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<h3>
Fabian Klötzl pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/figtree">Debian Med / figtree</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/figtree/commit/1819d7fa6f5aa74cb98c5ffa9be49505747a8f43">1819d7fa</a></strong>
<div>
<span>by Fabian Klötzl</span>
<i>at 2018-11-26T10:59:24Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.4.4</pre>
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<h4>14 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
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<li class="file-stats">
<a href="#bdc348bf75801c527f51cdeddc8edf027f7ef35a">
build.xml
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</li>
<li class="file-stats">
<a href="#9b1c57d655988fad9c569224abf94a44918fc467">
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+
doc/large_trees.md
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doc/shot1.png
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<li class="file-stats">
<a href="#aba10940eee7eba71a4376238006efb13bca1254">
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doc/shot2.png
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doc/shot3.png
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doc/shot4.png
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<a href="#e5e53e9a8b37ae5b597bd592de3451d7e71e9764">
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doc/shot5.png
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<a href="#9eca2e5bda2bd08effda108f1f6e7fedf6645fe7">
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−
lib/libquaqua64.dylib
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<li class="file-stats">
<a href="#4145536af19c61a3e73bf8c5f34a4b8f79fe2495">
release/Linux/scripts/figtree
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<li class="file-stats">
<a href="#7e30cd195ade384b348e0ce5a6e6d5f8994a2a26">
release/common/README.txt
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<li class="file-stats">
<a href="#9f7588c31a910e9bf63cbc6fb1f0d65d4d3abc75">
src/figtree/application/FigTreeApplication.java
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<a href="#05bc8dcd255d6aafcb4c19f8d927d01f0da79449">
src/figtree/treeviewer/TreePane.java
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<li class="file-stats">
<a href="#36719ec578b4d9f9fa23aeec997399ee0accb7e8">
src/figtree/treeviewer/painters/LabelPainter.java
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</li>
</ul>
<h4>Changes:</h4>
<li id="a5cc2925ca8258af241be7e5b0381edf30266302">
<a href="https://salsa.debian.org/med-team/figtree/commit/1819d7fa6f5aa74cb98c5ffa9be49505747a8f43#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,3 +7,4 @@ out/*</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">FigTree*</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">tests/*</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">examples/*</span>
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<td class="diff-line-num new new_line" data-linenumber="10" 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="LC10" class="line" lang="plaintext">.DS_Store</span></pre>
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<li id="bdc348bf75801c527f51cdeddc8edf027f7ef35a">
<a href="https://salsa.debian.org/med-team/figtree/commit/1819d7fa6f5aa74cb98c5ffa9be49505747a8f43#bdc348bf75801c527f51cdeddc8edf027f7ef35a"><strong>build.xml</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -102,8 +102,8 @@</td>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="xml"></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="xml"> <span class="nt" style="color: navy;"></target></span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="xml"></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="xml"> <span class="nt" style="color: navy;"><property</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"version"</span> <span class="na" style="color: teal;">value=</span><span class="s" style="color: #d14;">"1.4.<span class="idiff left right">3</span>"</span> <span class="nt" style="color: navy;">/></span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="xml"> <span class="nt" style="color: navy;"><property</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"version_number"</span> <span class="na" style="color: teal;">value=</span><span class="s" style="color: #d14;">"1.4.<span class="idiff left right">3</span>"</span> <span class="nt" style="color: navy;">/></span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" 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="LC105" class="line" lang="xml"> <span class="nt" style="color: navy;"><property</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"version"</span> <span class="na" style="color: teal;">value=</span><span class="s" style="color: #d14;">"1.4.<span class="idiff left right">4</span>"</span> <span class="nt" style="color: navy;">/></span></span>
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<td class="diff-line-num new new_line" data-linenumber="106" 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="LC106" class="line" lang="xml"> <span class="nt" style="color: navy;"><property</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"version_number"</span> <span class="na" style="color: teal;">value=</span><span class="s" style="color: #d14;">"1.4.<span class="idiff left right">4</span>"</span> <span class="nt" style="color: navy;">/></span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="xml"> <span class="nt" style="color: navy;"><property</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"release_dir"</span> <span class="na" style="color: teal;">value=</span><span class="s" style="color: #d14;">"release"</span> <span class="nt" style="color: navy;">/></span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="xml"> <span class="nt" style="color: navy;"><property</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"name"</span> <span class="na" style="color: teal;">value=</span><span class="s" style="color: #d14;">"FigTree"</span> <span class="nt" style="color: navy;">/></span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- Create the release directory --></span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="xml"> <span class="nt" style="color: navy;"><mkdir</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${Windows_package_dir}"</span> <span class="nt" style="color: navy;">/></span></span>
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128
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="xml"></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="xml"> <span class="nt" style="color: navy;"><property</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"launch4j.dir"</span> <span class="na" style="color: teal;">location=</span><span class="s" style="color: #d14;">"./launch4j"</span> <span class="nt" style="color: navy;">/></span></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="xml"></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="xml"> <span class="nt" style="color: navy;"><property</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"launch4j.dir"</span> <span class="na" style="color: teal;">location=</span><span class="s" style="color: #d14;">"${packaging_tools}/windows/launch4j"</span> <span class="nt" style="color: navy;">/></span></span>
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131
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="xml"> <span class="nt" style="color: navy;"><taskdef</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"launch4j"</span> <span class="na" style="color: teal;">classname=</span><span class="s" style="color: #d14;">"net.sf.launch4j.ant.Launch4jTask"</span></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="xml"> <span class="na" style="color: teal;">classpath=</span><span class="s" style="color: #d14;">"${launch4j.dir}/launch4j.jar :${launch4j.dir}/lib/xstream.jar"</span><span class="idiff left right"> </span><span class="nt" style="color: navy;">/></span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="xml"> <span class="na" style="color: teal;">classpath=</span><span class="s" style="color: #d14;">"${launch4j.dir}/launch4j.jar :${launch4j.dir}/lib/xstream.jar"</span><span class="nt" style="color: navy;">/></span></span>
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133
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="xml"></span>
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134
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="xml"> <span class="nt" style="color: navy;"><copy</span> <span class="na" style="color: teal;">file=</span><span class="s" style="color: #d14;">"${dist}/figtree.jar"</span> <span class="na" style="color: teal;">todir=</span><span class="s" style="color: #d14;">"${Windows_package_dir}/lib"</span><span class="nt" style="color: navy;">/></span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!--</span></span>
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136
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="xml"> <span class="nt" style="color: navy;"><copy</span> <span class="na" style="color: teal;">todir=</span><span class="s" style="color: #d14;">"${Windows_package_dir}/lib"</span><span class="nt" style="color: navy;">></span></span>
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137
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="xml"> <span class="nt" style="color: navy;"><fileset</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${Windows_dir}/lib"</span><span class="nt" style="color: navy;">/></span></span>
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138
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="xml"> <span class="nt" style="color: navy;"></copy></span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right"> --></span></span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="xml"></span>
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140
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="xml"> <span class="nt" style="color: navy;"><copy</span> <span class="na" style="color: teal;">todir=</span><span class="s" style="color: #d14;">"${Windows_package_dir}"</span><span class="nt" style="color: navy;">></span></span>
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141
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="xml"> <span class="nt" style="color: navy;"><fileset</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${common_dir}/"</span><span class="nt" style="color: navy;">/></span></span>
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142
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="xml"> <span class="nt" style="color: navy;"></copy></span></span>
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143
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="xml"></span>
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144
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="xml"> <span class="nt" style="color: navy;"><launch4j</span> <span class="na" style="color: teal;">configFile=</span><span class="s" style="color: #d14;">"${Windows_dir}/FigTree_launch4j.xml"</span></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="xml"> <span class="na" style="color: teal;">jar=</span><span class="s" style="color: #d14;">"${dist}/figtree.jar"</span></span>
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146
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="xml"> <span class="na" style="color: teal;">outfile=</span><span class="s" style="color: #d14;">"${Windows_package_dir}/${name} v${version}.exe"</span></span>
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147
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="xml"> <span class="na" style="color: teal;">fileVersion=</span><span class="s" style="color: #d14;">"${version_number}.0"</span></span>
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148
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="xml"> <span class="na" style="color: teal;">txtFileVersion=</span><span class="s" style="color: #d14;">"${version}"</span></span>
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149
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="xml"> <span class="na" style="color: teal;">productVersion=</span><span class="s" style="color: #d14;">"${version_number}.0"</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="xml"> <span class="na" style="color: teal;">txtProductVersion=</span><span class="s" style="color: #d14;">"${version}"</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="xml"> <span class="nt" style="color: navy;">/></span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="xml"> <span class="na" style="color: teal;">txtProductVersion=</span><span class="s" style="color: #d14;">"${version}"</span><span class="nt" style="color: navy;">/></span></span>
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152
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="xml"></span>
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153
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="xml"> <span class="nt" style="color: navy;"><zip</span> <span class="na" style="color: teal;">destfile=</span><span class="s" style="color: #d14;">"${release_dir}/${name} v${version}.zip"</span><span class="nt" style="color: navy;">></span></span>
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154
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="xml"> <span class="nt" style="color: navy;"><zipfileset</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${Windows_package_dir}"</span> <span class="na" style="color: teal;">prefix=</span><span class="s" style="color: #d14;">"${name} v${version}"</span><span class="nt" style="color: navy;">/></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="157" 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="153" 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">@@ -157,7 +153,7 @@</td>
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157
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="xml"> <span class="nt" style="color: navy;"><echo</span> <span class="na" style="color: teal;">message=</span><span class="s" style="color: #d14;">"Windows version release is finished."</span> <span class="nt" style="color: navy;">/></span></span>
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158
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="xml"> <span class="nt" style="color: navy;"></target></span></span>
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159
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="xml"></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="xml"> <span class="nt" style="color: navy;"><target</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"linux_unix_Release"</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="xml"> <span class="nt" style="color: navy;"><target</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"linux_unix_Release"</span><span class="idiff left"> </span><span class="na" style="color: teal;"><span class="idiff">depends=</span></span><span class="s" style="color: #d14;"><span class="idiff right">"dist"</span></span></span>
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161
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="xml"> <span class="na" style="color: teal;">description=</span><span class="s" style="color: #d14;">"release Linux/Unix version of FigTree"</span><span class="nt" style="color: navy;">></span></span>
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<td class="diff-line-num old_line" data-linenumber="162" 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">
162
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="xml"> <span class="nt" style="color: navy;"><delete</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${Linux_package_dir}"</span> <span class="nt" style="color: navy;">/></span></span>
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163
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- Create the release directory --></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="185" 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="181" 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">@@ -185,7 +181,9 @@</td>
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185
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="xml"> <span class="nt" style="color: navy;"><echo</span> <span class="na" style="color: teal;">message=</span><span class="s" style="color: #d14;">"Linux/Unix version release is finished."</span> <span class="nt" style="color: navy;">/></span></span>
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186
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="xml"> <span class="nt" style="color: navy;"></target></span></span>
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187
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="xml"></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="xml"> <span class="nt" style="color: navy;"><target</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"mac_release"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="xml"> <span class="nt" style="color: navy;"><property</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"AppleSigner"</span> <span class="na" style="color: teal;">value=</span><span class="s" style="color: #d14;">"Developer ID Application: Andrew Rambaut (9E4WXAQ6SE)"</span> <span class="nt" style="color: navy;">/></span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="xml"></span>
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<td class="diff-line-num new new_line" data-linenumber="186" 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">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="xml"> <span class="nt" style="color: navy;"><target</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"mac_release"</span> <span class="na" style="color: teal;">depends=</span><span class="s" style="color: #d14;">"dist"</span></span>
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189
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="xml"> <span class="na" style="color: teal;">description=</span><span class="s" style="color: #d14;">"release Mac version of FigTree"</span><span class="nt" style="color: navy;">></span></span>
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190
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="xml"> <span class="nt" style="color: navy;"><delete</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${Mac_package_dir}"</span> <span class="nt" style="color: navy;">/></span></span>
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<td class="diff-line-num old_line" data-linenumber="191" 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">
191
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- Create the release directory --></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="198" 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">@@ -200,7 +198,7 @@</td>
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200
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="xml"> <span class="nt" style="color: navy;"><fileset</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${Mac_dir}/QuickLook Plugin"</span><span class="nt" style="color: navy;">/></span></span>
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<td class="diff-line-num old_line" data-linenumber="201" 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">
201
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="xml"> <span class="nt" style="color: navy;"></copy></span></span>
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<td class="diff-line-num old_line" data-linenumber="202" 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">
202
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="xml"></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="xml"> <span class="nt" style="color: navy;"><taskdef</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"jarbundler"</span> <span class="na" style="color: teal;">classname=</span><span class="s" style="color: #d14;">"<span class="idiff left right">net.sourceforge</span>.jarbundler.JarBundler"</span><span class="nt" style="color: navy;">/></span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="xml"> <span class="nt" style="color: navy;"><taskdef</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"jarbundler"</span> <span class="na" style="color: teal;">classname=</span><span class="s" style="color: #d14;">"<span class="idiff left right">com.ultramixer</span>.jarbundler.JarBundler"</span><span class="nt" style="color: navy;">/></span></span>
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204
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="xml"></span>
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205
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- create a jar bundle for the mac --></span></span>
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<td class="diff-line-num old_line" data-linenumber="206" 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">
206
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="xml"> <span class="nt" style="color: navy;"><jarbundler</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${Mac_package_dir}"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="210" 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="208" 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">@@ -210,11 +208,12 @@</td>
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<td class="diff-line-num old_line" data-linenumber="210" 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">
210
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="xml"> <span class="na" style="color: teal;">stubfile=</span><span class="s" style="color: #d14;">"${packaging_tools}/mac/universalJavaApplicationStub"</span></span>
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211
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="xml"> <span class="na" style="color: teal;">useJavaXKey=</span><span class="s" style="color: #d14;">"true"</span></span>
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212
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="xml"> <span class="na" style="color: teal;">jvmversion=</span><span class="s" style="color: #d14;">"1.6+"</span></span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="xml"> <span class="na" style="color: teal;">vmoptions=</span><span class="s" style="color: #d14;">"-Xmx1024M"</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="xml"> <span class="na" style="color: teal;">vmoptions=</span><span class="s" style="color: #d14;">"-Xmx4096M"</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="xml"> <span class="na" style="color: teal;">highresolutioncapable=</span><span class="s" style="color: #d14;">"true"</span></span>
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214
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="xml"> <span class="na" style="color: teal;">arguments=</span><span class="s" style="color: #d14;">""</span></span>
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215
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="xml"> <span class="na" style="color: teal;">version=</span><span class="s" style="color: #d14;">"${version}"</span></span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="xml"> <span class="na" style="color: teal;">build=</span><span class="s" style="color: #d14;">"1"</span></span>
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217
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="xml"> <span class="na" style="color: teal;">copyright=</span><span class="s" style="color: #d14;">"${name} v${version}, Copyright 2006-201<span class="idiff left right">5</span>, Andrew Rambaut"</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="xml"> <span class="na" style="color: teal;">copyright=</span><span class="s" style="color: #d14;">"${name} v${version}, Copyright 2006-201<span class="idiff left right">8</span>, Andrew Rambaut"</span></span>
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218
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="xml"> <span class="na" style="color: teal;">bundleid=</span><span class="s" style="color: #d14;">"figtree"</span> <span class="nt" style="color: navy;">></span></span>
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219
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="xml"> <span class="nt" style="color: navy;"><javaproperty</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"apple.laf.useScreenMenuBar"</span> <span class="na" style="color: teal;">value=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: navy;">/></span></span>
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220
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219
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="xml"> <span class="nt" style="color: navy;"><jarfileset</span> <span class="na" style="color: teal;">dir=</span><span class="s" style="color: #d14;">"${dist}"</span><span class="nt" style="color: navy;">></span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -232,17 +231,21 @@</td>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="xml"> <span class="na" style="color: teal;">role=</span><span class="s" style="color: #d14;">"Editor"</span><span class="nt" style="color: navy;">/></span></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="xml"> <span class="nt" style="color: navy;"></jarbundler></span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="xml"></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- <span class="idiff left right">remove </span>code signing --></span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><<span class="idiff left right">!--</span></span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"><exec executable="/usr/bin/codesign"</span>></span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- code signing --></span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="xml"> <span class="nt" style="color: navy;"><<span class="idiff left">exec</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">executable=</span></span><span class="s" style="color: #d14;"><span class="idiff">"codesign"</span></span><span class="nt" style="color: navy;"><span class="idiff right">></span></span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="xml"> <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff"><arg</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">value=</span></span><span class="s" style="color: #d14;"><span class="idiff">"--deep"</span></span><span class="nt" style="color: navy;"><span class="idiff right">/</span>></span></span>
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238
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="xml"> <span class="nt" style="color: navy;"><arg</span> <span class="na" style="color: teal;">value=</span><span class="s" style="color: #d14;">"-s"</span><span class="nt" style="color: navy;">/></span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;"> <arg value="-"/></span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;"> <arg value="- -force"/> remove space from between minus signs</span></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;"> <arg value="${Mac_dir}/${name} v${version}/${name} v${version}.app"/></span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="xml"> <span class="nt" style="color: navy;"><arg</span> <span class="na" style="color: teal;">value=</span><span class="s" style="color: #d14;">"${AppleSigner}"</span><span class="nt" style="color: navy;">/></span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="xml"> <span class="nt" style="color: navy;"><arg</span> <span class="na" style="color: teal;">value=</span><span class="s" style="color: #d14;">"-v"</span><span class="nt" style="color: navy;">/></span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="xml"> <span class="nt" style="color: navy;"><arg</span> <span class="na" style="color: teal;">value=</span><span class="s" style="color: #d14;">"${Mac_package_dir}/${name} v${version}.app"</span><span class="nt" style="color: navy;">/></span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="xml"> <span class="nt" style="color: navy;"></exec></span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="xml"></span>
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<td class="diff-line-num new new_line" data-linenumber="243" 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">
243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- checking code signing --></span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="xml"> <span class="nt" style="color: navy;"><exec</span> <span class="na" style="color: teal;">executable=</span><span class="s" style="color: #d14;">"spctl"</span><span class="nt" style="color: navy;">></span></span>
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<td class="diff-line-num new new_line" data-linenumber="245" 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">
245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="xml"> <span class="nt" style="color: navy;"><arg</span> <span class="na" style="color: teal;">value=</span><span class="s" style="color: #d14;">"--assess"</span><span class="nt" style="color: navy;">/></span></span>
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<td class="diff-line-num new new_line" data-linenumber="246" 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">
246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="xml"> <span class="nt" style="color: navy;"><arg</span> <span class="na" style="color: teal;">value=</span><span class="s" style="color: #d14;">"--verbose=4"</span><span class="nt" style="color: navy;">/></span></span>
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<td class="diff-line-num new new_line" data-linenumber="247" 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">
247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="xml"> <span class="nt" style="color: navy;"><arg</span> <span class="na" style="color: teal;">value=</span><span class="s" style="color: #d14;">"${Mac_package_dir}/${name} v${version}.app"</span><span class="nt" style="color: navy;">/></span></span>
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242
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<td class="diff-line-num new_line" data-linenumber="248" 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">
248
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="xml"> <span class="nt" style="color: navy;"></exec></span></span>
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243
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<td class="diff-line-num new_line old" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;"> --></span></span>
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244
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="xml"> </span>
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245
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<td class="diff-line-num new_line old" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="xml"> <span class="nt" style="color: navy;"><echo</span> <span class="na" style="color: teal;">message=</span><span class="s" style="color: #d14;">"Building disk image."</span> <span class="nt" style="color: navy;">/></span></span>
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246
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="xml"></span>
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247
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<td class="diff-line-num new_line" data-linenumber="250" 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">
250
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- create disk image --></span></span>
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248
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<td class="diff-line-num new_line" data-linenumber="251" 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">
251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="xml"> <span class="nt" style="color: navy;"><exec</span> <span class="na" style="color: teal;">executable=</span><span class="s" style="color: #d14;">"/usr/bin/hdiutil"</span><span class="nt" style="color: navy;">></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="260" 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">@@ -257,6 +260,13 @@</td>
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257
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="xml"> <span class="nt" style="color: navy;"><arg</span> <span class="na" style="color: teal;">value=</span><span class="s" style="color: #d14;">"${release_dir}/${name} v${version}.dmg"</span><span class="nt" style="color: navy;">/></span></span>
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258
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="xml"> <span class="nt" style="color: navy;"></exec></span></span>
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259
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="xml"></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="xml"> <span class="nt" style="color: navy;"><exec</span> <span class="na" style="color: teal;">executable=</span><span class="s" style="color: #d14;">"codesign"</span><span class="nt" style="color: navy;">></span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="xml"> <span class="nt" style="color: navy;"><arg</span> <span class="na" style="color: teal;">value=</span><span class="s" style="color: #d14;">"-s"</span><span class="nt" style="color: navy;">/></span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="xml"> <span class="nt" style="color: navy;"><arg</span> <span class="na" style="color: teal;">value=</span><span class="s" style="color: #d14;">"${AppleSigner}"</span><span class="nt" style="color: navy;">/></span></span>
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<td class="diff-line-num new new_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="xml"> <span class="nt" style="color: navy;"><arg</span> <span class="na" style="color: teal;">value=</span><span class="s" style="color: #d14;">"-v"</span><span class="nt" style="color: navy;">/></span></span>
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<td class="diff-line-num new new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="xml"> <span class="nt" style="color: navy;"><arg</span> <span class="na" style="color: teal;">value=</span><span class="s" style="color: #d14;">"${release_dir}/${name} v${version}.dmg"</span><span class="nt" style="color: navy;">/></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="268" 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">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="xml"> <span class="nt" style="color: navy;"></exec></span></span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="xml"></span>
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="xml"> <span class="nt" style="color: navy;"><echo</span> <span class="na" style="color: teal;">message=</span><span class="s" style="color: #d14;">"Mac version release is finished."</span> <span class="nt" style="color: navy;">/></span></span>
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261
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="xml"> <span class="nt" style="color: navy;"></target></span></span>
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262
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="xml"></span>
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<a href="https://salsa.debian.org/med-team/figtree/commit/1819d7fa6f5aa74cb98c5ffa9be49505747a8f43#9b1c57d655988fad9c569224abf94a44918fc467"><strong>doc/large_trees.md</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown">If you open a large tree (in this case 1610 tips) you will see a complete mess:</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: teal;">shot1</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/rambaut/figtree/blob/master/doc/shot1.png</span><span class="p">)</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown">This is because the default tip label font size is too large. This means that the labels overlap but also take up most of the horizontal screen space, crushing the tree to the left. To fix this, you can shrink the font size (the minimum at the moment is 2pt):</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: teal;">shot2</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/rambaut/figtree/blob/master/doc/shot2.png</span><span class="p">)</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown">So now zoom the tree in the vertical axis only using the 'Expand' slider until the labels aren't overlapping any more. Essentially this creates a very long tree (that you can scroll up and down).</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: teal;">shot3</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/rambaut/figtree/blob/master/doc/shot3.png</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown">Now export as a PDF and you get a PDF of the same aspect ratio:</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: teal;">shot5</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/rambaut/figtree/blob/master/doc/shot5.png</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown">You can zoom in or create a multi-page print out (or a long poster on a continuous roll printer):</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: teal;">shot4</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/rambaut/figtree/blob/master/doc/shot4.png</span><span class="p">)</span></span></pre>
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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>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell">java <span class="nt" style="color: navy;">-Xms64m</span> <span class="nt" style="color: navy;">-Xmx512m</span> <span class="nt" style="color: navy;">-jar</span> lib/figtree.jar <span class="nv" style="color: teal;"><span class="idiff left right">$*</span></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell">java <span class="nt" style="color: navy;">-Xms64m</span> <span class="nt" style="color: navy;">-Xmx512m</span> <span class="nt" style="color: navy;">-jar</span> lib/figtree.jar <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: teal;"><span class="idiff">$@</span></span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"></span></pre>
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<li id="7e30cd195ade384b348e0ce5a6e6d5f8994a2a26">
<a href="https://salsa.debian.org/med-team/figtree/commit/1819d7fa6f5aa74cb98c5ffa9be49505747a8f43#7e30cd195ade384b348e0ce5a6e6d5f8994a2a26"><strong>release/common/README.txt</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"> FigTree v1.4.<span class="idiff left right">3 2006-2016</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"> FigTree v1.4.<span class="idiff left right">4 2006-2018</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"> Andrew Rambaut</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Institute of Evolutionary Biology</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +7,7 @@</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">UNIX/Linux/Mac OS X (command-line) version README</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Last updated: a.rambaut@ed.ac.uk - <span class="idiff left right">4th October 2016</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Last updated: a.rambaut@ed.ac.uk - <span class="idiff left right">25th November 2018</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Contents:</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">1) INTRODUCTION</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">@@ -27,6 +27,12 @@ FigTree is designed as a graphical viewer of phylogenetic trees and as a program</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">___________________________________________________________________________</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">2) VERSION HISTORY</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">v1.4.4 Released 25th November 2018</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Bugs fixed:</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> Issue 119: Various issues launching FigTree in Java 9</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> Issue 125: Cannot select nodes on HiDPI screens with scaling (thanks to Serafim Nenarokov for the fix)</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">v1.4.3 Released 4th October 2016</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">New features:</span>
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<li id="9f7588c31a910e9bf63cbc6fb1f0d65d4d3abc75">
<a href="https://salsa.debian.org/med-team/figtree/commit/1819d7fa6f5aa74cb98c5ffa9be49505747a8f43#9f7588c31a910e9bf63cbc6fb1f0d65d4d3abc75"><strong>src/figtree/application/FigTreeApplication.java</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">@@ -30,37 +30,27 @@</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">figtree</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">application</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.itextpdf.text.Document</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.itextpdf.text.DocumentException</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.itextpdf.text.pdf.PdfContentByte</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.itextpdf.text.pdf.PdfTemplate</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.itextpdf.text.pdf.PdfWriter</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">figtree.application.preferences.*</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">figtree.application.preferences.AppearancePreferencesSection</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">figtree.application.preferences.FontsPreferencesSection</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">figtree.treeviewer.ExtendedTreeViewer</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">jam.framework.*</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">jam.controlpalettes.BasicControlPalette</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">jam.controlpalettes.ControlPalette</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">jam.framework.*</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">jam.mac.Utils</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">jebl.evolution.io.ImportException</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">jebl.evolution.io.NewickImporter</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">jebl.evolution.trees.Tree</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.*</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.*</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.image.BufferedImage</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.*</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.lang.reflect.InvocationTargetException</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.lang.reflect.Method</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.net.URL</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.*</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.List</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">jebl.evolution.io.ImportException</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">jebl.evolution.io.NewickImporter</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">jebl.evolution.trees.Tree</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.imageio.ImageIO</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.*</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">ch.randelshofer.quaqua.QuaquaManager</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.apache.batik.dom.GenericDOMImplementation</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.apache.batik.svggen.SVGGraphics2D</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.w3c.dom.DOMImplementation</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Application class for FigTree including main() method for invoking it.</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Uses JAM Application classes to create a MultiDoc Application.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -76,8 +66,8 @@ import org.w3c.dom.DOMImplementation;</td>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FigTreeApplication</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="n" style="color: #333;">MultiDocApplication</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.4.<span class="idiff left right">3</span>"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">DATES</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2006-201<span class="idiff left right">6</span>"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.4.<span class="idiff left right">4</span>"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">DATES</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2006-201<span class="idiff left right">8</span>"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">FigTreeApplication</span> <span class="n" style="color: #333;">application</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="java"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="221" 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="211" 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">@@ -221,6 +211,12 @@ public class FigTreeApplication extends MultiDocApplication {</td>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="java"> <span class="n" style="color: #333;">centreLine</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"http://tree.bio.ed.ac.uk/"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">60</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="java"> <span class="n" style="color: #333;">centreLine</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Uses the Java Evolutionary Biology 2 Library (JEBL2)"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">60</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="java"> <span class="n" style="color: #333;">centreLine</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"http://jebl2.googlecode.com/"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">60</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="java"> <span class="n" style="color: #333;">centreLine</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Uses the iText PDF Library"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">60</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="java"> <span class="n" style="color: #333;">centreLine</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"http://itextpdf.com/"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">60</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="java"> <span class="n" style="color: #333;">centreLine</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Uses the Apache Batik Library"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">60</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="java"> <span class="n" style="color: #333;">centreLine</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"http://xmlgraphics.apache.org/batik/"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">60</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="java"> <span class="n" style="color: #333;">centreLine</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Uses the JDOM XML Library"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">60</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="java"> <span class="n" style="color: #333;">centreLine</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"http://www.jdom.org/"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">60</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="java"> <span class="n" style="color: #333;">centreLine</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Thanks to Alexei Drummond, Joseph Heled, Philippe Lemey, "</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">60</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="java"> <span class="n" style="color: #333;">centreLine</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Tulio de Oliveira, Oliver Pybus, Beth Shapiro & Marc Suchard"</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">60</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -232,7 +228,7 @@ public class FigTreeApplication extends MultiDocApplication {</td>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">" Example: figtree test.tree"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">" Example: figtree -graphic PDF test.tree test.pdf"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">" Example: figtree -graphic <span class="idiff left right">GIF -width 320 -height 320 test.tree test.gif</span>"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">" Example: figtree -graphic <span class="idiff left right">PNG -width 320 -height 320 test.tree test.png</span>"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="java"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="326" 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="322" 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">@@ -326,6 +322,7 @@ public class FigTreeApplication extends MultiDocApplication {</td>
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326
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="java"> <span class="n" style="color: #333;">javax</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">swing</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">SwingUtilities</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">invokeAndWait</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Runnable</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="java"> <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Only override the UI's necessary for ColorChooser and</span></span>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// FileChooser:</span></span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="java"> <span class="n" style="color: #333;">Set</span> <span class="n" style="color: #333;">includes</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">HashSet</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -337,23 +334,20 @@ public class FigTreeApplication extends MultiDocApplication {</td>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="java"> <span class="n" style="color: #333;">includes</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">add</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"SplitPane"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="java"> <span class="n" style="color: #333;">includes</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">add</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"TitledBorder"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="java"> <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="java"> <span class="n" style="color: #333;">QuaquaManager</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setIncludedUIs</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">includes</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">java</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">lang</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">NoClassDefFoundError</span> <span class="n" style="color: #333;">ncdfe</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// this is to protect against the figtree.jar being</span></span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// run on Mac OS without Quaqua on the classpath</span></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="java"> <span class="n" style="color: #333;">Class</span><span class="o" style="font-weight: 600;"><?></span> <span class="n" style="color: #333;">qm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Class</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">forName</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"ch.randelshofer.quaqua.QuaquaManager"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="java"> <span class="n" style="color: #333;">Method</span> <span class="n" style="color: #333;">method</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qm</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getMethod</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"setIncludedUIs"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Set</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">class</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="java"> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">invoke</span><span class="o" style="font-weight: 600;">(</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">includes</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="java"> <span class="n" style="color: #333;">UIManager</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setLookAndFeel</span><span class="o" style="font-weight: 600;">(</span></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="java"> <span class="s" style="color: #d14;">"ch.randelshofer.quaqua.QuaquaLookAndFeel"</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="java"> <span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="java"> <span class="n" style="color: #333;">lafLoaded</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Exception</span> <span class="n" style="color: #333;"><span class="idiff left right">e</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Exception</span> <span class="n" style="color: #333;"><span class="idiff left right">ignored</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="java"> <span class="o" style="font-weight: 600;">});</span></span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Exception</span> <span class="n" style="color: #333;"><span class="idiff left right">e</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Exception</span> <span class="n" style="color: #333;"><span class="idiff left right">ignored</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="java"> <span class="n" style="color: #333;">UIManager</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"SystemFont"</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Font</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Lucida Grande"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Font</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PLAIN</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">13</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -403,9 +397,9 @@ public class FigTreeApplication extends MultiDocApplication {</td>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="java"> <span class="s" style="color: #d14;">"Institute of Evolutionary Biology, University of Edinburgh.<br>"</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="java"> <span class="s" style="color: #d14;">"<a href=\"http://tree.bio.ed.ac.uk/\">http://tree.bio.ed.ac.uk/</a><br><br>"</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="java"> <span class="s" style="color: #d14;">"Source code available from:<br>"</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="java"> <span class="s" style="color: #d14;">"<a href=\"https://<span class="idiff left right">figtree.googlecode.com/\">http://figtree.googlecode.com</span>/</a><br><br>"</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="java"> <span class="s" style="color: #d14;">"<a href=\"https://<span class="idiff left right">github.com/rambaut/figtree\">http://github.com/rambaut/figtree</span>/</a><br><br>"</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="java"> <span class="s" style="color: #d14;">"Uses the Java Evolutionary Biology 2 Library (JEBL2)<br>"</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="java"> <span class="s" style="color: #d14;">"<a href=\"https://<span class="idiff left right">jebl2.googlecode.com/\">http://jebl2.googlecode.com</span>/</a><br><br>"</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="java"> <span class="s" style="color: #d14;">"<a href=\"https://<span class="idiff left right">github.com/rambaut/jebl2/\">http://github.com/rambaut/jebl2</span>/</a><br><br>"</span> <span class="o" style="font-weight: 600;">+</span></span>
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403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="java"> <span class="s" style="color: #d14;">"Thanks to Alexei Drummond, Joseph Heled, Philippe Lemey, <br>Tulio de Oliveira, Oliver Pybus, Beth Shapiro & Marc Suchard</center>"</span> <span class="o" style="font-weight: 600;">+</span></span>
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404
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="java"> <span class="s" style="color: #d14;">"</div></html>"</span><span class="o" style="font-weight: 600;">;</span></span>
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="java"></span>
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<a href="https://salsa.debian.org/med-team/figtree/commit/1819d7fa6f5aa74cb98c5ffa9be49505747a8f43#05bc8dcd255d6aafcb4c19f8d927d01f0da79449"><strong>src/figtree/treeviewer/TreePane.java</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">@@ -1170,7 +1170,7 @@ public class TreePane extends JComponent implements PainterListener, Printable {</td>
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1170
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1170
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<pre style="margin: 0;"> <span id="LC1170" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Node</span> <span class="n" style="color: #333;">node</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getExternalNodes</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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1171
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1171
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<pre style="margin: 0;"> <span id="LC1171" class="line" lang="java"> <span class="n" style="color: #333;">Shape</span> <span class="n" style="color: #333;">taxonLabelBound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tipLabelBounds</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">);</span></span>
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1172
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1172
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<pre style="margin: 0;"> <span id="LC1172" class="line" lang="java"></span>
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1173
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<pre style="margin: 0;">-<span id="LC1173" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">taxonLabelBound</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;"><span class="idiff left">g2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">hit</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">taxonLabelBound</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kc" style="font-weight: 600;"><span class="idiff right">false</span></span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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1173
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<pre style="margin: 0;">+<span id="LC1173" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">taxonLabelBound</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;"><span class="idiff left">taxonLabelBound</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">intersects</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">y</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">height</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff right">width</span></span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC1174" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">;</span></span>
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1175
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1175
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<pre style="margin: 0;"> <span id="LC1175" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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1176
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1176
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<pre style="margin: 0;"> <span id="LC1176" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1179,11 +1179,11 @@ public class TreePane extends JComponent implements PainterListener, Printable {</td>
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1179
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1179
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<pre style="margin: 0;"> <span id="LC1179" class="line" lang="java"></span>
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1180
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<pre style="margin: 0;"> <span id="LC1180" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Node</span> <span class="n" style="color: #333;">node</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getNodes</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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1181
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1181
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<pre style="margin: 0;"> <span id="LC1181" class="line" lang="java"> <span class="n" style="color: #333;">Shape</span> <span class="n" style="color: #333;">branchPath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transform</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">createTransformedShape</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">treeLayoutCache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getBranchPath</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">));</span></span>
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1182
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<pre style="margin: 0;">-<span id="LC1182" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">branchPath</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;"><span class="idiff left">g2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">hit</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">branchPath</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kc" style="font-weight: 600;"><span class="idiff right">true</span></span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC1182" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">branchPath</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;"><span class="idiff left">branchPath</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">intersects</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">y</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">height</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff right">width</span></span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC1183" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">;</span></span>
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1184
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1184
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<pre style="margin: 0;"> <span id="LC1184" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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1185
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<pre style="margin: 0;"> <span id="LC1185" class="line" lang="java"> <span class="n" style="color: #333;">Shape</span> <span class="n" style="color: #333;">collapsedShape</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transform</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">createTransformedShape</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">treeLayoutCache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getCollapsedShape</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">));</span></span>
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1186
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<pre style="margin: 0;">-<span id="LC1186" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">collapsedShape</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;"><span class="idiff left">g2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">hit</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">collapsedShape</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kc" style="font-weight: 600;"><span class="idiff right">false</span></span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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1186
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<pre style="margin: 0;">+<span id="LC1186" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">collapsedShape</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;"><span class="idiff left">collapsedShape</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">intersects</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">y</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">height</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff right">width</span></span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC1187" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC1188" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC1189" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1196,18 +1196,18 @@ public class TreePane extends JComponent implements PainterListener, Printable {</td>
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1196
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<pre style="margin: 0;"> <span id="LC1196" class="line" lang="java"> <span class="n" style="color: #333;">Set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Node</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">nodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">HashSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Node</span><span class="o" style="font-weight: 600;">>();</span></span>
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1197
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<pre style="margin: 0;"> <span id="LC1197" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Node</span> <span class="n" style="color: #333;">node</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getExternalNodes</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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1198
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<pre style="margin: 0;"> <span id="LC1198" class="line" lang="java"> <span class="n" style="color: #333;">Shape</span> <span class="n" style="color: #333;">taxonLabelBound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tipLabelBounds</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">);</span></span>
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1199
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<pre style="margin: 0;">-<span id="LC1199" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">taxonLabelBound</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;"><span class="idiff left">g2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">hit</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">taxonLabelBound</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kc" style="font-weight: 600;"><span class="idiff right">false</span></span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC1199" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">taxonLabelBound</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;"><span class="idiff left">taxonLabelBound</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">intersects</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">y</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">height</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff right">width</span></span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC1200" class="line" lang="java"> <span class="n" style="color: #333;">nodes</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">);</span></span>
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1201
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<pre style="margin: 0;"> <span id="LC1201" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC1202" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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1203
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<pre style="margin: 0;"> <span id="LC1203" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC1204" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Node</span> <span class="n" style="color: #333;">node</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getNodes</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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1205
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1205
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<pre style="margin: 0;"> <span id="LC1205" class="line" lang="java"> <span class="n" style="color: #333;">Shape</span> <span class="n" style="color: #333;">branchPath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transform</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">createTransformedShape</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">treeLayoutCache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getBranchPath</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">));</span></span>
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1206
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<pre style="margin: 0;">-<span id="LC1206" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">branchPath</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;"><span class="idiff left">g2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">hit</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">branchPath</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kc" style="font-weight: 600;"><span class="idiff right">true</span></span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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1206
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<pre style="margin: 0;">+<span id="LC1206" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">branchPath</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;"><span class="idiff left">branchPath</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">intersects</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">y</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">height</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff right">width</span></span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC1207" class="line" lang="java"> <span class="n" style="color: #333;">nodes</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">);</span></span>
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1208
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1208
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<pre style="margin: 0;"> <span id="LC1208" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC1209" class="line" lang="java"> <span class="n" style="color: #333;">Shape</span> <span class="n" style="color: #333;">collapsedShape</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transform</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">createTransformedShape</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">treeLayoutCache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getCollapsedShape</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">));</span></span>
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1210
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<pre style="margin: 0;">-<span id="LC1210" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">collapsedShape</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;"><span class="idiff left">g2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">hit</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">collapsedShape</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kc" style="font-weight: 600;"><span class="idiff right">false</span></span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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1210
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<pre style="margin: 0;">+<span id="LC1210" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">collapsedShape</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;"><span class="idiff left">collapsedShape</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">intersects</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">y</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">height</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff right">width</span></span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC1211" class="line" lang="java"> <span class="n" style="color: #333;">nodes</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">);</span></span>
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1212
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1212
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<pre style="margin: 0;"> <span id="LC1212" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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1213
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<pre style="margin: 0;"> <span id="LC1213" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2449,4 +2449,4 @@ public class TreePane extends JComponent implements PainterListener, Printable {</td>
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<pre style="margin: 0;"> <span id="LC2449" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC2450" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Node</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Shape</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">calloutPaths</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">HashMap</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Node</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Shape</span><span class="o" style="font-weight: 600;">>();</span></span>
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<pre style="margin: 0;"> <span id="LC2451" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC2452" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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<pre style="margin: 0;">+<span id="LC2452" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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<li id="36719ec578b4d9f9fa23aeec997399ee0accb7e8">
<a href="https://salsa.debian.org/med-team/figtree/commit/1819d7fa6f5aa74cb98c5ffa9be49505747a8f43#36719ec578b4d9f9fa23aeec997399ee0accb7e8"><strong>src/figtree/treeviewer/painters/LabelPainter.java</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">@@ -20,14 +20,8 @@</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">figtree</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">treeviewer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">painters</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.sun.tools.corba.se.idl.InterfaceEntry</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">jebl.evolution.trees.Tree</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">jebl.util.Attributable</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.*</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.text.NumberFormat</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Collection</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Set</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">figtree.treeviewer.decorators.Decorator</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="java"></span>
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