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GitLab

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<h3>

Andreas Tille pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/biojava4-live">Debian Med / biojava4-live</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/biojava4-live/commit/3aba982fef68dce7e73b2a29b7f07fee88bfcb0c">3aba982f</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-01-10T09:49:06Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 4.2.12</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/biojava4-live/commit/8d48abfeaece53f6aa10519dcddb356fd0240205">8d48abfe</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-01-10T10:33:38Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 4.2.12+dfsg</pre>

</li>

</ul>

<h4>29 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#eae1f8e4eee985cec491eebc50e5e27bb9b2c170">

biojava-aa-prop/pom.xml

</a>

</li>

<li class="file-stats">

<a href="#c521072b30695c9a39edd508f8132e5d36df975c">

biojava-alignment/pom.xml

</a>

</li>

<li class="file-stats">

<a href="#ef3263aa6a88d390f7b05598798eaa574644200f">

biojava-core/pom.xml

</a>

</li>

<li class="file-stats">

<a href="#c8eb86ae672dda5c63d549d5d561b24bac8603b6">

biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java

</a>

</li>

<li class="file-stats">

<a href="#ec64509af8ef0c0b83ce584250c53a9e179a35d7">

biojava-genome/pom.xml

</a>

</li>

<li class="file-stats">

<a href="#184b5673dd964353dc02ee87944303b467d3d155">

biojava-integrationtest/pom.xml

</a>

</li>

<li class="file-stats">

<a href="#dc21809df6dca39aab598512feab461669a06121">

biojava-modfinder/pom.xml

</a>

</li>

<li class="file-stats">

<a href="#fbe68b243f2c27bad79188712b2f1cef1b94a53b">

biojava-ontology/pom.xml

</a>

</li>

<li class="file-stats">

<a href="#20dfbfc7ba8f72600e13d2ecd32c9eae858f1b56">

biojava-phylo/pom.xml

</a>

</li>

<li class="file-stats">

<a href="#b50cb5175e0cabb113c6322d1bba1d5e14f82029">

biojava-protein-disorder/pom.xml

</a>

</li>

<li class="file-stats">

<a href="#7d8914fa09bceaff9477f6ec0ba8f629228de925">

biojava-sequencing/pom.xml

</a>

</li>

<li class="file-stats">

<a href="#97d9023e3b6aa8ede87066949adb144e3921bd59">

biojava-structure-gui/pom.xml

</a>

</li>

<li class="file-stats">

<a href="#bc75ba48356609052210fbf9f8f39f1d265b6c6e">

biojava-structure/pom.xml

</a>

</li>

<li class="file-stats">

<a href="#eaa9e59d5ea8eb17c7253f6af6e97b922791c6cb">

biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java

</a>

</li>

<li class="file-stats">

<a href="#3acb1c5c4dfcadec7cbaaf6c563ea7c1318e0947">

biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java

</a>

</li>

<li class="file-stats">

<a href="#fc5afcafbad3aa57eae2562032c7f9f7c8df9eb3">

biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java

</a>

</li>

<li class="file-stats">

<a href="#b718810c810230284c03cc47a47893ff188ffec6">

biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompGroupFactory.java

</a>

</li>

<li class="file-stats">

<a href="#c9544f544200a902cd1467f05515b3586169d9f4">

biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java

</a>

</li>

<li class="file-stats">

<a href="#cd1a85bfbcb2f8b5bfe993e88e9fdf07b5d1556f">

biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java

</a>

</li>

<li class="file-stats">

<a href="#fe1edc857045a7d0455eeeb9e81b445b8fce3865">

biojava-structure/src/main/java/org/biojava/nbio/structure/io/util/FileDownloadUtils.java

</a>

</li>

<li class="file-stats">

<a href="#7fb985a3aeb9a4f46da35200e130b1ef891eb9be">

biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.java

</a>

</li>

<li class="file-stats">

<a href="#efb614d21e140fe6ec68bf881794ca2b0b175e60">

biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomCache.java

</a>

</li>

<li class="file-stats">

<a href="#92a752fb8611c5f680cbf31058ac2f489a7cc933">

biojava-structure/src/test/java/org/biojava/nbio/structure/TestExperimentalTechniques.java

</a>

</li>

<li class="file-stats">

<a href="#75ee9ec412f2376a5ff1cd5c2e8f58aeadee5e26">

biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java

</a>

</li>

<li class="file-stats">

<a href="#c6e47bfa4a58cf7a8969a3bfc01aedad17cbc04a">

<span class="new-file">

+

biojava-structure/src/test/java/org/biojava/nbio/structure/test/util/GlobalsHelper.java

</span>

</a>

</li>

<li class="file-stats">

<a href="#f5518cde38547e1422e67390dd0063b16c3e160b">

<span class="new-file">

+

biojava-structure/src/test/resources/atp.cif.gz

</span>

</a>

</li>

<li class="file-stats">

<a href="#211138d0d9f7559842c8e636097db1e40f225ff4">

biojava-survival/pom.xml

</a>

</li>

<li class="file-stats">

<a href="#d776f6089be530cdb58291bc061f164083e9f1ae">

biojava-ws/pom.xml

</a>

</li>

<li class="file-stats">

<a href="#442292b8a7efeabbe4cc176709b833b1792140ec">

pom.xml

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="eae1f8e4eee985cec491eebc50e5e27bb9b2c170">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#eae1f8e4eee985cec491eebc50e5e27bb9b2c170"><strong>biojava-aa-prop/pom.xml</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,7 @@</td>

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2

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2

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="xml">    <span class="nt" style="color: navy;"><parent></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="xml">            <span class="nt" style="color: navy;"><artifactId></span>biojava<span class="nt" style="color: navy;"></artifactId></span></span>

</pre>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="xml">            <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5

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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC5" class="line" lang="xml">            <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="xml">            <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6" 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">

6

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<td class="diff-line-num new_line" data-linenumber="6" 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">

6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="xml">    <span class="nt" style="color: navy;"></parent></span></span>

</pre>

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<td class="diff-line-num 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">

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="xml">    <span class="nt" style="color: navy;"><modelVersion></span>4.0.0<span class="nt" style="color: navy;"></modelVersion></span></span>

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<td class="diff-line-num old_line" data-linenumber="8" 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">

8

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="xml">    <span class="nt" style="color: navy;"><artifactId></span>biojava-aa-prop<span class="nt" style="color: navy;"></artifactId></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="70" 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">@@ -70,12 +70,12 @@</td>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="xml">           <span class="nt" style="color: navy;"><dependency></span></span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="xml">                   <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="72" 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">

72

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72

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC72" class="line" lang="xml">                   <span class="nt" style="color: navy;"><artifactId></span>biojava-core<span class="nt" style="color: navy;"></artifactId></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="xml">                   <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="xml">                   <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="xml">           <span class="nt" style="color: navy;"></dependency></span></span>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="xml">           <span class="nt" style="color: navy;"><dependency></span></span>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="xml">                   <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="xml">                   <span class="nt" style="color: navy;"><artifactId></span>biojava-structure<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="xml">                   <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="xml">                   <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="xml">           <span class="nt" style="color: navy;"></dependency></span></span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="xml"></span>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="xml">           <span class="c" style="color: #998; font-style: italic;"><!-- logging dependencies (managed by parent pom, don't set versions or scopes here) --></span></span>

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<br>

</li>

<li id="c521072b30695c9a39edd508f8132e5d36df975c">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#c521072b30695c9a39edd508f8132e5d36df975c"><strong>biojava-alignment/pom.xml</strong></a>

<hr>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="xml">    <span class="nt" style="color: navy;"><parent></span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="xml">            <span class="nt" style="color: navy;"><artifactId></span>biojava<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="xml">            <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="xml">            <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="xml">            <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="xml">    <span class="nt" style="color: navy;"></parent></span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="xml">    <span class="nt" style="color: navy;"><artifactId></span>biojava-alignment<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="xml">   <span class="nt" style="color: navy;"><name></span>biojava-alignment<span class="nt" style="color: navy;"></name></span></span>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="xml">           <span class="nt" style="color: navy;"><dependency></span></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="xml">                   <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="xml">                   <span class="nt" style="color: navy;"><artifactId></span>biojava-core<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="xml">                   <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="xml">                   <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="xml">                   <span class="nt" style="color: navy;"><scope></span>compile<span class="nt" style="color: navy;"></scope></span></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="xml">           <span class="nt" style="color: navy;"></dependency></span></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="xml">           <span class="nt" style="color: navy;"><dependency></span></span>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="xml">           <span class="nt" style="color: navy;"><dependency></span></span>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="xml">                   <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="xml">                   <span class="nt" style="color: navy;"><artifactId></span>biojava-phylo<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="xml">                   <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="xml">                   <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="xml">           <span class="nt" style="color: navy;"></dependency></span></span>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="xml">   <span class="nt" style="color: navy;"></dependencies></span></span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="xml"><span class="nt" style="color: navy;"></project></span></span></pre>

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<br>

</li>

<li id="ef3263aa6a88d390f7b05598798eaa574644200f">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#ef3263aa6a88d390f7b05598798eaa574644200f"><strong>biojava-core/pom.xml</strong></a>

<hr>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="xml">    <span class="nt" style="color: navy;"><parent></span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="xml">            <span class="nt" style="color: navy;"><artifactId></span>biojava<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="xml">            <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="xml">            <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="xml">            <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="xml">    <span class="nt" style="color: navy;"></parent></span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="xml">    <span class="nt" style="color: navy;"><modelVersion></span>4.0.0<span class="nt" style="color: navy;"></modelVersion></span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="xml">    <span class="nt" style="color: navy;"><artifactId></span>biojava-core<span class="nt" style="color: navy;"></artifactId></span></span>

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<br>

</li>

<li id="c8eb86ae672dda5c63d549d5d561b24bac8603b6">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#c8eb86ae672dda5c63d549d5d561b24bac8603b6"><strong>biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.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">@@ -88,7 +88,7 @@ public class UniprotProxySequenceReader<C extends Compound> implements ProxySequ</td>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</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;">TREMBLID_PATTERN</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}"</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC89" 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;">Pattern</span> <span class="n" style="color: #333;">UP_AC_PATTERN</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Pattern</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">compile</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"("</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">SPID_PATTERN</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"|"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">TREMBLID_PATTERN</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">")"</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="java"></span>

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">uniprotbaseURL</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"http://www.uniprot.org"</span><span class="o" style="font-weight: 600;">;</span> <span class="c1" style="color: #998; font-style: italic;">//"http://pir.uniprot.org";</span></span>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">uniprotbaseURL</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"http<span class="idiff left right">s</span>://www.uniprot.org"</span><span class="o" style="font-weight: 600;">;</span> <span class="c1" style="color: #998; font-style: italic;">//"http://pir.uniprot.org";</span></span>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">uniprotDirectoryCache</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>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">CompoundSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">compoundSet</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="414" 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="414" 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">@@ -414,6 +414,61 @@ public class UniprotProxySequenceReader<C extends Compound> implements ProxySequ</td>

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<pre style="margin: 0;"> <span id="LC414" class="line" lang="java">         <span class="n" style="color: #333;">fw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">write</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toString</span><span class="o" style="font-weight: 600;">());</span></span>

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<pre style="margin: 0;"> <span id="LC415" class="line" lang="java">         <span class="n" style="color: #333;">fw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">close</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC416" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC417" class="line" lang="java"> </span>

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<pre style="margin: 0;">+<span id="LC418" 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="LC419" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * Open a URL connection.</span></span>

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<pre style="margin: 0;">+<span id="LC420" 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="LC421" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * Follows redirects.</span></span>

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<pre style="margin: 0;">+<span id="LC422" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @param url</span></span>

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<pre style="margin: 0;">+<span id="LC423" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @throws IOException </span></span>

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<pre style="margin: 0;">+<span id="LC424" 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="LC425" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">HttpURLConnection</span> <span class="nf" style="color: #900; font-weight: 600;">openURLConnection</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">URL</span> <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC426" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">// This method should be moved to a utility class in BioJava 5.0</span></span>

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<pre style="margin: 0;">+<span id="LC427" class="line" lang="java">         </span>

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<pre style="margin: 0;">+<span id="LC428" class="line" lang="java">         <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">timeout</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5000</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC429" class="line" lang="java">         <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">useragent</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"BioJava"</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC430" class="line" lang="java">         </span>

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<pre style="margin: 0;">+<span id="LC431" class="line" lang="java">         <span class="n" style="color: #333;">HttpURLConnection</span> <span class="n" style="color: #333;">conn</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">HttpURLConnection</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">openConnection</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="diff-line-num new new_line" data-linenumber="432" 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">

432

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<pre style="margin: 0;">+<span id="LC432" class="line" lang="java">         <span class="n" style="color: #333;">conn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setRequestProperty</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"User-Agent"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">useragent</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="433" 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">

433

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<pre style="margin: 0;">+<span id="LC433" class="line" lang="java">         <span class="n" style="color: #333;">conn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setInstanceFollowRedirects</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="434" 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">

434

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<pre style="margin: 0;">+<span id="LC434" class="line" lang="java">         <span class="n" style="color: #333;">conn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setConnectTimeout</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">timeout</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="435" 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">

435

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<pre style="margin: 0;">+<span id="LC435" class="line" lang="java">         <span class="n" style="color: #333;">conn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setReadTimeout</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">timeout</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="436" 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">

436

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<pre style="margin: 0;">+<span id="LC436" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="437" 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">

437

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<pre style="margin: 0;">+<span id="LC437" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">conn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getResponseCode</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="438" 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">

438

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<pre style="margin: 0;">+<span id="LC438" class="line" lang="java">         <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">HttpURLConnection</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">HTTP_MOVED_TEMP</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="439" 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">

439

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<pre style="margin: 0;">+<span id="LC439" class="line" lang="java">                         <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">HttpURLConnection</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">HTTP_MOVED_PERM</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="440" 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">

440

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<pre style="margin: 0;">+<span id="LC440" class="line" lang="java">                         <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">HttpURLConnection</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">HTTP_SEE_OTHER</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="441" 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">

441

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<pre style="margin: 0;">+<span id="LC441" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">// Redirect!</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="442" 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">

442

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<pre style="margin: 0;">+<span id="LC442" class="line" lang="java">                 <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">newUrl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">conn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getHeaderField</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Location"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="443" 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">

443

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<pre style="margin: 0;">+<span id="LC443" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="444" 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">

444

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<pre style="margin: 0;">+<span id="LC444" 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;">newUrl</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toString</span><span class="o" style="font-weight: 600;">()))</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="445" 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">

445

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<pre style="margin: 0;">+<span id="LC445" class="line" lang="java">                         <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IOException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Cyclic redirect detected at "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">newUrl</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="446" 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">

446

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<pre style="margin: 0;">+<span id="LC446" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="447" 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">

447

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<pre style="margin: 0;">+<span id="LC447" class="line" lang="java">                 </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="448" 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="LC448" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">// Preserve cookies</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="449" 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">

449

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<pre style="margin: 0;">+<span id="LC449" class="line" lang="java">                 <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">cookies</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">conn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getHeaderField</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Set-Cookie"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="450" 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">

450

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC450" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="451" 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">

451

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<pre style="margin: 0;">+<span id="LC451" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">// open the new connection again</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="452" 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">

452

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<pre style="margin: 0;">+<span id="LC452" class="line" lang="java">                 <span class="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">URL</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newUrl</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="453" 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">

453

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<pre style="margin: 0;">+<span id="LC453" class="line" lang="java">                 <span class="n" style="color: #333;">conn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">disconnect</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="454" 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">

454

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<pre style="margin: 0;">+<span id="LC454" class="line" lang="java">                 <span class="n" style="color: #333;">conn</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">HttpURLConnection</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">openConnection</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="455" 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">

455

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<pre style="margin: 0;">+<span id="LC455" 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;">cookies</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="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="456" 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">

456

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<pre style="margin: 0;">+<span id="LC456" class="line" lang="java">                         <span class="n" style="color: #333;">conn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setRequestProperty</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Cookie"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">cookies</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="457" 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">

457

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<pre style="margin: 0;">+<span id="LC457" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="458" 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">

458

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<pre style="margin: 0;">+<span id="LC458" class="line" lang="java">                 <span class="n" style="color: #333;">conn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addRequestProperty</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"User-Agent"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">useragent</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="459" 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">

459

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<pre style="margin: 0;">+<span id="LC459" class="line" lang="java">                 <span class="n" style="color: #333;">conn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setInstanceFollowRedirects</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="460" 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">

460

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC460" class="line" lang="java">                 <span class="n" style="color: #333;">conn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setConnectTimeout</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">timeout</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="461" 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">

461

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC461" class="line" lang="java">                 <span class="n" style="color: #333;">conn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setReadTimeout</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">timeout</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="462" 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">

462

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC462" class="line" lang="java">                 <span class="n" style="color: #333;">conn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">connect</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="463" 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">

463

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC463" class="line" lang="java">                 </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="464" 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">

464

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC464" class="line" lang="java">                 <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">conn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getResponseCode</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="465" 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">

465

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<pre style="margin: 0;">+<span id="LC465" class="line" lang="java">                 </span>

</pre>

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<pre style="margin: 0;">+<span id="LC466" class="line" lang="java">                 <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">info</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Redirecting from {} to {}"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">newUrl</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="467" 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="LC467" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="468" 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="LC468" class="line" lang="java">         <span class="n" style="color: #333;">conn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">connect</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="469" 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="LC469" class="line" lang="java">         </span>

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<td class="diff-line-num new old_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="470" 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="LC470" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">conn</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC471" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC472" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC473" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">StringBuilder</span> <span class="nf" style="color: #900; font-weight: 600;">fetchUniprotXML</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">uniprotURL</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC474" class="line" lang="java">                 <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">CompoundNotFoundException</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="423" 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="478" 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">@@ -423,11 +478,9 @@ public class UniprotProxySequenceReader<C extends Compound> implements ProxySequ</td>

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<pre style="margin: 0;"> <span id="LC478" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">attempt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC479" class="line" lang="java">         <span class="n" style="color: #333;">List</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">errorCodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ArrayList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">>();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC480" class="line" lang="java">         <span class="k" style="font-weight: 600;">while</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">attempt</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num old old_line" data-linenumber="426" 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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<td class="diff-line-num new_line old" data-linenumber="481" 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="LC426" class="line" lang="java">                 <span class="n" style="color: #333;">HttpURLConnection</span> <span class="n" style="color: #333;">uniprotConnection</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">HttpURLConnection</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">uniprot</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">openConnection</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="427" 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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<td class="diff-line-num new_line old" data-linenumber="481" 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="LC427" class="line" lang="java">                 <span class="n" style="color: #333;">uniprotConnection</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setRequestProperty</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"User-Agent"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"BioJava"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="428" 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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<td class="diff-line-num new_line old" data-linenumber="481" 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="LC428" class="line" lang="java">                 <span class="n" style="color: #333;">uniprotConnection</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">connect</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="481" 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="LC481" class="line" lang="java">                 <span class="n" style="color: #333;">HttpURLConnection</span> <span class="n" style="color: #333;">uniprotConnection</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">openURLConnection</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">uniprot</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC482" class="line" lang="java">                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">statusCode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">uniprotConnection</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getResponseCode</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;">-<span id="LC430" 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;">statusCode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left right">200</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="LC483" 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;">statusCode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left">HttpURLConnection</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff right">HTTP_OK</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="LC484" class="line" lang="java">                         <span class="n" style="color: #333;">BufferedReader</span> <span class="n" style="color: #333;">in</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BufferedReader</span><span class="o" style="font-weight: 600;">(</span></span>

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<pre style="margin: 0;"> <span id="LC485" class="line" lang="java">                                         <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">InputStreamReader</span><span class="o" style="font-weight: 600;">(</span></span>

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<pre style="margin: 0;"> <span id="LC486" class="line" lang="java">                                         <span class="n" style="color: #333;">uniprotConnection</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getInputStream</span><span class="o" style="font-weight: 600;">()));</span></span>

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<br>

</li>

<li id="ec64509af8ef0c0b83ce584250c53a9e179a35d7">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#ec64509af8ef0c0b83ce584250c53a9e179a35d7"><strong>biojava-genome/pom.xml</strong></a>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="xml">    <span class="nt" style="color: navy;"><parent></span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="xml">            <span class="nt" style="color: navy;"><artifactId></span>biojava<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="xml">            <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="xml">            <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="xml">            <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="xml">    <span class="nt" style="color: navy;"></parent></span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="xml">    <span class="nt" style="color: navy;"><modelVersion></span>4.0.0<span class="nt" style="color: navy;"></modelVersion></span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="xml">    <span class="nt" style="color: navy;"><artifactId></span>biojava-genome<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="xml">           <span class="nt" style="color: navy;"><dependency></span></span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="xml">                   <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="xml">                   <span class="nt" style="color: navy;"><artifactId></span>biojava-core<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="xml">                   <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="xml">                   <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="xml">                   <span class="nt" style="color: navy;"><scope></span>compile<span class="nt" style="color: navy;"></scope></span></span>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="xml">           <span class="nt" style="color: navy;"></dependency></span></span>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="xml">           <span class="nt" style="color: navy;"><dependency></span></span>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="xml">                   <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="xml">                   <span class="nt" style="color: navy;"><artifactId></span>biojava-alignment<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC94" class="line" lang="xml">                   <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="xml">                   <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="xml">                   <span class="nt" style="color: navy;"><scope></span>compile<span class="nt" style="color: navy;"></scope></span></span>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="xml">           <span class="nt" style="color: navy;"></dependency></span></span>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="xml">           <span class="nt" style="color: navy;"><dependency></span></span>

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<br>

</li>

<li id="184b5673dd964353dc02ee87944303b467d3d155">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#184b5673dd964353dc02ee87944303b467d3d155"><strong>biojava-integrationtest/pom.xml</strong></a>

<hr>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="xml">  <span class="nt" style="color: navy;"><parent></span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="xml">    <span class="nt" style="color: navy;"><artifactId></span>biojava<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="xml">    <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="xml">    <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="xml">    <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="xml">  <span class="nt" style="color: navy;"></parent></span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="xml">  <span class="nt" style="color: navy;"><artifactId></span>biojava-integrationtest<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="xml">  <span class="nt" style="color: navy;"><packaging></span>jar<span class="nt" style="color: navy;"></packaging></span></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="xml">    <span class="nt" style="color: navy;"><dependency></span></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="xml">           <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="xml">           <span class="nt" style="color: navy;"><artifactId></span>biojava-structure<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="xml">           <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="xml">           <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="xml">    <span class="nt" style="color: navy;"></dependency></span></span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="xml">           <span class="c" style="color: #998; font-style: italic;"><!-- logging dependencies (managed by parent pom, don't set versions or scopes here) --></span></span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="xml">           <span class="nt" style="color: navy;"><dependency></span></span>

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<br>

</li>

<li id="dc21809df6dca39aab598512feab461669a06121">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#dc21809df6dca39aab598512feab461669a06121"><strong>biojava-modfinder/pom.xml</strong></a>

<hr>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="xml">  <span class="nt" style="color: navy;"><parent></span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="xml">    <span class="nt" style="color: navy;"><artifactId></span>biojava<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="xml">    <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="xml">    <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="xml">    <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="xml">  <span class="nt" style="color: navy;"></parent></span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="xml">  <span class="nt" style="color: navy;"><artifactId></span>biojava-modfinder<span class="nt" style="color: navy;"></artifactId></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="xml">  <span class="nt" style="color: navy;"><name></span>biojava-modfinder<span class="nt" style="color: navy;"></name></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" 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="31" 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">@@ -31,7 +31,7 @@</td>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="xml">    <span class="nt" style="color: navy;"><dependency></span></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="xml">           <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="xml">           <span class="nt" style="color: navy;"><artifactId></span>biojava-structure<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="xml">           <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="xml">           <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="xml">           <span class="nt" style="color: navy;"><type></span>jar<span class="nt" style="color: navy;"></type></span></span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="xml">           <span class="nt" style="color: navy;"><scope></span>compile<span class="nt" style="color: navy;"></scope></span></span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="xml">    <span class="nt" style="color: navy;"></dependency></span></span>

</pre>

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<br>

</li>

<li id="fbe68b243f2c27bad79188712b2f1cef1b94a53b">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#fbe68b243f2c27bad79188712b2f1cef1b94a53b"><strong>biojava-ontology/pom.xml</strong></a>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="xml">  <span class="nt" style="color: navy;"><parent></span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="xml">    <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="xml">    <span class="nt" style="color: navy;"><artifactId></span>biojava<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="xml">    <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="xml">    <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="xml">  <span class="nt" style="color: navy;"></parent></span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="xml"></span>

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10" class="line" lang="xml">  <span class="nt" style="color: navy;"><artifactId></span>biojava-ontology<span class="nt" style="color: navy;"></artifactId></span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="20dfbfc7ba8f72600e13d2ecd32c9eae858f1b56">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#20dfbfc7ba8f72600e13d2ecd32c9eae858f1b56"><strong>biojava-phylo/pom.xml</strong></a>

<hr>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="xml">  <span class="nt" style="color: navy;"><parent></span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="xml">    <span class="nt" style="color: navy;"><artifactId></span>biojava<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="xml">    <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="xml">    <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="xml">    <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="xml">  <span class="nt" style="color: navy;"></parent></span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="xml">  <span class="nt" style="color: navy;"><modelVersion></span>4.0.0<span class="nt" style="color: navy;"></modelVersion></span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="xml">  <span class="nt" style="color: navy;"><artifactId></span>biojava-phylo<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="xml">    <span class="nt" style="color: navy;"><dependency></span></span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="xml">      <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="xml">      <span class="nt" style="color: navy;"><artifactId></span>biojava-core<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="xml">      <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="xml">      <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="xml">      <span class="nt" style="color: navy;"><scope></span>compile<span class="nt" style="color: navy;"></scope></span></span>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="xml">    <span class="nt" style="color: navy;"></dependency></span></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="xml">    <span class="nt" style="color: navy;"><dependency></span></span>

</pre>

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<br>

</li>

<li id="b50cb5175e0cabb113c6322d1bba1d5e14f82029">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#b50cb5175e0cabb113c6322d1bba1d5e14f82029"><strong>biojava-protein-disorder/pom.xml</strong></a>

<hr>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="xml">    <span class="nt" style="color: navy;"><parent></span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="xml">            <span class="nt" style="color: navy;"><artifactId></span>biojava<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="xml">            <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="xml">            <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="xml">            <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="xml">    <span class="nt" style="color: navy;"></parent></span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="xml">    <span class="nt" style="color: navy;"><artifactId></span>biojava-protein-disorder<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="xml">    <span class="nt" style="color: navy;"><packaging></span>jar<span class="nt" style="color: navy;"></packaging></span></span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="xml">           <span class="nt" style="color: navy;"><dependency></span></span>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="xml">                   <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="xml">                   <span class="nt" style="color: navy;"><artifactId></span>biojava-core<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="xml">                   <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="xml">                   <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="xml">           <span class="nt" style="color: navy;"></dependency></span></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="xml">           <span class="c" style="color: #998; font-style: italic;"><!-- logging dependencies (managed by parent pom, don't set versions or </span></span>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;">                        scopes here) --></span></span>

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<br>

</li>

<li id="7d8914fa09bceaff9477f6ec0ba8f629228de925">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#7d8914fa09bceaff9477f6ec0ba8f629228de925"><strong>biojava-sequencing/pom.xml</strong></a>

<hr>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="xml">    <span class="nt" style="color: navy;"><parent></span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="xml">            <span class="nt" style="color: navy;"><artifactId></span>biojava<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="xml">            <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="xml">            <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="xml">            <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="xml">    <span class="nt" style="color: navy;"></parent></span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="xml">    <span class="nt" style="color: navy;"><modelVersion></span>4.0.0<span class="nt" style="color: navy;"></modelVersion></span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="xml">    <span class="nt" style="color: navy;"><artifactId></span>biojava-sequencing<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="xml">           <span class="nt" style="color: navy;"><dependency></span></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="xml">                   <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="xml">                   <span class="nt" style="color: navy;"><artifactId></span>biojava-core<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="xml">                   <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="xml">                   <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="xml">                   <span class="nt" style="color: navy;"><scope></span>compile<span class="nt" style="color: navy;"></scope></span></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="xml">           <span class="nt" style="color: navy;"></dependency></span></span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="xml">           <span class="c" style="color: #998; font-style: italic;"><!-- logging dependencies (managed by parent pom, don't set versions or scopes here) --></span></span>

</pre>

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<br>

</li>

<li id="97d9023e3b6aa8ede87066949adb144e3921bd59">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#97d9023e3b6aa8ede87066949adb144e3921bd59"><strong>biojava-structure-gui/pom.xml</strong></a>

<hr>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="xml">    <span class="nt" style="color: navy;"><parent></span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="xml">        <span class="nt" style="color: navy;"><artifactId></span>biojava<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="xml">        <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="xml">        <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="xml">        <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="xml">    <span class="nt" style="color: navy;"></parent></span></span>

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8" class="line" lang="xml">    <span class="nt" style="color: navy;"><modelVersion></span>4.0.0<span class="nt" style="color: navy;"></modelVersion></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="xml">    <span class="nt" style="color: navy;"><artifactId></span>biojava-structure-gui<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="xml">        <span class="nt" style="color: navy;"><dependency></span></span>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="xml">            <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="xml">            <span class="nt" style="color: navy;"><artifactId></span>biojava-structure<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="xml">            <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="xml">            <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="xml">            <span class="nt" style="color: navy;"><scope></span>compile<span class="nt" style="color: navy;"></scope></span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="xml">        <span class="nt" style="color: navy;"></dependency></span></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="xml">        <span class="nt" style="color: navy;"><dependency></span></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="xml">            <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="xml">            <span class="nt" style="color: navy;"><artifactId></span>biojava-core<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="xml">            <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="xml">            <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="xml">            <span class="nt" style="color: navy;"><scope></span>compile<span class="nt" style="color: navy;"></scope></span></span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="xml">        <span class="nt" style="color: navy;"></dependency></span></span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="xml"></span>

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<br>

</li>

<li id="bc75ba48356609052210fbf9f8f39f1d265b6c6e">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#bc75ba48356609052210fbf9f8f39f1d265b6c6e"><strong>biojava-structure/pom.xml</strong></a>

<hr>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="xml">    <span class="nt" style="color: navy;"><parent></span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="xml">            <span class="nt" style="color: navy;"><artifactId></span>biojava<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="xml">            <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="xml">            <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="xml">            <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="xml">    <span class="nt" style="color: navy;"></parent></span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="xml">    <span class="nt" style="color: navy;"><artifactId></span>biojava-structure<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="xml">   <span class="nt" style="color: navy;"><name></span>biojava-structure<span class="nt" style="color: navy;"></name></span></span>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="xml">           <span class="nt" style="color: navy;"><dependency></span></span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="xml">                   <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="xml">                   <span class="nt" style="color: navy;"><artifactId></span>biojava-alignment<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="xml">                   <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="xml">                   <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="xml">                   <span class="nt" style="color: navy;"><scope></span>compile<span class="nt" style="color: navy;"></scope></span></span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="xml">           <span class="nt" style="color: navy;"></dependency></span></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="xml">           <span class="nt" style="color: navy;"><dependency></span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="xml">                   <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="xml">                   <span class="nt" style="color: navy;"><artifactId></span>biojava-core<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="xml">                   <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="xml">                   <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="xml">                   <span class="nt" style="color: navy;"><scope></span>compile<span class="nt" style="color: navy;"></scope></span></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="xml">           <span class="nt" style="color: navy;"></dependency></span></span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="xml"></span>

</pre>

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</li>

<li id="eaa9e59d5ea8eb17c7253f6af6e97b922791c6cb">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#eaa9e59d5ea8eb17c7253f6af6e97b922791c6cb"><strong>biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="119" 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="119" 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">@@ -119,6 +119,11 @@ public class StructureIO {</td>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">setAtomCache</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">AtomCache</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">){</span></span>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="java">         <span class="n" style="color: #333;">cache</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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<td class="diff-line-num new old_line" data-linenumber="122" 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="LC122" class="line" lang="java"> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="123" 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="LC123" 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;">AtomCache</span> <span class="nf" style="color: #900; font-weight: 600;">getAtomCache</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="122" 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="LC124" class="line" lang="java">         <span class="n" style="color: #333;">checkInitAtomCache</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="125" 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="LC125" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cache</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="126" 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="LC126" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC128" 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="LC129" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * Returns the first biologicalAssembly that is available for a protein structure. For more documentation on quaternary structures see:</span></span>

</pre>

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<br>

</li>

<li id="3acb1c5c4dfcadec7cbaaf6c563ea7c1318e0947">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#3acb1c5c4dfcadec7cbaaf6c563ea7c1318e0947"><strong>biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="636" 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="636" 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">@@ -636,6 +636,7 @@ public class CathInstallation implements CathDatabase{</td>

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<pre style="margin: 0;"> <span id="LC636" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC637" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">downloadFileFromRemote</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">URL</span> <span class="n" style="color: #333;">remoteURL</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">localFile</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span><span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC638" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//        System.out.println("downloading " + remoteURL + " to: " + localFile);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC639" class="line" lang="java">         <span class="n" style="color: #333;">LOGGER</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">info</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Downloading file {} to local file {}"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">remoteURL</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">localFile</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC640" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC641" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">timeS</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">currentTimeMillis</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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641

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<pre style="margin: 0;"> <span id="LC642" class="line" lang="java">         <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">tempFile</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">File</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">createTempFile</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">FileDownloadUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getFilePrefix</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">localFile</span><span class="o" style="font-weight: 600;">),</span> <span class="s" style="color: #d14;">"."</span><span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">FileDownloadUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getFileExtension</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">localFile</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="665" 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="666" 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">@@ -665,7 +666,7 @@ public class CathInstallation implements CathDatabase{</td>

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<pre style="margin: 0;"> <span id="LC666" class="line" lang="java">                 <span class="n" style="color: #333;">disp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">disp</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">1024.0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC667" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC668" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">timeE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">currentTimeMillis</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="668" 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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<td class="diff-line-num new_line old" data-linenumber="669" 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="LC668" class="line" lang="java">         <span class="n" style="color: #333;">LOGGER</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">info</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Downloaded <span class="idiff left">file {} ({}) to local file {} in {} sec."</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">remoteURL</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">String</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">format</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"%.1f"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">disp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">unit</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">localFile</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">timeE</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">timeS</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)/</span></span><span class="mi" style="color: #099;"><span class="idiff right">1000</span></span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC669" class="line" lang="java">         <span class="n" style="color: #333;">LOGGER</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">info</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Downloaded <span class="idiff left">{} in {} sec. to {}"</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">String</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">format</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"%.1f"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">disp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">unit</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">timeE</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">timeS</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)/</span></span><span class="mi" style="color: #099;"><span class="idiff">1000</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 right">localFile</span></span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC670" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC671" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC672" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">domainDescriptionFileAvailable</span><span class="o" style="font-weight: 600;">(){</span></span>

</pre>

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<br>

</li>

<li id="fc5afcafbad3aa57eae2562032c7f9f7c8df9eb3">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#fc5afcafbad3aa57eae2562032c7f9f7c8df9eb3"><strong>biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="35" 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">@@ -35,6 +35,7 @@ import java.io.File;</td>

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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;">java.io.IOException</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="36" 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">

36

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC36" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.InputStream</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="37" 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">

37

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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;">java.net.URL</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="38" 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="LC38" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.nio.file.Files</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

38

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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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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;">java.text.ParseException</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<td class="diff-line-num new_line" data-linenumber="40" 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">

40

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC40" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.text.SimpleDateFormat</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="40" 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">

40

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<td class="diff-line-num new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC41" 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>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="127" 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="128" 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">@@ -127,6 +128,9 @@ public abstract class LocalPDBDirectory implements StructureIOFile {</td>

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<td class="diff-line-num old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</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;">lineSplit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getProperty</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"file.separator"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="131" 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="LC131" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/** Minimum size for a valid structure file (CIF or PDB), in bytes */</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="132" 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="LC132" 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="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">MIN_PDB_FILE_SIZE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">;</span>  <span class="c1" style="color: #998; font-style: italic;">// Empty gzip files are 20bytes. Add a few more for buffer.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="133" 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="LC133" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">List</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="402" 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="406" 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">@@ -402,8 +406,9 @@ public abstract class LocalPDBDirectory implements StructureIOFile {</td>

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<td class="diff-line-num old_line" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC406" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * Attempts to delete all versions of a structure from the local directory.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC407" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @param pdbId</span></span>

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<pre style="margin: 0;"> <span id="LC408" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @return True if one or more files were deleted</span></span>

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<pre style="margin: 0;">+<span id="LC409" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @throws IOException if the file cannot be deleted</span></span>

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<pre style="margin: 0;"> <span id="LC410" 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="LC406" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">deleteStructure</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">pdbId</span><span class="o" style="font-weight: 600;">){</span></span>

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<pre style="margin: 0;">+<span id="LC411" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">deleteStructure</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">pdbId</span><span class="o" style="font-weight: 600;">)</span><span class="idiff left"> </span><span class="kd" style="font-weight: 600;"><span class="idiff">throws</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">IOException</span></span><span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC412" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">deleted</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC413" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">// Force getLocalFile to check in obsolete locations</span></span>

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<pre style="margin: 0;"> <span id="LC414" class="line" lang="java">         <span class="n" style="color: #333;">ObsoleteBehavior</span> <span class="n" style="color: #333;">obsolete</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getObsoleteBehavior</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="421" 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">@@ -421,7 +426,7 @@ public abstract class LocalPDBDirectory implements StructureIOFile {</td>

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<pre style="margin: 0;"> <span id="LC426" class="line" lang="java">                         <span class="c1" style="color: #998; font-style: italic;">// delete file</span></span>

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<pre style="margin: 0;"> <span id="LC427" class="line" lang="java">                         <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">existing</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">delete</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC428" 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;">success</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="LC424" class="line" lang="java">                                 <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;"><span class="idiff left right">info</span></span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Deleting "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">existing</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getAbsolutePath</span><span class="o" style="font-weight: 600;">());</span></span>

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<td class="diff-line-num new new_line" data-linenumber="429" 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="LC429" class="line" lang="java">                                 <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;"><span class="idiff left right">debug</span></span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Deleting "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">existing</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getAbsolutePath</span><span class="o" style="font-weight: 600;">());</span></span>

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<pre style="margin: 0;"> <span id="LC430" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC431" class="line" lang="java">                         <span class="n" style="color: #333;">deleted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">deleted</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">success</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC432" class="line" lang="java"></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="435" 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">@@ -430,7 +435,7 @@ public abstract class LocalPDBDirectory implements StructureIOFile {</td>

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<pre style="margin: 0;"> <span id="LC435" 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;">parent</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="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC436" class="line" lang="java">                                 <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">delete</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC437" 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;">success</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num new_line old" data-linenumber="438" 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="LC433" class="line" lang="java">                                         <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;"><span class="idiff left right">info</span></span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Deleting "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getAbsolutePath</span><span class="o" style="font-weight: 600;">());</span></span>

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<pre style="margin: 0;">+<span id="LC438" class="line" lang="java">                                         <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;"><span class="idiff left right">debug</span></span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Deleting "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getAbsolutePath</span><span class="o" style="font-weight: 600;">());</span></span>

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<pre style="margin: 0;"> <span id="LC439" class="line" lang="java">                                 <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC440" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC441" class="line" lang="java"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="660" 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="665" 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">@@ -660,8 +665,9 @@ public abstract class LocalPDBDirectory implements StructureIOFile {</td>

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<pre style="margin: 0;"> <span id="LC665" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * Searches for previously downloaded files</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC666" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @param pdbId</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC667" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @return A file pointing to the existing file, or null if not found</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="668" 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="LC668" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @throws IOException If the file exists but is empty and can't be deleted</span></span>

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<pre style="margin: 0;"> <span id="LC669" 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="LC664" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">File</span> <span class="nf" style="color: #900; font-weight: 600;">getLocalFile</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">pdbId</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC670" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">File</span> <span class="nf" style="color: #900; font-weight: 600;">getLocalFile</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">pdbId</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;"><span class="idiff left">throws</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">IOException</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">{</span></span>

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665

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<pre style="margin: 0;"> <span id="LC671" class="line" lang="java"></span>

</pre>

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672

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<pre style="margin: 0;"> <span id="LC672" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">// Search for existing files</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="667" 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">

667

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<td class="diff-line-num new_line" data-linenumber="673" 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">

673

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<pre style="margin: 0;"> <span id="LC673" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="687" 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="693" 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">@@ -687,6 +693,11 @@ public abstract class LocalPDBDirectory implements StructureIOFile {</td>

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<td class="diff-line-num old_line" data-linenumber="687" 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">

687

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<td class="diff-line-num new_line" data-linenumber="693" 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">

693

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<pre style="margin: 0;"> <span id="LC693" 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;">String</span> <span class="n" style="color: #333;">ex</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">getExtensions</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">){</span></span>

</pre>

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688

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<td class="diff-line-num new_line" data-linenumber="694" 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">

694

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<pre style="margin: 0;"> <span id="LC694" class="line" lang="java">                                 <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">searchdir</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pdbId</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toLowerCase</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ex</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="689" 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">

689

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<td class="diff-line-num new_line" data-linenumber="695" 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">

695

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<pre style="margin: 0;"> <span id="LC695" 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;">f</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">exists</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="696" 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">

696

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<pre style="margin: 0;">+<span id="LC696" class="line" lang="java">                                         <span class="c1" style="color: #998; font-style: italic;">// delete files that are too short to have contents</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="690" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="697" 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">

697

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC697" 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;">f</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">MIN_PDB_FILE_SIZE</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="690" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="698" 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">

698

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<pre style="margin: 0;">+<span id="LC698" class="line" lang="java">                                                 <span class="n" style="color: #333;">Files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">delete</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toPath</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="699" 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">

699

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<pre style="margin: 0;">+<span id="LC699" class="line" lang="java">                                                 <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="700" 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="LC700" class="line" lang="java">                                         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="690" 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">

690

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<td class="diff-line-num new_line" data-linenumber="701" 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">

701

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<pre style="margin: 0;"> <span id="LC701" class="line" lang="java">                                         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="691" 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">

691

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<td class="diff-line-num new_line" data-linenumber="702" 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">

702

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<pre style="margin: 0;"> <span id="LC702" class="line" lang="java">                                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="692" 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">

692

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<td class="diff-line-num new_line" data-linenumber="703" 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">

703

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC703" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="697" 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="708" 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">@@ -697,9 +708,11 @@ public abstract class LocalPDBDirectory implements StructureIOFile {</td>

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<td class="diff-line-num old_line" data-linenumber="697" 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">

697

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<td class="diff-line-num new_line" data-linenumber="708" 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">

708

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<pre style="margin: 0;"> <span id="LC708" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="698" 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">

698

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<td class="diff-line-num new_line" data-linenumber="709" 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">

709

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC709" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="710" 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">

710

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<pre style="margin: 0;"> <span id="LC710" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">checkFileExists</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">pdbId</span><span class="o" style="font-weight: 600;">){</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="711" 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="LC700" class="line" lang="java">         <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span>  <span class="n" style="color: #333;">getLocalFile</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pdbId</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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701

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<td class="diff-line-num new_line old" data-linenumber="711" 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="LC701" 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;">path</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>

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702

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<td class="diff-line-num new_line old" data-linenumber="711" 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="LC702" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="711" 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">

711

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<pre style="margin: 0;">+<span id="LC711" 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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<td class="diff-line-num new new_line" data-linenumber="712" 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">

712

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC712" class="line" lang="java">                 <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span>  <span class="n" style="color: #333;">getLocalFile</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pdbId</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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713

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<pre style="margin: 0;">+<span id="LC713" 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;">path</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>

</pre>

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714

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<pre style="margin: 0;">+<span id="LC714" class="line" lang="java">                         <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC715" 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;">IOException</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{}</span></span>

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703

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716

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<pre style="margin: 0;"> <span id="LC716" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC717" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC718" class="line" lang="java"></span>

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<br>

</li>

<li id="b718810c810230284c03cc47a47893ff188ffec6">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#b718810c810230284c03cc47a47893ff188ffec6"><strong>biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompGroupFactory.java</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="68" 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="68" 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">@@ -68,9 +68,8 @@ public class ChemCompGroupFactory {</td>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * again. Note that this change can have unexpected behavior of</span></span>

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69

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * code executed afterwards.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="70" 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">

70

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70

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * <p></span></span>

</pre>

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71

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<td class="diff-line-num new_line old" data-linenumber="71" 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="LC71" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * Changing the provider does not reset the cache, so Chemical</span></span>

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<td class="diff-line-num old old_line" data-linenumber="72" 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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<td class="diff-line-num new_line old" data-linenumber="71" 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="LC72" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * Component definitions already downloaded from previous providers</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="73" 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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<td class="diff-line-num new_line old" data-linenumber="71" 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="LC73" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * will be used. To reset the cache see {@link #getCache()).</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * Changing the provider also resets the cache, so any groups</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * previously accessed will be reread or re-downloaded.</span></span>

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<pre style="margin: 0;"> <span id="LC73" 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="LC74" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * @param provider</span></span>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       */</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">@@ -84,6 +83,15 @@ public class ChemCompGroupFactory {</td>

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<pre style="margin: 0;"> <span id="LC83" 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;">ChemCompProvider</span> <span class="nf" style="color: #900; font-weight: 600;">getChemCompProvider</span><span class="o" style="font-weight: 600;">(){</span></span>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="java">          <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">chemCompProvider</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="java">  <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="java">  </span>

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<pre style="margin: 0;">+<span id="LC87" 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="LC88" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * Force the in-memory cache to be reset.</span></span>

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<pre style="margin: 0;">+<span id="LC89" 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="LC90" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * Note that the ChemCompProvider may have additional memory or disk caches that need to be cleared too.</span></span>

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<pre style="margin: 0;">+<span id="LC91" 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="LC92" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">clearCache</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="LC93" class="line" lang="java">          <span class="n" style="color: #333;">cache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">clear</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="java">  <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC96" 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;">Group</span> <span class="nf" style="color: #900; font-weight: 600;">getGroupFromChemCompDictionary</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">recordName</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="LC97" class="line" lang="java"></span>

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<li id="c9544f544200a902cd1467f05515b3586169d9f4">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#c9544f544200a902cd1467f05515b3586169d9f4"><strong>biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="42" 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="42" 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">@@ -42,6 +42,7 @@ import java.util.zip.GZIPOutputStream;</td>

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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;">org.biojava.nbio.core.util.InputStreamProvider</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.align.util.HTTPConnectionTools</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.align.util.UserConfiguration</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="45" 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="LC45" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.io.LocalPDBDirectory</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.io.mmcif.model.ChemComp</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.slf4j.Logger</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.slf4j.LoggerFactory</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="85" 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="86" 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">@@ -85,6 +86,8 @@ public class DownloadChemCompProvider implements ChemCompProvider {</td>

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<td class="diff-line-num old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="java">          <span class="n" style="color: #333;">protectedIDs</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;">"AUX"</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="java">          <span class="n" style="color: #333;">protectedIDs</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;">"NUL"</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="java">  <span class="o" style="font-weight: 600;">}</span></span>

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<td class="diff-line-num new old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="89" 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="LC89" class="line" lang="java">  </span>

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<td class="diff-line-num new old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="90" 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="LC90" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">ChemCompProvider</span> <span class="n" style="color: #333;">fallback</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="c1" style="color: #998; font-style: italic;">// Fallback provider if the download fails</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="java">  <span class="cm" style="color: #998; font-style: italic;">/** by default we will download only some of the files. User has to request that all files should be downloaded...</span></span>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       *</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="92" 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="95" 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">@@ -92,25 +95,28 @@ public class DownloadChemCompProvider implements ChemCompProvider {</td>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="java">  <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">downloadAll</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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96

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC96" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="94" 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">

94

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<td class="diff-line-num new_line" data-linenumber="97" 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">

97

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">DownloadChemCompProvider</span><span class="o" style="font-weight: 600;">(){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="95" 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">

95

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<td class="diff-line-num new_line old" data-linenumber="98" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC95" class="line" lang="java">          <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">debug</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Initialising DownloadChemCompProvider"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="96" 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">

96

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<td class="diff-line-num new_line old" data-linenumber="98" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC96" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="97" 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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<td class="diff-line-num new_line old" data-linenumber="98" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC97" class="line" lang="java">          <span class="c1" style="color: #998; font-style: italic;">// note that path is static, so this is just to make sure that all non-static methods will have path initialised</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="98" 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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<td class="diff-line-num new_line old" data-linenumber="98" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC98" class="line" lang="java">          <span class="n" style="color: #333;">initPath</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC98" class="line" lang="java">          <span class="k" style="font-weight: 600;">this</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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC99" class="line" lang="java">  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC100" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC101" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">DownloadChemCompProvider</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">cacheFilePath</span><span class="o" style="font-weight: 600;">){</span></span>

</pre>

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<td class="diff-line-num old_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">

102

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<td class="diff-line-num 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">

102

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC102" class="line" lang="java">         <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">debug</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Initialising DownloadChemCompProvider"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="103" 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">

103

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<td class="diff-line-num new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="java"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC104" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">// note that path is static, so this is just to make sure that all non-static methods will have path initialised</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="105" 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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<td class="diff-line-num new_line old" data-linenumber="105" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC105" class="line" lang="java">         <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cacheFilePath</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_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">

</td>

<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">

105

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<pre style="margin: 0;">+<span id="LC105" 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;">cacheFilePath</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="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<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">

106

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC106" class="line" lang="java">                 <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cacheFilePath</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

107

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC107" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

106

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<td class="diff-line-num new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="110" 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="LC108" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">initPath</span><span class="o" style="font-weight: 600;">(){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="109" 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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<td class="diff-line-num new_line old" data-linenumber="110" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC109" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * Get this provider's cache path</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="112" 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="LC112" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @return</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="113" 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="LC113" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      */</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="114" 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="LC114" 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;">File</span> <span class="nf" style="color: #900; font-weight: 600;">getPath</span><span class="o" style="font-weight: 600;">(){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC115" 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;">path</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="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="java">                 <span class="n" style="color: #333;">UserConfiguration</span> <span class="n" style="color: #333;">config</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">UserConfiguration</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="java">                 <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getCacheFilePath</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="119" 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="LC119" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="127" 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="133" 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">@@ -127,7 +133,7 @@ public class DownloadChemCompProvider implements ChemCompProvider {</td>

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<td class="diff-line-num old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">// this makes sure there is a file separator between every component,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">// if path has a trailing file separator or not, it will work for both cases</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="130" 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="LC130" class="line" lang="java">         <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left right">path</span></span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">CHEM_COMP_CACHE_DIRECTORY</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="136" 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">

136

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="java">         <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">getPath</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>,</span> <span class="n" style="color: #333;">CHEM_COMP_CACHE_DIRECTORY</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="java">         <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dir</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"components.cif.gz"</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="139" 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">

139

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span> <span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">exists</span><span class="o" style="font-weight: 600;">())</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="161" 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="167" 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">@@ -161,7 +167,7 @@ public class DownloadChemCompProvider implements ChemCompProvider {</td>

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<td class="diff-line-num old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="java"></span>

</pre>

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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">

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<td class="diff-line-num new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="java">         <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">info</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Installing individual chem comp files ..."</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="164" 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="LC164" class="line" lang="java">         <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left right">path</span></span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">CHEM_COMP_CACHE_DIRECTORY</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="165" 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="LC170" class="line" lang="java">         <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">getPath</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>,</span> <span class="n" style="color: #333;">CHEM_COMP_CACHE_DIRECTORY</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="java">         <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dir</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"components.cif.gz"</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC173" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="212" 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="218" 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">@@ -212,7 +218,7 @@ public class DownloadChemCompProvider implements ChemCompProvider {</td>

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<td class="diff-line-num old_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      */</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">writeID</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">contents</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">currentID</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span><span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="java"></span>

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<td class="diff-line-num new_line old" data-linenumber="221" 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="LC215" class="line" lang="java">         <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">localName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">DownloadChemCompProvider</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="na" style="color: teal;">getLocalFileName</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">currentID</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="216" 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="LC221" class="line" lang="java">         <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">localName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getLocalFileName</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">currentID</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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="java">         <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">(</span> <span class="n" style="color: #333;">PrintWriter</span> <span class="n" style="color: #333;">pw</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">PrintWriter</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">GZIPOutputStream</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FileOutputStream</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">localName</span><span class="o" style="font-weight: 600;">)))</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="LC224" class="line" lang="java"></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="278" 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">@@ -272,7 +278,10 @@ public class DownloadChemCompProvider implements ChemCompProvider {</td>

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<pre style="margin: 0;"> <span id="LC278" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="java">                         <span class="n" style="color: #333;">ChemComp</span> <span class="n" style="color: #333;">chemComp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dict</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getChemComp</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">recordName</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC280" class="line" lang="java"></span>

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<pre style="margin: 0;">-<span id="LC275" class="line" lang="java">                         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">chemComp</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="276" 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="LC281" class="line" lang="java">                         <span class="c1" style="color: #998; font-style: italic;">// May be null if the file was corrupt. Fall back on ReducedChemCompProvider in that case</span></span>

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<td class="diff-line-num new old_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="282" 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="LC282" 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;">chemComp</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="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="283" 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="LC283" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">chemComp</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="284" 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="LC284" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC286" 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;">IOException</span> <span class="n" style="color: #333;">e</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="LC287" class="line" lang="java"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="296" 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="305" 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">@@ -296,9 +305,12 @@ public class DownloadChemCompProvider implements ChemCompProvider {</td>

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">// see https://github.com/biojava/biojava/issues/315</span></span>

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<pre style="margin: 0;"> <span id="LC307" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">// probably a network error happened. Try to use the ReducedChemCOmpProvider</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="308" 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="LC299" class="line" lang="java">         <span class="n" style="color: #333;">ReducedChemCompProvider</span> <span class="n" style="color: #333;">reduced</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ReducedChemCompProvider</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="diff-line-num new old_line" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="308" 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="LC308" 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;">fallback</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="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC309" class="line" lang="java">                 <span class="n" style="color: #333;">fallback</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ReducedChemCompProvider</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="java"></span>

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<pre style="margin: 0;">-<span id="LC301" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">reduced</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getChemComp</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">recordName</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="302" 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="LC312" class="line" lang="java">         <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">warn</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Falling back to ReducedChemCompProvider for {}. This could indicate a network error."</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">recordName</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC313" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fallback</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getChemComp</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">recordName</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC314" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC315" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC316" class="line" lang="java"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="313" 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="325" 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">@@ -313,16 +325,15 @@ public class DownloadChemCompProvider implements ChemCompProvider {</td>

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="java">                 <span class="n" style="color: #333;">recordName</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"_"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">recordName</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC326" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC327" class="line" lang="java"></span>

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<pre style="margin: 0;">-<span id="LC316" class="line" lang="java">         <span class="n" style="color: #333;">initPath</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="diff-line-num new_line old" data-linenumber="328" 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="LC317" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="318" 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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<td class="diff-line-num new_line old" data-linenumber="328" 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="LC318" class="line" lang="java">         <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">CHEM_COMP_CACHE_DIRECTORY</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="328" 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="LC328" class="line" lang="java">         <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">getPath</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">CHEM_COMP_CACHE_DIRECTORY</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC329" 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;">f</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">exists</span><span class="o" style="font-weight: 600;">()){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC330" class="line" lang="java">                 <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">info</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Creating directory "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC331" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_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">

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<pre style="margin: 0;"> <span id="LC332" class="line" lang="java">                 <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">mkdir</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="diff-line-num old_line" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC333" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">// we've checked in initPath that path is writable, so there's no need to check if it succeeds</span></span>

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<td class="diff-line-num old_line" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC334" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">// in the unlikely case that in the meantime it isn't writable at least we log an error</span></span>

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<pre style="margin: 0;">-<span id="LC325" 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;">success</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">error</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Directory {} could not be created"</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="326" 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="LC335" 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;">success</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="336" 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="LC336" class="line" lang="java">                         <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">error</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Directory {} could not be created"</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">f</span><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>

</pre>

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<pre style="margin: 0;"> <span id="LC338" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC339" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="337" 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="348" 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">@@ -337,6 +348,14 @@ public class DownloadChemCompProvider implements ChemCompProvider {</td>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="java">         <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fileName</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC350" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="351" 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="LC351" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">// delete files that are too short to have contents</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="352" 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="LC352" 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;">f</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">LocalPDBDirectory</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">MIN_PDB_FILE_SIZE</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="353" 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="LC353" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">// Delete defensively.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="354" 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="LC354" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">// Note that if delete is unsuccessful, we re-download the file anyways</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="355" 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="LC355" class="line" lang="java">                 <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">delete</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC356" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC357" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC358" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC359" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">exists</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC360" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC361" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<br>

</li>

<li id="cd1a85bfbcb2f8b5bfe993e88e9fdf07b5d1556f">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#cd1a85bfbcb2f8b5bfe993e88e9fdf07b5d1556f"><strong>biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="212" 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="212" 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">@@ -212,6 +212,9 @@ public class SimpleMMcifParser implements MMcifParser {</td>

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<td class="diff-line-num old_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">// the first line is a data_PDBCODE line, test if this looks like a mmcif file</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="java">         <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">readLine</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="215" 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="LC215" class="line" lang="java">         <span class="k" style="font-weight: 600;">while</span><span class="o" style="font-weight: 600;">(</span> <span class="n" style="color: #333;">line</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="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">isEmpty</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">startsWith</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">COMMENT_CHAR</span><span class="o" style="font-weight: 600;">)))</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="216" 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="LC216" class="line" lang="java">                 <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">readLine</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="java">         <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="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">line</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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">startsWith</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">MMCIF_TOP_HEADER</span><span class="o" style="font-weight: 600;">)){</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="java">                 <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">error</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"This does not look like a valid mmCIF file! The first line should start with 'data_', but is: '"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"'"</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;">triggerDocumentEnd</span><span class="o" style="font-weight: 600;">();</span></span>

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<br>

</li>

<li id="fe1edc857045a7d0455eeeb9e81b445b8fce3865">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#fe1edc857045a7d0455eeeb9e81b445b8fce3865"><strong>biojava-structure/src/main/java/org/biojava/nbio/structure/io/util/FileDownloadUtils.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">@@ -21,9 +21,6 @@</td>

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<pre style="margin: 0;"> <span id="LC21" 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="LC22" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">org</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">biojava</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">nbio</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">structure</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">io</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">util</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="java"></span>

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<td class="diff-line-num old old_line" data-linenumber="24" 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="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.slf4j.Logger</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new_line old" data-linenumber="24" 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="LC25" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.slf4j.LoggerFactory</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new_line old" data-linenumber="24" 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="LC26" class="line" lang="java"></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.io.File</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;">java.io.FileInputStream</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 class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.FileOutputStream</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="36" 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="33" 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">@@ -36,6 +33,15 @@ import java.net.URLConnection;</td>

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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;">java.nio.channels.Channels</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;">java.nio.channels.FileChannel</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;">java.nio.channels.ReadableByteChannel</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="36" 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="LC36" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.nio.file.FileVisitResult</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="37" 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="LC37" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.nio.file.Files</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="38" 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="LC38" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.nio.file.Path</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="39" 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="LC39" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.nio.file.Paths</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="40" 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="LC40" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.nio.file.SimpleFileVisitor</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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;">java.nio.file.attribute.BasicFileAttributes</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="42" 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="LC42" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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;">org.slf4j.Logger</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.slf4j.LoggerFactory</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="java"></span>

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<td class="diff-line-num old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC46" 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;">FileDownloadUtils</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="java"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="240" 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="246" 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">@@ -240,6 +246,41 @@ public class FileDownloadUtils {</td>

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<td class="diff-line-num old_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="java">         <span class="n" style="color: #333;">connection</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setConnectTimeout</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">timeout</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">connection</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="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">

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="249" 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="LC249" class="line" lang="java"> </span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="250" 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="LC250" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="251" 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="LC251" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * Recursively delete a folder & contents</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="252" 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="LC252" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      *</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="253" 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="LC253" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @param dir directory to delete</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="254" 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">

254

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<pre style="margin: 0;">+<span id="LC254" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      */</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="255" 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="LC255" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">deleteDirectory</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Path</span> <span class="n" style="color: #333;">dir</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="256" 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">

256

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<pre style="margin: 0;">+<span id="LC256" 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;">dir</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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">Files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">exists</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dir</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="257" 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">

257

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<pre style="margin: 0;">+<span id="LC257" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="258" 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="LC258" class="line" lang="java">         <span class="n" style="color: #333;">Files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">walkFileTree</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dir</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">SimpleFileVisitor</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Path</span><span class="o" style="font-weight: 600;">>()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="259" 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">

259

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<pre style="margin: 0;">+<span id="LC259" class="line" lang="java">         <span class="nd">@Override</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="260" 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="LC260" class="line" lang="java">         <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">FileVisitResult</span> <span class="nf" style="color: #900; font-weight: 600;">visitFile</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Path</span> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">BasicFileAttributes</span> <span class="n" style="color: #333;">attrs</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="261" 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="LC261" class="line" lang="java">             <span class="n" style="color: #333;">Files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">delete</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="262" 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">

262

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="java">             <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">FileVisitResult</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">CONTINUE</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="263" 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">

263

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="264" 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="LC264" class="line" lang="java"></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="265" 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="LC265" class="line" lang="java">         <span class="nd">@Override</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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">

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="java">         <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">FileVisitResult</span> <span class="nf" style="color: #900; font-weight: 600;">postVisitDirectory</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Path</span> <span class="n" style="color: #333;">dir</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">IOException</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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">

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<pre style="margin: 0;">+<span id="LC267" 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;">e</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="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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">

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="java">                 <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="269" 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="LC269" class="line" lang="java">             <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="270" 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="LC270" class="line" lang="java">             <span class="n" style="color: #333;">Files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">delete</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dir</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="271" 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">

271

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="java">             <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">FileVisitResult</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">CONTINUE</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="272" 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">

272

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="273" 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">

273

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="java">     <span class="o" style="font-weight: 600;">});</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="274" 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">

274

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="275" 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">

275

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="276" 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">

276

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * Recursively delete a folder & contents</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="277" 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">

277

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      *</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="278" 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="LC278" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @param dir directory to delete</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="279" 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="LC279" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      */</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="280" 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="LC280" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">deleteDirectory</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">dir</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="281" 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">

281

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="java">         <span class="n" style="color: #333;">deleteDirectory</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Paths</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;">dir</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="282" 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">

282

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="283" 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="LC283" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC284" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC286" class="line" lang="java">         <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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</table>

<br>

</li>

<li id="7fb985a3aeb9a4f46da35200e130b1ef891eb9be">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#7fb985a3aeb9a4f46da35200e130b1ef891eb9be"><strong>biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.java</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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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">@@ -81,7 +81,7 @@ public class CeSymmResult {</td>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="java">          <span class="c1" style="color: #998; font-style: italic;">// If the refinement was attempted</span></span>

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<pre style="margin: 0;"> <span id="LC82" 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;">params</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getRefineMethod</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">RefineMethod</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">NOT_REFINED</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="LC83" class="line" lang="java">                  <span class="c1" style="color: #998; font-style: italic;">// Check for minimum length</span></span>

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<pre style="margin: 0;">-<span id="LC84" 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;">multipleAlignment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getCoreLength</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getMinCoreLength</span><span class="o" style="font-weight: 600;">())</span></span>

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<pre style="margin: 0;">+<span id="LC84" 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;">multipleAlignment</span><span class="idiff left"> </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">null</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">multipleAlignment</span></span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getCoreLength</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getMinCoreLength</span><span class="o" style="font-weight: 600;">())</span></span>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="java">                          <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="java">                  <span class="c1" style="color: #998; font-style: italic;">// Allow 90% of original TM-Score theshold</span></span>

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<pre style="margin: 0;"> <span id="LC87" 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;">multipleAlignment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getScore</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">MultipleAlignmentScorer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">AVGTM_SCORE</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">params</span></span>

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<br>

</li>

<li id="efb614d21e140fe6ec68bf881794ca2b0b175e60">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#efb614d21e140fe6ec68bf881794ca2b0b175e60"><strong>biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomCache.java</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="46" 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">@@ -46,7 +46,7 @@ public class TestAtomCache {</td>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">AtomCache</span> <span class="n" style="color: #333;">cache</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>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="java">  <span class="nd">@Before</span></span>

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<pre style="margin: 0;">-<span id="LC49" 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;">setUp</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="LC49" 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;">setUp</span><span class="o" style="font-weight: 600;">()</span> <span class="kd" style="font-weight: 600;"><span class="idiff left">throws</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">IOException</span></span><span class="idiff right"> </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="n" style="color: #333;">cache</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">AtomCache</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>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="java">          <span class="c1" style="color: #998; font-style: italic;">// Delete files which were cached in previous tests</span></span>

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<li id="92a752fb8611c5f680cbf31058ac2f489a7cc933">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#92a752fb8611c5f680cbf31058ac2f489a7cc933"><strong>biojava-structure/src/test/java/org/biojava/nbio/structure/TestExperimentalTechniques.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">@@ -31,7 +31,7 @@ import static org.junit.Assert.*;</td>

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<pre style="margin: 0;"> <span id="LC31" 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;">TestExperimentalTechniques</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="nd">@Test</span></span>

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<pre style="margin: 0;">-<span id="LC34" 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;">test<span class="idiff left right">4LNC</span></span><span class="o" style="font-weight: 600;">()</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">StructureException</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="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;">test<span class="idiff left right">6F2Q</span></span><span class="o" style="font-weight: 600;">()</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">StructureException</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>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="java">          <span class="c1" style="color: #998; font-style: italic;">// a multiple experimental techniques PDB entry (X-RAY + NEUTRON DIFFRACTION)</span></span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="java"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="40" 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="40" 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">@@ -40,9 +40,9 @@ public class TestExperimentalTechniques {</td>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="java">          <span class="n" style="color: #333;">StructureIO</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setAtomCache</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cache</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>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="java">          <span class="n" style="color: #333;">cache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setUseMmCif</span><span class="o" style="font-weight: 600;">(</span><span class="kc" style="font-weight: 600;">false</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="n" style="color: #333;">Structure</span> <span class="n" style="color: #333;">sPdb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StructureIO</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getStructure</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"<span class="idiff left right">4LNC</span>"</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="n" style="color: #333;">Structure</span> <span class="n" style="color: #333;">sPdb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StructureIO</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getStructure</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"<span class="idiff left right">6F2Q</span>"</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 class="n" style="color: #333;">cache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setUseMmCif</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="LC45" class="line" lang="java">          <span class="n" style="color: #333;">Structure</span> <span class="n" style="color: #333;">sCif</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StructureIO</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getStructure</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"<span class="idiff left right">4LNC</span>"</span><span class="o" style="font-weight: 600;">);</span></span>

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45

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="java">          <span class="n" style="color: #333;">Structure</span> <span class="n" style="color: #333;">sCif</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StructureIO</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getStructure</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"<span class="idiff left right">6F2Q</span>"</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC46" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="java">          <span class="n" style="color: #333;">comparePdbToCif</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sPdb</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sCif</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>

</pre>

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<br>

</li>

<li id="75ee9ec412f2376a5ff1cd5c2e8f58aeadee5e26">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#75ee9ec412f2376a5ff1cd5c2e8f58aeadee5e26"><strong>biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java</strong></a>

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<pre style="margin: 0;"> <span id="LC20" 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="LC21" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">org</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">biojava</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">nbio</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">structure</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">align</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">util</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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="23" 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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<td class="diff-line-num new_line old" data-linenumber="23" 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="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.*</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="23" 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="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">static</span> <span class="n" style="color: #333;">org</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">junit</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="24" 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="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">static</span> <span class="n" style="color: #333;">org</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">junit</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertNotNull</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="25" 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="LC25" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">static</span> <span class="n" style="color: #333;">org</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">junit</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertNull</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="26" 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="LC26" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">static</span> <span class="n" style="color: #333;">org</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">junit</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertTrue</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="24" 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="LC27" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">static</span> <span class="n" style="color: #333;">org</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">junit</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">fail</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="24" 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="LC28" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="29" 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="LC29" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.File</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="30" 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">

30

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC30" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.FileOutputStream</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="31" 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">

31

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC31" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.IOException</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="32" 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">

32

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC32" 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>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="33" 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">

33

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<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;">java.nio.file.Files</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="34" 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">

34

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC34" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.nio.file.Path</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="35" 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">

35

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC35" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.nio.file.Paths</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="36" 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">

36

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC36" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.text.ParseException</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="37" 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">

37

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC37" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.text.SimpleDateFormat</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="38" 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">

38

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC38" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Date</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="39" 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">

39

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC39" 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>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="40" 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">

40

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC40" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Locale</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

41

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<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;">java.util.zip.GZIPOutputStream</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="42" 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">

42

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC42" class="line" lang="java"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

43

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<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;">org.biojava.nbio.structure.AtomPositionMap</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

44

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC44" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.Chain</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="45" 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">

45

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC45" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.Group</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="46" 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">

46

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC46" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.ResidueRangeAndLength</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="47" 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">

47

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC47" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.Structure</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<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;">org.biojava.nbio.structure.StructureException</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="49" 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">

49

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC49" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.StructureIO</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="50" 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">

50

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<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;">org.biojava.nbio.structure.StructureIdentifier</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="51" 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">

51

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC51" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.StructureTools</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="52" 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">

52

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<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;">org.biojava.nbio.structure.SubstructureIdentifier</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" 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">

24

</td>

<td class="diff-line-num new_line" data-linenumber="53" 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">

53

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC53" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.io.LocalPDBDirectory</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="25" 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">

25

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<td class="diff-line-num new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC54" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="26" 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">

26

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<td class="diff-line-num new_line" data-linenumber="55" 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">

55

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC55" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="27" 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">

27

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<td class="diff-line-num new_line" data-linenumber="56" 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">

56

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC56" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.io.MMCIFFileReader</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="28" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC57" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="28" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC58" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="28" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC59" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.io.mmcif.model.ChemComp</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="28" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC60" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.io.util.FileDownloadUtils</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC61" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.scop.ScopDatabase</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="29" 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">

29

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<td class="diff-line-num new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC62" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.scop.ScopFactory</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="30" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC63" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.test.util.GlobalsHelper</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="30" 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">

30

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<td class="diff-line-num new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC64" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.junit.After</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="31" 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">

31

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<td class="diff-line-num new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC65" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.junit.Before</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="32" 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">

32

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<td class="diff-line-num new_line" data-linenumber="66" 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">

66

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC66" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.junit.Test</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="33" 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="LC33" class="line" lang="java"></span>

</pre>

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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;">java.io.File</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;">java.io.IOException</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;">java.text.ParseException</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;">java.text.SimpleDateFormat</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;">java.util.Date</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;">java.util.List</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;">java.util.Locale</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>

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<td class="diff-line-num old old_line" data-linenumber="42" 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="LC42" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">static</span> <span class="n" style="color: #333;">org</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">junit</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">Assert</span><span class="o" style="font-weight: 600;">.*;</span></span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.slf4j.Logger</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 class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.slf4j.LoggerFactory</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>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -49,22 +75,24 @@ import static org.junit.Assert.*;</td>

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<pre style="margin: 0;"> <span id="LC75" 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="LC76" 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;">AtomCacheTest</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="java"></span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">Logger</span> <span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LoggerFactory</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getLogger</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">AtomCacheTest</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>

</pre>

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<td class="diff-line-num new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">AtomCache</span> <span class="n" style="color: #333;">cache</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">previousPDB_DIR</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="java">  <span class="nd">@Before</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC82" 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;">setUp</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="57" 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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<td class="diff-line-num new_line old" data-linenumber="83" 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="LC57" class="line" lang="java">          <span class="n" style="color: #333;">previousPDB_DIR</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getProperty</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">UserConfiguration</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PDB_DIR</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="java">          <span class="n" style="color: #333;">GlobalsHelper</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">pushState</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="java">          </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="java">          <span class="n" style="color: #333;">cache</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">AtomCache</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="java">          <span class="n" style="color: #333;">cache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setObsoleteBehavior</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ObsoleteBehavior</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">FETCH_OBSOLETE</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="java">          <span class="n" style="color: #333;">StructureIO</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setAtomCache</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cache</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="88" 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="LC88" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="java">          <span class="c1" style="color: #998; font-style: italic;">// Use a fixed SCOP version for stability</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="java">          <span class="n" style="color: #333;">ScopFactory</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setScopDatabase</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ScopFactory</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">VERSION_1_75B</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="java">  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="java">  <span class="nd">@After</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC94" 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;">tearDown</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="LC66" 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;">previousPDB_DIR</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>

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<td class="diff-line-num old old_line" data-linenumber="67" 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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<td class="diff-line-num new_line old" data-linenumber="95" 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="LC67" 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;">setProperty</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">UserConfiguration</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PDB_DIR</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">previousPDB_DIR</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="java">          <span class="n" style="color: #333;">GlobalsHelper</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">restoreState</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="java">  <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="java">  <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="312" 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="340" 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">@@ -312,4 +340,125 @@ public class AtomCacheTest {</td>

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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="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC342" class="line" lang="java"> </span>

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<td class="diff-line-num new old_line" data-linenumber="315" 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="LC343" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC344" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * Test for #703 - Chemical component cache poisoning</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC345" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC346" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * Handle empty CIF files</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" 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="LC347" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @throws IOException</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC348" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @throws StructureException</span></span>

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<pre style="margin: 0;">+<span id="LC349" 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="LC350" class="line" lang="java"> <span class="nd">@Test</span></span>

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<pre style="margin: 0;">+<span id="LC351" 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;">testEmptyChemComp</span><span class="o" style="font-weight: 600;">()</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">StructureException</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="352" 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="LC352" class="line" lang="java">         <span class="n" style="color: #333;">Path</span> <span class="n" style="color: #333;">tmpCache</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Paths</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;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getProperty</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"java.io.tmpdir"</span><span class="o" style="font-weight: 600;">),</span><span class="s" style="color: #d14;">"BIOJAVA_TEST_CACHE"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="353" 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="LC353" class="line" lang="java">         <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">info</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Testing AtomCache at {}"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tmpCache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toString</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="354" 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="LC354" 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;">setProperty</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">UserConfiguration</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PDB_DIR</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tmpCache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toString</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="355" 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="LC355" 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;">setProperty</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">UserConfiguration</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PDB_CACHE_DIR</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tmpCache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toString</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="356" 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="LC356" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="357" 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="LC357" class="line" lang="java">         <span class="n" style="color: #333;">FileDownloadUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">deleteDirectory</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tmpCache</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="358" 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="LC358" class="line" lang="java">         <span class="n" style="color: #333;">Files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">createDirectory</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tmpCache</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="359" 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="LC359" class="line" lang="java">         <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC360" class="line" lang="java">                 <span class="n" style="color: #333;">cache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setPath</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tmpCache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toString</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="361" 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="LC361" class="line" lang="java">                 <span class="n" style="color: #333;">cache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setCachePath</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tmpCache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toString</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="362" 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="LC362" class="line" lang="java">                 <span class="n" style="color: #333;">cache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setUseMmCif</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="363" 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="LC363" class="line" lang="java">                 <span class="n" style="color: #333;">ChemCompGroupFactory</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setChemCompProvider</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">DownloadChemCompProvider</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tmpCache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toString</span><span class="o" style="font-weight: 600;">()));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC364" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC365" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">// Create an empty chemcomp</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" 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="LC366" class="line" lang="java">                 <span class="n" style="color: #333;">Path</span> <span class="n" style="color: #333;">chemCompCif</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmpCache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">resolve</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Paths</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="s" style="color: #d14;">"chemcomp"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"ATP.cif.gz"</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC367" class="line" lang="java">                 <span class="n" style="color: #333;">Files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">createDirectories</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">chemCompCif</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getParent</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="368" 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">

368

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<pre style="margin: 0;">+<span id="LC368" class="line" lang="java">                 <span class="n" style="color: #333;">Files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">createFile</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">chemCompCif</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="369" 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">

369

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<pre style="margin: 0;">+<span id="LC369" class="line" lang="java">                 <span class="n" style="color: #333;">assertTrue</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">exists</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">chemCompCif</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="370" 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">

370

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<pre style="margin: 0;">+<span id="LC370" class="line" lang="java">                 <span class="n" style="color: #333;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">size</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">chemCompCif</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="371" 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">

371

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<pre style="margin: 0;">+<span id="LC371" class="line" lang="java">                 </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="372" 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">

372

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<pre style="margin: 0;">+<span id="LC372" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">// Copy stub file into place</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="373" 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">

373

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<pre style="margin: 0;">+<span id="LC373" class="line" lang="java">                 <span class="n" style="color: #333;">Path</span> <span class="n" style="color: #333;">testCif</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmpCache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">resolve</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Paths</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="s" style="color: #d14;">"data"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"structures"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"divided"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"mmCIF"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"ab"</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"1abc.cif.gz"</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="374" 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">

374

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<pre style="margin: 0;">+<span id="LC374" class="line" lang="java">                 <span class="n" style="color: #333;">Files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">createDirectories</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">testCif</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getParent</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="375" 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">

375

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<pre style="margin: 0;">+<span id="LC375" class="line" lang="java">                 <span class="n" style="color: #333;">URL</span> <span class="n" style="color: #333;">resource</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AtomCacheTest</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 class="na" style="color: teal;">getResource</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"/atp.cif.gz"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="376" 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">

376

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<pre style="margin: 0;">+<span id="LC376" class="line" lang="java">                 <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">src</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">resource</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getPath</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="377" 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">

377

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<pre style="margin: 0;">+<span id="LC377" class="line" lang="java">                 <span class="n" style="color: #333;">FileDownloadUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">copy</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">testCif</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toFile</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="378" 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">

378

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC378" class="line" lang="java">                 </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="379" 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">

379

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<pre style="margin: 0;">+<span id="LC379" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">// Load structure</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

380

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<pre style="margin: 0;">+<span id="LC380" class="line" lang="java">                 <span class="n" style="color: #333;">Structure</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getStructure</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"1ABC"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="381" 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">

381

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<pre style="margin: 0;">+<span id="LC381" class="line" lang="java">                 </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

382

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<pre style="margin: 0;">+<span id="LC382" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">// Should have re-downloaded the file</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="383" 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">

383

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<pre style="margin: 0;">+<span id="LC383" class="line" lang="java">                 <span class="n" style="color: #333;">assertTrue</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">size</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">chemCompCif</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">LocalPDBDirectory</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">MIN_PDB_FILE_SIZE</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

384

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<pre style="margin: 0;">+<span id="LC384" class="line" lang="java">                 </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="385" 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">

385

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<pre style="margin: 0;">+<span id="LC385" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">// Structure should have valid ChemComp now</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="386" 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">

386

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<pre style="margin: 0;">+<span id="LC386" class="line" lang="java">                 <span class="n" style="color: #333;">assertNotNull</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="387" 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">

387

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<pre style="margin: 0;">+<span id="LC387" class="line" lang="java">                 </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="388" 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">

388

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<pre style="margin: 0;">+<span id="LC388" class="line" lang="java">                 <span class="n" style="color: #333;">Group</span> <span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getChainByPDB</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"A"</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">getAtomGroup</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="389" 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">

389

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<pre style="margin: 0;">+<span id="LC389" class="line" lang="java">                 <span class="n" style="color: #333;">assertTrue</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getPDBName</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"ATP"</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="390" 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">

390

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<pre style="margin: 0;">+<span id="LC390" class="line" lang="java">                 </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="391" 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">

391

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<pre style="margin: 0;">+<span id="LC391" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">// should be unknown</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="392" 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">

392

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<pre style="margin: 0;">+<span id="LC392" class="line" lang="java">                 <span class="n" style="color: #333;">ChemComp</span> <span class="n" style="color: #333;">chem</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getChemComp</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="393" 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">

393

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC393" class="line" lang="java">                 <span class="n" style="color: #333;">assertNotNull</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">chem</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="394" 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">

394

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC394" class="line" lang="java">                 <span class="n" style="color: #333;">assertTrue</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">chem</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getAtoms</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">size</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="395" 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">

395

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC395" class="line" lang="java">                 <span class="n" style="color: #333;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"NON-POLYMER"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">chem</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getType</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="396" 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">

396

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC396" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">finally</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="315" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="397" 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">

397

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC397" class="line" lang="java">                 <span class="n" style="color: #333;">FileDownloadUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">deleteDirectory</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tmpCache</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="315" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="398" 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">

398

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC398" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="315" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="399" 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">

399

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC399" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="315" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="400" 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">

400

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC400" class="line" lang="java"> </span>

</pre>

</td>

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401

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<pre style="margin: 0;">+<span id="LC401" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="402" 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="LC402" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * Test for #703 - Chemical component cache poisoning</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="403" 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="LC403" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * </span></span>

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<td class="diff-line-num new new_line" data-linenumber="404" 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="LC404" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * Handle empty CIF files</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="405" 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">

405

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<pre style="margin: 0;">+<span id="LC405" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @throws IOException</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="406" 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="LC406" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @throws StructureException</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC407" 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="LC408" class="line" lang="java"> <span class="nd">@Test</span></span>

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<td class="diff-line-num new new_line" data-linenumber="409" 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="LC409" 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;">testEmptyGZChemComp</span><span class="o" style="font-weight: 600;">()</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">StructureException</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="410" 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="LC410" class="line" lang="java">         </span>

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<td class="diff-line-num new new_line" data-linenumber="411" 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="LC411" class="line" lang="java">         <span class="n" style="color: #333;">Path</span> <span class="n" style="color: #333;">tmpCache</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Paths</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;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getProperty</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"java.io.tmpdir"</span><span class="o" style="font-weight: 600;">),</span><span class="s" style="color: #d14;">"BIOJAVA_TEST_CACHE"</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="412" 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="LC412" class="line" lang="java">         <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">info</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Testing AtomCache at {}"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tmpCache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toString</span><span class="o" style="font-weight: 600;">());</span></span>

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<td class="diff-line-num new new_line" data-linenumber="413" 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="LC413" 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;">setProperty</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">UserConfiguration</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PDB_DIR</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tmpCache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toString</span><span class="o" style="font-weight: 600;">());</span></span>

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<td class="diff-line-num new new_line" data-linenumber="414" 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="LC414" 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;">setProperty</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">UserConfiguration</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PDB_CACHE_DIR</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tmpCache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toString</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="415" 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="LC415" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="416" 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="LC416" class="line" lang="java">         <span class="n" style="color: #333;">FileDownloadUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">deleteDirectory</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tmpCache</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="417" 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="LC417" class="line" lang="java">         <span class="n" style="color: #333;">Files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">createDirectory</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tmpCache</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="418" 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">

418

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<pre style="margin: 0;">+<span id="LC418" class="line" lang="java">         <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="419" 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">

419

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<pre style="margin: 0;">+<span id="LC419" class="line" lang="java">                 <span class="n" style="color: #333;">cache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setPath</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tmpCache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toString</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="420" 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">

420

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<pre style="margin: 0;">+<span id="LC420" class="line" lang="java">                 <span class="n" style="color: #333;">cache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setCachePath</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tmpCache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toString</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="421" 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">

421

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<pre style="margin: 0;">+<span id="LC421" class="line" lang="java">                 <span class="n" style="color: #333;">cache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setUseMmCif</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>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="422" 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">

422

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<pre style="margin: 0;">+<span id="LC422" class="line" lang="java">                 <span class="n" style="color: #333;">ChemCompGroupFactory</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setChemCompProvider</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">DownloadChemCompProvider</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tmpCache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toString</span><span class="o" style="font-weight: 600;">()));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="423" 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">

423

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<pre style="margin: 0;">+<span id="LC423" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="424" 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">

424

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<pre style="margin: 0;">+<span id="LC424" class="line" lang="java">                 </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="425" 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">

425

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<pre style="margin: 0;">+<span id="LC425" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">// Create an empty chemcomp</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="426" 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">

426

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<pre style="margin: 0;">+<span id="LC426" class="line" lang="java">                 <span class="n" style="color: #333;">Path</span> <span class="n" style="color: #333;">sub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmpCache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">resolve</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Paths</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="s" style="color: #d14;">"chemcomp"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"ATP.cif.gz"</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="427" 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">

427

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<pre style="margin: 0;">+<span id="LC427" class="line" lang="java">                 <span class="n" style="color: #333;">Files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">createDirectories</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sub</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getParent</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="428" 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">

428

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<pre style="margin: 0;">+<span id="LC428" class="line" lang="java">                 <span class="k" style="font-weight: 600;">try</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">GZIPOutputStream</span> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">GZIPOutputStream</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FileOutputStream</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sub</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toFile</span><span class="o" style="font-weight: 600;">())))</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="429" 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">

429

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<pre style="margin: 0;">+<span id="LC429" class="line" lang="java">                         <span class="c1" style="color: #998; font-style: italic;">// don't write anything</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="430" 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="LC430" class="line" lang="java">                         <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">flush</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="431" 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">

431

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<pre style="margin: 0;">+<span id="LC431" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="432" 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="LC432" class="line" lang="java">                 <span class="n" style="color: #333;">assertTrue</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">exists</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sub</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="433" 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="LC433" class="line" lang="java">                 <span class="n" style="color: #333;">assertTrue</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">Files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">size</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sub</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">Files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">size</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sub</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">LocalPDBDirectory</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">MIN_PDB_FILE_SIZE</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC434" class="line" lang="java">                 </span>

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<pre style="margin: 0;">+<span id="LC435" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">// Copy stub file into place</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC436" class="line" lang="java">                 <span class="n" style="color: #333;">Path</span> <span class="n" style="color: #333;">testCif</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmpCache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">resolve</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Paths</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="s" style="color: #d14;">"data"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"structures"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"divided"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"mmCIF"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"ab"</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"1abc.cif.gz"</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC437" class="line" lang="java">                 <span class="n" style="color: #333;">Files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">createDirectories</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">testCif</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getParent</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC438" class="line" lang="java">                 <span class="n" style="color: #333;">URL</span> <span class="n" style="color: #333;">resource</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AtomCacheTest</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 class="na" style="color: teal;">getResource</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"/atp.cif.gz"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC439" class="line" lang="java">                 <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">src</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">resource</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getPath</span><span class="o" style="font-weight: 600;">());</span></span>

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<pre style="margin: 0;">+<span id="LC440" class="line" lang="java">                 <span class="n" style="color: #333;">FileDownloadUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">copy</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">testCif</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toFile</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC441" class="line" lang="java">                 </span>

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<pre style="margin: 0;">+<span id="LC442" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">// Load structure</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC443" class="line" lang="java">                 <span class="n" style="color: #333;">Structure</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getStructure</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"1ABC"</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC444" class="line" lang="java">                 </span>

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<pre style="margin: 0;">+<span id="LC445" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">// Should have re-downloaded the file</span></span>

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<pre style="margin: 0;">+<span id="LC446" class="line" lang="java">                 <span class="n" style="color: #333;">assertTrue</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">size</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sub</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">LocalPDBDirectory</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">MIN_PDB_FILE_SIZE</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC447" class="line" lang="java">                 </span>

</pre>

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<pre style="margin: 0;">+<span id="LC448" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">// Structure should have valid ChemComp</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC449" class="line" lang="java">                 <span class="n" style="color: #333;">assertNotNull</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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450

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<pre style="margin: 0;">+<span id="LC450" class="line" lang="java">                 </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="451" 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">

451

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<pre style="margin: 0;">+<span id="LC451" class="line" lang="java">                 <span class="n" style="color: #333;">Group</span> <span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getChainByPDB</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"A"</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">getAtomGroup</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="452" 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">

452

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<pre style="margin: 0;">+<span id="LC452" class="line" lang="java">                 <span class="n" style="color: #333;">assertTrue</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getPDBName</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"ATP"</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="453" 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">

453

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<pre style="margin: 0;">+<span id="LC453" class="line" lang="java">                 </span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="454" 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">

454

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<pre style="margin: 0;">+<span id="LC454" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">// should be unknown</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="455" 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">

455

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<pre style="margin: 0;">+<span id="LC455" class="line" lang="java">                 <span class="n" style="color: #333;">ChemComp</span> <span class="n" style="color: #333;">chem</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getChemComp</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="456" 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">

456

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<pre style="margin: 0;">+<span id="LC456" class="line" lang="java">                 <span class="n" style="color: #333;">assertNotNull</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">chem</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="457" 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">

457

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<pre style="margin: 0;">+<span id="LC457" class="line" lang="java">                 <span class="n" style="color: #333;">assertTrue</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">chem</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getAtoms</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">size</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="458" 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">

458

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<pre style="margin: 0;">+<span id="LC458" class="line" lang="java">                 <span class="n" style="color: #333;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"NON-POLYMER"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">chem</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getType</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="459" 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">

459

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<pre style="margin: 0;">+<span id="LC459" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">finally</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="460" 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">

460

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<pre style="margin: 0;">+<span id="LC460" class="line" lang="java">                 <span class="n" style="color: #333;">FileDownloadUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">deleteDirectory</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tmpCache</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="461" 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">

461

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<pre style="margin: 0;">+<span id="LC461" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="462" 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">

462

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<pre style="margin: 0;">+<span id="LC462" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="463" 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">

463

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<pre style="margin: 0;">+<span id="LC463" class="line" lang="java"> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="315" 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">

315

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<td class="diff-line-num new_line" data-linenumber="464" 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">

464

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<pre style="margin: 0;"> <span id="LC464" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>

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<br>

</li>

<li id="c6e47bfa4a58cf7a8969a3bfc01aedad17cbc04a">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#c6e47bfa4a58cf7a8969a3bfc01aedad17cbc04a"><strong>biojava-structure/src/test/java/org/biojava/nbio/structure/test/util/GlobalsHelper.java</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">org</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">biojava</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">nbio</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">structure</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">test</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">util</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Deque</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.LinkedList</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.NoSuchElementException</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.StructureIO</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.align.util.AtomCache</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<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">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.align.util.UserConfiguration</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="11" 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">

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="12" 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">

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.io.mmcif.ChemCompProvider</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="14" 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">

14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.scop.ScopDatabase</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="15" 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">

15

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.biojava.nbio.structure.scop.ScopFactory</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC16" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="17" 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="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="18" 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="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Helper class to manage all the global state changes in BioJava.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="19" 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="LC19" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * For instance, this should be used in tests before modifying PDB_PATH. </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC20" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="21" 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">

21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Used by tests during setup and teardown to ensure a clean environment</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="23" 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="LC23" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This class is a singleton.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="24" 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">

24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @author Spencer Bliven</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="25" 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">

25

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="26" 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="LC26" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="27" 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="LC27" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">GlobalsHelper</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="28" 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="LC28" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="29" 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="LC29" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PathInfo</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="30" 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="LC30" class="line" lang="java">          <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">pdbPath</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="java">          <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">pdbCachePath</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 class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">AtomCache</span> <span class="n" style="color: #333;">atomCache</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="33" 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="LC33" class="line" lang="java">          <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">ChemCompProvider</span> <span class="n" style="color: #333;">chemCompProvider</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="34" 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="LC34" class="line" lang="java">          <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">downloadChemCompProviderPath</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="35" 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="LC35" class="line" lang="java">          <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">ScopDatabase</span> <span class="n" style="color: #333;">scop</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>

</pre>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="java">          <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">PathInfo</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="java">                  <span class="n" style="color: #333;">pdbPath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getProperty</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">UserConfiguration</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PDB_DIR</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>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="java">                  <span class="n" style="color: #333;">pdbCachePath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getProperty</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">UserConfiguration</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PDB_CACHE_DIR</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>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="java">                  <span class="n" style="color: #333;">atomCache</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StructureIO</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getAtomCache</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="n" style="color: #333;">chemCompProvider</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ChemCompGroupFactory</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getChemCompProvider</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="n" style="color: #333;">downloadChemCompProviderPath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DownloadChemCompProvider</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getPath</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">getPath</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="n" style="color: #333;">scop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ScopFactory</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getSCOP</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 class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="java">  <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>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="java">  <span class="c1" style="color: #998; font-style: italic;">// Saves defaults as stack</span></span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">Deque</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">PathInfo</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">stack</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">LinkedList</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="kd" style="font-weight: 600;">static</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="c1" style="color: #998; font-style: italic;">// Save default state</span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="java">          <span class="n" style="color: #333;">pushState</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="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="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;">       * GlobalsHelper should not be instantiated.</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;">       */</span></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="nf" style="color: #900; font-weight: 600;">GlobalsHelper</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="LC58" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="59" 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="LC59" class="line" lang="java">  <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="60" 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="LC60" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * Save current global state to the stack</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="61" 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">

61

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       */</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="62" 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="LC62" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">pushState</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="63" 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="LC63" class="line" lang="java">          <span class="n" style="color: #333;">PathInfo</span> <span class="n" style="color: #333;">paths</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">PathInfo</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="64" 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="LC64" class="line" lang="java">          <span class="n" style="color: #333;">stack</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addFirst</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">paths</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="java">  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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66

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="java">  </span>

</pre>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="java">  <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * Sets a new PDB_PATH and PDB_CACHE_PATH consistently.</span></span>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * </span></span>

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<td class="diff-line-num new new_line" data-linenumber="70" 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="LC70" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * Previous values can be restored with {@link #restoreState()}.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * @param path</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       */</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="73" 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="LC73" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">setPdbPath</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">cachePath</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="java">          <span class="n" style="color: #333;">pushState</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="75" 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="LC75" 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;">path</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;">cachePath</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="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="java">                  <span class="n" style="color: #333;">UserConfiguration</span> <span class="n" style="color: #333;">config</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">UserConfiguration</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;">+<span id="LC77" 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;">path</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="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="java">                          <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getPdbFilePath</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="79" 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">

79

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="java">                  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC80" 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;">cachePath</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="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="java">                          <span class="n" style="color: #333;">cachePath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getCacheFilePath</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="java">                  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="java">          <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC84" 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;">setProperty</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">UserConfiguration</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PDB_DIR</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="85" 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="LC85" 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;">setProperty</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">UserConfiguration</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PDB_CACHE_DIR</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="86" 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="LC86" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="java">          <span class="n" style="color: #333;">AtomCache</span> <span class="n" style="color: #333;">cache</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">AtomCache</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="88" 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="LC88" class="line" lang="java">          <span class="n" style="color: #333;">StructureIO</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setAtomCache</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cache</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="89" 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="LC89" class="line" lang="java">          </span>

</pre>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="java">          <span class="c1" style="color: #998; font-style: italic;">// Note side effect setting the path for all DownloadChemCompProvider due to static state</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="91" 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="LC91" class="line" lang="java">          <span class="n" style="color: #333;">ChemCompProvider</span> <span class="n" style="color: #333;">provider</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">DownloadChemCompProvider</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="92" 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="LC92" class="line" lang="java">          <span class="n" style="color: #333;">ChemCompGroupFactory</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setChemCompProvider</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">provider</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="93" 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="LC93" class="line" lang="java">  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="94" 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">

94

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="java">  </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="95" 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">

95

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC95" class="line" lang="java">  <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="96" 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">

96

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * Restore global state to the previous settings</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="97" 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">

97

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * @throws NoSuchElementException if there is no prior state to restore</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="98" 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">

98

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       */</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="99" 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">

99

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">restoreState</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="100" 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">

100

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="java">         <span class="n" style="color: #333;">PathInfo</span> <span class="n" style="color: #333;">paths</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stack</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">removeFirst</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="101" 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">

101

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="java">         </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="102" 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">

102

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<pre style="margin: 0;">+<span id="LC102" 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;">paths</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">pdbPath</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="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="103" 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">

103

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<pre style="margin: 0;">+<span id="LC103" 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;">clearProperty</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">UserConfiguration</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PDB_DIR</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="104" 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">

104

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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">

105

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<pre style="margin: 0;">+<span id="LC105" 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;">setProperty</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">UserConfiguration</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PDB_DIR</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">paths</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">pdbPath</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<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">

106

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

107

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">paths</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">pdbCachePath</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="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

108

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<pre style="margin: 0;">+<span id="LC108" 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;">clearProperty</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">UserConfiguration</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PDB_CACHE_DIR</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="109" 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">

109

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

110

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="java">                 <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setProperty</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">UserConfiguration</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PDB_CACHE_DIR</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">paths</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">pdbCachePath</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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111

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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112

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="java"></span>

</pre>

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113

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="java">         <span class="n" style="color: #333;">StructureIO</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setAtomCache</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">paths</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">atomCache</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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114

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="java">         </span>

</pre>

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115

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">// Use side effect setting the path for all DownloadChemCompProvider due to static state</span></span>

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="java">         <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">DownloadChemCompProvider</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">paths</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">downloadChemCompProviderPath</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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117

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="java">         </span>

</pre>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="java">         <span class="n" style="color: #333;">ChemCompGroupFactory</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setChemCompProvider</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">paths</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">chemCompProvider</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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119

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="java">         </span>

</pre>

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120

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="java">         <span class="n" style="color: #333;">ScopFactory</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setScopDatabase</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">paths</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">scop</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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121

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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122

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="java"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="123" 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="LC123" class="line" lang="java"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>

</td>

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</table>

<br>

</li>

<li id="f5518cde38547e1422e67390dd0063b16c3e160b">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#f5518cde38547e1422e67390dd0063b16c3e160b"><strong>biojava-structure/src/test/resources/atp.cif.gz</strong></a>

<hr>

No preview for this file type

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<li id="211138d0d9f7559842c8e636097db1e40f225ff4">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#211138d0d9f7559842c8e636097db1e40f225ff4"><strong>biojava-survival/pom.xml</strong></a>

<hr>

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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">@@ -4,7 +4,7 @@</td>

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4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="xml">    <span class="nt" style="color: navy;"><parent></span></span>

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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="xml">        <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

</pre>

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6

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6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="xml">        <span class="nt" style="color: navy;"><artifactId></span>biojava<span class="nt" style="color: navy;"></artifactId></span></span>

</pre>

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7

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="xml">        <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="xml">        <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="xml">    <span class="nt" style="color: navy;"></parent></span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="xml"></span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="xml">    <span class="nt" style="color: navy;"><artifactId></span>biojava-survival<span class="nt" style="color: navy;"></artifactId></span></span>

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<br>

</li>

<li id="d776f6089be530cdb58291bc061f164083e9f1ae">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#d776f6089be530cdb58291bc061f164083e9f1ae"><strong>biojava-ws/pom.xml</strong></a>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="xml">    <span class="nt" style="color: navy;"><parent></span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="xml">            <span class="nt" style="color: navy;"><artifactId></span>biojava<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="xml">            <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="xml">            <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="xml">            <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="xml">    <span class="nt" style="color: navy;"></parent></span>    </span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="xml">    <span class="nt" style="color: navy;"><artifactId></span>biojava-ws<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="xml">    <span class="nt" style="color: navy;"><name></span>biojava-ws<span class="nt" style="color: navy;"></name></span></span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="xml">           <span class="nt" style="color: navy;"><dependency></span></span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="xml">                   <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="xml">                   <span class="nt" style="color: navy;"><artifactId></span>biojava-core<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="xml">                   <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="xml">                   <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="xml">                   <span class="nt" style="color: navy;"><scope></span>compile<span class="nt" style="color: navy;"></scope></span></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="xml">           <span class="nt" style="color: navy;"></dependency></span></span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="xml">           <span class="nt" style="color: navy;"><dependency></span></span>

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<br>

</li>

<li id="442292b8a7efeabbe4cc176709b833b1792140ec">

<a href="https://salsa.debian.org/med-team/biojava4-live/compare/9eaa739bafda061ec60a5a2851afd718e8a2c032...8d48abfeaece53f6aa10519dcddb356fd0240205#442292b8a7efeabbe4cc176709b833b1792140ec"><strong>pom.xml</strong></a>

<hr>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="xml">   <span class="nt" style="color: navy;"><groupId></span>org.biojava<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="xml">   <span class="nt" style="color: navy;"><artifactId></span>biojava<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="xml">   <span class="nt" style="color: navy;"><packaging></span>pom<span class="nt" style="color: navy;"></packaging></span></span>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="xml">   <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="xml">   <span class="nt" style="color: navy;"><version></span>4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="xml">   <span class="nt" style="color: navy;"><name></span>biojava<span class="nt" style="color: navy;"></name></span></span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="xml">   <span class="nt" style="color: navy;"><description></span>BioJava is an open-source project dedicated to providing a Java framework for processing biological</span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="xml">        data. It provides analytical and statistical routines, parsers for common file formats and allows the</span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="xml">           <span class="nt" style="color: navy;"><developerConnection></span>scm:git:git@github.com:biojava/biojava.git<span class="nt" style="color: navy;"></developerConnection></span></span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="xml">           <span class="nt" style="color: navy;"><url></span>https://github.com/biojava/biojava<span class="nt" style="color: navy;"></url></span></span>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="xml"></span>

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="xml">           <span class="nt" style="color: navy;"><tag></span>biojava-4.2.1<span class="idiff left right">1</span><span class="nt" style="color: navy;"></tag></span></span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="xml">           <span class="nt" style="color: navy;"><tag></span>biojava-4.2.1<span class="idiff left right">2</span><span class="nt" style="color: navy;"></tag></span></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="xml">   <span class="nt" style="color: navy;"></scm></span></span>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="xml"></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="xml">   <span class="c" style="color: #998; font-style: italic;"><!-- This section required for release at Maven Central. For a full list </span></span>

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="xml">                                  <span class="nt" style="color: navy;"><version></span>2.10.3<span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="xml">                                  <span class="nt" style="color: navy;"><configuration></span></span>

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="xml">                                          <span class="c" style="color: #998; font-style: italic;"><!-- we need to allow script in comments or otherwise we can't use google analytics js in footer below - JD 2017-06-06 --></span></span>

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<pre style="margin: 0;">-<span id="LC215" class="line" lang="xml">                                          <span class="nt" style="color: navy;"><additionalparam></span>--allow-script-in-comments<span class="nt" style="color: navy;"></additionalparam></span></span>

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="xml">                                          <span class="c" style="color: #998; font-style: italic;"><!-- requires java 8u121</span></span>

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;">                                               <additionalparam>--><!--allow-script-in-comments</additionalparam></span></span>

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;">                                               <maxmemory>256m</maxmemory></span></span>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;">                                               <footer>&lt;script src="http://www.google-analytics.com/urchin.js"</span></span>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;">                                                       type="text/javascript"&gt;_uacct =</span></span>

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="xml">                                  <span class="nt" style="color: navy;"></configuration></span></span>

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="xml">                                  <span class="nt" style="color: navy;"><version></span>2.7<span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="xml">                          <span class="nt" style="color: navy;"><plugin></span></span>

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="xml">                                  <span class="nt" style="color: navy;"><groupId></span>org.apache.maven.plugins<span class="nt" style="color: navy;"></groupId></span></span>

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="xml">                                  <span class="nt" style="color: navy;"><artifactId></span>maven-deploy-plugin<span class="nt" style="color: navy;"></artifactId></span></span>

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="xml">                                  <span class="nt" style="color: navy;"><version></span>2.8.2<span class="nt" style="color: navy;"></version></span></span>

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="xml">                          <span class="nt" style="color: navy;"></plugin></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="xml"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC282" class="line" lang="xml">                  <span class="nt" style="color: navy;"></plugins></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="xml">          <span class="nt" style="color: navy;"></pluginManagement></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC284" class="line" lang="xml"></span>

</pre>

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