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<h3>

Julien Y. Dutheil pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/libbpp-phyl">Debian Med / libbpp-phyl</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/libbpp-phyl/commit/2d1077e72fbc569cc82e62fdb6d37456a0e1a745">2d1077e7</a></strong>

<div>

<span>by Julien Y. Dutheil</span>

<i>at 2018-08-19T11:47:42Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.4.1</pre>

</li>

</ul>

<h4>12 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">

CMakeLists.txt

</a>

</li>

<li class="file-stats">

<a href="#3fa7b3d8e9b1a6a923cff77497ab817d9f94b6c0">

Doxyfile

</a>

</li>

<li class="file-stats">

<a href="#a1bac226baa6d9b0093f4b128ccc7db75e1135a8">

bpp-phyl.spec

</a>

</li>

<li class="file-stats">

<a href="#90ae7aade236f810e4663b380aaedf3ba91ac7a6">

src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp

</a>

</li>

<li class="file-stats">

<a href="#3e757d14dd92c8ad19e501170ef5ceadae88819e">

src/Bpp/Phyl/Io/IoTree.h

</a>

</li>

<li class="file-stats">

<a href="#32c58bb7469f3dc59f40fa7339ea9deaa1473c5a">

src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp

</a>

</li>

<li class="file-stats">

<a href="#e27fa4628a99ba480f20266fb8ada4e2f21ad189">

src/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp

</a>

</li>

<li class="file-stats">

<a href="#4dfe99812103586056d7135fb6526ad70cf35319">

src/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.h

</a>

</li>

<li class="file-stats">

<a href="#20c15b53567a1bfa97f67b8fbf718c40eb3757d7">

src/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.h

</a>

</li>

<li class="file-stats">

<a href="#dc0e3009002fd02356548aa69de4e096e557f607">

src/Bpp/Phyl/Model/SubstitutionModelSet.h

</a>

</li>

<li class="file-stats">

<a href="#c278ae6ea381687a7f6bafac197e4aecb99b5d3a">

src/Bpp/Phyl/TreeTemplateTools.cpp

</a>

</li>

<li class="file-stats">

<a href="#6e5c49a7992a9c6a7f368cbc8844c5d323183b08">

test/test_likelihood_nh.cpp

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">

<a href="https://salsa.debian.org/med-team/libbpp-phyl/commit/2d1077e72fbc569cc82e62fdb6d37456a0e1a745#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="95" style="width: 35px; color: rgba(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="95" style="width: 35px; color: rgba(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">@@ -95,10 +95,10 @@ ENDIF(NO_DEP_CHECK)</td>

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<td class="diff-line-num old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Packager</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC96" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_NAME <span class="s2" style="color: #d14;">"libbpp-phyl"</span><span class="p">)</span></span>

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<td class="diff-line-num old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

97

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<td class="diff-line-num new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC97" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_VENDOR <span class="s2" style="color: #d14;">"Bio++ Development Team"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

98

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<td class="diff-line-num new_line old" data-linenumber="98" style="width: 35px; color: rgba(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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC98" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_VERSION <span class="s2" style="color: #d14;">"2.4.<span class="idiff left right">0</span>"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="99" 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="98" 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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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_VERSION <span class="s2" style="color: #d14;">"2.4.<span class="idiff left right">1</span>"</span><span class="p">)</span></span>

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<td class="diff-line-num old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC99" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_VERSION_MAJOR <span class="s2" style="color: #d14;">"2"</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC100" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_VERSION_MINOR <span class="s2" style="color: #d14;">"4"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="101" style="width: 35px; color: rgba(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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<td class="diff-line-num new_line old" data-linenumber="101" style="width: 35px; color: rgba(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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC101" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_VERSION_PATCH <span class="s2" style="color: #d14;">"<span class="idiff left right">0</span>"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="102" 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="101" 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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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_VERSION_PATCH <span class="s2" style="color: #d14;">"<span class="idiff left right">1</span>"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_DESCRIPTION_SUMMARY <span class="s2" style="color: #d14;">"The Bio++ Phylogenetics library"</span><span class="p">)</span></span>

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<td class="diff-line-num old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

103

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<td class="diff-line-num new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_RESOURCE_FILE_LICENSE <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/COPYING.txt"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

104

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<td class="diff-line-num new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_RESOURCE_FILE_AUTHORS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/AUTHORS.txt"</span><span class="p">)</span></span>

</pre>

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<br>

</li>

<li id="3fa7b3d8e9b1a6a923cff77497ab817d9f94b6c0">

<a href="https://salsa.debian.org/med-team/libbpp-phyl/commit/2d1077e72fbc569cc82e62fdb6d37456a0e1a745#3fa7b3d8e9b1a6a923cff77497ab817d9f94b6c0"><strong>Doxyfile</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="38" style="width: 35px; color: rgba(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="38" style="width: 35px; color: rgba(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">@@ -38,7 +38,7 @@ PROJECT_NAME           = bpp-phyl</td>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"># could be handy for archiving the generated documentation or if some version</span>

</pre>

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39

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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"># control system is used.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

40

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<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

40

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

41

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<td class="diff-line-num new_line old" data-linenumber="41" style="width: 35px; color: rgba(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="LC41" class="line" lang="plaintext">PROJECT_NUMBER         = 2.4.<span class="idiff left right">0</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="42" 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="41" 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">

41

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">PROJECT_NUMBER         = 2.4.<span class="idiff left right">1</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"># Using the PROJECT_BRIEF tag one can provide an optional one line description</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"># for a project that appears at the top of each page and should give viewer a</span>

</pre>

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<br>

</li>

<li id="a1bac226baa6d9b0093f4b128ccc7db75e1135a8">

<a href="https://salsa.debian.org/med-team/libbpp-phyl/commit/2d1077e72fbc569cc82e62fdb6d37456a0e1a745#a1bac226baa6d9b0093f4b128ccc7db75e1135a8"><strong>bpp-phyl.spec</strong></a>

<hr>

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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">@@ -3,7 +3,7 @@</td>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">URL: https://github.com/BioPP/bpp-phyl</span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>

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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Name: bpp-phyl</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(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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<td class="diff-line-num new_line old" data-linenumber="6" style="width: 35px; color: rgba(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="LC6" class="line" lang="plaintext">Version: <span class="idiff left right">1.4.0</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" 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="6" 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">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Version: <span class="idiff left right">2.4.1</span></span>

</pre>

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7

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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Release: 1%{?dist}</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">License: CECILL-2.0</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Vendor: The Bio++ Project</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="85" style="width: 35px; color: rgba(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="85" style="width: 35px; color: rgba(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">@@ -85,6 +85,8 @@ rm -rf $RPM_BUILD_ROOT</td>

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext">%{_prefix}/include/*</span>

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<td class="diff-line-num old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="plaintext"></span>

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<td class="diff-line-num old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="plaintext">%changelog</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="88" 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="88" 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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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">* Mon Aug 13 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.1-1</span>

</pre>

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89

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">- Compatibility update gcc8</span>

</pre>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext">* Mon Mar 12 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.0-1</span>

</pre>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext">- Increased interface number</span>

</pre>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext">- Removed dynamic exceptions specifications.</span>

</pre>

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<br>

</li>

<li id="90ae7aade236f810e4663b380aaedf3ba91ac7a6">

<a href="https://salsa.debian.org/med-team/libbpp-phyl/commit/2d1077e72fbc569cc82e62fdb6d37456a0e1a745#90ae7aade236f810e4663b380aaedf3ba91ac7a6"><strong>src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="138" style="width: 35px; color: rgba(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="138" style="width: 35px; color: rgba(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">@@ -138,13 +138,14 @@ TransitionModel* BppOTransitionModelFormat::readTransitionModel(</td>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">nestedModel</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// update only for transition models</span></span>

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp">    <span class="n" style="color: #333;">updateParameters_</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(),</span> <span class="n" style="color: #333;">args</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">parseArguments</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="145" 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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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp">      <span class="n" style="color: #333;">initialize_</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">else</span></span>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp">    <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">(</span><span class="n" style="color: #333;">BppOSubstitutionModelFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">alphabet</span><span class="p">,</span> <span class="n" style="color: #333;">modelDescription</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">parseArguments</span><span class="p">));</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="cpp">  <span class="n" style="color: #333;">updateParameters_</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(),</span> <span class="n" style="color: #333;">args</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC146" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">parseArguments</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC147" class="line" lang="cpp">    <span class="n" style="color: #333;">initialize_</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC148" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

149

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">release</span><span class="p">();</span></span>

</pre>

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151

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp"><span class="p">}</span></span></pre>

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<br>

</li>

<li id="3e757d14dd92c8ad19e501170ef5ceadae88819e">

<a href="https://salsa.debian.org/med-team/libbpp-phyl/commit/2d1077e72fbc569cc82e62fdb6d37456a0e1a745#3e757d14dd92c8ad19e501170ef5ceadae88819e"><strong>src/Bpp/Phyl/Io/IoTree.h</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,7 +5,7 @@</td>

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5

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5

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>

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6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

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<td class="diff-line-num new_line old" data-linenumber="8" style="width: 35px; color: rgba(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="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">Copyright or © or Copr. <span class="idiff left right">CNRS</span>, (November 16, 2004)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="9" 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="8" 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">

8

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">Copyright or © or Copr. <span class="idiff left right">Bio++ Development Team</span>, (November 16, 2004)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">This software is a computer program whose purpose is to provide classes</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">for phylogenetic data analysis.</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="170" style="width: 35px; color: rgba(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="170" style="width: 35px; color: rgba(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">@@ -170,7 +170,7 @@ class AbstractOTree:</td>

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="c">        <span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">,</span> <span class="n" style="color: #333;">output</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="c">        <span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="c">      <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC173" class="line" lang="c">      <span class="n" style="color: #333;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">IOException</span> <span class="n" style="color: #333;">e</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="174" 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="173" 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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<pre style="margin: 0;">+<span id="LC173" class="line" lang="c">      <span class="n" style="color: #333;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">IOException</span><span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span> <span class="n" style="color: #333;">e</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="c">        <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="c">          <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">ss</span> <span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC176" class="line" lang="c">          <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">what</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Problem writing tree to file "</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> Is the file path correct and do \</span></span>

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<br>

</li>

<li id="32c58bb7469f3dc59f40fa7339ea9deaa1473c5a">

<a href="https://salsa.debian.org/med-team/libbpp-phyl/commit/2d1077e72fbc569cc82e62fdb6d37456a0e1a745#32c58bb7469f3dc59f40fa7339ea9deaa1473c5a"><strong>src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="138" style="width: 35px; color: rgba(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="138" style="width: 35px; color: rgba(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">@@ -138,7 +138,7 @@ void DRASRTreeLikelihoodData::initLikelihoods(const Node* node, const SiteContai</td>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp">      <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sequences</span><span class="p">.</span><span class="n" style="color: #333;">getSequence</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getName</span><span class="p">());</span></span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC141" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">SequenceNotFoundException</span> <span class="n" style="color: #333;">snfe</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">SequenceNotFoundException</span><span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span> <span class="n" style="color: #333;">snfe</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">SequenceNotFoundException</span><span class="p">(</span><span class="s" style="color: #d14;">"DRASRTreeLikelihoodData::initTreelikelihoods. Leaf name in tree not found in site conainer: "</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getName</span><span class="p">()));</span></span>

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<pre style="margin: 0;"> <span id="LC144" 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="241" style="width: 35px; color: rgba(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="241" style="width: 35px; color: rgba(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">@@ -241,7 +241,7 @@ SitePatterns* DRASRTreeLikelihoodData::initLikelihoodsWithPatterns(const Node* n</td>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp">      <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">subSequences</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getSequence</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getName</span><span class="p">());</span></span>

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC244" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">SequenceNotFoundException</span> <span class="n" style="color: #333;">snfe</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">SequenceNotFoundException</span><span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span> <span class="n" style="color: #333;">snfe</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">SequenceNotFoundException</span><span class="p">(</span><span class="s" style="color: #d14;">"HomogeneousTreeLikelihood::initTreelikelihoodsWithPatterns. Leaf name in tree not found in site conainer: "</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getName</span><span class="p">()));</span></span>

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp">    <span class="p">}</span></span>

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</li>

<li id="e27fa4628a99ba480f20266fb8ada4e2f21ad189">

<a href="https://salsa.debian.org/med-team/libbpp-phyl/commit/2d1077e72fbc569cc82e62fdb6d37456a0e1a745#e27fa4628a99ba480f20266fb8ada4e2f21ad189"><strong>src/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp</strong></a>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">  knowledge of the CeCILL license and that you accept its terms.</span></span>

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<pre style="margin: 0;"> <span id="LC37" 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="LC38" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"># include "AbstractCodonAAFitnessSubstitutionModel.h"</span></span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "AbstractCodonAAFitnessSubstitutionModel.h"</span></span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <Bpp/Seq/Alphabet/AlphabetTools.h></span></span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC43" 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;">bpp</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC44" 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;">std</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC46" 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="LC47" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"><span class="n" style="color: #333;">AbstractCodonAAFitnessSubstitutionModel</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AbstractCodonAAFitnessSubstitutionModel</span><span class="p">(</span><span class="n" style="color: #333;">FrequenciesSet</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pfitset</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">GeneticCode</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pgencode</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">prefix</span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cpp">  <span class="n" style="color: #333;">AbstractParameterAliasable</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="p">),</span> <span class="n" style="color: #333;">pfitset_</span><span class="p">(</span><span class="n" style="color: #333;">pfitset</span><span class="p">),</span> <span class="n" style="color: #333;">pgencode_</span><span class="p">(</span><span class="n" style="color: #333;">pgencode</span><span class="p">),</span> <span class="n" style="color: #333;">fitName_</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp">  <span class="n" style="color: #333;">AbstractParameterAliasable</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="p">),</span> <span class="n" style="color: #333;">pfitset_</span><span class="p">(</span><span class="n" style="color: #333;">pfitset</span><span class="p">),</span> <span class="n" style="color: #333;">pgencode_</span><span class="p">(</span><span class="n" style="color: #333;">pgencode</span><span class="p">),</span> <span class="n" style="color: #333;">fitName_</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">)<span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">stateMap_</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">pfitset</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">getStateMap</span></span><span class="p"><span class="idiff right">())</span></span></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC46" 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">pfitset_</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">getAlphabet</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">getAlphabetType</span></span><span class="p"><span class="idiff">()</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="s" style="color: #d14;"><span class="idiff right">"Proteic"</span></span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC51" 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">AlphabetTools</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">isProteicAlphabet</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">pfitset_</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">getAlphabet</span></span><span class="p"><span class="idiff right">())</span>)</span></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"AbstractCodonAAFitnessSubstitutionModel::AbstractCodonAAFitnessSubstitutionModel need Proteic Fitness."</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp">  </span>

</pre>

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp">  <span class="n" style="color: #333;">fitName_</span><span class="o" style="font-weight: 600;"><span class="idiff left">=</span></span><span class="s" style="color: #d14;"><span class="idiff right">"fit_"</span></span><span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pfitset_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNamespace</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp">  <span class="n" style="color: #333;">fitName_</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"fit_"</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pfitset_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNamespace</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp">  <span class="n" style="color: #333;">pfitset_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setNamespace</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">fitName_</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="cpp">  <span class="n" style="color: #333;">stateMap_</span><span class="o" style="font-weight: 600;">=&</span><span class="n" style="color: #333;">pfitset_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getStateMap</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp">  </span>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp">  <span class="n" style="color: #333;">addParameters_</span><span class="p">(</span><span class="n" style="color: #333;">pfitset_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getParameters</span><span class="p">());</span></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"><span class="p">}</span></span>

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</li>

<li id="4dfe99812103586056d7135fb6526ad70cf35319">

<a href="https://salsa.debian.org/med-team/libbpp-phyl/commit/2d1077e72fbc569cc82e62fdb6d37456a0e1a745#4dfe99812103586056d7135fb6526ad70cf35319"><strong>src/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.h</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="90" style="width: 35px; color: rgba(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="90" style="width: 35px; color: rgba(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">@@ -90,7 +90,6 @@ namespace bpp</td>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     * @param pmodel shared_ptr to an amino_acid generator</span></span>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     * @param pgencode the genetic code</span></span>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     * @param prefix the Namespace</span></span>

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     * @param statemap the statemap</span></span>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     * @param paramSynRate is true iff synonymous rate is parameterised</span></span>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     *       (default=false).</span></span>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     */</span></span>

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<li id="20c15b53567a1bfa97f67b8fbf718c40eb3757d7">

<a href="https://salsa.debian.org/med-team/libbpp-phyl/commit/2d1077e72fbc569cc82e62fdb6d37456a0e1a745#20c15b53567a1bfa97f67b8fbf718c40eb3757d7"><strong>src/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.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">@@ -93,7 +93,6 @@ namespace bpp</td>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     *</span></span>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     * @param pgencode the genetic code</span></span>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     * @param prefix the Namespace</span></span>

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     * @param statemap the statemap</span></span>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     */</span></span>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c">    <span class="n" style="color: #333;">AbstractCodonBGCSubstitutionModel</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c">      <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">GeneticCode</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pgencode</span><span class="p">,</span></span>

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<li id="dc0e3009002fd02356548aa69de4e096e557f607">

<a href="https://salsa.debian.org/med-team/libbpp-phyl/commit/2d1077e72fbc569cc82e62fdb6d37456a0e1a745#dc0e3009002fd02356548aa69de4e096e557f607"><strong>src/Bpp/Phyl/Model/SubstitutionModelSet.h</strong></a>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="c">  <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="c">    <span class="n" style="color: #333;">try</span></span>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="c">    <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC272" class="line" lang="c">      <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left">dynamic_cast</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">SubstitutionModel</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="n" style="color: #333;">getModel</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="LC272" class="line" lang="c">      <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;"><span class="idiff left">&</span></span><span class="n" style="color: #333;"><span class="idiff">dynamic_cast</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">SubstitutionModel</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&></span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">*</span></span><span class="n" style="color: #333;">getModel</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="LC273" class="line" lang="c">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC274" class="line" lang="c">    <span class="n" style="color: #333;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bad_cast</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">bc</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC275" class="line" lang="c">    <span class="p">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="282" style="width: 35px; color: rgba(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="282" style="width: 35px; color: rgba(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">@@ -282,7 +282,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC282" class="line" lang="c">  <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="c">    <span class="n" style="color: #333;">try</span></span>

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<pre style="margin: 0;"> <span id="LC284" class="line" lang="c">    <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC285" class="line" lang="c">      <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left">dynamic_cast</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">SubstitutionModel</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="n" style="color: #333;">getModel</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="LC285" class="line" lang="c">      <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;"><span class="idiff left">&</span></span><span class="n" style="color: #333;"><span class="idiff">dynamic_cast</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">SubstitutionModel</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&></span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">*</span></span><span class="n" style="color: #333;">getModel</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="LC286" class="line" lang="c">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC287" class="line" lang="c">    <span class="n" style="color: #333;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bad_cast</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">bc</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="c">    <span class="p">{</span></span>

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<br>

</li>

<li id="c278ae6ea381687a7f6bafac197e4aecb99b5d3a">

<a href="https://salsa.debian.org/med-team/libbpp-phyl/commit/2d1077e72fbc569cc82e62fdb6d37456a0e1a745#c278ae6ea381687a7f6bafac197e4aecb99b5d3a"><strong>src/Bpp/Phyl/TreeTemplateTools.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="241" style="width: 35px; color: rgba(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">@@ -241,7 +241,7 @@ TreeTemplateTools::Element TreeTemplateTools::getElement(const string& elt)</td>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp">      <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC244" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">exception</span> <span class="n" style="color: #333;">e</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span> <span class="n" style="color: #333;">e</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp">  <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">IOException</span><span class="p">(</span><span class="s" style="color: #d14;">"Bad tree description: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">elt</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp">  <span class="p">}</span></span>

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<br>

</li>

<li id="6e5c49a7992a9c6a7f368cbc8844c5d323183b08">

<a href="https://salsa.debian.org/med-team/libbpp-phyl/commit/2d1077e72fbc569cc82e62fdb6d37456a0e1a745#6e5c49a7992a9c6a7f368cbc8844c5d323183b08"><strong>test/test_likelihood_nh.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">@@ -89,14 +89,14 @@ int main() {</td>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp">  <span class="n" style="color: #333;">DiscreteDistribution</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rdist</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">GammaDiscreteRateDistribution</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nsites</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1000</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nrep</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">20</span></span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nrep</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">3</span></span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nmodels</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modelSet</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNumberOfModels</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp">  <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">thetas</span><span class="p">(</span><span class="n" style="color: #333;">nmodels</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp">  <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">thetasEst1</span><span class="p">(</span><span class="n" style="color: #333;">nmodels</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp">  <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">thetasEst2</span><span class="p">(</span><span class="n" style="color: #333;">nmodels</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC98" 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;">size_t</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;">nmodels</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC99" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">theta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RandomTools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">giveRandomNumberBetweenZeroAndEntry</span><span class="p">(</span><span class="mf" style="color: #099;">0.9<span class="idiff left">9</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="mf" style="color: #099;"><span class="idiff right">0.0</span>05</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">theta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RandomTools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">giveRandomNumberBetweenZeroAndEntry</span><span class="p">(</span><span class="mf" style="color: #099;">0.9</span><span class="p"><span class="idiff left">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff right">0.</span>05</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp">    <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Theta"</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="s" style="color: #d14;">" set to "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">theta</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp">    <span class="n" style="color: #333;">modelSet</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setParameterValue</span><span class="p">(</span><span class="s" style="color: #d14;">"T92.theta_"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">TextTools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">toString</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="n" style="color: #333;">theta</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

102

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp">    <span class="n" style="color: #333;">thetas</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;">theta</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="119" style="width: 35px; color: rgba(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="119" style="width: 35px; color: rgba(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">@@ -119,11 +119,11 @@ int main() {</td>

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<td class="diff-line-num old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp">    <span class="n" style="color: #333;">tl2</span><span class="p">.</span><span class="n" style="color: #333;">initialize</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp">   </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OptimizationTools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">optimizeNumericalParameters2</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="cpp">        <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tl</span><span class="p">,</span> <span class="n" style="color: #333;">tl</span><span class="p">.</span><span class="n" style="color: #333;">getParameters</span><span class="p">(),</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="123" 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="122" 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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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp">        <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tl</span><span class="p">,</span> <span class="n" style="color: #333;">tl</span><span class="p">.</span><span class="n" style="color: #333;">get<span class="idiff left right">SubstitutionModel</span>Parameters</span><span class="p">(),</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp">        <span class="mf" style="color: #099;">0.0001</span><span class="p">,</span> <span class="mi" style="color: #099;">10000</span><span class="p">,</span> <span class="n" style="color: #333;">messenger</span><span class="p">,</span> <span class="n" style="color: #333;">profiler</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">OptimizationTools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">OPTIMIZATION_NEWTON</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

125

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<td class="diff-line-num new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OptimizationTools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">optimizeNumericalParameters2</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC126" class="line" lang="cpp">        <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tl2</span><span class="p">,</span> <span class="n" style="color: #333;">tl2</span><span class="p">.</span><span class="n" style="color: #333;">getParameters</span><span class="p">(),</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="127" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="126" 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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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp">        <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tl2</span><span class="p">,</span> <span class="n" style="color: #333;">tl2</span><span class="p">.</span><span class="n" style="color: #333;">get<span class="idiff left right">SubstitutionModel</span>Parameters</span><span class="p">(),</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

127

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<td class="diff-line-num new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp">        <span class="mf" style="color: #099;">0.0001</span><span class="p">,</span> <span class="mi" style="color: #099;">10000</span><span class="p">,</span> <span class="n" style="color: #333;">messenger</span><span class="p">,</span> <span class="n" style="color: #333;">profiler</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">OptimizationTools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">OPTIMIZATION_NEWTON</span><span class="p">);</span></span>

</pre>

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128

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<td class="diff-line-num new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

128

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp"></span>

</pre>

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129

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129

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp">    <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">c1</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;">tl</span><span class="p">.</span><span class="n" style="color: #333;">getValue</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">c2</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;">tl2</span><span class="p">.</span><span class="n" style="color: #333;">getValue</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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