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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/cluster3">Debian Med / cluster3</a>
</h3>
<h4>
Commits:
</h4>
<ul>
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<strong><a href="https://salsa.debian.org/med-team/cluster3/commit/291de8a8e6299c799d2049f717568ab55fe72e9d">291de8a8</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-01-26T23:49:09Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.57</pre>
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</ul>
<h4>15 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
ChangeLog
</a>
</li>
<li class="file-stats">
<a href="#9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8">
NEWS
</a>
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<li class="file-stats">
<a href="#09be8533ff0a6ee5d577f971145ed449399fcda4">
configure
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<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
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<li class="file-stats">
<a href="#d27331e1afdde20a1d695ac4894094e0ceb2e79d">
doc/cluster.pdf
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<li class="file-stats">
<a href="#9b4e041d30f93d599aa9615be65e032940cf5f1e">
doc/cluster3.pdf
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<li class="file-stats">
<a href="#a406fd7883bf280c9dac05db7948d306292f5dd9">
mac/English.lproj/AboutPanel.xib
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<li class="file-stats">
<a href="#dabc12039aed8e862bb7cb610878db90c4a171f9">
mac/Info.plist
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<li class="file-stats">
<a href="#0a44e0614f23c2dd71257e5e32cb02e9a295dbfd">
perl/Cluster.pm
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<li class="file-stats">
<a href="#bb5afbfb42ef4ae77e927ad9a39bb8c7f6a27963">
python/__init__.py
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<li class="file-stats">
<a href="#4da3d46fb2a93582b1b2d09328d2b529636f7d32">
python/test/test_Cluster.py
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<li class="file-stats">
<a href="#cef7c3e0339a15adc388ac4a9747b77227826683">
src/cluster.c
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<li class="file-stats">
<a href="#d0a709faa909252ae246c0d6c1212099d4cc6343">
src/cluster.h
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<li class="file-stats">
<a href="#ad9733d1a5d8c7c1d3a59b30ea7bfa6e2780f674">
src/command.c
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<h4>Changes:</h4>
<li id="00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
<a href="https://salsa.debian.org/med-team/cluster3/commit/291de8a8e6299c799d2049f717568ab55fe72e9d#00fe7828d56d7a3ee4030d6cea057cf13f50e70c"><strong>ChangeLog</strong></a>
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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="LC1" class="line" lang="plaintext">2018.11.22</span>
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<td class="diff-line-num new new_line" data-linenumber="2" 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="LC2" class="line" lang="plaintext">Fixed memory leaks in kcluster and treecluster in src/cluster.c, and in</span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext">Hierarchical and KMeans in src/command.c; these memory leaks occurred when</span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext">memory allocation failed.</span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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="LC5" class="line" lang="plaintext">Fixed a bug in the distancematrix function Bio/Cluster/__init__.py, where the </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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="plaintext">weight argument was not properly initialized if it had the default value None,</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">causing the function to fail.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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1
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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="LC9" class="line" lang="plaintext">2018.04.29</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="LC10" class="line" lang="plaintext">In the Python wrapper python/clustermodule.c, use PyTree_new to initialize Tree</span>
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<td class="diff-line-num old_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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<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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">objects instead of PyTree_init, as Tree objects are immutable. Check if the</span>
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<li id="9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8">
<a href="https://salsa.debian.org/med-team/cluster3/commit/291de8a8e6299c799d2049f717568ab55fe72e9d#9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8"><strong>NEWS</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">2018.04.29</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">In the Python wrapper python/clustermodule.c, use PyTree_new to initialize Tree</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">objects instead of PyTree_init, as Tree objects are immutable. Check if the</span>
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<td class="diff-line-num old old_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext">argument passed are nodes by using PyType_IsSubtype instead of comparing against</span>
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<td class="diff-line-num old old_line" data-linenumber="5" 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">
5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">PyNodeType directly, as Node in __init__.py is a subtype of Node in</span>
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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">clustermodule.c.</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Rewrote indexing code for PyTree for Python3.</span>
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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Fixed a bug in Tree.cut in Bio/Cluster/__init__.py, which calculated the indices</span>
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<td class="diff-line-num old old_line" data-linenumber="9" 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">
9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">but did not return them. Updated the documentation for Tree.cut and Tree.sort</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">in Bio/Cluster/__init__.py. Added tests for Tree.cut. Updated the documentation</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">for Pycluster.</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Fixed a bug in src/cluster.c where a NULL pointer was freed if memory</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">allocation failed.</span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2018.11.22</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Fixed memory leaks in kcluster and treecluster in src/cluster.c, and in</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Hierarchical and KMeans in src/command.c; these memory leaks occurred when</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">memory allocation failed.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Fixed a bug in the distancematrix function Bio/Cluster/__init__.py, where the </span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">weight argument was not properly initialized if it had the default value None,</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">causing the function to fail.</span></pre>
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<li id="09be8533ff0a6ee5d577f971145ed449399fcda4">
<a href="https://salsa.debian.org/med-team/cluster3/commit/291de8a8e6299c799d2049f717568ab55fe72e9d#09be8533ff0a6ee5d577f971145ed449399fcda4"><strong>configure</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#! /bin/sh</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Guess values for system-dependent variables and create Makefiles.</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Generated by GNU Autoconf 2.69 for cluster 1.5<span class="idiff left right">6</span>.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Generated by GNU Autoconf 2.69 for cluster 1.5<span class="idiff left right">7</span>.</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.</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">@@ -577,8 +577,8 @@ MAKEFLAGS=</td>
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577
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577
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Identity of this package.</span></span>
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578
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<pre style="margin: 0;"> <span id="LC578" class="line" lang="shell"><span class="nv" style="color: teal;">PACKAGE_NAME</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'cluster'</span></span>
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579
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="shell"><span class="nv" style="color: teal;">PACKAGE_TARNAME</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'cluster'</span></span>
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580
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<pre style="margin: 0;">-<span id="LC580" class="line" lang="shell"><span class="nv" style="color: teal;">PACKAGE_VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'1.5<span class="idiff left right">6</span>'</span></span>
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581
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<pre style="margin: 0;">-<span id="LC581" class="line" lang="shell"><span class="nv" style="color: teal;">PACKAGE_STRING</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'cluster 1.5<span class="idiff left right">6</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="shell"><span class="nv" style="color: teal;">PACKAGE_VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'1.5<span class="idiff left right">7</span>'</span></span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="shell"><span class="nv" style="color: teal;">PACKAGE_STRING</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'cluster 1.5<span class="idiff left right">7</span>'</span></span>
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582
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582
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="shell"><span class="nv" style="color: teal;">PACKAGE_BUGREPORT</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">''</span></span>
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583
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583
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="shell"><span class="nv" style="color: teal;">PACKAGE_URL</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">''</span></span>
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584
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="shell"></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">@@ -1273,7 +1273,7 @@ if test "$ac_init_help" = "long"; then</td>
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1273
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<pre style="margin: 0;"> <span id="LC1273" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Omit some internal or obsolete options to make the list less imposing.</span></span>
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1274
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<pre style="margin: 0;"> <span id="LC1274" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># This message is too long to be a string in the A/UX 3.1 sh.</span></span>
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<pre style="margin: 0;"> <span id="LC1275" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: teal;">_ACEOF</span></span>
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<pre style="margin: 0;">-<span id="LC1276" class="line" lang="shell"><span class="sh" style="color: #d14;">\`configure' configures cluster 1.5<span class="idiff left right">6</span> to adapt to many kinds of systems.</span></span>
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<pre style="margin: 0;">+<span id="LC1276" class="line" lang="shell"><span class="sh" style="color: #d14;">\`configure' configures cluster 1.5<span class="idiff left right">7</span> to adapt to many kinds of systems.</span></span>
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1277
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<pre style="margin: 0;"> <span id="LC1277" class="line" lang="shell"></span>
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1278
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<pre style="margin: 0;"> <span id="LC1278" class="line" lang="shell"><span class="sh" style="color: #d14;">Usage: </span><span class="nv" style="color: teal;">$0</span><span class="sh" style="color: #d14;"> [OPTION]... [VAR=VALUE]...</span></span>
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<pre style="margin: 0;"> <span id="LC1279" class="line" lang="shell"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1343,7 +1343,7 @@ fi</td>
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1343
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<pre style="margin: 0;"> <span id="LC1343" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC1344" class="line" lang="shell"><span class="k" style="font-weight: 600;">if </span><span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: navy;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$ac_init_help</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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1345
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<pre style="margin: 0;"> <span id="LC1345" class="line" lang="shell"><span class="k" style="font-weight: 600;"> case</span> <span class="nv" style="color: teal;">$ac_init_help</span> <span class="k" style="font-weight: 600;">in</span></span>
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1346
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<pre style="margin: 0;">-<span id="LC1346" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>short <span class="p">|</span> recursive <span class="p">)</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Configuration of cluster 1.5<span class="idiff left right">6</span>:"</span><span class="p">;;</span></span>
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<pre style="margin: 0;">+<span id="LC1346" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>short <span class="p">|</span> recursive <span class="p">)</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Configuration of cluster 1.5<span class="idiff left right">7</span>:"</span><span class="p">;;</span></span>
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1347
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1347
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<pre style="margin: 0;"> <span id="LC1347" class="line" lang="shell"> <span class="k" style="font-weight: 600;">esac</span></span>
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1348
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1348
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<pre style="margin: 0;"> <span id="LC1348" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="sh" style="color: #d14;">\</span><span class="no" style="color: teal;">_ACEOF</span></span>
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1349
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<pre style="margin: 0;"> <span id="LC1349" class="line" lang="shell"></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">@@ -1440,7 +1440,7 @@ fi</td>
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<pre style="margin: 0;"> <span id="LC1440" class="line" lang="shell"><span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: navy;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$ac_init_help</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">exit</span> <span class="nv" style="color: teal;">$ac_status</span></span>
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<pre style="margin: 0;"> <span id="LC1441" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="nv" style="color: teal;">$ac_init_version</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC1442" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="sh" style="color: #d14;">\</span><span class="no" style="color: teal;">_ACEOF</span></span>
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<pre style="margin: 0;">-<span id="LC1443" class="line" lang="shell"><span class="sh" style="color: #d14;">cluster configure 1.5<span class="idiff left right">6</span></span></span>
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<pre style="margin: 0;">+<span id="LC1443" class="line" lang="shell"><span class="sh" style="color: #d14;">cluster configure 1.5<span class="idiff left right">7</span></span></span>
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<pre style="margin: 0;"> <span id="LC1444" class="line" lang="shell"><span class="sh" style="color: #d14;">generated by GNU Autoconf 2.69</span></span>
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<pre style="margin: 0;"> <span id="LC1445" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC1446" class="line" lang="shell"><span class="sh" style="color: #d14;">Copyright (C) 2012 Free Software Foundation, Inc.</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">@@ -1859,7 +1859,7 @@ cat >config.log <<_ACEOF</td>
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<pre style="margin: 0;"> <span id="LC1859" class="line" lang="shell"><span class="sh" style="color: #d14;">This file contains any messages produced by compilers while</span></span>
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<pre style="margin: 0;"> <span id="LC1860" class="line" lang="shell"><span class="sh" style="color: #d14;">running configure, to aid debugging if configure makes a mistake.</span></span>
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<pre style="margin: 0;"> <span id="LC1861" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC1862" class="line" lang="shell"><span class="sh" style="color: #d14;">It was created by cluster </span><span class="nv" style="color: teal;">$as_me</span><span class="sh" style="color: #d14;"> 1.5<span class="idiff left right">6</span>, which was</span></span>
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<pre style="margin: 0;">+<span id="LC1862" class="line" lang="shell"><span class="sh" style="color: #d14;">It was created by cluster </span><span class="nv" style="color: teal;">$as_me</span><span class="sh" style="color: #d14;"> 1.5<span class="idiff left right">7</span>, which was</span></span>
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<pre style="margin: 0;"> <span id="LC1863" class="line" lang="shell"><span class="sh" style="color: #d14;">generated by GNU Autoconf 2.69. Invocation command line was</span></span>
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<pre style="margin: 0;"> <span id="LC1864" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC1865" class="line" lang="shell"><span class="sh" style="color: #d14;"> </span><span class="nv" style="color: teal;">$ $0</span><span class="sh" style="color: #d14;"> </span><span class="nv" style="color: teal;">$@</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">@@ -2723,7 +2723,7 @@ fi</td>
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<pre style="margin: 0;"> <span id="LC2723" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC2724" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Define the identity of the package.</span></span>
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<pre style="margin: 0;"> <span id="LC2725" class="line" lang="shell"> <span class="nv" style="color: teal;">PACKAGE</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'cluster'</span></span>
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<pre style="margin: 0;">-<span id="LC2726" class="line" lang="shell"> <span class="nv" style="color: teal;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'1.5<span class="idiff left right">6</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC2726" class="line" lang="shell"> <span class="nv" style="color: teal;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'1.5<span class="idiff left right">7</span>'</span></span>
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<pre style="margin: 0;"> <span id="LC2727" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC2728" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC2729" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;">>></span>confdefs.h <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: teal;">_ACEOF</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6009" style="width: 35px; color: rgba(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">@@ -6009,7 +6009,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1</td>
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6009
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<pre style="margin: 0;"> <span id="LC6009" class="line" lang="shell"><span class="sh" style="color: #d14;"># report actual input values of CONFIG_FILES etc. instead of their</span></span>
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6010
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6010
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<pre style="margin: 0;"> <span id="LC6010" class="line" lang="shell"><span class="sh" style="color: #d14;"># values after options handling.</span></span>
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6011
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6011
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<pre style="margin: 0;"> <span id="LC6011" class="line" lang="shell"><span class="sh" style="color: #d14;">ac_log="</span></span>
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<pre style="margin: 0;">-<span id="LC6012" class="line" lang="shell"><span class="sh" style="color: #d14;">This file was extended by cluster </span><span class="nv" style="color: teal;">$as_me</span><span class="sh" style="color: #d14;"> 1.5<span class="idiff left right">6</span>, which was</span></span>
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<pre style="margin: 0;">+<span id="LC6012" class="line" lang="shell"><span class="sh" style="color: #d14;">This file was extended by cluster </span><span class="nv" style="color: teal;">$as_me</span><span class="sh" style="color: #d14;"> 1.5<span class="idiff left right">7</span>, which was</span></span>
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<pre style="margin: 0;"> <span id="LC6013" class="line" lang="shell"><span class="sh" style="color: #d14;">generated by GNU Autoconf 2.69. Invocation command line was</span></span>
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<pre style="margin: 0;"> <span id="LC6014" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC6015" class="line" lang="shell"><span class="sh" style="color: #d14;"> CONFIG_FILES = </span><span class="nv" style="color: teal;">$CONFIG_FILES</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">@@ -6075,7 +6075,7 @@ _ACEOF</td>
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6075
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<pre style="margin: 0;"> <span id="LC6075" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;">>></span><span class="nv" style="color: teal;">$CONFIG_STATUS</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: teal;">_ACEOF</span><span class="sh" style="color: #d14;"> || ac_write_fail=1</span></span>
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6076
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6076
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<pre style="margin: 0;"> <span id="LC6076" class="line" lang="shell"><span class="sh" style="color: #d14;">ac_cs_config="`</span><span class="nv" style="color: teal;">$as_echo</span><span class="sh" style="color: #d14;"> "</span><span class="nv" style="color: teal;">$ac_configure_args</span><span class="sh" style="color: #d14;">" | sed 's/^ //; s/[\\""\`\</span><span class="nv" style="color: teal;">$]</span><span class="sh" style="color: #d14;">/\\\\&/g'`"</span></span>
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6077
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<pre style="margin: 0;"> <span id="LC6077" class="line" lang="shell"><span class="sh" style="color: #d14;">ac_cs_version="\\</span></span>
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<pre style="margin: 0;">-<span id="LC6078" class="line" lang="shell"><span class="sh" style="color: #d14;">cluster config.status 1.5<span class="idiff left right">6</span></span></span>
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<pre style="margin: 0;">+<span id="LC6078" class="line" lang="shell"><span class="sh" style="color: #d14;">cluster config.status 1.5<span class="idiff left right">7</span></span></span>
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<pre style="margin: 0;"> <span id="LC6079" class="line" lang="shell"><span class="sh" style="color: #d14;">configured by </span><span class="nv" style="color: teal;">$0</span><span class="sh" style="color: #d14;">, generated by GNU Autoconf 2.69,</span></span>
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<pre style="margin: 0;"> <span id="LC6080" class="line" lang="shell"><span class="sh" style="color: #d14;"> with options \\"\</span><span class="nv" style="color: teal;">$ac_cs_config</span><span class="sh" style="color: #d14;">\\"</span></span>
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6081
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<pre style="margin: 0;"> <span id="LC6081" class="line" lang="shell"></span>
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<a href="https://salsa.debian.org/med-team/cluster3/commit/291de8a8e6299c799d2049f717568ab55fe72e9d#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</strong></a>
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<pre style="margin: 0;"> <span id="LC1" 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="LC2" class="line" lang="plaintext">AC_INIT(cluster, 1.5<span class="idiff left right">6</span>)</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">AC_INIT(cluster, 1.5<span class="idiff left right">7</span>)</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">AC_CONFIG_SRCDIR(src/cluster.c)</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">AM_INIT_AUTOMAKE</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">AC_CONFIG_HEADERS(config.h)</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">@@ -29,7 +29,7 @@</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="xml"> <span class="nt" style="color: navy;"><textFieldCell</span> <span class="na" style="color: teal;">key=</span><span class="s" style="color: #d14;">"cell"</span> <span class="na" style="color: teal;">sendsActionOnEndEditing=</span><span class="s" style="color: #d14;">"YES"</span> <span class="na" style="color: teal;">alignment=</span><span class="s" style="color: #d14;">"left"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"12"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="xml"> <span class="nt" style="color: navy;"><font</span> <span class="na" style="color: teal;">key=</span><span class="s" style="color: #d14;">"font"</span> <span class="na" style="color: teal;">metaFont=</span><span class="s" style="color: #d14;">"system"</span><span class="nt" style="color: navy;">/></span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="xml"> <span class="nt" style="color: navy;"><string</span> <span class="na" style="color: teal;">key=</span><span class="s" style="color: #d14;">"title"</span><span class="nt" style="color: navy;">></span>Cluster 3.0</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="xml">using the C Clustering Library version 1.5<span class="idiff left right">6</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="xml">using the C Clustering Library version 1.5<span class="idiff left right">7</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="xml"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="xml">Cluster was originally written by Michael Eisen (eisen 'AT' rana.lbl.gov).</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="xml">Copyright 1998-99 Stanford University.</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="p"><</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">k</span><span class="mh" style="color: #099;">e</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">y</span><span class="p">></span><span class="l">CFBundleSignature</span><span class="p"><</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">/k</span><span class="mh" style="color: #099;">e</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">y</span><span class="p">></span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="p"><</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">string</span><span class="p">></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">????</span><span class="p"><</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">/string</span><span class="p">></span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="p"><</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">k</span><span class="mh" style="color: #099;">e</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">y</span><span class="p">></span><span class="l">CFBundleVersion</span><span class="p"><</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">/k</span><span class="mh" style="color: #099;">e</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">y</span><span class="p">></span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="p"><</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">string</span><span class="p">></span><span class="l">C</span><span class="w" style="color: #bbb;"> </span><span class="l">Clustering</span><span class="w" style="color: #bbb;"> </span><span class="l">Library</span><span class="w" style="color: #bbb;"> </span><span class="l">1.5<span class="idiff left right">6</span></span><span class="p"><</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">/string</span><span class="p">></span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="p"><</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">string</span><span class="p">></span><span class="l">C</span><span class="w" style="color: #bbb;"> </span><span class="l">Clustering</span><span class="w" style="color: #bbb;"> </span><span class="l">Library</span><span class="w" style="color: #bbb;"> </span><span class="l">1.5<span class="idiff left right">7</span></span><span class="p"><</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">/string</span><span class="p">></span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="p"><</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">k</span><span class="mh" style="color: #099;">e</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">y</span><span class="p">></span><span class="l">NSMainNibFile</span><span class="p"><</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">/k</span><span class="mh" style="color: #099;">e</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">y</span><span class="p">></span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="p"><</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">string</span><span class="p">></span><span class="l">MainMenu</span><span class="p"><</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">/string</span><span class="p">></span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plist"><span class="w" style="color: #bbb;"> </span><span class="p"><</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">k</span><span class="mh" style="color: #099;">e</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">y</span><span class="p">></span><span class="l">NSPrincipalClass</span><span class="p"><</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">/k</span><span class="mh" style="color: #099;">e</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">y</span><span class="p">></span></span>
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<a href="https://salsa.debian.org/med-team/cluster3/commit/291de8a8e6299c799d2049f717568ab55fe72e9d#0a44e0614f23c2dd71257e5e32cb02e9a295dbfd"><strong>perl/Cluster.pm</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">@@ -32,7 +32,7 @@ use DynaLoader;</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="perl"><span class="nb" style="color: #0086b3;">require</span> <span class="nv" style="color: teal;">Exporter</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="perl"><span class="nv" style="color: teal;">$VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1.5<span class="idiff left right">6</span>'</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="perl"><span class="nv" style="color: teal;">$VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1.5<span class="idiff left right">7</span>'</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="perl"><span class="nv" style="color: teal;">$DEBUG</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="LC37" class="line" lang="perl"><span class="nv" style="color: teal;">@ISA</span> <span class="o" style="font-weight: 600;">=</span> <span class="sx" style="color: #d14;">qw(DynaLoader Exporter)</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="perl"></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">@@ -779,7 +779,7 @@ See the scripts in the examples subdirectory of the package.</td>
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<pre style="margin: 0;"> <span id="LC779" class="line" lang="perl"></span>
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780
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<pre style="margin: 0;"> <span id="LC780" class="line" lang="perl"><span class="s" style="color: #d14;">=over 4</span></span>
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<pre style="margin: 0;"> <span id="LC781" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC782" class="line" lang="perl"><span class="s" style="color: #d14;">=item * C Clustering Library version 1.5<span class="idiff left right">6 (2018.04.29</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="perl"><span class="s" style="color: #d14;">=item * C Clustering Library version 1.5<span class="idiff left right">7 (2018.11.22</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC783" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC784" class="line" lang="perl"><span class="s" style="color: #d14;">=head1 TO DO</span></span>
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<pre style="margin: 0;"> <span id="LC785" class="line" lang="perl"></span>
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<a href="https://salsa.debian.org/med-team/cluster3/commit/291de8a8e6299c799d2049f717568ab55fe72e9d#bb5afbfb42ef4ae77e927ad9a39bb8c7f6a27963"><strong>python/__init__.py</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">@@ -473,9 +473,14 @@ def distancematrix(data, mask=None, weight=None, transpose=False, dist='e'):</td>
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473
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="python"><span class="s" style="color: #d14;"> [4., 2., 6., 0.]</span></span>
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__check_data</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC476" class="line" lang="python"> <span class="n" style="color: #333;">mask</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__check_mask</span><span class="p">(</span><span class="n" style="color: #333;">mask</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;">shape</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC477" class="line" lang="python"> <span class="n" style="color: #333;">n</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;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">transpose</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC478" class="line" lang="python"> <span class="n" style="color: #333;">matrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">empty</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'d'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">)]</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="python"> <span class="n" style="color: #333;">shape</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;">shape</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="python"> <span class="n" style="color: #333;">mask</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__check_mask</span><span class="p">(</span><span class="n" style="color: #333;">mask</span><span class="p">,</span> <span class="n" style="color: #333;">shape</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">transpose</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="python"> <span class="n" style="color: #333;">ndata</span><span class="p">,</span> <span class="n" style="color: #333;">nitems</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">shape</span></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="python"> <span class="n" style="color: #333;">nitems</span><span class="p">,</span> <span class="n" style="color: #333;">ndata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">shape</span></span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="python"> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__check_weight</span><span class="p">(</span><span class="n" style="color: #333;">weight</span><span class="p">,</span> <span class="n" style="color: #333;">ndata</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="python"> <span class="n" style="color: #333;">matrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">empty</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'d'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">nitems</span><span class="p">)]</span></span>
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="python"> <span class="n" style="color: #333;">_cluster</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">distancematrix</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">mask</span><span class="p">,</span> <span class="n" style="color: #333;">weight</span><span class="p">,</span> <span class="n" style="color: #333;">transpose</span><span class="p">,</span> <span class="n" style="color: #333;">dist</span><span class="p">,</span> <span class="n" style="color: #333;">matrix</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">matrix</span></span>
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="python"></span>
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<li id="4da3d46fb2a93582b1b2d09328d2b529636f7d32">
<a href="https://salsa.debian.org/med-team/cluster3/commit/291de8a8e6299c799d2049f717568ab55fe72e9d#4da3d46fb2a93582b1b2d09328d2b529636f7d32"><strong>python/test/test_Cluster.py</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">@@ -1154,6 +1154,52 @@ class TestCluster(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC1154" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">clusterid</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">],</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1155" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">error</span><span class="p">,</span> <span class="mf" style="color: #099;">7.680</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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1156
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1156
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<pre style="margin: 0;"> <span id="LC1156" class="line" lang="python"></span>
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1157
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<pre style="margin: 0;">+<span id="LC1157" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># check if default weights can be used</span></span>
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1158
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<pre style="margin: 0;">+<span id="LC1158" class="line" lang="python"> <span class="n" style="color: #333;">matrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">distancematrix</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">mask</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">mask</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1159" 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">
1159
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<pre style="margin: 0;">+<span id="LC1159" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="mf" style="color: #099;">1.687</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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1160
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<pre style="margin: 0;">+<span id="LC1160" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="1161" 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">
1161
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<pre style="margin: 0;">+<span id="LC1161" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="mf" style="color: #099;">21.365</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1162" 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">
1162
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<pre style="margin: 0;">+<span id="LC1162" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="mf" style="color: #099;">38.560</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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1163
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<pre style="margin: 0;">+<span id="LC1163" class="line" lang="python"></span>
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1164
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<pre style="margin: 0;">+<span id="LC1164" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="mf" style="color: #099;">4.900</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1165" 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">
1165
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<pre style="margin: 0;">+<span id="LC1165" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="mf" style="color: #099;">7.793</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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1166
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<pre style="margin: 0;">+<span id="LC1166" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="mf" style="color: #099;">22.490</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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1167
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<pre style="margin: 0;">+<span id="LC1167" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="1168" 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">
1168
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<pre style="margin: 0;">+<span id="LC1168" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="mf" style="color: #099;">3.687</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1169" 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">
1169
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<pre style="margin: 0;">+<span id="LC1169" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="mf" style="color: #099;">6.367</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1170" 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">
1170
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<pre style="margin: 0;">+<span id="LC1170" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="mf" style="color: #099;">22.025</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1171" 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">
1171
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<pre style="margin: 0;">+<span id="LC1171" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="mf" style="color: #099;">0.087</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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1172
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<pre style="margin: 0;">+<span id="LC1172" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="1173" 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">
1173
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<pre style="margin: 0;">+<span id="LC1173" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="mf" style="color: #099;">0.040</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1174" 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">
1174
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<pre style="margin: 0;">+<span id="LC1174" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="mf" style="color: #099;">2.890</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1175" 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">
1175
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<pre style="margin: 0;">+<span id="LC1175" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="mf" style="color: #099;">34.810</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1176" 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">
1176
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<pre style="margin: 0;">+<span id="LC1176" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="mf" style="color: #099;">0.640</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1177" 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">
1177
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<pre style="margin: 0;">+<span id="LC1177" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">][</span><span class="mi" style="color: #099;">4</span><span class="p">],</span> <span class="mf" style="color: #099;">0.490</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1178" 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">
1178
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<pre style="margin: 0;">+<span id="LC1178" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="1179" 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">
1179
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<pre style="margin: 0;">+<span id="LC1179" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="mf" style="color: #099;">1.557</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1180" 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">
1180
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<pre style="margin: 0;">+<span id="LC1180" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="mf" style="color: #099;">0.990</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1181" 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">
1181
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<pre style="margin: 0;">+<span id="LC1181" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="mf" style="color: #099;">34.065</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1182" 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">
1182
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<pre style="margin: 0;">+<span id="LC1182" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="mf" style="color: #099;">3.937</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1183" 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">
1183
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<pre style="margin: 0;">+<span id="LC1183" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">][</span><span class="mi" style="color: #099;">4</span><span class="p">],</span> <span class="mf" style="color: #099;">3.017</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1184" 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">
1184
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<pre style="margin: 0;">+<span id="LC1184" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">][</span><span class="mi" style="color: #099;">5</span><span class="p">],</span> <span class="mf" style="color: #099;">3.610</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1185" 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">
1185
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<pre style="margin: 0;">+<span id="LC1185" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="1186" 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">
1186
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<pre style="margin: 0;">+<span id="LC1186" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="mf" style="color: #099;">14.005</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1187" 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">
1187
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<pre style="margin: 0;">+<span id="LC1187" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="mf" style="color: #099;">9.050</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1188" 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">
1188
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<pre style="margin: 0;">+<span id="LC1188" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="mf" style="color: #099;">65.610</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1189" 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">
1189
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<pre style="margin: 0;">+<span id="LC1189" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="mf" style="color: #099;">30.465</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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1190
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<pre style="margin: 0;">+<span id="LC1190" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">][</span><span class="mi" style="color: #099;">4</span><span class="p">],</span> <span class="mf" style="color: #099;">27.380</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1191" 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">
1191
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<pre style="margin: 0;">+<span id="LC1191" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">][</span><span class="mi" style="color: #099;">5</span><span class="p">],</span> <span class="mf" style="color: #099;">0.000</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1192" 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">
1192
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<pre style="margin: 0;">+<span id="LC1192" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">][</span><span class="mi" style="color: #099;">6</span><span class="p">],</span> <span class="mf" style="color: #099;">16.385</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1193" 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">
1193
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<pre style="margin: 0;">+<span id="LC1193" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="1194" 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">
1194
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<pre style="margin: 0;">+<span id="LC1194" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="mf" style="color: #099;">14.167</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1195" 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">
1195
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<pre style="margin: 0;">+<span id="LC1195" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="mf" style="color: #099;">25.553</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1196" 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">
1196
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<pre style="margin: 0;">+<span id="LC1196" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="mf" style="color: #099;">0.010</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1197" 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">
1197
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<pre style="margin: 0;">+<span id="LC1197" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="mf" style="color: #099;">17.187</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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1198
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<pre style="margin: 0;">+<span id="LC1198" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">4</span><span class="p">],</span> <span class="mf" style="color: #099;">16.380</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1199" 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">
1199
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<pre style="margin: 0;">+<span id="LC1199" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">5</span><span class="p">],</span> <span class="mf" style="color: #099;">33.640</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1200" 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">
1200
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<pre style="margin: 0;">+<span id="LC1200" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">6</span><span class="p">],</span> <span class="mf" style="color: #099;">22.497</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1201" 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">
1201
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<pre style="margin: 0;">+<span id="LC1201" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">][</span><span class="mi" style="color: #099;">7</span><span class="p">],</span> <span class="mf" style="color: #099;">36.745</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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1202
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<pre style="margin: 0;">+<span id="LC1202" class="line" lang="python"></span>
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1157
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<td class="diff-line-num new_line" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1203
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<pre style="margin: 0;"> <span id="LC1203" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_pca</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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1158
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<td class="diff-line-num new_line" data-linenumber="1204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1204
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<pre style="margin: 0;"> <span id="LC1204" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">TestCluster</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">module</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'Bio.Cluster'</span><span class="p">:</span></span>
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1159
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<td class="diff-line-num new_line" data-linenumber="1205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1205
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<pre style="margin: 0;"> <span id="LC1205" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Cluster</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">pca</span></span>
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<a href="https://salsa.debian.org/med-team/cluster3/commit/291de8a8e6299c799d2049f717568ab55fe72e9d#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="41" style="width: 35px; color: rgba(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">@@ -41,7 +41,7 @@ class test_Pycluster(Command):</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Pycluster"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"1.5<span class="idiff left right">6</span>"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"1.5<span class="idiff left right">7</span>"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"The C Clustering Library"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">author</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Michiel de Hoon"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">author_email</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"michiel.dehoon 'AT' riken.jp"</span><span class="p">,</span></span>
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<li id="cef7c3e0339a15adc388ac4a9747b77227826683">
<a href="https://salsa.debian.org/med-team/cluster3/commit/291de8a8e6299c799d2049f717568ab55fe72e9d#cef7c3e0339a15adc388ac4a9747b77227826683"><strong>src/cluster.c</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">@@ -2732,8 +2732,8 @@ number of clusters is larger than the number of elements being clustered,</td>
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2732
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<pre style="margin: 0;"> <span id="LC2732" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">npass</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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2733
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2733
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<pre style="margin: 0;"> <span id="LC2733" class="line" lang="c"> <span class="p">{</span> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">tclusterid</span><span class="p">);</span></span>
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2734
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2734
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<pre style="margin: 0;"> <span id="LC2734" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">mapping</span><span class="p">);</span></span>
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2735
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<pre style="margin: 0;">-<span id="LC2735" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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2736
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2735
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<pre style="margin: 0;"> <span id="LC2735" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC2736" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2737" class="line" lang="c"> <span class="p">}</span></span>
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2738
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<pre style="margin: 0;"> <span id="LC2738" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC2739" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'m'</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3859" style="width: 35px; color: rgba(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="3859" style="width: 35px; color: rgba(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">@@ -3859,6 +3859,7 @@ If a memory error occurs, treecluster returns NULL.</td>
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3859
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3859
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<pre style="margin: 0;"> <span id="LC3859" class="line" lang="c"> <span class="p">{</span> <span class="n" style="color: #333;">distmatrix</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;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">));</span></span>
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3860
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3860
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<pre style="margin: 0;"> <span id="LC3860" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">distmatrix</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="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="cm" style="color: #998; font-style: italic;">/* Not enough memory available */</span></span>
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3861
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3861
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<pre style="margin: 0;"> <span id="LC3861" class="line" lang="c"> <span class="p">{</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">distmatrix</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="LC3862" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">distmatrix</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC3863" 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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<pre style="margin: 0;"> <span id="LC3864" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC3865" class="line" lang="c"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/cluster3/commit/291de8a8e6299c799d2049f717568ab55fe72e9d#d0a709faa909252ae246c0d6c1212099d4cc6343"><strong>src/cluster.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">@@ -38,7 +38,7 @@</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># include <windows.h></span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define CLUSTERVERSION "1.5<span class="idiff left right">6</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define CLUSTERVERSION "1.5<span class="idiff left right">7</span>"</span></span>
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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="cm" style="color: #998; font-style: italic;">/* Chapter 2 */</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">clusterdistance</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nrows</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ncolumns</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">data</span><span class="p">,</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;">mask</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/cluster3/commit/291de8a8e6299c799d2049f717568ab55fe72e9d#ad9733d1a5d8c7c1d3a59b30ea7bfa6e2780f674"><strong>src/command.c</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">@@ -242,6 +242,7 @@ Hierarchical(char genemetric, char arraymetric, char method, char* jobname)</td>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="c"> <span class="p">{</span> <span class="n" style="color: #333;">ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HierarchicalCluster</span><span class="p">(</span><span class="n" style="color: #333;">outputfile</span><span class="p">,</span> <span class="n" style="color: #333;">genemetric</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC243" 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;">ok</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="c"> <span class="p">{</span> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: Failed to allocate sufficient memory for clustering</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">outputfile</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">@@ -255,6 +256,7 @@ Hierarchical(char genemetric, char arraymetric, char method, char* jobname)</td>
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="c"> <span class="p">{</span> <span class="n" style="color: #333;">ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HierarchicalCluster</span><span class="p">(</span><span class="n" style="color: #333;">outputfile</span><span class="p">,</span> <span class="n" style="color: #333;">arraymetric</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="p">);</span></span>
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256
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<td class="diff-line-num new_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
257
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<pre style="margin: 0;"> <span id="LC257" 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;">ok</span><span class="p">)</span></span>
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257
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258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="c"> <span class="p">{</span> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: Failed to allocate sufficient memory for clustering</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">);</span></span>
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258
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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259
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="c"> <span class="p">}</span></span>
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260
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">outputfile</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -339,10 +341,12 @@ static void KMeans(char genemetric, char arraymetric, int k, int r,</td>
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339
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341
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">NodeMap</span><span class="p">);</span></span>
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340
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342
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ok</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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341
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343
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="c"> <span class="p">{</span> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: Failed to allocate sufficient memory for clustering</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">);</span></span>
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342
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345
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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343
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346
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="c"> <span class="p">}</span></span>
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344
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347
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ok</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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345
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348
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="c"> <span class="p">{</span> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: Failed to allocate sufficient memory for saving file</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">);</span></span>
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346
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350
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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351
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="c"> <span class="p">}</span></span>
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348
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352
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="373" style="width: 35px; color: rgba(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="377" style="width: 35px; color: rgba(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">@@ -373,11 +377,11 @@ static void KMeans(char genemetric, char arraymetric, int k, int r,</td>
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373
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377
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="c"> <span class="p">}</span></span>
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374
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378
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="c"> <span class="p">}</span></span>
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375
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379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">genemetric</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">arraymetric</span><span class="p">)</span></span>
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376
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="c"> <span class="n" style="color: #333;">sprintf</span><span class="idiff left"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="p"><span class="idiff right">,</span></span><span class="s" style="color: #d14;">"%s_K_G%d_A%d.cdt"</span><span class="p">,</span> <span class="n" style="color: #333;">jobname</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="380" 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">
380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="c"> <span class="n" style="color: #333;">sprintf</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">"%s_K_G%d_A%d.cdt"</span><span class="p">,</span> <span class="n" style="color: #333;">jobname</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>
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377
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<td class="diff-line-num new_line" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">genemetric</span><span class="p">)</span></span>
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378
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="c"> <span class="n" style="color: #333;">sprintf</span><span class="idiff left"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="p"><span class="idiff right">,</span></span><span class="s" style="color: #d14;">"%s_K_G%d.cdt"</span><span class="p">,</span> <span class="n" style="color: #333;">jobname</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="382" 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">
382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="c"> <span class="n" style="color: #333;">sprintf</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">"%s_K_G%d.cdt"</span><span class="p">,</span> <span class="n" style="color: #333;">jobname</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>
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379
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<td class="diff-line-num new_line" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">arraymetric</span><span class="p">)</span></span>
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380
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="c"> <span class="n" style="color: #333;">sprintf</span><span class="idiff left"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="p"><span class="idiff right">,</span></span><span class="s" style="color: #d14;">"%s_K_A%d.cdt"</span><span class="p">,</span> <span class="n" style="color: #333;">jobname</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="384" 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">
384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="c"> <span class="n" style="color: #333;">sprintf</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">"%s_K_A%d.cdt"</span><span class="p">,</span> <span class="n" style="color: #333;">jobname</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>
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381
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Now write the data file */</span></span>
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382
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<td class="diff-line-num new_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
386
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="c"> <span class="n" style="color: #333;">outputfile</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="s" style="color: #d14;">"wt"</span><span class="p">);</span></span>
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383
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387
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<pre style="margin: 0;"> <span id="LC387" 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;">outputfile</span><span class="p">)</span> <span class="n" style="color: #333;">printf</span> <span class="p">(</span><span class="s" style="color: #d14;">"Failed to open output file %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;">filename</span><span class="p">);</span></span>
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