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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/mptp">Debian Med / mptp</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mptp/commit/ff0ad8f44917d839e4fb521072a611db1fec4b49">ff0ad8f4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-04-27T07:15:46+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.2.3</pre>
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<h4>12 changed files:</h4>
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<li class="file-stats">
<a href="#458e1d0f85716e3c7c27857fb05bfd41d637ba7c">
ChangeLog.md
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
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<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
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<li class="file-stats">
<a href="#0e766443d2ebc74860970a223861f9bc7b7c049f">
man/mptp.1
</a>
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<li class="file-stats">
<a href="#67e794015a01b8816bd16290e5f8538236da8245">
src/Makefile.am
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<li class="file-stats">
<a href="#7442ac311dbfd89059322cc1ea0b6ab7ac8d6493">
src/auto.c
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<li class="file-stats">
<a href="#0d3f46c95760f46c2070dd4bc4374809da5018a2">
<span class="new-file">
+
src/hash.c
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<li class="file-stats">
<a href="#42b6da528fada3a76ec21058091b5a090bd6a625">
<span class="new-file">
+
src/list.c
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<li class="file-stats">
<a href="#91197b4433b6a20331e46f63a38dfda8981df1c1">
src/mptp.h
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<li class="file-stats">
<a href="#a84dd12c0a2a7a35be02ff3fb545cdba7ab7c61b">
src/rtree.c
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<li class="file-stats">
<a href="#67c319180cbcafb0d1d073f70f07d14aff317006">
src/util.c
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<li class="file-stats">
<a href="#3cf18ed6089d7a27c4c0c91ff1ff520726e97d79">
src/utree.c
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<h4>Changes:</h4>
<li id="458e1d0f85716e3c7c27857fb05bfd41d637ba7c">
<a href="https://salsa.debian.org/med-team/mptp/commit/ff0ad8f44917d839e4fb521072a611db1fec4b49#458e1d0f85716e3c7c27857fb05bfd41d637ba7c"><strong>ChangeLog.md</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" style="width: 35px; color: rgba(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">@@ -2,6 +2,11 @@</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="LC2" class="line" lang="markdown">All notable changes to <span class="sb" style="color: #d14;">`mptp`</span> will be documented in this file.</span>
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown">This project adheres to <span class="p">[</span><span class="nv" style="color: teal;">Semantic Versioning</span><span class="p">](</span><span class="sx" style="color: #d14;">http://semver.org/</span><span class="p">)</span>.</span>
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(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="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [0.2.3] - 2017-07-25</span></span>
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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">
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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="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Fixed</span></span>
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<td class="diff-line-num new new_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="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="p"> -</span> Replaced hsearch which was causing problems on APPLE with custom hashtable</span>
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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">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="p"> -</span> Corrected file name in error messages when failing to open files</span>
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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [0.2.2] - 2017-01-31</span></span>
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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">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Fixed</span></span>
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(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="LC12" class="line" lang="markdown"><span class="p"> -</span> Regular expressions now allow scientific notation when parsing branch lengths</span>
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<br>
</li>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/mptp/commit/ff0ad8f44917d839e4fb521072a611db1fec4b49#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Species <span class="idiff left right">Delimitation</span></span></span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Species <span class="idiff left right">delimitation using the multi-rate Poisson Tree Processes (mPTP)</span></span></span>
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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="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">![License</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/license-AGPL-blue.svg</span><span class="p">)</span>](http://www.gnu.org/licenses/agpl-3.0.en.html)</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/Pas-Kapli/mptp.svg?branch=master</span><span class="p">)</span>](https://travis-ci.<span class="idiff left right">com</span>/Pas-Kapli/mptp)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/Pas-Kapli/mptp.svg?branch=master</span><span class="p">)</span>](https://travis-ci.<span class="idiff left right">org</span>/Pas-Kapli/mptp)</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Introduction</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="59" style="width: 35px; color: rgba(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="59" style="width: 35px; color: rgba(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">@@ -59,7 +59,7 @@ On a Debian-based Linux system, the four packages can be installed</td>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown">using the command</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">sudo </span>apt-get install libgsl0-dev flex bison autotools-dev</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">sudo </span>apt-get install libgsl0-dev flex bison autotools-dev<span class="idiff left right"> autoconf</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="markdown">Optionally, you can install the bash auto-completion for mptp. To do that,</span>
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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -121,6 +121,13 @@ and `doc`. We recommend making a copy or a symbolic link to the mptp binary</td>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="markdown">to the mptp man page <span class="sb" style="color: #d14;">`man/mptp.1`</span> in a folder included in your <span class="sb" style="color: #d14;">`$MANPATH`</span>. The</span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="markdown">PDF version of the manual is available in <span class="sb" style="color: #d14;">`doc/mptp_manual.pdf`</span>.</span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Implementation details and method description</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="markdown">Please see the manuscript for details:</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="markdown">Kapli T, Lutteropp S, Zhang J, Kobert K, Pavlidis P, Stamatakis A, Flouri T. (2016) Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinformatics 33(11):1630-1638. doi:<span class="p">[</span><span class="nv" style="color: teal;">10.1093/bioinformatics/btx025</span><span class="p">](</span><span class="sx" style="color: #d14;">https://doi.org/10.1093/bioinformatics/btx025</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Command-line options</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="193" style="width: 35px; color: rgba(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="200" style="width: 35px; color: rgba(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">@@ -193,30 +200,30 @@ The code is currently licensed under the [GNU Affero General Public License vers</td>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Code</span></span>
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195
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="markdown"></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right"> File | Description</span></span></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="markdown"><span class="idiff left right">--------------------|----------------</span></span>
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<td class="diff-line-num old old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**arch.c**</span></span><span class="idiff right"> | Architecture specific code (Mac/Linux).</span></span>
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<td class="diff-line-num old old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**auto.c**</span></span><span class="idiff right"> | Code for auto-detecting minimum branch length.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
200
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<td class="diff-line-num new_line old" data-linenumber="203" style="width: 35px; color: rgba(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="LC200" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**aic.c**</span></span><span class="idiff right"> | Code for Bayesian Single- and multi-rate PTP.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
201
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<td class="diff-line-num new_line old" data-linenumber="203" style="width: 35px; color: rgba(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="LC201" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**mptp.c**</span></span><span class="idiff right"> | Main file handling command-line parameters and executing corresponding parts.</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**mptp.h**</span></span><span class="idiff right"> | MPTP Header file.</span></span>
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203
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<td class="diff-line-num new_line old" data-linenumber="203" style="width: 35px; color: rgba(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="LC203" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**dp.c**</span></span><span class="idiff right"> | Single- and multi-rate DP heuristics for solving the PTP problem.</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**fasta.c**</span></span><span class="idiff right"> | Code for reading FASTA files.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
205
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<td class="diff-line-num new_line old" data-linenumber="203" style="width: 35px; color: rgba(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="LC205" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**lex_rtree.l**</span></span><span class="idiff right"> | Lexical analyzer parsing newick rooted trees.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
206
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<td class="diff-line-num new_line old" data-linenumber="203" style="width: 35px; color: rgba(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="LC206" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**lex_utree.l**</span></span><span class="idiff right"> | Lexical analyzer parsing newick unrooted trees.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
207
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<td class="diff-line-num new_line old" data-linenumber="203" style="width: 35px; color: rgba(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="LC207" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**likelihood.c**</span></span><span class="idiff right"> | Likelihood rated functions.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
208
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<td class="diff-line-num new_line old" data-linenumber="203" style="width: 35px; color: rgba(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="LC208" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**Makefile.am**</span></span><span class="idiff right"> | Automake file for generating Makefile.in.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
209
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<td class="diff-line-num new_line old" data-linenumber="203" style="width: 35px; color: rgba(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="LC209" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**maps.c**</span></span><span class="idiff right"> | Character mapping arrays for converting sequences to the internal representation.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
210
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<td class="diff-line-num new_line old" data-linenumber="203" style="width: 35px; color: rgba(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="LC210" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**multirun.c**</span></span><span class="idiff right"> | Functions to execute multiple MCMC runs and compute ASD of support values.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**output.c**</span></span><span class="idiff right"> | Output related files.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
212
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<td class="diff-line-num new_line old" data-linenumber="203" style="width: 35px; color: rgba(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="LC212" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**parse_rtree.y**</span></span><span class="idiff right"> | Functions for parsing rooted trees in newick format.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
213
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<td class="diff-line-num new_line old" data-linenumber="203" style="width: 35px; color: rgba(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="LC213" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**parse_utree.y**</span></span><span class="idiff right"> | Functions for parsing unrooted trees in newick format.</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
214
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<td class="diff-line-num new_line old" data-linenumber="203" style="width: 35px; color: rgba(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="LC214" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**random.c**</span></span><span class="idiff right"> | Functions for creating a random delimitation.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**rtree.c**</span></span><span class="idiff right"> | Rooted tree manipulation functions.</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**svg.c**</span></span><span class="idiff right"> | SVG visualization of delimited tree.</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**svg_landscape.c**</span></span><span class="idiff right"> | SVG visualization of likelihood landscape.</span></span>
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218
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**util.c**</span></span><span class="idiff right"> | Various common utility functions.</span></span>
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219
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="markdown"><span class="gs" style="font-weight: 600;"><span class="idiff left">**utree.c**</span></span><span class="idiff right"> | Unrooted tree manipulation functions.</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="markdown"><span class="idiff left right">| File | Description |</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="markdown"><span class="idiff left right">| --------------------| --------------------------------------------------------------------------------- |</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="markdown"><span class="idiff left">| </span><span class="gs" style="font-weight: 600;"><span class="idiff">**arch.c**</span></span><span class="idiff right"> | Architecture specific code (Mac/Linux). |</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="markdown"><span class="idiff left">| </span><span class="gs" style="font-weight: 600;"><span class="idiff">**auto.c**</span></span><span class="idiff right"> | Code for auto-detecting minimum branch length. |</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="markdown"><span class="idiff left">| </span><span class="gs" style="font-weight: 600;"><span class="idiff">**aic.c**</span></span><span class="idiff right"> | Code for Bayesian Single- and multi-rate PTP. |</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="markdown"><span class="idiff left">| </span><span class="gs" style="font-weight: 600;"><span class="idiff">**mptp.c**</span></span><span class="idiff right"> | Main file handling command-line parameters and executing corresponding parts. |</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="markdown"><span class="idiff left">| </span><span class="gs" style="font-weight: 600;"><span class="idiff">**mptp.h**</span></span><span class="idiff right"> | MPTP Header file. |</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="markdown"><span class="idiff left">| </span><span class="gs" style="font-weight: 600;"><span class="idiff">**dp.c**</span></span><span class="idiff right"> | Single- and multi-rate DP heuristics for solving the PTP problem. |</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="markdown"><span class="idiff left">| </span><span class="gs" style="font-weight: 600;"><span class="idiff">**fasta.c**</span></span><span class="idiff right"> | Code for reading FASTA files. |</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="markdown"><span class="idiff left">| </span><span class="gs" style="font-weight: 600;"><span class="idiff">**lex_rtree.l**</span></span><span class="idiff right"> | Lexical analyzer parsing newick rooted trees. |</span></span>
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<td class="diff-line-num new new_line" data-linenumber="213" 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">
213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="markdown"><span class="idiff left">| </span><span class="gs" style="font-weight: 600;"><span class="idiff">**lex_utree.l**</span></span><span class="idiff right"> | Lexical analyzer parsing newick unrooted trees. |</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="markdown"><span class="idiff left">| </span><span class="gs" style="font-weight: 600;"><span class="idiff">**likelihood.c**</span></span><span class="idiff right"> | Likelihood rated functions. |</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="markdown"><span class="idiff left">| </span><span class="gs" style="font-weight: 600;"><span class="idiff">**Makefile.am**</span></span><span class="idiff right"> | Automake file for generating Makefile.in. |</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="markdown"><span class="idiff left">| </span><span class="gs" style="font-weight: 600;"><span class="idiff">**maps.c**</span></span><span class="idiff right"> | Character mapping arrays for converting sequences to the internal representation. |</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="markdown"><span class="idiff left">| </span><span class="gs" style="font-weight: 600;"><span class="idiff">**multirun.c**</span></span><span class="idiff right"> | Functions to execute multiple MCMC runs and compute ASD of support values. |</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="markdown"><span class="idiff left">| </span><span class="gs" style="font-weight: 600;"><span class="idiff">**output.c**</span></span><span class="idiff right"> | Output related files. |</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="markdown"><span class="idiff left">| </span><span class="gs" style="font-weight: 600;"><span class="idiff">**parse_rtree.y**</span></span><span class="idiff right"> | Functions for parsing rooted trees in newick format. |</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="markdown"><span class="idiff left">| </span><span class="gs" style="font-weight: 600;"><span class="idiff">**parse_utree.y**</span></span><span class="idiff right"> | Functions for parsing unrooted trees in newick format. |</span></span>
</pre>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="markdown"><span class="idiff left">| </span><span class="gs" style="font-weight: 600;"><span class="idiff">**random.c**</span></span><span class="idiff right"> | Functions for creating a random delimitation. |</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="markdown"><span class="idiff left">| </span><span class="gs" style="font-weight: 600;"><span class="idiff">**rtree.c**</span></span><span class="idiff right"> | Rooted tree manipulation functions. |</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="markdown"><span class="idiff left">| </span><span class="gs" style="font-weight: 600;"><span class="idiff">**svg.c**</span></span><span class="idiff right"> | SVG visualization of delimited tree. |</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="markdown"><span class="idiff left">| </span><span class="gs" style="font-weight: 600;"><span class="idiff">**svg_landscape.c**</span></span><span class="idiff right"> | SVG visualization of likelihood landscape. |</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="markdown"><span class="idiff left">| </span><span class="gs" style="font-weight: 600;"><span class="idiff">**util.c**</span></span><span class="idiff right"> | Various common utility functions. |</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="markdown"><span class="idiff left">| </span><span class="gs" style="font-weight: 600;"><span class="idiff">**utree.c**</span></span><span class="idiff right"> | Unrooted tree manipulation functions. |</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## The team</span></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="235" style="width: 35px; color: rgba(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">@@ -228,6 +235,12 @@ The code is currently licensed under the [GNU Affero General Public License vers</td>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="markdown"><span class="p">*</span> Alexandros Stamatakis</span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="markdown"><span class="p">*</span> Tom<span class="ni" style="color: purple;">áš</span> Flouri</span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Citing mPTP</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="markdown">Please cite the following publication if you use mPTP:</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="markdown">Kapli T, Lutteropp S, Zhang J, Kobert K, Pavlidis P, Stamatakis A, Flouri T. (2016) Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinformatics 33(11):1630-1638. doi:<span class="p">[</span><span class="nv" style="color: teal;">10.1093/bioinformatics/btx025</span><span class="p">](</span><span class="sx" style="color: #d14;">https://doi.org/10.1093/bioinformatics/btx025</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="markdown"><span class="gh" style="color: #999;"># References</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="markdown"><span class="p">*</span> Zhang J., Kapli P., Pavlidis P., Stamatakis A. (2013)</span>
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<li id="87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
<a href="https://salsa.debian.org/med-team/mptp/commit/ff0ad8f44917d839e4fb521072a611db1fec4b49#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,7 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"># Process this file with autoconf to produce a configure script.</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">AC_PREREQ([2.63])</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">AC_INIT([mptp], [0.2.<span class="idiff left right">2</span>], [Tomas.Flouri@h-its.org])</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">AC_INIT([mptp], [0.2.<span class="idiff left right">3</span>], [Tomas.Flouri@h-its.org])</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">AM_INIT_AUTOMAKE([subdir-objects])</span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">AC_LANG([C])</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">AC_CONFIG_SRCDIR([src/mptp.c])</span>
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<a href="https://salsa.debian.org/med-team/mptp/commit/ff0ad8f44917d839e4fb521072a611db1fec4b49#0e766443d2ebc74860970a223861f9bc7b7c049f"><strong>man/mptp.1</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">@@ -351,5 +351,8 @@ Fixed regular expressions to allow scientific notation for branch lengths when</td>
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351
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351
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="plaintext">parsing trees. Improved the accuracy of ASV score by also taking into account</span>
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="plaintext">tips forming coalescent roots. Fixed memory leaks that occur when parsing</span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="plaintext">incorrectly formatted trees.</span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="plaintext">.TP</span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="plaintext">.BR v0.2.3\~ "released July 25th, 2017"</span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="plaintext">Replaced hsearch() with custom hashtable. Fixed minor output error messages.</span>
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="plaintext">.RE</span>
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355
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="plaintext">.LP</span></pre>
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<a href="https://salsa.debian.org/med-team/mptp/commit/ff0ad8f44917d839e4fb521072a611db1fec4b49#67e794015a01b8816bd16290e5f8538236da8245"><strong>src/Makefile.am</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">@@ -26,4 +26,6 @@ rtree.c \</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="make">svg.c <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="make">svg_landscape.c <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="make">util.c <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="make">utree.c</span></pre>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="make">utree.c <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="make">hash.c <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="make">list.c</span></pre>
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<a href="https://salsa.debian.org/med-team/mptp/commit/ff0ad8f44917d839e4fb521072a611db1fec4b49#7442ac311dbfd89059322cc1ea0b6ab7ac8d6493"><strong>src/auto.c</strong></a>
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<pre style="margin: 0;"> <span id="LC1" 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="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Copyright (C) 2015 Tomas Flouri</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Copyright (C) 2015<span class="idiff left right">-2017</span> Tomas Flouri</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> This program is free software: you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> it under the terms of the GNU Affero General Public License as</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -159,30 +159,6 @@ static int cb_short_trees(rtree_t * node)</td>
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="c"></span>
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="c"><span class="p">}</span></span>
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161
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="c"></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">hash_tips</span><span class="p">(</span><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">root</span><span class="p">)</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="c"><span class="p">{</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="c"></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* obtain an array of pointers to tip names */</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="c"> <span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">tipnodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">**</span><span class="p">)</span><span class="n" style="color: #333;">xmalloc</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)(</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">leaves</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="c"> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">));</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="c"> <span class="n" style="color: #333;">rtree_query_tipnodes</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">tipnodes</span><span class="p">);</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="c"></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* create a libc hash table of size tip_count */</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="c"> <span class="n" style="color: #333;">hcreate</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)(</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">leaves</span><span class="p">));</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="c"></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* populate a libc hash table with tree tip labels */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">leaves</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="c"> <span class="n" style="color: #333;">ENTRY</span> <span class="n" style="color: #333;">entry</span><span class="p">;</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="c"> <span class="n" style="color: #333;">entry</span><span class="p">.</span><span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tipnodes</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;">label</span><span class="p">;</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="c"> <span class="n" style="color: #333;">entry</span><span class="p">.</span><span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="n" style="color: #333;">tipnodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="c"> <span class="n" style="color: #333;">hsearch</span><span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">,</span> <span class="n" style="color: #333;">ENTER</span><span class="p">);</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="c"> <span class="p">}</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">tipnodes</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">set_encode_sequence</span><span class="p">(</span><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">node</span><span class="p">,</span></span>
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187
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sequence</span><span class="p">,</span></span>
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188
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">seqlen</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -211,22 +187,47 @@ static void link_sequences(rtree_t * root, char ** headers, char ** sequence, lo</td>
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211
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="c"><span class="p">{</span></span>
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212
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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213
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="c"></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* obtain an array of pointers to tip names */</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="c"> <span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">tipnodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">**</span><span class="p">)</span><span class="n" style="color: #333;">xmalloc</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)(</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">leaves</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="c"> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">));</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="c"> <span class="n" style="color: #333;">rtree_query_tipnodes</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">tipnodes</span><span class="p">);</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="c"></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* create a libc hash table of size tip_count */</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="c"> <span class="n" style="color: #333;">hashtable_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ht</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashtable_create</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">leaves</span><span class="p">);</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="c"></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* populate a libc hash table with tree tip labels */</span></span>
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214
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">leaves</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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215
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="c"> <span class="p">{</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="c"> <span class="n" style="color: #333;">ENTRY</span> <span class="n" style="color: #333;">query</span><span class="p">;</span></span>
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217
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// printf("Linking %s\n", headers[i]);</span></span>
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218
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="c"> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">headers</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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219
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="c"> <span class="n" style="color: #333;">ENTRY</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">found</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="c"> <span class="n" style="color: #333;">pair_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pair</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">pair_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">xmalloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">pair_t</span><span class="p">));</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="c"> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tipnodes</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;">label</span><span class="p">;</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="c"> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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220
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="c"></span>
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221
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="c"> <span class="n" style="color: #333;">found</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hsearch</span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">,</span><span class="n" style="color: #333;">FIND</span><span class="p">);</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">hashtable_insert</span><span class="p">(</span><span class="n" style="color: #333;">ht</span><span class="p">,</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="c"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">pair</span><span class="p">,</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="c"> <span class="n" style="color: #333;">hash_fnv</span><span class="p">(</span><span class="n" style="color: #333;">tipnodes</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;">label</span><span class="p">),</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="c"> <span class="n" style="color: #333;">hashtable_paircmp</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="209" 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">
209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="c"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Duplicate taxon (%s)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">tipnodes</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;">label</span><span class="p">);</span></span>
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222
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">found</span><span class="p">)</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="c"> <span class="p">}</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="c"></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">leaves</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="c"> <span class="p">{</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="c"> <span class="n" style="color: #333;">pair_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashtable_find</span><span class="p">(</span><span class="n" style="color: #333;">ht</span><span class="p">,</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="c"> <span class="n" style="color: #333;">headers</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="c"> <span class="n" style="color: #333;">hash_fnv</span><span class="p">(</span><span class="n" style="color: #333;">headers</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]),</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="c"> <span class="n" style="color: #333;">hashtable_paircmp</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">query</span><span class="p">)</span></span>
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224
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="c"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Sequence with header %s does not appear in the tree"</span><span class="p">,</span> <span class="n" style="color: #333;">headers</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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225
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="c"> </span>
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226
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="c"> <span class="n" style="color: #333;">set_encode_sequence</span><span class="p">(<span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">rtree_t</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="p"><span class="idiff">)(</span></span><span class="n" style="color: #333;"><span class="idiff">found</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">data</span></span><span class="p"><span class="idiff right">)</span>,</span> <span class="n" style="color: #333;">sequence</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">pll_map_nt</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="c"> <span class="n" style="color: #333;">set_encode_sequence</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">tipnodes</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">query</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">index</span></span><span class="p"><span class="idiff right">]</span>,</span> <span class="n" style="color: #333;">sequence</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">pll_map_nt</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">tipnodes</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="c"> <span class="n" style="color: #333;">hashtable_destroy</span><span class="p">(</span><span class="n" style="color: #333;">ht</span><span class="p">,</span><span class="n" style="color: #333;">free</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">all_pairwise_dist</span><span class="p">(</span><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">tip_node_list</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tip_list_count</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">seqlen</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="c"><span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -263,14 +264,9 @@ void detect_min_bl(rtree_t * rtree)</td>
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="c"> <span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">load_fasta</span><span class="p">(</span><span class="n" style="color: #333;">rtree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">leaves</span><span class="p">,</span> <span class="n" style="color: #333;">headers</span><span class="p">,</span> <span class="n" style="color: #333;">seqdata</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="c"> <span class="n" style="color: #333;">hash_tips</span><span class="p">(</span><span class="n" style="color: #333;">rtree</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* find sequences in hash table and link them with the corresponding taxa */</span></span>
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269
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="c"> <span class="n" style="color: #333;">link_sequences</span><span class="p">(</span><span class="n" style="color: #333;">rtree</span><span class="p">,</span> <span class="n" style="color: #333;">headers</span><span class="p">,</span> <span class="n" style="color: #333;">seqdata</span><span class="p">,</span> <span class="n" style="color: #333;">seqlen</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* destroy hash table */</span></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="c"> <span class="n" style="color: #333;">hdestroy</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get inner nodes that are roots of of the largest short subtrees. Short are</span></span>
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> such subtrees where all branch lengths within them are less or equal to</span></span>
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> opt_subtree_short. The largest such subtrees are those that are not</span></span>
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<a href="https://salsa.debian.org/med-team/mptp/commit/ff0ad8f44917d839e4fb521072a611db1fec4b49#0d3f46c95760f46c2070dd4bc4374809da5018a2"><strong>src/hash.c</strong></a>
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<pre style="margin: 0;">+<span id="LC1" 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="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Copyright (C) 2015-2017 Tomas Flouri</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> This program is free software: you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> it under the terms of the GNU Affero General Public License as</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> published by the Free Software Foundation, either version 3 of the</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> License, or (at your option) any later version.</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> This program is distributed in the hope that it will be useful,</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> GNU Affero General Public License for more details.</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> You should have received a copy of the GNU Affero General Public License</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> along with this program. If not, see <http://www.gnu.org/licenses/>.</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Contact: Tomas Flouri <Tomas.Flouri@h-its.org>,</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Heidelberg Institute for Theoretical Studies,</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "mptp.h"</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="c"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Daniel J. Bernstein 2a hash function */</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="nf" style="color: #900; font-weight: 600;">hash_djb2a</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">s</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">hash</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5381</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">++</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"> <span class="n" style="color: #333;">hash</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">hash</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">hash</span><span class="p">)</span> <span class="o" style="font-weight: 600;">^</span> <span class="n" style="color: #333;">c</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* hash*33 ^ c */</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">hash</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Fowler–Noll–Vo 1a hash function */</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="nf" style="color: #900; font-weight: 600;">hash_fnv</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">s</span><span class="p">)</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">hash</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">14695981039346656037UL</span><span class="p">;</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">++</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="c"> <span class="n" style="color: #333;">hash</span> <span class="o" style="font-weight: 600;">^=</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="c"> <span class="n" style="color: #333;">hash</span> <span class="o" style="font-weight: 600;">*=</span> <span class="mi" style="color: #099;">1099511628211UL</span><span class="p">;</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">hash</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">ht_item_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">hashitem_create</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c"> <span class="n" style="color: #333;">ht_item_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hi</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">ht_item_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">xmalloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">ht_item_t</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="c"> <span class="n" style="color: #333;">hi</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">key</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"> <span class="n" style="color: #333;">hi</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">hi</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">hashtable_strcmp</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">y</span><span class="p">)</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">strcmp</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="c"><span class="p">}</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">hashtable_ptrcmp</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">y</span><span class="p">)</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">hashtable_paircmp</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">stored</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">query</span><span class="p">)</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="c"><span class="p">{</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="c"> <span class="n" style="color: #333;">pair_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">stored_pair</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">pair_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">stored</span><span class="p">;</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">query_label</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">query</span><span class="p">;</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">stored_pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">label</span><span class="p">,</span> <span class="n" style="color: #333;">query_label</span><span class="p">);</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="c"><span class="p">}</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="c"></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">hashtable_find</span><span class="p">(</span><span class="n" style="color: #333;">hashtable_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ht</span><span class="p">,</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">x</span><span class="p">,</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">hash</span><span class="p">,</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cb_cmp</span><span class="p">)(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="p">))</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c"><span class="p">{</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hash</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">table_size</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="c"> <span class="n" style="color: #333;">list_item_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">li</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">list_item_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">entries</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">head</span><span class="p">);</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="c"></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">li</span><span class="p">)</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"> <span class="p">{</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="c"> <span class="n" style="color: #333;">ht_item_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hi</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">ht_item_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="n" style="color: #333;">li</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">);</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">hash</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">hi</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">key</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">cb_cmp</span><span class="p">(</span><span class="n" style="color: #333;">hi</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">hi</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="c"> <span class="n" style="color: #333;">li</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">li</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">;</span> </span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="c"> <span class="p">}</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="c"></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="c"> <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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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="c"><span class="p">}</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="c"> </span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="c"></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="c"><span class="n" style="color: #333;">hashtable_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">hashtable_create</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">items_count</span><span class="p">)</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="c"><span class="p">{</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="c"></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">items_count</span><span class="p">)</span> <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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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="c"></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* compute a size of at least double the items count that is a</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> multiple of 2 */</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="c"> <span class="n" style="color: #333;">items_count</span> <span class="o" style="font-weight: 600;"><<=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">items_count</span><span class="p">)</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="c"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;"><<=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="c"></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* allocate and init hash table */</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="c"> <span class="n" style="color: #333;">hashtable_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ht</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">hashtable_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">xmalloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">hashtable_t</span><span class="p">));</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="c"> <span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">table_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="c"> <span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">entries_count</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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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="c"></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* allocate and init entries array */</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="c"> <span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">entries</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">list_t</span> <span class="o" style="font-weight: 600;">**</span><span class="p">)</span><span class="n" style="color: #333;">xmalloc</span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">list_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">));</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="c"> <span class="p">{</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="c"> <span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">entries</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">list_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">xmalloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">list_t</span><span class="p">));</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="c"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">entries</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">list_t</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="c"> <span class="p">}</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="c"></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ht</span><span class="p">;</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="c"><span class="p">}</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="c"></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">hashtable_insert</span><span class="p">(</span><span class="n" style="color: #333;">hashtable_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ht</span><span class="p">,</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">x</span><span class="p">,</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">hash</span><span class="p">,</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cb_cmp</span><span class="p">)(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="p">))</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="c"><span class="p">{</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* size is always a multiple of 2 and greater than 2 */</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hash</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">table_size</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="c"></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="c"> <span class="n" style="color: #333;">list_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">entries</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">];</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="c"></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="c"></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hashtable_find</span><span class="p">(</span><span class="n" style="color: #333;">ht</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">hash</span><span class="p">,</span> <span class="n" style="color: #333;">cb_cmp</span><span class="p">))</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="c"></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="c"> <span class="n" style="color: #333;">ht_item_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">item</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashitem_create</span><span class="p">(</span><span class="n" style="color: #333;">hash</span><span class="p">,</span><span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c"> <span class="n" style="color: #333;">list_append</span><span class="p">(</span><span class="n" style="color: #333;">list</span><span class="p">,</span> <span class="n" style="color: #333;">item</span><span class="p">);</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="c"></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="c"> <span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">entries_count</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="c"></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="c"><span class="p">}</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="c"></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">hashtable_destroy</span><span class="p">(</span><span class="n" style="color: #333;">hashtable_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ht</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cb_dealloc</span><span class="p">)(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="p">))</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="c"><span class="p">{</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" data-linenumber="157" 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">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cb_dealloc</span><span class="p">)</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">table_size</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="161" 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">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="c"> <span class="n" style="color: #333;">list_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">entries</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="163" 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">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="c"> <span class="n" style="color: #333;">list_item_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">head</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">head</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="164" 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">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">head</span><span class="p">)</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="166" 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">
166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="c"> <span class="n" style="color: #333;">ht_item_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hi</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">ht_item_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="n" style="color: #333;">head</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">);</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="c"> <span class="n" style="color: #333;">cb_dealloc</span><span class="p">(</span><span class="n" style="color: #333;">hi</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="c"> <span class="n" style="color: #333;">head</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">head</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">;</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="c"> <span class="p">}</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="c"> <span class="p">}</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="c"> <span class="p">}</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="c"></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">table_size</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="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">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="c"> <span class="n" style="color: #333;">list_clear</span><span class="p">(</span><span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">entries</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">free</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">entries</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="c"> <span class="p">}</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">entries</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="179" 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">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">ht</span><span class="p">);</span> </span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="c"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/mptp/commit/ff0ad8f44917d839e4fb521072a611db1fec4b49#42b6da528fada3a76ec21058091b5a090bd6a625"><strong>src/list.c</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Copyright (C) 2015 Tomas Flouri</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="c"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> This program is free software: you can redistribute it and/or modify</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> it under the terms of the GNU Affero General Public License as</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> published by the Free Software Foundation, either version 3 of the</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> License, or (at your option) any later version.</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> This program is distributed in the hope that it will be useful,</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> GNU Affero General Public License for more details.</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="c"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> You should have received a copy of the GNU Affero General Public License</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> along with this program. If not, see <http://www.gnu.org/licenses/>.</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="c"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Contact: Tomas Flouri <Tomas.Flouri@h-its.org>,</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Heidelberg Institute for Theoretical Studies,</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "mptp.h"</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define DEF_LIST_APPEND 0</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define DEF_LIST_PREPEND 1</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">list_insert</span><span class="p">(</span><span class="n" style="color: #333;">list_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">list</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">where</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">list</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* create list item */</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"> <span class="n" style="color: #333;">list_item_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">item</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">list_item_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">xmalloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">list_item_t</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"> <span class="n" style="color: #333;">item</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* if list is empty */</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">count</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">head</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tail</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">item</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="c"> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="c"> <span class="n" style="color: #333;">item</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* append */</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">where</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">DEF_LIST_APPEND</span><span class="p">)</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="c"> <span class="p">{</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="c"> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tail</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">item</span><span class="p">;</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="c"> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tail</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">item</span><span class="p">;</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="c"> <span class="n" style="color: #333;">item</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="c"> <span class="p">}</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="c"></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* prepend */</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="c"> <span class="n" style="color: #333;">item</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">head</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="c"> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">head</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">item</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="c"></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="c"><span class="p">}</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">list_append</span><span class="p">(</span><span class="n" style="color: #333;">list_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">list</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="c"><span class="p">{</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="c"> <span class="n" style="color: #333;">list_insert</span><span class="p">(</span><span class="n" style="color: #333;">list</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">DEF_LIST_APPEND</span><span class="p">);</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="c"><span class="p">}</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="c"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">list_prepend</span><span class="p">(</span><span class="n" style="color: #333;">list_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">list</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c"><span class="p">{</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="c"> <span class="n" style="color: #333;">list_insert</span><span class="p">(</span><span class="n" style="color: #333;">list</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">DEF_LIST_PREPEND</span><span class="p">);</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"><span class="p">}</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c"></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">list_clear</span><span class="p">(</span><span class="n" style="color: #333;">list_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">list</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cb_dealloc</span><span class="p">)(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="p">))</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="c"><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="74" 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">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">list</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" data-linenumber="76" 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">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"> <span class="n" style="color: #333;">list_item_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">head</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">head</span><span class="p">;</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" data-linenumber="78" 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">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">head</span><span class="p">)</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="80" 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">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="c"> <span class="n" style="color: #333;">list_item_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">head</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="c"> <span class="n" style="color: #333;">head</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">head</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="82" 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">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cb_dealloc</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="83" 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">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="c"> <span class="n" style="color: #333;">cb_dealloc</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="84" 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">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">);</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="c"> <span class="p">}</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" data-linenumber="87" 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">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="c"> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">head</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tail</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c"> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">count</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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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"><span class="p">}</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="c"></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="c"><span class="n" style="color: #333;">list_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">list_create</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="c"><span class="p">{</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="c"> <span class="n" style="color: #333;">list_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">list_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">xmalloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">list_t</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="c"> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">count</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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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="c"> <span class="n" style="color: #333;">list_append</span><span class="p">(</span><span class="n" style="color: #333;">list</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">);</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">list</span><span class="p">;</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="c"><span class="p">}</span></span></pre>
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<li id="91197b4433b6a20331e46f63a38dfda8981df1c1">
<a href="https://salsa.debian.org/med-team/mptp/commit/ff0ad8f44917d839e4fb521072a611db1fec4b49#91197b4433b6a20331e46f63a38dfda8981df1c1"><strong>src/mptp.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">@@ -177,6 +177,38 @@ typedef struct pll_fasta</td>
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177
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">stripped</span><span class="p">[</span><span class="mi" style="color: #099;">256</span><span class="p">];</span></span>
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178
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="c"><span class="p">}</span> <span class="n" style="color: #333;">pll_fasta_t</span><span class="p">;</span></span>
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179
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="c"></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">list_item_s</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="c"><span class="p">{</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">data</span><span class="p">;</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">list_item_s</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">next</span><span class="p">;</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="c"><span class="p">}</span> <span class="n" style="color: #333;">list_item_t</span><span class="p">;</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="c"></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">list_s</span></span>
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<td class="diff-line-num new new_line" data-linenumber="187" 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">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="c"><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="188" 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">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="c"> <span class="n" style="color: #333;">list_item_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">head</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="189" 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">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="c"> <span class="n" style="color: #333;">list_item_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tail</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="190" 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">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">count</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="191" 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">
191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="c"><span class="p">}</span> <span class="n" style="color: #333;">list_t</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="192" 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">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" data-linenumber="193" 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">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">ht_item_s</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="c"><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="195" 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">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">key</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="196" 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">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">value</span><span class="p">;</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="c"><span class="p">}</span> <span class="n" style="color: #333;">ht_item_t</span><span class="p">;</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" data-linenumber="199" 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">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">hashtable_s</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="c"><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="201" 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">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">table_size</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="202" 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">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">entries_count</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="203" 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">
203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="c"> <span class="n" style="color: #333;">list_t</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">entries</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="204" 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">
204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="c"><span class="p">}</span> <span class="n" style="color: #333;">hashtable_t</span><span class="p">;</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" data-linenumber="206" 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">
206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">pair_s</span></span>
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<td class="diff-line-num new new_line" data-linenumber="207" 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">
207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="c"><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="208" 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">
208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">label</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="209" 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">
209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="c"><span class="p">}</span> <span class="n" style="color: #333;">pair_t</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="c"></span>
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* macros */</span></span>
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="c"></span>
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MIN(a,b) ((a) < (b) ? (a) : (b))</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -313,9 +345,6 @@ rtree_t * rtree_clone(rtree_t * node, rtree_t * parent);</td>
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313
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rtree_traverse_postorder</span><span class="p">(</span><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">root</span><span class="p">,</span></span>
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314
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346
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cbtrav</span><span class="p">)(</span><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">),</span></span>
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315
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347
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="c"> <span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">outbuffer</span><span class="p">);</span></span>
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316
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="c"><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">rtree_tipstring_nodes</span><span class="p">(</span><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">root</span><span class="p">,</span></span>
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317
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tipstring</span><span class="p">,</span></span>
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318
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tiplist_count</span><span class="p">);</span></span>
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348
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="c"><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">get_outgroup_lca</span><span class="p">(</span><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">root</span><span class="p">);</span></span>
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320
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349
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="c"><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rtree_lca</span><span class="p">(</span><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">root</span><span class="p">,</span></span>
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321
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="c"> <span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">tip_nodes</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="417" style="width: 35px; color: rgba(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">@@ -417,3 +446,40 @@ void aic_mcmc(rtree_t * tree,</td>
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417
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446
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">seed</span><span class="p">,</span></span>
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418
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447
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<pre style="margin: 0;"> <span id="LC447" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mcmc_min_logl</span><span class="p">,</span></span>
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419
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448
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<pre style="margin: 0;"> <span id="LC448" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mcmc_max_logl</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* functions in hash.c */</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">hash_djb2a</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="c"></span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">hash_fnv</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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455
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hashtable_strcmp</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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457
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hashtable_ptrcmp</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="c"></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hashtable_paircmp</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">stored</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">query</span><span class="p">);</span></span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="c"></span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hashtable_find</span><span class="p">(</span><span class="n" style="color: #333;">hashtable_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ht</span><span class="p">,</span></span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">x</span><span class="p">,</span></span>
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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">hash</span><span class="p">,</span></span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cb_cmp</span><span class="p">)(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="p">));</span></span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="c"></span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="c"><span class="n" style="color: #333;">hashtable_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hashtable_create</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">items_count</span><span class="p">);</span></span>
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468
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hashtable_insert</span><span class="p">(</span><span class="n" style="color: #333;">hashtable_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ht</span><span class="p">,</span></span>
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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">x</span><span class="p">,</span></span>
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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">hash</span><span class="p">,</span></span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cb_cmp</span><span class="p">)(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* functions in list.c */</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">list_append</span><span class="p">(</span><span class="n" style="color: #333;">list_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">list</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">data</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">list_prepend</span><span class="p">(</span><span class="n" style="color: #333;">list_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">list</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">data</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">list_clear</span><span class="p">(</span><span class="n" style="color: #333;">list_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">list</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cb_dealloc</span><span class="p">)(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="c"><span class="n" style="color: #333;">list_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">list_create</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">data</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">hashtable_destroy</span><span class="p">(</span><span class="n" style="color: #333;">hashtable_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ht</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cb_dealloc</span><span class="p">)(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="p">));</span></span></pre>
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<a href="https://salsa.debian.org/med-team/mptp/commit/ff0ad8f44917d839e4fb521072a611db1fec4b49#a84dd12c0a2a7a35be02ff3fb545cdba7ab7c61b"><strong>src/rtree.c</strong></a>
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<pre style="margin: 0;"> <span id="LC1" 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="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Copyright (C) 2015 Tomas Flouri</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Copyright (C) 2015<span class="idiff left right">-2017</span> Tomas Flouri</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> This program is free software: you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> it under the terms of the GNU Affero General Public License as</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -427,9 +427,9 @@ rtree_t * rtree_clone(rtree_t * node, rtree_t * parent)</td>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">clone</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="c"><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">**</span> <span class="nf" style="color: #900; font-weight: 600;">rtree_tipstring_nodes</span><span class="p">(</span><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">root</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tipstring</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tiplist_count</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="c"><span class="k" style="font-weight: 600;"><span class="idiff left">static</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">**</span> <span class="nf" style="color: #900; font-weight: 600;">rtree_tipstring_nodes</span><span class="p">(</span><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">root</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="c"> <span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tipstring</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="c"> <span class="idiff left right"> </span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tiplist_count</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="c"> <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;">k</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -438,8 +438,6 @@ rtree_t ** rtree_tipstring_nodes(rtree_t * root,</td>
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">taxon</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">taxon_len</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="c"> <span class="n" style="color: #333;">ENTRY</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">found</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">tipstring</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tipstring</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="sc" style="color: #d14;">','</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="c"> <span class="n" style="color: #333;">commas_count</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -452,14 +450,19 @@ rtree_t ** rtree_tipstring_nodes(rtree_t * root,</td>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="c"> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* create a hashtable of tip labels */</span></span>
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="c"> <span class="n" style="color: #333;">h<span class="idiff left">create</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="p"><span class="idiff">)(</span></span><span class="n" style="color: #333;"><span class="idiff">root</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">leaves</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="c"> <span class="n" style="color: #333;">h<span class="idiff left">ashtable_t</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ht</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">hashtable_create</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">root</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">leaves</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)(</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">leaves</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="c"> <span class="n" style="color: #333;">ENTRY</span> <span class="n" style="color: #333;">entry</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="c"> <span class="n" style="color: #333;">entry</span><span class="p">.</span><span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">node_list</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;">label</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC461" class="line" lang="c"> <span class="n" style="color: #333;">entry</span><span class="p">.</span><span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">node_list</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="LC462" class="line" lang="c"> <span class="n" style="color: #333;">hsearch</span><span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">,</span><span class="n" style="color: #333;">ENTER</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="c"> <span class="n" style="color: #333;">pair_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pair</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">pair_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">xmalloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">pair_t</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="c"> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">node_list</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;">label</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="c"> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">hashtable_insert</span><span class="p">(</span><span class="n" style="color: #333;">ht</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="c"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">pair</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="c"> <span class="n" style="color: #333;">hash_fnv</span><span class="p">(</span><span class="n" style="color: #333;">node_list</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;">label</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="c"> <span class="n" style="color: #333;">hashtable_paircmp</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="c"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Duplicate taxon (%s)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">node_list</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;">label</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tipstring</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -475,16 +478,16 @@ rtree_t ** rtree_tipstring_nodes(rtree_t * root,</td>
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="c"> <span class="n" style="color: #333;">taxon</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xstrndup</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">taxon_len</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* search tip in hash table */</span></span>
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<pre style="margin: 0;">-<span id="LC478" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">ENTRY</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">query</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<pre style="margin: 0;">-<span id="LC479" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">query</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">key</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">taxon</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">found</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">NULL</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">found</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">hsearch</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">query</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">FIND</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">pair_t</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">query</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">hashtable_find</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ht</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="c"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">taxon</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="c"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">hash_fnv</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">taxon</span></span><span class="p"><span class="idiff right">),</span></span></span>
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="c"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff right">hashtable_paircmp</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;"><span class="idiff left right">found</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;"><span class="idiff left right">query</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="c"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Taxon %s in does not appear in the tree"</span><span class="p">,</span> <span class="n" style="color: #333;">taxon</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* store pointer in output list */</span></span>
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="c"> <span class="n" style="color: #333;">out_node_list</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">rtree_t</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="p"><span class="idiff">)(</span></span><span class="n" style="color: #333;"><span class="idiff">found</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">data</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="c"> <span class="n" style="color: #333;">out_node_list</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">node_list</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">query</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">index</span></span><span class="p"><span class="idiff right">]</span>;</span></span>
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488
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491
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="c"></span>
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489
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492
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* free tip label, and move to the beginning of next tip if available */</span></span>
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490
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493
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">taxon</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="494" style="width: 35px; color: rgba(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="497" style="width: 35px; color: rgba(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">@@ -494,7 +497,7 @@ rtree_t ** rtree_tipstring_nodes(rtree_t * root,</td>
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494
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497
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="c"> <span class="p">}</span></span>
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495
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498
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="c"></span>
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496
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499
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* kill the hash table */</span></span>
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497
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="c"> <span class="n" style="color: #333;">h<span class="idiff left">destroy</span></span><span class="p"><span class="idiff right">(</span>);</span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="c"> <span class="n" style="color: #333;">h<span class="idiff left">ashtable_destroy</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ht</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">free</span></span><span class="p">);</span></span>
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498
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501
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="c"></span>
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499
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502
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">node_list</span><span class="p">);</span></span>
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503
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="c"></span>
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<a href="https://salsa.debian.org/med-team/mptp/commit/ff0ad8f44917d839e4fb521072a611db1fec4b49#67c319180cbcafb0d1d073f70f07d14aff317006"><strong>src/util.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="165" style="width: 35px; color: rgba(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="165" style="width: 35px; color: rgba(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">@@ -165,7 +165,7 @@ FILE * xopen(const char * filename, const char * mode)</td>
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165
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="c"><span class="p">{</span></span>
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166
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">);</span></span>
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167
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">out</span><span class="p">)</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="c"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot open file %s"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">opt_outfil</span>e</span><span class="p">);</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="c"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot open file %s"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">filenam</span>e</span><span class="p">);</span></span>
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169
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="c"></span>
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170
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">out</span><span class="p">;</span></span>
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171
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="c"><span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/mptp/commit/ff0ad8f44917d839e4fb521072a611db1fec4b49#3cf18ed6089d7a27c4c0c91ff1ff520726e97d79"><strong>src/utree.c</strong></a>
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<pre style="margin: 0;"> <span id="LC1" 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="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Copyright (C) 2015 Tomas Flouri</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Copyright (C) 2015<span class="idiff left right">-2017</span> Tomas Flouri</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> This program is free software: you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> it under the terms of the GNU Affero General Public License as</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -471,8 +471,6 @@ static utree_t ** utree_tipstring_nodes(utree_t * root,</td>
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">taxon</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">taxon_len</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="c"> <span class="n" style="color: #333;">ENTRY</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">found</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">tipstring</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tipstring</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="sc" style="color: #d14;">','</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="c"> <span class="n" style="color: #333;">commas_count</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -485,14 +483,19 @@ static utree_t ** utree_tipstring_nodes(utree_t * root,</td>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="c"> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">utree_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* create a hashtable of tip labels */</span></span>
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<pre style="margin: 0;">-<span id="LC488" class="line" lang="c"> <span class="n" style="color: #333;">h<span class="idiff left">create</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="p"><span class="idiff right">)</span></span><span class="n" style="color: #333;">utree_tip_count</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="c"> <span class="n" style="color: #333;">h<span class="idiff left">ashtable_t</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ht</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">hashtable_create</span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">utree_tip_count</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">utree_tip_count</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="c"> <span class="n" style="color: #333;">ENTRY</span> <span class="n" style="color: #333;">entry</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="c"> <span class="n" style="color: #333;">entry</span><span class="p">.</span><span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">node_list</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;">label</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="c"> <span class="n" style="color: #333;">entry</span><span class="p">.</span><span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">node_list</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="LC495" class="line" lang="c"> <span class="n" style="color: #333;">hsearch</span><span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">,</span><span class="n" style="color: #333;">ENTER</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="c"> <span class="n" style="color: #333;">pair_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pair</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">pair_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">xmalloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">pair_t</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="c"> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">node_list</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;">label</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="c"> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">hashtable_insert</span><span class="p">(</span><span class="n" style="color: #333;">ht</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="c"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">pair</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="c"> <span class="n" style="color: #333;">hash_fnv</span><span class="p">(</span><span class="n" style="color: #333;">node_list</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;">label</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="c"> <span class="n" style="color: #333;">hashtable_paircmp</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="c"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Duplicate taxon (%s)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">node_list</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;">label</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tipstring</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="508" style="width: 35px; color: rgba(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="511" style="width: 35px; color: rgba(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">@@ -508,16 +511,16 @@ static utree_t ** utree_tipstring_nodes(utree_t * root,</td>
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508
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="c"> <span class="n" style="color: #333;">taxon</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xstrndup</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">taxon_len</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* search tip in hash table */</span></span>
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<pre style="margin: 0;">-<span id="LC511" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">ENTRY</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">query</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">query</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">key</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">taxon</span></span><span class="p"><span class="idiff right">;</span></span></span>
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513
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">found</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">NULL</span></span><span class="p"><span class="idiff right">;</span></span></span>
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514
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">found</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">hsearch</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">query</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">FIND</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">pair_t</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">query</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">hashtable_find</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ht</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="c"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">taxon</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="c"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">hash_fnv</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">taxon</span></span><span class="p"><span class="idiff right">),</span></span></span>
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="c"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff right">hashtable_paircmp</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;"><span class="idiff left right">found</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;"><span class="idiff left right">query</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="c"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Taxon %s does not appear in the tree"</span><span class="p">,</span> <span class="n" style="color: #333;">taxon</span><span class="p">);</span></span>
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521
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="c"></span>
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522
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<pre style="margin: 0;"> <span id="LC522" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* store pointer in output list */</span></span>
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="c"> <span class="n" style="color: #333;">out_node_list</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">utree_t</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="p"><span class="idiff">)(</span></span><span class="n" style="color: #333;"><span class="idiff">found</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">data</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="c"> <span class="n" style="color: #333;">out_node_list</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">node_list</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">query</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">index</span></span><span class="p"><span class="idiff right">]</span>;</span></span>
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524
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* free tip label, and move to the beginning of next tip if available */</span></span>
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">taxon</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -527,7 +530,7 @@ static utree_t ** utree_tipstring_nodes(utree_t * root,</td>
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* kill the hash table */</span></span>
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="c"> <span class="n" style="color: #333;">h<span class="idiff left">destroy</span></span><span class="p"><span class="idiff right">(</span>);</span></span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="c"> <span class="n" style="color: #333;">h<span class="idiff left">ashtable_destroy</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ht</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">free</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">node_list</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="c"></span>
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