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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/megan-ce">Debian Med / megan-ce</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/megan-ce/-/commit/7b6b15aa9c22b523ca340fbaa012d252f1cfb171">7b6b15aa</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-01-10T17:39:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Don't build class needing unpackaged Contrasts dependency
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/megan-ce/-/commit/d653d7e9d4ef7aff3e1b66ee7bc3f203b1741be8">d653d7e9</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-01-10T17:41:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Using a replacement class for BCrypt
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/megan-ce/-/commit/8c9a491c0da78ddd763cf1707d18a8fda0f51378">8c9a491c</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-01-10T17:53:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Making the right method calls to sis-jhdf5 classes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/megan-ce/-/commit/8a62fa33c45added37c86cdc115d2d563fd7c93f">8a62fa33</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-01-10T18:10:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Setting myself as uploader
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/megan-ce/-/commit/f4b620fd57b5ce2c0687aba084e5ae7d4203a0a0">f4b620fd</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-01-10T18:11:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">The binary package is Architecture: all
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/megan-ce/-/commit/b3346e9588031988167ec7862803530129a2c67f">b3346e95</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-01-10T18:12:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Setting the right name for the built jar file in d/jlibs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/megan-ce/-/commit/3c8d5bf9740b3f3de345185ec386199b1fe0c630">3c8d5bf9</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-01-10T18:12:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating the manifest in d/manifest
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/megan-ce/-/commit/5b9bfca866260c7d554574d1b2b78564214a3e3d">5b9bfca8</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-01-10T18:14:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Setting Standards version to 4.6.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/megan-ce/-/commit/deaa513a94de3468a753ea1994b0d2c572e8d980">deaa513a</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-01-14T17:27:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding manpage
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/megan-ce/-/commit/a945597b88684b6db296f217fa0b5df196dc61ff">a945597b</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-01-14T17:28:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Providing an executable file to launch the jar of megan, setting the manifest consistently
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/megan-ce/-/commit/def5c3e38fed499579d0d051f5c6897af95ee35a">def5c3e3</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-01-14T17:28:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating the list of dependencies as needed
</pre>
</li>
</ul>
<h4>12 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#2f4ef18936ac3e079b9336fb8aec3e59442e655c">
<span class="new-file">
+
debian/bin/megan
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#c1c6e8d19f85cbe117af7f4626eacb7c3309cbcb">
debian/jlibs
</a>
</li>
<li class="file-stats">
<a href="#09661b26dadd0f6da66651a045417e1c81207c10">
debian/manifest
</a>
</li>
<li class="file-stats">
<a href="#911bf7cf0f233a3b606224b2d64e61a3cd1cd459">
<span class="new-file">
+
debian/manpages/megan.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#b79158473afc33ce0a70f27a67caaf86c2528f8b">
<span class="new-file">
+
debian/megan-ce.install
</span>
</a>
</li>
<li class="file-stats">
<a href="#1c4823842ff5821a225f8696e2d00eba99211edf">
<span class="new-file">
+
debian/megan-ce.manpages
</span>
</a>
</li>
<li class="file-stats">
<a href="#58096a22352a450bf0c15855466c9199a445adc7">
<span class="new-file">
+
debian/patches/BCrypt_replacement.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#4b3ce65a28eb2bbd5d873c6019e53a8a16884cdf">
<span class="new-file">
+
debian/patches/altering_calls_to_sis-jhdf5.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#8666ebcd61bca28421615be4803729b3e0c71c0e">
debian/patches/fix_class_path.patch
</a>
</li>
<li class="file-stats">
<a href="#b634a4a45a43e47f913e27f3cb3d6af45b75af4f">
<span class="new-file">
+
debian/patches/omit_ComputeContrastsCommand.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="2f4ef18936ac3e079b9336fb8aec3e59442e655c">
<a href="https://salsa.debian.org/med-team/megan-ce/-/compare/04602583e555ec51cd59259c58ad2fc13b942c22...def5c3e38fed499579d0d051f5c6897af95ee35a#2f4ef18936ac3e079b9336fb8aec3e59442e655c"><strong>debian/bin/megan</strong></a>
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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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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
</pre>
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<td class="new_line diff-line-num new" 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="shell"><span class="c" style="color: #998; font-style: italic;"># The upstream website recommends to launch megan by running 'ant run'.</span></span>
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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># We launch the software by calling java with the args in antbuild/build.xml.</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell">java <span class="nt" style="color: #000080;">-Xshare</span>:off <span class="nt" style="color: #000080;">-server</span> <span class="nt" style="color: #000080;">-Xmx4G</span> <span class="nt" style="color: #000080;">-Duser</span>.language<span class="o" style="font-weight: 600;">=</span>en <span class="nt" style="color: #000080;">-Duser</span>.region<span class="o" style="font-weight: 600;">=</span>US <span class="nt" style="color: #000080;">-jar</span> /usr/share/java/megan.jar <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/megan-ce/-/compare/04602583e555ec51cd59259c58ad2fc13b942c22...def5c3e38fed499579d0d051f5c6897af95ee35a#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: megan-ce</span>
</pre>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org>,</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Pierre Gruet <pgt@debian.org></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</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">@@ -12,18 +13,25 @@ Build-Depends: debhelper-compat (= 13),</td>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> libcommons-math3-java,</span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libjama-java,</span>
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14
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> libgoogle-gson-java,</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> libjbcrypt-java,</span>
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15
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> libopenjfx-java,</span>
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16
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> libsis-jhdf5-java,</span>
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17
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> libxerial-sqlite-jdbc-java</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.4</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">6.0</span></span>
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19
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/megan-ce</span>
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20
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/megan-ce.git</span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Homepage: https://github.com/danielhuson/megan-ce</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Package: megan-ce</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">Architecture: any</span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">Depends: ${java:Depends},</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Depends: default-jre,</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> ${java:Depends},</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> libjloda-java,</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> libjbcrypt-java,</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> libopenjfx-java,</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> libsis-jhdf5-java,</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> libxerial-sqlite-jdbc-java,</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">Description: MEGAN Community Edition</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> MEGAN Community Edition - Interactive exploration and analysis of large-</span>
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<a href="https://salsa.debian.org/med-team/megan-ce/-/compare/04602583e555ec51cd59259c58ad2fc13b942c22...def5c3e38fed499579d0d051f5c6897af95ee35a#c1c6e8d19f85cbe117af7f4626eacb7c3309cbcb"><strong>debian/jlibs</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">antbuild/megan<span class="idiff left right">-ce</span>.jar</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">antbuild/megan.jar</span></pre>
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<a href="https://salsa.debian.org/med-team/megan-ce/-/compare/04602583e555ec51cd59259c58ad2fc13b942c22...def5c3e38fed499579d0d051f5c6897af95ee35a#09661b26dadd0f6da66651a045417e1c81207c10"><strong>debian/manifest</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">/usr/share/java/megan<span class="idiff left right">-ce</span>.jar:</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> Main-Class: megan<span class="idiff left">-ce</span>.Megan<span class="idiff right">Run</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> Class-Path: /usr/share/java/<span class="idiff left">jloda</span>.jar /usr/share/java/co<span class="idiff">lt</span>.jar /usr/share/java/<span class="idiff">commons-codec</span>.jar /usr/share/java/<span class="idiff">commons-math3</span>.jar /usr/share/java/<span class="idiff">gson</span>.jar /usr/share/java/<span class="idiff">openjfx/jre/lib/ext/jfxr</span>t.jar /usr/share/java/j<span class="idiff">am</span>a.jar /usr/share/java/s<span class="idiff">pring3-web</span>.jar /usr/share/java/<span class="idiff right">controlsfx</span>.jar</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">/usr/share/java/megan.jar:</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> Main-Class: megan<span class="idiff left">.main</span>.Megan<span class="idiff right">6</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Class-Path: /usr/share/java/<span class="idiff left">colt</span>.jar /usr/share/java/co<span class="idiff">mmons-math3</span>.jar /usr/share/java/<span class="idiff">gson.jar /usr/share/java/jama.jar /usr/share/java/javafx-base</span>.jar<span class="idiff">"</span> /usr/share/java/<span class="idiff">javafx-controls.jar /usr/share/java/javafx-fxml</span>.jar /usr/share/java/<span class="idiff">javafx-graphics</span>.jar /usr/share/java/<span class="idiff">javafx-swing.jar /usr/share/java/jbcryp</span>t.jar /usr/share/java/j<span class="idiff">lod</span>a.jar /usr/share/java/s<span class="idiff">is-jhdf5</span>.jar /usr/share/java/<span class="idiff right">xerial-sqlite-jdbc</span>.jar</span></pre>
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<a href="https://salsa.debian.org/med-team/megan-ce/-/compare/04602583e555ec51cd59259c58ad2fc13b942c22...def5c3e38fed499579d0d051f5c6897af95ee35a#911bf7cf0f233a3b606224b2d64e61a3cd1cd459"><strong>debian/manpages/megan.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH MEGAN 1 "January 2022"</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">megan \- Interactive explorer and analyzer of microbiome sequencing data</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.B megan</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.RI [ options ]</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.SH OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.BR \-f, \-\-files \fIfile\fR...</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">MEGAN RMA file(s) to open</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.TP</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.BR \-p, \-\-propertiesFile \fIfile\fR</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Properties file</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.TP</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.BR +w, \-\-hideMessageWindow</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Hide message window</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.TP</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.BR \-S, \-\-silentMode</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Silent mode</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.BR \-d, \-\-debug</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Debug mode</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.SH SEE ALSO</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/megan6</span></pre>
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<a href="https://salsa.debian.org/med-team/megan-ce/-/compare/04602583e555ec51cd59259c58ad2fc13b942c22...def5c3e38fed499579d0d051f5c6897af95ee35a#b79158473afc33ce0a70f27a67caaf86c2528f8b"><strong>debian/megan-ce.install</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="n" style="color: #333;">debian</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bin</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">megan</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bin</span></span></pre>
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<a href="https://salsa.debian.org/med-team/megan-ce/-/compare/04602583e555ec51cd59259c58ad2fc13b942c22...def5c3e38fed499579d0d051f5c6897af95ee35a#1c4823842ff5821a225f8696e2d00eba99211edf"><strong>debian/megan-ce.manpages</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/manpages/megan.1</span></pre>
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<li id="58096a22352a450bf0c15855466c9199a445adc7">
<a href="https://salsa.debian.org/med-team/megan-ce/-/compare/04602583e555ec51cd59259c58ad2fc13b942c22...def5c3e38fed499579d0d051f5c6897af95ee35a#58096a22352a450bf0c15855466c9199a445adc7"><strong>debian/patches/BCrypt_replacement.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: using a replacement BCrypt implementation, which is Debian-packaged</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2022-01-08</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/src/megan/ms/Utilities.java</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/megan/ms/Utilities.java</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -20,8 +20,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> package megan.ms;</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import at.favre.lib.crypto.bcrypt.BCrypt;</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import jloda.util.Basic;</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+//import at.favre.lib.crypto.bcrypt.BCrypt;</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.mindrot.jbcrypt.BCrypt;</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+//import jloda.util.Basic;</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> import megan.daa.connector.ClassificationBlockDAA;</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> import megan.daa.io.ByteInputStream;</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> import megan.daa.io.ByteOutputStream;</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="p">@@ -124,10 +125,12 @@</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> public static String computeBCryptHash(byte[] password) {</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return Basic.toString(BCrypt.withDefaults().hash(6, SALT, password));</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ //return Basic.toString(BCrypt.withDefaults().hash(6, SALT, password));</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return BCrypt.hashpw(new String(password), BCrypt.gensalt(6));</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> public static boolean verify (char[] password,String bcryptHash) {</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return BCrypt.verifyer().verify(password,bcryptHash).verified;</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ //return BCrypt.verifyer().verify(password,bcryptHash).verified;</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return BCrypt.checkpw(new String(password), bcryptHash);</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> }</span></pre>
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<a href="https://salsa.debian.org/med-team/megan-ce/-/compare/04602583e555ec51cd59259c58ad2fc13b942c22...def5c3e38fed499579d0d051f5c6897af95ee35a#4b3ce65a28eb2bbd5d873c6019e53a8a16884cdf"><strong>debian/patches/altering_calls_to_sis-jhdf5.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: rewriting some calls to classes of sis-jhdf5</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> Many times methods are called, which are not in the class of the object they</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> are applied to. We implement the right calls.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Last-Update: 2022-01-09</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff">--- a/src/megan/biom/biom2/Biom2ParserTest.java</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/megan/biom/biom2/Biom2ParserTest.java</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">@@ -73,7 +73,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> classifications.add(taxonomyNameMetadata);</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> // System.err.println("Elements: " + reader.getDataSetInformation("/observation/metadata/"+taxonomyNameMetadata).getNumberOfElements());</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final MDArray<String> array = reader.readStringMDArray("/observation/metadata/" + taxonomyNameMetadata);</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final MDArray<String> array = reader.string().readMDArray("/observation/metadata/" + taxonomyNameMetadata);</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> /*</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> int[] dimensions = array.dimensions();</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> if (dimensions.length == 2) {</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/megan/biom/biom2/ImportBiom2Taxonomy.java</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/megan/biom/biom2/ImportBiom2Taxonomy.java</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="p">@@ -48,7 +48,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> for (final String metaKey : reader.getGroupMembers("/observation/metadata")) {</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> if (Basic.getIndexIgnoreCase(metaKey, keys) != -1) {</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pathArray = reader.readStringMDArray("/observation/metadata/" + metaKey);</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pathArray = reader.string().readMDArray("/observation/metadata/" + metaKey);</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> dimensions = pathArray.dimensions();</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> if (dimensions != null && dimensions.length > 0)</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> break;</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="p">@@ -111,7 +111,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> public static boolean hasTaxonomyMetadata(IHDF5Reader reader) {</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> for (final String metaKey : reader.getGroupMembers("/observation/metadata")) {</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> if (Basic.getIndexIgnoreCase(metaKey, keys) != -1) {</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final MDArray<String> pathArray = reader.readStringMDArray("/observation/metadata/" + metaKey);</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final MDArray<String> pathArray = reader.string().readMDArray("/observation/metadata/" + metaKey);</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> final int[] dimensions = pathArray.dimensions();</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> if (dimensions != null && dimensions.length > 0)</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> return true;</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/megan/biom/biom2/TopLevelAttributes.java</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/megan/biom/biom2/TopLevelAttributes.java</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="p">@@ -93,14 +93,14 @@</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> private void read(IHDF5Reader reader) throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> try {</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- id = reader.getStringAttribute("/", "id");</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- type = reader.getStringAttribute("/", "type");</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- formatURL = reader.getStringAttribute("/", "format-url");</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- formatVersion = reader.getIntArrayAttribute("/", "format-version");</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- generatedBy = reader.getStringAttribute("/", "generated-by");</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- creationDate = reader.getStringAttribute("/", "creation-date");</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- shape = reader.getIntArrayAttribute("/", "shape");</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- nnz = reader.getIntAttribute("/", "nnz");</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ id = reader.string().getAttr("/", "id");</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ type = reader.string().getAttr("/", "type");</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ formatURL = reader.string().getAttr("/", "format-url");</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ formatVersion = reader.int32().getArrayAttr("/", "format-version");</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ generatedBy = reader.string().getAttr("/", "generated-by");</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ creationDate = reader.string().getAttr("/", "creation-date");</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ shape = reader.int32().getArrayAttr("/", "shape");</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ nnz = reader.int32().getAttr("/", "nnz");</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> } catch (Exception ex) {</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> System.err.println("BIOM2 parser: Some required top-level attribute(s) missing.");</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> throw new IOException(ex);</span></pre>
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<li id="8666ebcd61bca28421615be4803729b3e0c71c0e">
<a href="https://salsa.debian.org/med-team/megan-ce/-/compare/04602583e555ec51cd59259c58ad2fc13b942c22...def5c3e38fed499579d0d051f5c6897af95ee35a#8666ebcd61bca28421615be4803729b3e0c71c0e"><strong>debian/patches/fix_class_path.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,7 @@ Last-Update: 2022-01-08</td>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Description: setting paths of Debian jars used during the build</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/antbuild/build.xml</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/antbuild/build.xml</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="p">@@ -22,22 +22,<span class="idiff left right">29</span> @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -22,22 +22,<span class="idiff left right">30</span> @@</span></span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> <property name="ant.build.javac.target" value="13"/>--></span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> </span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> <property name="jfxDir" value="../../javafx/lib"/></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" style="width: 35px; color: rgba(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="22" style="width: 35px; color: rgba(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">@@ -22,6 +22,7 @@ Description: setting paths of Debian jars used during the build</td>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <fileset dir="/usr/share/java/" includes="javafx-fxml.jar"/></span></span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <fileset dir="/usr/share/java/" includes="javafx-graphics.jar"/></span></span>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <fileset dir="/usr/share/java/" includes="javafx-swing.jar"/></span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <fileset dir="/usr/share/java/" includes="jbcrypt.jar"/></span></span>
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <fileset dir="/usr/share/java/" includes="jloda.jar"/></span></span>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <fileset dir="/usr/share/java/" includes="sis-jhdf5.jar"/></span></span>
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <fileset dir="/usr/share/java/" includes="xerial-sqlite-jdbc.jar"/></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -38,7 +39,7 @@ Description: setting paths of Debian jars used during the build</td>
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38
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"> <fileset dir="../antbuild" includes="megan.jar"/></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="diff"> </path></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"><span class="p">@@ -48,10 +5<span class="idiff left right">5</span>,6 @@</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="p">@@ -48,10 +5<span class="idiff left right">6</span>,6 @@</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"> <mkdir dir="${buildModulesDir}/megan"/></span>
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43
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"> </target></span>
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44
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="49" style="width: 35px; color: rgba(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="50" style="width: 35px; color: rgba(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">@@ -49,7 +50,7 @@ Description: setting paths of Debian jars used during the build</td>
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49
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> <target name="copy_sources" depends="init"></span>
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50
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"> <copy todir="${buildSrcDir}/megan"></span>
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51
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"> <fileset dir="../src"/></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"><span class="p">@@ -98,7 +10<span class="idiff left right">1</span>,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="p">@@ -98,7 +10<span class="idiff left right">2</span>,6 @@</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"> <delete dir="${buildModulesDir}" includeEmptyDirs="true"/></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"> <delete dir="${buildSrcDir}" includeEmptyDirs="true"/></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> <delete file="megan.jar"/></span>
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<li id="b634a4a45a43e47f913e27f3cb3d6af45b75af4f">
<a href="https://salsa.debian.org/med-team/megan-ce/-/compare/04602583e555ec51cd59259c58ad2fc13b942c22...def5c3e38fed499579d0d051f5c6897af95ee35a#b634a4a45a43e47f913e27f3cb3d6af45b75af4f"><strong>debian/patches/omit_ComputeContrastsCommand.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: omitting a class, as its dependency Contrasts is not packaged</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2022-01-08</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/src/megan/groups/commands/ComputeContrastsCommand.java</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ /dev/null</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -1,195 +0,0 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-/*</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * ComputeContrastsCommand.java Copyright (C) 2020. Daniel H. Huson</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- *</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * (Some files contain contributions from other authors, who are then mentioned separately.)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- *</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * This program is free software: you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * it under the terms of the GNU General Public License as published by</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * the Free Software Foundation, either version 3 of the License, or</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * (at your option) any later version.</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- *</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * This program is distributed in the hope that it will be useful,</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * GNU General Public License for more details.</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- *</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * You should have received a copy of the GNU General Public License</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * along with this program. If not, see <http://www.gnu.org/licenses/>.</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- *</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- */</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-package megan.groups.commands;</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import contrasts.Contrasts;</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import jloda.graph.Graph;</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import jloda.graph.Node;</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import jloda.graph.NodeData;</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import jloda.swing.commands.CommandBase;</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import jloda.swing.commands.ICommand;</span></span>
</pre>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import jloda.util.Basic;</span></span>
</pre>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import jloda.util.Pair;</span></span>
</pre>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import jloda.util.ProgramProperties;</span></span>
</pre>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import jloda.util.parse.NexusStreamParser;</span></span>
</pre>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import megan.classification.Classification;</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import megan.classification.ClassificationManager;</span></span>
</pre>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import megan.core.Director;</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import megan.core.Document;</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import megan.data.IName2IdMap;</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import megan.groups.GroupsViewer;</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import megan.viewer.ClassificationViewer;</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import javax.swing.*;</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import java.awt.*;</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import java.awt.event.ActionEvent;</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import java.awt.event.KeyEvent;</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import java.util.List;</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import java.util.*;</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-/**</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * * compute contrasts command</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * * Daniel Huson, 8.2014</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- */</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-public class ComputeContrastsCommand extends CommandBase implements ICommand {</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public String getSyntax() {</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return "compute contrasts data={" + Basic.toString(ClassificationManager.getAllSupportedClassifications(), ",") + "}";</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- /**</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * parses the given command and executes it</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- *</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * @param np</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * @throws java.io.IOException</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- */</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @Override</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void apply(NexusStreamParser np) throws Exception {</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- np.matchIgnoreCase("compute contrasts data=");</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final String viewerName = np.getWordMatchesIgnoringCase(Basic.toString(ClassificationManager.getAllSupportedClassifications(), " "));</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- np.matchIgnoreCase(";");</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (getViewer() instanceof GroupsViewer) {</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final GroupsViewer viewer = (GroupsViewer) getViewer();</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final Document doc = viewer.getDir().getDocument();</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final Pair<String, String> twoGroupIds = viewer.getGroupsPanel().getTwoSelectedGroups();</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (twoGroupIds != null) {</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ArrayList<String> first = new ArrayList<>();</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (String sample : doc.getSampleNames()) {</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (doc.getSampleAttributeTable().getGroupId(sample).equals(twoGroupIds.getFirst()))</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- first.add(sample);</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ArrayList<String> second = new ArrayList<>();</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (String sample : doc.getSampleNames()) {</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (doc.getSampleAttributeTable().getGroupId(sample).equals(twoGroupIds.getSecond()))</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- second.add(sample);</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final String[] samples = doc.getSampleNamesAsArray();</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (first.size() > 0 && second.size() > 0) {</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- // compute data map for contrasts:</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Map<String, Map<String, Double>> data = new HashMap<>();</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- int numberOfNodes = 0;</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final IName2IdMap name2IdMap;</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final ClassificationViewer classificationViewer = (ClassificationViewer) ((Director) getDir()).getViewerByClassName(viewerName);</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final Graph graph = classificationViewer.getGraph();</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- name2IdMap = classificationViewer.getClassification().getName2IdMap();</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (Node v = graph.getFirstNode(); v != null; v = graph.getNextNode(v)) {</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- int classId = (Integer) v.getInfo();</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (classId > 0) {</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- NodeData nd = (NodeData) v.getData();</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (int t = 0; t < samples.length; t++) {</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String sample = samples[t];</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Map<String, Double> classId2Counts = data.computeIfAbsent(sample, k -> new HashMap<>());</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- classId2Counts.put(name2IdMap.get(classId), (double) (v.getOutDegree() > 0 ? nd.getAssigned()[t] : nd.getSummarized()[t]));</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- numberOfNodes++;</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final Contrasts contrasts = new Contrasts();</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- try {</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Basic.hideSystemErr();</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- contrasts.apply(data);</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- } finally {</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Basic.restoreSystemErr();</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- executeImmediately("show window=message;");</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- System.out.println("\nContrasts for " + viewerName + " assignments on " + numberOfNodes + " nodes:");</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- System.out.println("Group " + twoGroupIds.getFirst() + ": " + Basic.toString(first, ","));</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- System.out.println("Group " + twoGroupIds.getSecond() + ": " + Basic.toString(second, ","));</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- System.out.println("Results for group " + twoGroupIds.getFirst() + " vs group " + twoGroupIds.getSecond() + ":");</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Map<String, Double> results = contrasts.getSplitScores(first.toArray(new String[0]), second.toArray(new String[0]));</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SortedSet<Pair<Double, String>> sorted = new TreeSet<>();</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- System.out.println(String.format("%-20s\tScore", viewerName));</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (String taxon : results.keySet()) {</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- double value = results.get(taxon); // clamp to range -1 1</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (value < -1)</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- value = -1;</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else if (value > 1)</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- value = 1;</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sorted.add(new Pair<>(-value, taxon)); // negative sign to sort from high to low...</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- System.out.println("Number of results: " + sorted.size());</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- System.out.println("--------------------------------------");</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (Pair<Double, String> pair : sorted) {</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if ((-pair.getFirst()) >= 0)</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- System.out.println(String.format("%-20s\t %1.4f", pair.getSecond(), (-pair.getFirst())));</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- System.out.println(String.format("%-20s\t%1.4f", pair.getSecond(), (-pair.getFirst())));</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- System.out.println("--------------------------------------");</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- viewer.setIgnoreNextUpdateAll(true); // this prevents loss of selection</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void actionPerformed(ActionEvent event) {</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- List<String> openViewers = new ArrayList<>();</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (String name : ClassificationManager.getAllSupportedClassifications()) {</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (((Director) getDir()).getViewerByClassName(name) != null)</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- openViewers.add(name);</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (!openViewers.contains(Classification.Taxonomy))</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- openViewers.add(Classification.Taxonomy);</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (openViewers.size() == 1) {</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- execute("compute contrasts data=" + openViewers.get(0) + ";");</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- } else if (openViewers.size() > 1) {</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String[] choices = openViewers.toArray(new String[0]);</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String result = (String) JOptionPane.showInputDialog(getViewer().getFrame(), "Choose viewer", "Choose viewer", JOptionPane.PLAIN_MESSAGE, ProgramProperties.getProgramIcon(), choices, choices[0]);</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (result != null)</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- execute("compute contrasts data=" + result + ";");</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public boolean isApplicable() {</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return (getViewer() instanceof GroupsViewer) && (((GroupsViewer) getViewer()).getGroupsPanel().getTwoSelectedGroups() != null);</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public String getName() {</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return "Compute Contrasts...";</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public String getDescription() {</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return "Computes contrasts on two selected groups";</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public ImageIcon getIcon() {</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return null;</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public boolean isCritical() {</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return true;</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public KeyStroke getAcceleratorKey() {</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx());</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/megan-ce/-/compare/04602583e555ec51cd59259c58ad2fc13b942c22...def5c3e38fed499579d0d051f5c6897af95ee35a#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,3 +2,6 @@ build.patch</td>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">fix_class_path.patch</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">do_not_check_for_update.patch</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">no_module_info.patch</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">omit_ComputeContrastsCommand.patch</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">BCrypt_replacement.patch</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">altering_calls_to_sis-jhdf5.patch</span></pre>
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