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<h3>
Julien Y. Dutheil pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/libbpp-raa">Debian Med / libbpp-raa</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libbpp-raa/commit/7506d6dd0e2d1ba1e3e922649c2aebe3ddd528e6">7506d6dd</a></strong>
<div>
<span>by Julien Y. Dutheil</span>
<i>at 2018-08-22T07:04:21Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.4.1</pre>
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
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<li class="file-stats">
<a href="#3fa7b3d8e9b1a6a923cff77497ab817d9f94b6c0">
Doxyfile
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<li class="file-stats">
<a href="#8e8baa9f086fe67459b25b82470d5442a8054d99">
bpp-raa.spec
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<li class="file-stats">
<a href="#b987ffd067ea9e31cb7274f9eb3298d776f2991a">
<span class="deleted-file">
−
header.html
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<li class="file-stats">
<a href="#1709b3d94b205ec5a6782d1075600a0b57fd6323">
src/Bpp/Raa/RAA.cpp
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<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/libbpp-raa/commit/7506d6dd0e2d1ba1e3e922649c2aebe3ddd528e6#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -104,10 +104,10 @@ ENDIF(NO_DEP_CHECK)</td>
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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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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Packager</span></span>
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<td class="diff-line-num old_line" data-linenumber="105" style="width: 35px; color: rgba(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="105" style="width: 35px; color: rgba(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="LC105" 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-raa"</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="106" style="width: 35px; color: rgba(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="106" style="width: 35px; color: rgba(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="LC106" 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="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="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>
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<td class="diff-line-num new old_line" data-linenumber="108" 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="107" 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">
107
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<pre style="margin: 0;">+<span id="LC107" 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="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
108
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<td class="diff-line-num new_line" data-linenumber="108" style="width: 35px; color: rgba(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="LC108" 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 old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
109
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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(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="LC109" 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>
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<pre style="margin: 0;">-<span id="LC110" 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>
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<td class="diff-line-num new old_line" data-linenumber="111" 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="110" 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">
110
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<pre style="margin: 0;">+<span id="LC110" 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>
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111
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<td class="diff-line-num new_line" data-linenumber="111" style="width: 35px; color: rgba(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="LC111" 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++ Remote Acnuc Access library"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC112" 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;">${</span><span class="nv" style="color: teal;">CMAKE_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/COPYING.txt"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_RESOURCE_FILE_AUTHORS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</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>
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<a href="https://salsa.debian.org/med-team/libbpp-raa/commit/7506d6dd0e2d1ba1e3e922649c2aebe3ddd528e6#3fa7b3d8e9b1a6a923cff77497ab817d9f94b6c0"><strong>Doxyfile</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">@@ -38,7 +38,7 @@ PROJECT_NAME = bpp-raa</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>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"># control system is used.</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"></span>
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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>
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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>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"></span>
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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>
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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>
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<li id="8e8baa9f086fe67459b25b82470d5442a8054d99">
<a href="https://salsa.debian.org/med-team/libbpp-raa/commit/7506d6dd0e2d1ba1e3e922649c2aebe3ddd528e6#8e8baa9f086fe67459b25b82470d5442a8054d99"><strong>bpp-raa.spec</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">@@ -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-raa</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Name: bpp-raa</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Version: 2.4.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Version: 2.4.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Release: 1%{?dist}</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">License: CECILL-2.0</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Vendor: The Bio++ Project</span>
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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>
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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">@@ -90,8 +90,10 @@ rm -rf $RPM_BUILD_ROOT</td>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext">%{_prefix}/include/*</span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext">%changelog</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">* Mon Aug 13 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.1-1</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">- Compatibility gcc8.</span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext">* Mon Feb 26 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.0-1</span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext">- Increased interface number</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">- Increased interface number<span class="idiff left right">.</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext">- Removed dynamic exceptions specifications.</span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext">* Tue Jun 06 2017 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.3.1-1</span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext">- Increased interface number</span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="html"><span class="nt" style="color: navy;"><html</span> <span class="na" style="color: teal;">xmlns=</span><span class="s" style="color: #d14;">"http://www.w3.org/1999/xhtml"</span> <span class="na" style="color: teal;">xml:lang=</span><span class="s" style="color: #d14;">"en"</span> <span class="na" style="color: teal;">lang=</span><span class="s" style="color: #d14;">"en"</span><span class="nt" style="color: navy;">></span></span>
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<a href="https://salsa.debian.org/med-team/libbpp-raa/commit/7506d6dd0e2d1ba1e3e922649c2aebe3ddd528e6#1709b3d94b205ec5a6782d1075600a0b57fd6323"><strong>src/Bpp/Raa/RAA.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">@@ -262,7 +262,7 @@ Sequence* RAA::translateCDS(int seqrank)</td>
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="cpp"> <span class="n" style="color: #333;">Sprot</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BasicSequence</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sname</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pstring</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">AlphabetTools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PROTEIN_ALPHABET</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">BadCharException</span> <span class="n" style="color: #333;">e</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">BadCharException</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="LC266" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">sname</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">pstring</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -283,14 +283,7 @@ Sequence* RAA::translateCDS(const string& name)</td>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rank</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="cpp"> <span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">Sprot</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="cpp"> <span class="n" style="color: #333;">Sprot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">translateCDS</span><span class="p">(</span><span class="n" style="color: #333;">rank</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">BadCharException</span> <span class="n" style="color: #333;">e</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">e</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"> <span class="n" style="color: #333;">Sprot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">translateCDS</span><span class="p">(</span><span class="n" style="color: #333;">rank</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Sprot</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="cpp"></span>
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