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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/biojava4-live">Debian Med / biojava4-live</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/biojava4-live/-/commit/b5af80dfc8544077e7040cbf49bdf920c9c685fc">b5af80df</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-12-12T21:09:36+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Depending again on libjgrapht0.8-java instead of libjgrapht-java so that the package builds
</pre>
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<strong><a href="https://salsa.debian.org/med-team/biojava4-live/-/commit/b531add7f664d8c35aa93d2eb1f46de9d45384ff">b531add7</a></strong>
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<span>by Pierre Gruet</span>
<i>at 2021-12-12T22:14:46+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Excluding more tests needing the network
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<strong><a href="https://salsa.debian.org/med-team/biojava4-live/-/commit/5e4f9a2ce270623849dd7648843f2365e06ca6c6">5e4f9a2c</a></strong>
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<span>by Pierre Gruet</span>
<i>at 2021-12-12T22:52:30+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#7d0e38ebad7c01125c531c7fefc0d248fadf9366">
debian/patches/skip_network_related_tests
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/biojava4-live/-/compare/6ea5ecb247ea1e7f69d9848466f33049770178f3...5e4f9a2ce270623849dd7648843f2365e06ca6c6#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">biojava4</span><span class="p">-</span><span class="n" style="color: #333;">live</span> <span class="p">(</span><span class="m" style="color: #099;">4.2.12</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">6</span><span class="p">)</span> <span class="n" style="color: #333;">unstable</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Team</span> <span class="n" style="color: #333;">upload</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Depending</span> <span class="n" style="color: #333;">again</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">libjgrapht0</span><span class="m" style="color: #099;">.8</span><span class="p">-</span><span class="n" style="color: #333;">java</span> <span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">libjgrapht</span><span class="p">-</span><span class="n" style="color: #333;">java</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Excluding</span> <span class="n" style="color: #333;">more</span> <span class="n" style="color: #333;">tests</span> <span class="n" style="color: #333;">needing</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">network</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"> <span class="p">--</span> <span class="n" style="color: #333;">Pierre</span> <span class="n" style="color: #333;">Gruet</span> <span class="p"><</span><span class="n" style="color: #333;">pgt</span><span class="p">@</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span> <span class="n" style="color: #333;">Sun</span><span class="p">,</span> <span class="m" style="color: #099;">12</span> <span class="n" style="color: #333;">Dec</span> <span class="m" style="color: #099;">2021</span> <span class="m" style="color: #099;">22</span><span class="p">:</span><span class="m" style="color: #099;">15</span><span class="p">:</span><span class="m" style="color: #099;">47</span> <span class="p">+</span><span class="m" style="color: #099;">0100</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="mosel"><span class="n" style="color: #333;">biojava4</span><span class="p">-</span><span class="n" style="color: #333;">live</span> <span class="p">(</span><span class="m" style="color: #099;">4.2.12</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">5</span><span class="p">)</span> <span class="n" style="color: #333;">unstable</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Team</span> <span class="n" style="color: #333;">upload</span><span class="p">.</span></span>
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<a href="https://salsa.debian.org/med-team/biojava4-live/-/compare/6ea5ecb247ea1e7f69d9848466f33049770178f3...5e4f9a2ce270623849dd7648843f2365e06ca6c6#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,7 +27,7 @@ Build-Depends-Indep: libcommons-dbcp-java,</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> liblog4j2-java,</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> libslf4j-java,</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> libxmlunit-java,</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> libjgrapht-java,</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> libjgrapht<span class="idiff left right">0.8</span>-java,</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> libjaxb-api-java,</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> libjaxb-java,</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> libnetx-java,</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">@@ -56,7 +56,7 @@ Depends: ${java:Depends},</td>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"> libguava-java,</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext"> libslf4j-java,</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"> libcommons-math-java,</span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext"> libjgrapht-java,</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> libjgrapht<span class="idiff left right">0.8</span>-java,</span>
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"> libvecmath-java</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext">Suggests: java-virtual-machine,</span>
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext"> libbiojava4-java,</span>
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<li id="7d0e38ebad7c01125c531c7fefc0d248fadf9366">
<a href="https://salsa.debian.org/med-team/biojava4-live/-/compare/6ea5ecb247ea1e7f69d9848466f33049770178f3...5e4f9a2ce270623849dd7648843f2365e06ca6c6#7d0e38ebad7c01125c531c7fefc0d248fadf9366"><strong>debian/patches/skip_network_related_tests</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">@@ -5,7 +5,7 @@ Last-Updated: 2016-12-09</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -67,21 +67,6 @@</span><span class="idiff left right"> public class GenbankCookbookTest {</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -67,21 +67,6 @@</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> public void testProcess() throws Throwable {</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> /*</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,7 +29,7 @@ Forwarded: no</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"> //Try with the GenbankReaderHelper</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="p">@@ -67,20 +67,6 @@</span><span class="idiff left right"> public class NonstandardProteinCompoundT</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="p">@@ -67,20 +67,6 @@</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"> private void testUniprot(String uniprotID) throws CompoundNotFoundException, IOException {</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"> </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">@@ -52,7 +52,7 @@ Forwarded: no</td>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"><span class="p">@@ -75,90 +75,11 @@</span><span class="idiff left right"> public class GenbankProxySequenceReaderT</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="p">@@ -75,90 +75,11 @@</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> public void testFeatures() throws IOException, InterruptedException, CompoundNotFoundException {</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">@@ -143,3 +143,47 @@ Forwarded: no</td>
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/biojava-core/src/test/java/org/biojava/nbio/core/search/io/SearchIOTest.java</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/biojava-core/src/test/java/org/biojava/nbio/core/search/io/SearchIOTest.java</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="p">@@ -27,6 +27,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> import org.junit.AfterClass;</span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> import org.junit.Before;</span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> import org.junit.BeforeClass;</span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.junit.Ignore;</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> import org.junit.Test;</span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> import static org.junit.Assert.*;</span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"> </span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="p">@@ -78,6 +79,7 @@</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> /**</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> * Constructor test specifying Factory</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> */</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore("Attemps to use the network")</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> @Test</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> public void testConstructorWithoutFactoryGuess() {</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> String resource = "/org/biojava/nbio/core/search/io/blast/testBlastReport.blastxml";</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="p">@@ -95,6 +97,7 @@</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> /**</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> * Constructor test specifying Factory and using a evalue threshold filter</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> */</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore("Attemps to use the network")</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> @Test</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> public void testConstructorWithEvalueHspFilter() {</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"> //</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastXMLParserTest.java</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastXMLParserTest.java</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="p">@@ -31,6 +31,7 @@</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> import org.junit.AfterClass;</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> import org.junit.Before;</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> import org.junit.BeforeClass;</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.junit.Ignore;</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"> import org.junit.Test;</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> import static org.junit.Assert.*;</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> import org.junit.Ignore;</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"><span class="p">@@ -84,6 +85,7 @@</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> /**</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"> * Test of createObjects method, of class BlastXMLParser.</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"> */</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore("Attempts to use the network")</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> @Test</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> public void testCreateObjects() throws Exception {</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> System.out.println("createObjects");</span></pre>
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