.9552196629051225 0.02140744778728731</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="plaintext">65 0.021<span class="idiff left right">03532247533653 0.951598294835963 0.02736638268870059</span></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="plaintext">66 2.<span class="idiff left right">487852398499066e-12 0.001508335280479298 0.9984916647170328</span></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="plaintext">67 0.42<span class="idiff left right">85637071264611 0.4453317244021789 0.1261045684713601</span></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="plaintext">68 <span class="idiff left right">2.969924066760578e-05 0.3944298203381409 0.6055404804211916</span></span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="plaintext">69 4.<span class="idiff left right">031355426340145e-07 0.1664020635500504 0.833597533314407</span></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="plaintext">70 0.12<span class="idiff left right">73454140934302 0.8173961651470001 0.05525842075956964</span></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="plaintext">71 0.08<span class="idiff left right">804086160724707 0.7893213431723116 0.1226377952204414</span></span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="plaintext">72 0.024<span class="idiff left right">43240135146625 0.9545298532451186 0.02103774540341517</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="plaintext">73 0.05<span class="idiff left right">234553025846337 0.6702418194719839 0.2774126502695526</span></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="plaintext">74 0.84<span class="idiff left right">47543711358414 0.1547870241018713 0.0004586047622872992</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="plaintext">75 0.004<span class="idiff left right">873253850134324 0.688165050247081 0.3069616959027847</span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="plaintext">76 1.2<span class="idiff left right">15507587476473e-06 0.324213536788662 0.6757852477037506</span></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="plaintext">77 0.88<span class="idiff left right">77821246335438 0.1119876342691656 0.0002302410972905876</span></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="plaintext">78 0.64<span class="idiff left right">74357779532641 0.3375800380785697 0.01498418396816613</span></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="plaintext">79 0.3<span class="idiff left right">289377286767906 0.6678388150535354 0.003223456269673978</span></span>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="plaintext">80 0.88<span class="idiff left right">69026108142981 0.1129464993884068 0.0001508897972951693</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="plaintext">81 0.71<span class="idiff left right">82778008443462 0.2765511055442251 0.005171093611428542</span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="plaintext">82 0.63<span class="idiff left right">08413283365097 0.3514009690982259 0.01775770256526435</span></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="plaintext">83 9.<span class="idiff left right">028853568587064e-07 0.1856358307924804 0.8143632663221626</span></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="plaintext">84 9.<span class="idiff left right">578642651884824e-05 0.7224526121172409 0.2774516014562403</span></span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="plaintext">85 0.880<span class="idiff left right">15102949012 0.1196527963948851 0.0001961741149948456</span></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="plaintext">86 0.88<span class="idiff left right">16214532222431 0.1181563232843053 0.0002222234934517179</span></span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="plaintext">87 1.<span class="idiff left right">458685175204862e-08 0.01433090814099288 0.9856690772721554</span></span>
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="plaintext">88 0.63<span class="idiff left right">08413283365097 0.3514009690982259 0.01775770256526435</span></span>
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="plaintext">89 0.81<span class="idiff left right">09004627962602 0.1879271868981504 0.00117235030558950</span>7</span>
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349
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="plaintext">90 0.007<span class="idiff left right">317318166084692 0.8065097276778674 0.18617295415604</span>8</span>
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350
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="plaintext">91 0.47<span class="idiff left right">48123679645572 0.4369598848359741 0.08822774719946876</span></span></pre>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext">Rate/Site Rate=0.058<span class="idiff left right">54805862606752 Rate=1 Rate=3.640709855148721</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext">1 2.<span class="idiff left right">123821587431194e-05 0.4947413693869718 0.5052373923971539</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext">2 0.84<span class="idiff left right">54805150711112 0.1540601357267516 0.0004593492021371499</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext">3 0.71<span class="idiff left right">71925566791651 0.2768902378686959 0.005917205452138728</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext">4 0.90<span class="idiff left right">23145803022071 0.09758878362629728 9.663607149571083</span>e-05</span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext">5 0.58<span class="idiff left right">29266831612094 0.3853448893780992 0.03172842746069128</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext">6 0.88<span class="idiff left right">74735538558555 0.112375266611063 0.0001511795330813065</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext">7 0.70<span class="idiff left right">1299413788691 0.2917569503013152 0.006943635909993886</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext">8 0.52<span class="idiff left right">58486059883327 0.4174124792416061 0.05673891477006113</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext">9 0.0010<span class="idiff left right">5308734360597 0.276277684611205 0.7226692280451891</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext">10 0.<span class="idiff left right">1004481920361048 0.803041524604753 0.09651028335914213</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext">11 0.81<span class="idiff left right">94140603392319 0.1796652296204631 0.0009207100403048468</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext">12 0.67<span class="idiff left right">17772510719154 0.3175824655859811 0.01064028334210353</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext">13 0.86<span class="idiff left right">46165745664404 0.1348900071698753 0.0004934182636844576</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext">14 0.56<span class="idiff left right">24375756998519 0.3976449726649919 0.03991745163515635</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext">15 0.88<span class="idiff left right">22191864215847 0.1175582554811163 0.0002225580972989534</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="plaintext">16 0.88<span class="idiff left right">22191864215847 0.1175582554811163 0.0002225580972989534</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext">17 0.84<span class="idiff left right">54805150711112 0.1540601357267516 0.0004593492021371499</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext">18 0.032<span class="idiff left right">983308732931 0.533976079941317 0.4330406113257519</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="plaintext">19 0.66<span class="idiff left right">45919677056602 0.3237958727235673 0.0116121595707726</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext">20 0.15<span class="idiff left right">97162578236267 0.806602473647518 0.0336812685288552</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="plaintext">21 6.<span class="idiff left right">497561809983018e-05 0.752623218955946 0.2473118054259542</span></span>
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<td class="diff-line-num new new_line" data-linenumber="281" 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">
281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="plaintext">22 <span class="idiff left right">6.147883799728457e-05 0.2014919290070293 0.7984465921549734</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="plaintext">23 0.84<span class="idiff left right">54805150711112 0.1540601357267516 0.0004593492021371499</span></span>
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<td class="diff-line-num new new_line" data-linenumber="283" 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">
283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="plaintext">24 1.<span class="idiff left right">810178742010458e-06 0.4157701039029758 0.5842280859182822</span></span>
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<td class="diff-line-num new new_line" data-linenumber="284" 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">
284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="plaintext">25 0.72<span class="idiff left right">59101630303384 0.2689168565046722 0.005172980464989402</span></span>
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<td class="diff-line-num new new_line" data-linenumber="285" 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">
285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="plaintext">26 1.<span class="idiff left right">883724016460931e-07 0.09287622280393867 0.9071235888236596</span></span>
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<td class="diff-line-num new new_line" data-linenumber="286" 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">
286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext">27 0.58<span class="idiff left right">96752507993037 0.3809199870370982 0.02940476216359821</span></span>
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<td class="diff-line-num new new_line" data-linenumber="287" 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">
287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="plaintext">28 7.<span class="idiff left right">593295246048614e-14 0.0007914383645691474 0.999208561635355</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="plaintext">29 0.905<span class="idiff left right">5057132759483 0.09441475725209994 7.952947195176931</span>e-05</span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="plaintext">30 0.47<span class="idiff left right">15021983865639 0.437031098794566 0.09146670281887008</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="plaintext">31 0.00019<span class="idiff left right">79673775266633 0.4298989878010734 0.569903044821400</span>1</span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="plaintext">32 0.70<span class="idiff left right">1299413788691 0.2917569503013152 0.006943635909993886</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="plaintext">33 0.81<span class="idiff left right">94140603392319 0.1796652296204631 0.0009207100403048468</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="plaintext">34 0.29<span class="idiff left right">60737907520586 0.6994108450666394 0.004515364181301996</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="plaintext">35 0.35<span class="idiff left right">59604560803941 0.641988793260765 0.002050750658840959</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext">36 0.001<span class="idiff left right">30942674258278 0.8934690314170927 0.1052215418403245</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext">37 0.011<span class="idiff left right">80978530471919 0.9021622904359465 0.08602792425933428</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext">38 0.29<span class="idiff left right">41041942604504 0.7004973263923493 0.005398479347200226</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext">39 0.0001<span class="idiff left right">44144499790302 0.3558514471530856 0.6440044083471241</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext">40 0.0002<span class="idiff left right">529699651473707 0.5439158494238194 0.4558311806110331</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext">41 0.2<span class="idiff left right">120674596489594 0.7760798923706854 0.01185264798035508</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext">42 0.<span class="idiff left right">7007026627516525 0.2924393477253602 0.006857989522987185</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext">43 0.48<span class="idiff left right">41294396612101 0.432198077596047 0.08367248274274289</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext">44 0.0<span class="idiff left right">301228872990572 0.9580405078359099 0.01183660486503293</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext">45 0.18<span class="idiff left right">93248839788894 0.7931688778993868 0.01750623812172373</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext">46 0.003<span class="idiff left right">359794088751816 0.5672274449584306 0.4294127609528174</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext">47 0.6<span class="idiff left right">3009891120623 0.3515230881722035 0.0183780006215666</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="plaintext">48 0.02<span class="idiff left right">206748041476434 0.9525836698066102 0.02534884977862542</span></span>
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<td class="diff-line-num new new_line" data-linenumber="308" 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">
308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="plaintext">49 0.013<span class="idiff left right">56591438428317 0.9153066291745316 0.07112745644118525</span></span>
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<td class="diff-line-num new new_line" data-linenumber="309" 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">
309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext">50 0.22<span class="idiff left right">40745276745924 0.7652910993933291 0.01063437293207849</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext">51 2.<span class="idiff left right">492645830161824e-08 0.1138985168648641 0.8861014582086777</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext">52 0.88<span class="idiff left right">22191864215847 0.1175582554811163 0.0002225580972989534</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="plaintext">53 0.82<span class="idiff left right">11660693180184 0.1780655702426055 0.00076836043937605</span>27</span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext">54 0.01<span class="idiff left right">100295212811388 0.8906447613794071 0.09835228649247904</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="plaintext">55 0.28<span class="idiff left right">33340811759865 0.7103263732591142 0.0063395455648993</span>68</span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="plaintext">56 0.905<span class="idiff left right">5057132759483 0.09441475725209994 7.952947195176931</span>e-05</span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="plaintext">57 0.00<span class="idiff left right">7045975624482142 0.7878804894327445 0.2050735349427733</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="plaintext">58 0.82<span class="idiff left right">40613622898397 0.1752111065414368 0.000727531168723411</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="plaintext">59 0.004<span class="idiff left right">581163540158042 0.6639752834793526 0.3314435529804894</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="plaintext">60 0.58<span class="idiff left right">96752507993037 0.3809199870370982 0.02940476216359821</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="plaintext">61 0.10<span class="idiff left right">7806169745878 0.8101927135133216 0.08200111674080049</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="plaintext">62 0.06<span class="idiff left right">861334373069095 0.7377206297197041 0.193666026549605</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="plaintext">63 0.012<span class="idiff left right">42704838986371 0.9103215529754771 0.0772513986346591</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="plaintext">64 0.023<span class="idiff left right">90636440935269 0.9546094186710312 0.02148421691961612</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="plaintext">65 0.021<span class="idiff left right">51934533944069 0.9510277882954953 0.02745286636506417</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="plaintext">66 2.<span class="idiff left right">671166083534726e-12 0.001517686866166226 0.9984823131311625</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="plaintext">67 0.42<span class="idiff left right">95450384222473 0.4442725968259071 0.1261823647518457</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="plaintext">68 <span class="idiff left right">3.079998533959148e-05 0.3944141398788535 0.605555060135807</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="plaintext">69 4.<span class="idiff left right">243743084525438e-07 0.1666422297263941 0.8333573458992974</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="plaintext">70 0.12<span class="idiff left right">88881665397853 0.8157663699880722 0.05534546347214257</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="plaintext">71 0.08<span class="idiff left right">913564852994389 0.7880791269944257 0.1227852244756305</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="plaintext">72 0.024<span class="idiff left right">99602234463322 0.9538989055654777 0.02110507208988902</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="plaintext">73 0.05<span class="idiff left right">300541149090041 0.6693935635419703 0.2776010249671293</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="plaintext">74 0.84<span class="idiff left right">54805150711112 0.1540601357267516 0.0004593492021371499</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="plaintext">75 0.004<span class="idiff left right">981355134669857 0.687674094236646 0.3073445506286841</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="plaintext">76 1.2<span class="idiff left right">75841252079727e-06 0.3240141526912666 0.6759845714674814</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="plaintext">77 0.88<span class="idiff left right">83601983297144 0.1114092796932183 0.0002305219770671781</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="plaintext">78 0.64<span class="idiff left right">85688357833093 0.3364376246912923 0.01499353952539858</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="plaintext">79 0.3<span class="idiff left right">321969903648257 0.6645777090928409 0.003225300542333516</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="plaintext">80 0.88<span class="idiff left right">74735538558555 0.112375266611063 0.0001511795330813065</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="plaintext">81 0.71<span class="idiff left right">93517468744175 0.2754744374209876 0.005173815704594973</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="plaintext">82 0.63<span class="idiff left right">19797015005985 0.3502496321154693 0.01777066638393202</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="plaintext">83 9.<span class="idiff left right">451297855017863e-07 0.1857524199000273 0.8142466349701873</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="plaintext">84 9.<span class="idiff left right">483309866743794e-05 0.7215660287271692 0.2783391381741632</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="plaintext">85 0.880<span class="idiff left right">7566499603399 0.119046866631502 0.0001964834081581603</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="plaintext">86 0.88<span class="idiff left right">22191864215847 0.1175582554811163 0.0002225580972989534</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="plaintext">87 1.<span class="idiff left right">512672292179054e-08 0.01436080404814105 0.985639180825136</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="plaintext">88 0.63<span class="idiff left right">19797015005985 0.3502496321154693 0.01777066638393202</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="plaintext">89 0.81<span class="idiff left right">17475469052963 0.1870790581657977 0.00117339492890614</span>7</span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="plaintext">90 0.007<span class="idiff left right">483970311633406 0.8060983721720208 0.186417657516345</span>8</span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="plaintext">91 0.47<span class="idiff left right">58571278249646 0.4358530605425494 0.08828981163248605</span></span></pre>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d8a6fecc5558ddf14f61e62f2bf14fe1a9ea9fff#3bbc19efb5ab1243a9d0c4627a24ef88cf1f3ca0"><strong>tests/hbltests/Results/HIVSweden.out_MODEL_-1.nex</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">@@ -37,8 +37,8 @@ END;</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">BEGIN HYPHY;</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">global c=0.9051395<span class="idiff left right">111492303</span>;</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">global kappa=0.40524221<span class="idiff left right">64401616</span>;</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">global c=0.9051395<span class="idiff left right">450601901</span>;</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">global kappa=0.40524221<span class="idiff left right">78470169</span>;</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">modelMatrix={61,61};</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">modelMatrix[0][1]:=kappa*c*t;</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">modelMatrix[0][2]:=t;</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">@@ -638,29 +638,29 @@ ACCEPT_ROOTED_TREES=0;</td>
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="plaintext">UseModel (theModel);</span>
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<pre style="margin: 0;"> <span id="LC639" class="line" lang="plaintext">Tree givenTree=(((U68496,U68497)Node3,(U68501,(U68502,(U68503,((((U68504,U68506)Node15,U68505)Node14,U68507)Node13,U68508)Node12)Node10)Node8)Node6)Node2,U68498,(U68499,U68500)Node6_1);</span>
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<pre style="margin: 0;"> <span id="LC640" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC641" class="line" lang="plaintext">givenTree.U68496.t=0.1932757<span class="idiff left right">871041837</span>;</span>
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<pre style="margin: 0;">-<span id="LC642" class="line" lang="plaintext">givenTree.U68497.t=0.6442091<span class="idiff left right">652256334</span>;</span>
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<pre style="margin: 0;">-<span id="LC643" class="line" lang="plaintext">givenTree.Node3.t=1.244091<span class="idiff left right">415592038</span>;</span>
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<pre style="margin: 0;">-<span id="LC644" class="line" lang="plaintext">givenTree.U68501.t=1.072314<span class="idiff left right">201483783</span>;</span>
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<pre style="margin: 0;">-<span id="LC645" class="line" lang="plaintext">givenTree.U68502.t=1.55536<span class="idiff left right">9080763556</span>;</span>
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<pre style="margin: 0;">-<span id="LC646" class="line" lang="plaintext">givenTree.U68503.t=1.573795<span class="idiff left right">705681594</span>;</span>
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<pre style="margin: 0;">-<span id="LC647" class="line" lang="plaintext">givenTree.U68504.t=0.1545017<span class="idiff left right">84041082</span>;</span>
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<pre style="margin: 0;">-<span id="LC648" class="line" lang="plaintext">givenTree.U68506.t=0.572443<span class="idiff left right">9233580223</span>;</span>
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<pre style="margin: 0;">-<span id="LC649" class="line" lang="plaintext">givenTree.Node15.t=0.4520764<span class="idiff left right">356621616</span>;</span>
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<pre style="margin: 0;">-<span id="LC650" class="line" lang="plaintext">givenTree.U68505.t=0.2464768<span class="idiff left right">788725834</span>;</span>
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<pre style="margin: 0;">-<span id="LC651" class="line" lang="plaintext">givenTree.Node14.t=0.2982771<span class="idiff left right">643141667</span>;</span>
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<pre style="margin: 0;">-<span id="LC652" class="line" lang="plaintext">givenTree.U68507.t=0.497436<span class="idiff left right">2344804469</span>;</span>
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<pre style="margin: 0;">-<span id="LC653" class="line" lang="plaintext">givenTree.Node13.t=0.2831885<span class="idiff left right">640218609</span>;</span>
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<pre style="margin: 0;">-<span id="LC654" class="line" lang="plaintext">givenTree.U68508.t=1.613919<span class="idiff left right">93653481</span>;</span>
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<pre style="margin: 0;">-<span id="LC655" class="line" lang="plaintext">givenTree.Node12.t=0.4115609<span class="idiff left right">436825465</span>;</span>
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<pre style="margin: 0;">-<span id="LC656" class="line" lang="plaintext">givenTree.Node10.t=0.5209728<span class="idiff left right">609075241</span>;</span>
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<pre style="margin: 0;">-<span id="LC657" class="line" lang="plaintext">givenTree.Node8.t=0.273999<span class="idiff left right">403135316</span>6;</span>
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<pre style="margin: 0;">-<span id="LC658" class="line" lang="plaintext">givenTree.Node6.t=0.3910850<span class="idiff left right">665208743</span>;</span>
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<pre style="margin: 0;">-<span id="LC659" class="line" lang="plaintext">givenTree.Node2.t=0.192207<span class="idiff left right">6567933305</span>;</span>
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<pre style="margin: 0;">-<span id="LC660" class="line" lang="plaintext">givenTree.U68498.t=0.4102499<span class="idiff left right">915642663</span>;</span>
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="plaintext">givenTree.U68499.t=0.2311741<span class="idiff left right">941445719</span>;</span>
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<pre style="margin: 0;">-<span id="LC662" class="line" lang="plaintext">givenTree.U68500.t=0.8119659<span class="idiff left right">49396724</span>6;</span>
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="plaintext">givenTree.Node6_1.t=0.6788164<span class="idiff left right">927550273</span>;</span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="plaintext">givenTree.U68496.t=0.1932757<span class="idiff left right">790297635</span>;</span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="plaintext">givenTree.U68497.t=0.6442091<span class="idiff left right">360697517</span>;</span>
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643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="plaintext">givenTree.Node3.t=1.244091<span class="idiff left right">350196699</span>;</span>
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644
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="plaintext">givenTree.U68501.t=1.072314<span class="idiff left right">145612458</span>;</span>
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645
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="plaintext">givenTree.U68502.t=1.55536<span class="idiff left right">8999549274</span>;</span>
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646
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="plaintext">givenTree.U68503.t=1.573795<span class="idiff left right">636757062</span>;</span>
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647
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="plaintext">givenTree.U68504.t=0.1545017<span class="idiff left right">778755618</span>;</span>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="plaintext">givenTree.U68506.t=0.572443<span class="idiff left right">8957384254</span>;</span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="plaintext">givenTree.Node15.t=0.4520764<span class="idiff left right">15208067</span>;</span>
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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="plaintext">givenTree.U68505.t=0.2464768<span class="idiff left right">693858635</span>;</span>
</pre>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="plaintext">givenTree.Node14.t=0.2982771<span class="idiff left right">493845721</span>;</span>
</pre>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="plaintext">givenTree.U68507.t=0.497436<span class="idiff left right">0955659346</span>;</span>
</pre>
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653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="plaintext">givenTree.Node13.t=0.2831885<span class="idiff left right">574728508</span>;</span>
</pre>
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654
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="plaintext">givenTree.U68508.t=1.613919<span class="idiff left right">861191977</span>;</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="664" 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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655
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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="LC655" class="line" lang="plaintext">givenTree.Node12.t=0.4115609<span class="idiff left right">2487671</span>;</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="664" 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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656
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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="LC656" class="line" lang="plaintext">givenTree.Node10.t=0.5209728<span class="idiff left right">334125625</span>;</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="664" 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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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="plaintext">givenTree.Node8.t=0.273999<span class="idiff left right">397471021</span>6;</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="664" 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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658
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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="LC658" class="line" lang="plaintext">givenTree.Node6.t=0.3910850<span class="idiff left right">502827137</span>;</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="659" 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">
659
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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="LC659" class="line" lang="plaintext">givenTree.Node2.t=0.192207<span class="idiff left right">7082389846</span>;</span>
</pre>
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="plaintext">givenTree.U68498.t=0.4102499<span class="idiff left right">738247144</span>;</span>
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="plaintext">givenTree.U68499.t=0.2311741<span class="idiff left right">894617957</span>;</span>
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="plaintext">givenTree.U68500.t=0.8119659<span class="idiff left right">11842013</span>6;</span>
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="plaintext">givenTree.Node6_1.t=0.6788164<span class="idiff left right">71820221</span>;</span>
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="plaintext">DataSet ds = ReadDataFile(USE_NEXUS_FILE_DATA);</span>
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="plaintext">DataSetFilter filteredData = CreateFilter(ds,3,"0-272","0,1,5-8,10,9,11,12,2-4","TAA,TAG,TGA");</span>
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="plaintext">ASSUME_REVERSIBLE_MODELS=0;</span>
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<li id="96e4cef3847de919b0f245e8443e6befe26c217b">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d8a6fecc5558ddf14f61e62f2bf14fe1a9ea9fff#96e4cef3847de919b0f245e8443e6befe26c217b"><strong>tests/hbltests/Results/HIVSweden.out_MODEL_0.nex</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">@@ -37,11 +37,11 @@ END;</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">BEGIN HYPHY;</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">global W=0.078540<span class="idiff left right">92332840576</span>;</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">global W=0.078540<span class="idiff left right">89951899505</span>;</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">W:<1;</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">global P=0.4830173<span class="idiff left right">42736387</span>6;</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">global P=0.4830173<span class="idiff left right">1729503</span>6;</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">P:<1;</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext">global kappa=0.38639<span class="idiff left right">39052192686</span>;</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">global kappa=0.38639<span class="idiff left right">15314909612</span>;</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">c.weights={1,2};</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">c.weights[0][0]:=P;</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">@@ -654,29 +654,29 @@ ACCEPT_ROOTED_TREES=0;</td>
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<pre style="margin: 0;"> <span id="LC654" class="line" lang="plaintext">UseModel (theModel);</span>
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<pre style="margin: 0;"> <span id="LC655" class="line" lang="plaintext">Tree givenTree=(((U68496,U68497)Node3,(U68501,(U68502,(U68503,((((U68504,U68506)Node15,U68505)Node14,U68507)Node13,U68508)Node12)Node10)Node8)Node6)Node2,U68498,(U68499,U68500)Node6_1);</span>
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC657" class="line" lang="plaintext">givenTree.U68496.t=0.3014658<span class="idiff left right">105724962</span>;</span>
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<pre style="margin: 0;">-<span id="LC658" class="line" lang="plaintext">givenTree.U68497.t=1.058937<span class="idiff left right">175876235</span>;</span>
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<pre style="margin: 0;">-<span id="LC659" class="line" lang="plaintext">givenTree.Node3.t=2.08174<span class="idiff left right">8321243699</span>;</span>
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<pre style="margin: 0;">-<span id="LC660" class="line" lang="plaintext">givenTree.U68501.t=1.76433<span class="idiff left right">1517307145</span>;</span>
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="plaintext">givenTree.U68502.t=2.673570<span class="idiff left right">235134937</span>;</span>
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<pre style="margin: 0;">-<span id="LC662" class="line" lang="plaintext">givenTree.U68503.t=2.699658<span class="idiff left right">423145014</span>;</span>
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="plaintext">givenTree.U68504.t=0.243154<span class="idiff left right">063524979</span>;</span>
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<pre style="margin: 0;">-<span id="LC664" class="line" lang="plaintext">givenTree.U68506.t=0.90380<span class="idiff left right">78207510426</span>;</span>
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<pre style="margin: 0;">-<span id="LC665" class="line" lang="plaintext">givenTree.Node15.t=0.715349<span class="idiff left right">4550371319</span>;</span>
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<pre style="margin: 0;">-<span id="LC666" class="line" lang="plaintext">givenTree.U68505.t=0.395653<span class="idiff left right">7768124779</span>;</span>
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<pre style="margin: 0;">-<span id="LC667" class="line" lang="plaintext">givenTree.Node14.t=0.4993<span class="idiff left right">396138326727</span>;</span>
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<pre style="margin: 0;">-<span id="LC668" class="line" lang="plaintext">givenTree.U68507.t=0.773734<span class="idiff left right">3409382251</span>;</span>
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<pre style="margin: 0;">-<span id="LC669" class="line" lang="plaintext">givenTree.Node13.t=0.27714<span class="idiff left right">39596307402</span>;</span>
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<pre style="margin: 0;">-<span id="LC670" class="line" lang="plaintext">givenTree.U68508.t=2.851718<span class="idiff left right">598450606</span>;</span>
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<pre style="margin: 0;">-<span id="LC671" class="line" lang="plaintext">givenTree.Node12.t=0.747826<span class="idiff left right">31031285</span>6;</span>
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<pre style="margin: 0;">-<span id="LC672" class="line" lang="plaintext">givenTree.Node10.t=0.823204<span class="idiff left right">3891596889</span>;</span>
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<pre style="margin: 0;">-<span id="LC673" class="line" lang="plaintext">givenTree.Node8.t=0.30935<span class="idiff left right">58783899246</span>;</span>
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<pre style="margin: 0;">-<span id="LC674" class="line" lang="plaintext">givenTree.Node6.t=0.640299<span class="idiff left right">4000640408</span>;</span>
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<pre style="margin: 0;">-<span id="LC675" class="line" lang="plaintext">givenTree.Node2.t=0.304288<span class="idiff left right">6856398082</span>;</span>
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<pre style="margin: 0;">-<span id="LC676" class="line" lang="plaintext">givenTree.U68498.t=0.638790<span class="idiff left right">5520441879</span>;</span>
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<pre style="margin: 0;">-<span id="LC677" class="line" lang="plaintext">givenTree.U68499.t=0.35940<span class="idiff left right">49973891654</span>;</span>
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<pre style="margin: 0;">-<span id="LC678" class="line" lang="plaintext">givenTree.U68500.t=1.31997<span class="idiff left right">7303229773</span>;</span>
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<pre style="margin: 0;">-<span id="LC679" class="line" lang="plaintext">givenTree.Node6_1.t=1.138047<span class="idiff left right">087568419</span>;</span>
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="plaintext">givenTree.U68496.t=0.3014658<span class="idiff left right">876783538</span>;</span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="plaintext">givenTree.U68497.t=1.058937<span class="idiff left right">965054783</span>;</span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="plaintext">givenTree.Node3.t=2.08174<span class="idiff left right">984846752</span>;</span>
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660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="plaintext">givenTree.U68501.t=1.76433<span class="idiff left right">3870286974</span>;</span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="plaintext">givenTree.U68502.t=2.673570<span class="idiff left right">567299918</span>;</span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="plaintext">givenTree.U68503.t=2.699658<span class="idiff left right">069558426</span>;</span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="plaintext">givenTree.U68504.t=0.243154<span class="idiff left right">1588198822</span>;</span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="plaintext">givenTree.U68506.t=0.90380<span class="idiff left right">84521967604</span>;</span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="plaintext">givenTree.Node15.t=0.715349<span class="idiff left right">8168088975</span>;</span>
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666
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="plaintext">givenTree.U68505.t=0.395653<span class="idiff left right">9001874164</span>;</span>
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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="plaintext">givenTree.Node14.t=0.4993<span class="idiff left right">402949067045</span>;</span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="plaintext">givenTree.U68507.t=0.773734<span class="idiff left right">6315034068</span>;</span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="plaintext">givenTree.Node13.t=0.27714<span class="idiff left right">5717534158</span>;</span>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="plaintext">givenTree.U68508.t=2.851718<span class="idiff left right">049074558</span>;</span>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="plaintext">givenTree.Node12.t=0.747826<span class="idiff left right">726614586</span>6;</span>
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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="plaintext">givenTree.Node10.t=0.823204<span class="idiff left right">8503168657</span>;</span>
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673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="plaintext">givenTree.Node8.t=0.30935<span class="idiff left right">7412100375</span>;</span>
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674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="plaintext">givenTree.Node6.t=0.640299<span class="idiff left right">7546627597</span>;</span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="plaintext">givenTree.Node2.t=0.304288<span class="idiff left right">7273137687</span>;</span>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="plaintext">givenTree.U68498.t=0.638790<span class="idiff left right">9451494354</span>;</span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="plaintext">givenTree.U68499.t=0.35940<span class="idiff left right">52835330087</span>;</span>
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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="plaintext">givenTree.U68500.t=1.31997<span class="idiff left right">9691408115</span>;</span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="plaintext">givenTree.Node6_1.t=1.138047<span class="idiff left right">66964687</span>;</span>
</pre>
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680
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680
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<pre style="margin: 0;"> <span id="LC680" class="line" lang="plaintext">DataSet ds = ReadDataFile(USE_NEXUS_FILE_DATA);</span>
</pre>
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681
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681
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<pre style="margin: 0;"> <span id="LC681" class="line" lang="plaintext">DataSetFilter filteredData = CreateFilter(ds,3,"0-272","0,1,5-8,10,9,11,12,2-4","TAA,TAG,TGA");</span>
</pre>
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<pre style="margin: 0;"> <span id="LC682" class="line" lang="plaintext">ASSUME_REVERSIBLE_MODELS=0;</span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d8a6fecc5558ddf14f61e62f2bf14fe1a9ea9fff#dc4367ca74d002d80f8b7061c05e7d0232904a74"><strong>tests/hbltests/Results/HIVSweden.out_MODEL_1.nex</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">@@ -37,15 +37,15 @@ END;</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">BEGIN HYPHY;</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">global P2=0.708<span class="idiff left right">705612029199</span>;</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">global P2=0.708<span class="idiff left right">1253811493516</span>;</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">P2:<1;</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">global W_1=0.058<span class="idiff left right">03551904096559</span>;</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">global W_1=0.058<span class="idiff left right">54805862606752</span>;</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">W_1:<1;</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext">global W_2=3.64<span class="idiff left right">547161773776</span>;</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">global W_2=3.64<span class="idiff left right">0709855148721</span>;</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">W_2:>1;</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">global P1=0.37<span class="idiff left right">38941254448849</span>;</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">global P1=0.37<span class="idiff left right">47723001916182</span>;</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">P1:<1;</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext">global kappa=0.359<span class="idiff left right">5872901133234</span>;</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">global kappa=0.359<span class="idiff left right">7040016204291</span>;</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext">c.weights={1,3};</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">c.weights[0][0]:=P1;</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">@@ -660,29 +660,29 @@ ACCEPT_ROOTED_TREES=0;</td>
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<pre style="margin: 0;"> <span id="LC660" class="line" lang="plaintext">UseModel (theModel);</span>
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="plaintext">Tree givenTree=(((U68496,U68497)Node3,(U68501,(U68502,(U68503,((((U68504,U68506)Node15,U68505)Node14,U68507)Node13,U68508)Node12)Node10)Node8)Node6)Node2,U68498,(U68499,U68500)Node6_1);</span>
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="plaintext">givenTree.U68496.t=0.181<span class="idiff left right">8762919281609</span>;</span>
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<td class="diff-line-num old old_line" data-linenumber="664" 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="LC664" class="line" lang="plaintext">givenTree.U68497.t=0.630<span class="idiff left right">0551440548584</span>;</span>
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<pre style="margin: 0;">-<span id="LC665" class="line" lang="plaintext">givenTree.Node3.t=1.24<span class="idiff left right">2477534620</span>252;</span>
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<pre style="margin: 0;">-<span id="LC666" class="line" lang="plaintext">givenTree.U68501.t=1.052<span class="idiff left right">718749766851</span>;</span>
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<pre style="margin: 0;">-<span id="LC667" class="line" lang="plaintext">givenTree.U68502.t=1.74<span class="idiff left right">5690425208843</span>;</span>
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<td class="diff-line-num old old_line" data-linenumber="668" 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="LC668" class="line" lang="plaintext">givenTree.U68503.t=1.77<span class="idiff left right">2661631401772</span>;</span>
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<td class="diff-line-num old old_line" data-linenumber="669" 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="LC669" class="line" lang="plaintext">givenTree.U68504.t=0.146<span class="idiff left right">1819892700968</span>;</span>
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<td class="diff-line-num old old_line" data-linenumber="670" 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="LC670" class="line" lang="plaintext">givenTree.U68506.t=0.5<span class="idiff left right">19705091019830</span>5;</span>
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<pre style="margin: 0;">-<span id="LC671" class="line" lang="plaintext">givenTree.Node15.t=0.416<span class="idiff left right">25119485480</span>48;</span>
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<pre style="margin: 0;">-<span id="LC672" class="line" lang="plaintext">givenTree.U68505.t=0.24<span class="idiff left right">080463265513</span>26;</span>
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<pre style="margin: 0;">-<span id="LC673" class="line" lang="plaintext">givenTree.Node14.t=0.275<span class="idiff left right">23510860759</span>9;</span>
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<pre style="margin: 0;">-<span id="LC674" class="line" lang="plaintext">givenTree.U68507.t=0.47<span class="idiff left right">66147197519663</span>;</span>
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<td class="diff-line-num old old_line" data-linenumber="675" 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="LC675" class="line" lang="plaintext">givenTree.Node13.t=0.00<span class="idiff left right">7124632417842378</span>;</span>
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<pre style="margin: 0;">-<span id="LC676" class="line" lang="plaintext">givenTree.U68508.t=1.94<span class="idiff left right">0263089445053</span>;</span>
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<pre style="margin: 0;">-<span id="LC677" class="line" lang="plaintext">givenTree.Node12.t=0.50<span class="idiff left right">74844030410871</span>;</span>
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<td class="diff-line-num old old_line" data-linenumber="678" 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="LC678" class="line" lang="plaintext">givenTree.Node10.t=0.50<span class="idiff left right">64503192192543</span>;</span>
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<td class="diff-line-num old old_line" data-linenumber="679" 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="LC679" class="line" lang="plaintext">givenTree.Node8.t=0.180<span class="idiff left right">7141019606832</span>;</span>
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<td class="diff-line-num old old_line" data-linenumber="680" 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="LC680" class="line" lang="plaintext">givenTree.Node6.t=0.393<span class="idiff left right">4552618450088</span>;</span>
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<td class="diff-line-num old old_line" data-linenumber="681" 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">
681
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<pre style="margin: 0;">-<span id="LC681" class="line" lang="plaintext">givenTree.Node2.t=0.189<span class="idiff left right">4290890321033</span>;</span>
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<td class="diff-line-num old old_line" data-linenumber="682" 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="LC682" class="line" lang="plaintext">givenTree.U68498.t=0.333<span class="idiff left right">581631786244</span>;</span>
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<td class="diff-line-num old old_line" data-linenumber="683" 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">
683
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<pre style="margin: 0;">-<span id="LC683" class="line" lang="plaintext">givenTree.U68499.t=0.187<span class="idiff left right">4655318656705</span>;</span>
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<td class="diff-line-num old old_line" data-linenumber="684" 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">
684
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<pre style="margin: 0;">-<span id="LC684" class="line" lang="plaintext">givenTree.U68500.t=0.799<span class="idiff left right">2046138178572</span>;</span>
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<td class="diff-line-num old old_line" data-linenumber="685" 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">
685
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<pre style="margin: 0;">-<span id="LC685" class="line" lang="plaintext">givenTree.Node6_1.t=0.74<span class="idiff left right">79255472650597</span>;</span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="plaintext">givenTree.U68496.t=0.181<span class="idiff left right">9372645612003</span>;</span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="plaintext">givenTree.U68497.t=0.630<span class="idiff left right">5701510272947</span>;</span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="plaintext">givenTree.Node3.t=1.24<span class="idiff left right">4260990073</span>252;</span>
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666
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="plaintext">givenTree.U68501.t=1.052<span class="idiff left right">08595250357</span>;</span>
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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="plaintext">givenTree.U68502.t=1.74<span class="idiff left right">6445328113835</span>;</span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="plaintext">givenTree.U68503.t=1.77<span class="idiff left right">4938469552289</span>;</span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="plaintext">givenTree.U68504.t=0.146<span class="idiff left right">3724860825859</span>;</span>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="plaintext">givenTree.U68506.t=0.5<span class="idiff left right">20005798176746</span>5;</span>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="plaintext">givenTree.Node15.t=0.416<span class="idiff left right">69140006946</span>48;</span>
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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="plaintext">givenTree.U68505.t=0.24<span class="idiff left right">10553615390</span>26;</span>
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673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="plaintext">givenTree.Node14.t=0.275<span class="idiff left right">452069507696</span>9;</span>
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674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="plaintext">givenTree.U68507.t=0.47<span class="idiff left right">71824473110387</span>;</span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="plaintext">givenTree.Node13.t=0.00<span class="idiff left right">6305605103123437</span>;</span>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="plaintext">givenTree.U68508.t=1.94<span class="idiff left right">4259154790765</span>;</span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="plaintext">givenTree.Node12.t=0.50<span class="idiff left right">81406979260248</span>;</span>
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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="plaintext">givenTree.Node10.t=0.50<span class="idiff left right">74584441922946</span>;</span>
</pre>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="plaintext">givenTree.Node8.t=0.180<span class="idiff left right">8898503811754</span>;</span>
</pre>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="plaintext">givenTree.Node6.t=0.393<span class="idiff left right">9031724767187</span>;</span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="plaintext">givenTree.Node2.t=0.189<span class="idiff left right">6556393922262</span>;</span>
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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="plaintext">givenTree.U68498.t=0.333<span class="idiff left right">7924593752155</span>;</span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="plaintext">givenTree.U68499.t=0.187<span class="idiff left right">5734352334583</span>;</span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="plaintext">givenTree.U68500.t=0.799<span class="idiff left right">8185516002427</span>;</span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="plaintext">givenTree.Node6_1.t=0.74<span class="idiff left right">92860788646263</span>;</span>
</pre>
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686
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686
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<pre style="margin: 0;"> <span id="LC686" class="line" lang="plaintext">DataSet ds = ReadDataFile(USE_NEXUS_FILE_DATA);</span>
</pre>
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687
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687
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<pre style="margin: 0;"> <span id="LC687" class="line" lang="plaintext">DataSetFilter filteredData = CreateFilter(ds,3,"0-272","0,1,5-8,10,9,11,12,2-4","TAA,TAG,TGA");</span>
</pre>
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688
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688
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<pre style="margin: 0;"> <span id="LC688" class="line" lang="plaintext">ASSUME_REVERSIBLE_MODELS=0;</span>
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<li id="1dea2190f9519da2b039674a61e37385e9584c01">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/d8a6fecc5558ddf14f61e62f2bf14fe1a9ea9fff#1dea2190f9519da2b039674a61e37385e9584c01"><strong>tests/hbltests/libv3/MEME-partitioned.wbf</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,7 +20,7 @@ fscanf ("data/CD2.nex.MEME.json","Raw",json);</td>
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20
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">assert (check_value (</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> ((meme.json["fits"])["<span class="idiff left right">Unconstrained model"])["Log Likelihood"], -3466.56</span>, 0.001), "Incorrect log-likelihood for the Global MG94xREV model");</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> ((meme.json["fits"])["<span class="idiff left right">Global MG94xREV"])["Log Likelihood"], -3466.57</span>, 0.001), "Incorrect log-likelihood for the Global MG94xREV model");</span>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">p_values = (((meme.json["MLE"])["content"])["0"])[-1][6];</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="60" style="width: 35px; color: rgba(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">@@ -60,10 +60,9 @@ function confirm_site (site, p, dict, kind) {</td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"> return FALSE;</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext">}</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext">utility.ForEachPair (p_values,"_index_", "_p_",</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"> " </span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext"> confirm_site (_index_[0], _p_, test.expected_positives, 1))</span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext"> ");</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">for (_index_,_p_; in; p_values) {</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> confirm_site (_index_, _p_, test.expected_positives, 1);</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">}</span>
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67
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"></span>
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68
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">assert (check_value (</span>
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69
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"> test.lrt_sum, 20.33, 0.05), "More than 5% difference in cumulative LRT for positively selected sites");</span>
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