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View results here -> <a href="http://emmy.rcsb.org:8080/cruisecontrol/buildresults/biojava-legacy?log=log20110125005252Lbuild.5">http://emmy.rcsb.org:8080/cruisecontrol/buildresults/biojava-legacy?log=log20110125005252Lbuild.5</a><p>
<table xmlns:lxslt="http://xml.apache.org/xslt" align="center" cellpadding="2" cellspacing="0" border="0" class="header" width="98%">
<tr>
<th class="big" colspan="2">BUILD COMPLETE -
build.5
</th>
</tr>
<tr>
<th>Date of build:</th>
<td>2011-01-25T08:52:52</td>
</tr>
<tr>
<th>Time to build:</th>
<td>13 minute(s) 50 second(s)</td>
</tr>
<tr>
<th>Last changed:</th>
<td>2011-01-25T05:42:33</td>
</tr>
<tr>
<th>Last log entry:</th>
<td>Fix unexpected throwing of exception when invoking symbols(SymbolList seq) on circular locations</td>
</tr>
</table><p>
<p>
<table xmlns="http://www.w3.org/TR/html4/strict.dtd" align="center" cellpadding="2" cellspacing="0" border="0" width="98%">
<tr class="compile-sectionheader">
<td>Initial Messages</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Scanning for projects...<br/></span><span class="compile-data">[INFO] Reactor build order: <br/></span><span class="compile-data">[INFO] biojava-legacy<br/></span><span class="compile-data">[INFO] bytecode<br/></span><span class="compile-data">[INFO] core<br/></span><span class="compile-data">[INFO] alignment<br/></span><span class="compile-data">[INFO] biosql<br/></span><span class="compile-data">[INFO] blast<br/></span><span class="compile-data">[INFO] das<br/></span><span class="compile-data">[INFO] sequencing<br/></span><span class="compile-data">[INFO] gui<br/></span><span class="compile-data">[INFO] phylo<br/></span><span class="compile-data">[INFO] Searching repository for plugin with prefix: 'source'.<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building biojava-legacy<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>site:attach-descriptor {execution: default-attach-descriptor}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/pom.xml to /home/andreas/.m2/repository/org/biojava/biojava-legacy/1.8.1-SNAPSHOT/biojava-legacy-1.8.1-SNAPSHOT.pom<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Not executing Javadoc as the project is not a Java classpath-capable package<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>site:attach-descriptor {execution: default-attach-descriptor}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/pom.xml to /home/andreas/.m2/repository/org/biojava/biojava-legacy/1.8.1-SNAPSHOT/biojava-legacy-1.8.1-SNAPSHOT.pom<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava-legacy/1.8.1-SNAPSHOT/biojava-legacy-1.8.1-SNAPSHOT.pom<br/></span><span class="compile-data">7K uploaded (biojava-legacy-1.8.1-SNAPSHOT.pom)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:biojava-legacy'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:biojava-legacy:1.8.1-SNAPSHOT'<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building bytecode<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-legacy/bytecode/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/bytecode/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 44 source files to /opt/cruise/projects/biojava-legacy/bytecode/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/bytecode/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] No tests to run.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/bytecode/target/bytecode-1.8.1-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/bytecode/target/bytecode-1.8.1-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/bytecode/1.8.1-SNAPSHOT/bytecode-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/bytecode/target/bytecode-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">3 warnings<br/></span><span class="compile-data">[WARNING] Javadoc Warnings<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/bytecode/src/main/java/org/biojava/utils/bytecode/ByteCode.java:1351: warning
- @param argument "lockVar" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/bytecode/src/main/java/org/biojava/utils/bytecode/CodeContext.java:139: warning
- @for.developer is an unknown tag.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/bytecode/src/main/java/org/biojava/utils/bytecode/CodeField.java:79: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/bytecode/target/bytecode-1.8.1-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/bytecode/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/bytecode/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] No tests to run.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/bytecode/target/bytecode-1.8.1-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/bytecode/1.8.1-SNAPSHOT/bytecode-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/bytecode/target/bytecode-1.8.1-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/bytecode/1.8.1-SNAPSHOT/bytecode-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/bytecode/target/bytecode-1.8.1-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/bytecode/1.8.1-SNAPSHOT/bytecode-1.8.1-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/bytecode/1.8.1-SNAPSHOT/bytecode-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">94K uploaded (bytecode-1.8.1-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:bytecode'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:bytecode:1.8.1-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Uploading project information for bytecode 1.8.1-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/bytecode/1.8.1-SNAPSHOT/bytecode-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">59K uploaded (bytecode-1.8.1-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/bytecode/1.8.1-SNAPSHOT/bytecode-1.8.1-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">250K uploaded (bytecode-1.8.1-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building core<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-legacy/core/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 29 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 1063 source files to /opt/cruise/projects/biojava-legacy/core/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 51 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 146 source files to /opt/cruise/projects/biojava-legacy/core/target/test-classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/core/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.utils.lsid.LifeScienceIdentifierTest<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SymbolListTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.101 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleDocRefAuthorTest<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetExtendedName<br/></span><span class="compile-data">testIsConsortium<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec<br/></span><span class="compile-data">Running org.biojavax.ga.functions.SimpleMutationFunctionTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec<br/></span><span class="compile-data">Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.273 sec<br/></span><span class="compile-data">Running org.biojava.bio.dp.EmissionStateEventTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.SimpleRichLocationTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec<br/></span><span class="compile-data">Running org.biojava.bio.search.SeqContentPatternTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojavax.EmptyRichAnnotationTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testContains<br/></span><span class="compile-data">testKeys<br/></span><span class="compile-data">testAsMap<br/></span><span class="compile-data">testClear<br/></span><span class="compile-data">testGetNoteSet<br/></span><span class="compile-data">testSetNoteSet<br/></span><span class="compile-data">testGetProperty<br/></span><span class="compile-data">testGetNote<br/></span><span class="compile-data">testSetProperty<br/></span><span class="compile-data">testAddNote<br/></span><span class="compile-data">testRemoveProperty<br/></span><span class="compile-data">testRemoveNote<br/></span><span class="compile-data">testContainsProperty<br/></span><span class="compile-data">Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.FeatureFilterTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.Bug2255Test<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.065 sec<br/></span><span class="compile-data">Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleDocRefTest<br/></span><span class="compile-data">testGetLocation<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testSetRemark<br/></span><span class="compile-data">testSetCrossref<br/></span><span class="compile-data">testGetAuthors<br/></span><span class="compile-data">testGetAuthorList<br/></span><span class="compile-data">testGetCRC<br/></span><span class="compile-data">testGetRemark<br/></span><span class="compile-data">testGetCrossref<br/></span><span class="compile-data">testGetTitle<br/></span><span class="compile-data">Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.io.SmartSequenceBuilderTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.41 sec<br/></span><span class="compile-data">Running org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest<br/></span><span class="compile-data">java.lang.NullPointerException: table is null.<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.addTable(SimpleSymbolPropertyTableDB.java:145)<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testAddTable(SimpleSymbolPropertyTableDBTest.java:113)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:168)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:134)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:110)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:128)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:113)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:124)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:232)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:227)<br/></span><span class="compile-data"> at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">java.lang.NullPointerException: name is null.<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:172)<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:126)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:168)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:134)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:110)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:128)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:113)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:124)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:232)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:227)<br/></span><span class="compile-data"> at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">org.biojava.bio.seq.db.IllegalIDException: No table found with name test.<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:175)<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:134)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:168)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:134)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:110)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:128)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:113)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:124)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:232)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:227)<br/></span><span class="compile-data"> at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec<br/></span><span class="compile-data">Running org.biojava.bio.dist.DistributionTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.filter.FilterTransformerTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 sec<br/></span><span class="compile-data">Running org.biojavax.ontology.SimpleComparableOntologyTest<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetDescription<br/></span><span class="compile-data">testSetDescription<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetTerm<br/></span><span class="compile-data">testContainsTerm<br/></span><span class="compile-data">testGetOrCreateTerm<br/></span><span class="compile-data">testGetOrImportTerm<br/></span><span class="compile-data">testCreateTerm<br/></span><span class="compile-data">testImportTerm<br/></span><span class="compile-data">testCreateTriple<br/></span><span class="compile-data">testDeleteTerm<br/></span><span class="compile-data">testGetTriples<br/></span><span class="compile-data">testSetTripleSet<br/></span><span class="compile-data">testGetTripleSet<br/></span><span class="compile-data">testGetTerms<br/></span><span class="compile-data">testSetTermSet<br/></span><span class="compile-data">testGetTermSet<br/></span><span class="compile-data">testContainsTriple<br/></span><span class="compile-data">testCreateVariable<br/></span><span class="compile-data">testGetOps<br/></span><span class="compile-data">Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.indexdb.IndexToolsTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.ProteinToolsTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojavax.bio.SimpleBioEntryTest<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testGetAnnotation<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetDescription<br/></span><span class="compile-data">testSetDescription<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetRankedCrossRefs<br/></span><span class="compile-data">testSetTaxon<br/></span><span class="compile-data">testGetNoteSet<br/></span><span class="compile-data">testSetNoteSet<br/></span><span class="compile-data">testGetComments<br/></span><span class="compile-data">testGetRankedDocRefs<br/></span><span class="compile-data">testGetRelationships<br/></span><span class="compile-data">testSetIdentifier<br/></span><span class="compile-data">testSetDivision<br/></span><span class="compile-data">testGetAccession<br/></span><span class="compile-data">testGetDivision<br/></span><span class="compile-data">testGetIdentifier<br/></span><span class="compile-data">testGetNamespace<br/></span><span class="compile-data">testGetTaxon<br/></span><span class="compile-data">testGetVersion<br/></span><span class="compile-data">testAddRankedCrossRef<br/></span><span class="compile-data">testRemoveRankedCrossRef<br/></span><span class="compile-data">testAddRankedDocRef<br/></span><span class="compile-data">testRemoveRankedDocRef<br/></span><span class="compile-data">testAddComment<br/></span><span class="compile-data">testRemoveComment<br/></span><span class="compile-data">testAddRelationship<br/></span><span class="compile-data">testRemoveRelationship<br/></span><span class="compile-data">testSetRankedCrossRefs<br/></span><span class="compile-data">Tests run: 32, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleRichAnnotationTest<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testContains<br/></span><span class="compile-data">testKeys<br/></span><span class="compile-data">testAsMap<br/></span><span class="compile-data">testClear<br/></span><span class="compile-data">testGetNoteSet<br/></span><span class="compile-data">testSetNoteSet<br/></span><span class="compile-data">testGetProperty<br/></span><span class="compile-data">testGetNote<br/></span><span class="compile-data">testSetProperty<br/></span><span class="compile-data">testAddNote<br/></span><span class="compile-data">testRemoveProperty<br/></span><span class="compile-data">testRemoveNote<br/></span><span class="compile-data">testContainsProperty<br/></span><span class="compile-data">testGetPropertys<br/></span><span class="compile-data">testRemoveProperty2<br/></span><span class="compile-data">Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.PointLocationTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.MergeAnnotationTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec<br/></span><span class="compile-data">Running org.biojava.bio.dp.DPSerializationTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.io.SymbolListCharSequenceTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.CodonPrefToolsTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.126 sec<br/></span><span class="compile-data">Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.io.LocationFormatterTest<br/></span><span class="compile-data">Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.179 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.Bug2249_2248Test<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojava.utils.walker.WalkerFactoryTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec<br/></span><span class="compile-data">Running org.biojavax.ga.functions.SimpleCrossOverFunctionTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleCrossRefTest<br/></span><span class="compile-data">testGetAnnotation<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetNoteSet<br/></span><span class="compile-data">testSetNoteSet<br/></span><span class="compile-data">testGetAccession<br/></span><span class="compile-data">testGetVersion<br/></span><span class="compile-data">testGetDbname<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Running org.biojavax.ga.functions.AbstractMutationFunctionTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.DoubleAlphabetTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.impl.ViewSequenceTest<br/></span><span class="compile-data">template: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any
annotation={geneID=braca1}<br/></span><span class="compile-data">orignal: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any
annotation={geneID=braca1}<br/></span><span class="compile-data">copy: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any
annotation={geneID=braca1}<br/></span><span class="compile-data">template: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any
annotation={geneID=braca1}<br/></span><span class="compile-data">orignal: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any
annotation={geneID=braca1}<br/></span><span class="compile-data">copy: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any
annotation={geneID=braca1}<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.TestSoftMaskedAlphabet<br/></span><span class="compile-data">Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.IntegerAlphabetTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SimpleSymbolListTest<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.EMBLFormatTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SimpleSymbolEventTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.utils.walker.WalkerTest<br/></span><span class="compile-data">Increasing counter: Overlaps([20,50])<br/></span><span class="compile-data">Increasing counter: Overlaps([20,50])<br/></span><span class="compile-data">Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature)<br/></span><span class="compile-data">Increasing counter: And(Overlaps([20,50]) , ByClass(org.biojava.bio.seq.StrandedFeature))<br/></span><span class="compile-data">Increasing counter: Overlaps([20,50])<br/></span><span class="compile-data">Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature)<br/></span><span class="compile-data">Increasing counter: ByClass(org.biojava.bio.seq.ComponentFeature)<br/></span><span class="compile-data">Increasing counter: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))<br/></span><span class="compile-data">Increasing counter: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)))<br/></span><span class="compile-data">OverlapsLocation: Overlaps([20,50])<br/></span><span class="compile-data">Feature: ByClass(org.biojava.bio.seq.StrandedFeature)<br/></span><span class="compile-data">OverlapsLocation: Overlaps([20,50])<br/></span><span class="compile-data">Feature: ByClass(org.biojava.bio.seq.StrandedFeature)<br/></span><span class="compile-data">Feature: ByClass(org.biojava.bio.seq.ComponentFeature)<br/></span><span class="compile-data">Feature: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))<br/></span><span class="compile-data">Feature: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)))<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec<br/></span><span class="compile-data">Running org.biojava.utils.RepeatedCharSequenceTest<br/></span><span class="compile-data">JAM<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.FilterUtilsTest<br/></span><span class="compile-data">Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleRankedDocRefTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testSetRank<br/></span><span class="compile-data">testGetRank<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetDocumentReference<br/></span><span class="compile-data">testGetStart<br/></span><span class="compile-data">testGetEnd<br/></span><span class="compile-data">testSetLocation<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.RichLocationToolsTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.impl.ViewSeqSerializationTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 sec<br/></span><span class="compile-data">Running org.biojava.utils.regex.PatternCheckerTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.MergeLocationTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojavax.ontology.SimpleComparableTermTest<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testGetAnnotation<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetDescription<br/></span><span class="compile-data">testSetDescription<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetRankedCrossRefs<br/></span><span class="compile-data">testSetIdentifier<br/></span><span class="compile-data">testGetIdentifier<br/></span><span class="compile-data">testAddRankedCrossRef<br/></span><span class="compile-data">testRemoveRankedCrossRef<br/></span><span class="compile-data">testSetRankedCrossRefs<br/></span><span class="compile-data">testAddSynonym<br/></span><span class="compile-data">testRemoveSynonym<br/></span><span class="compile-data">testGetSynonyms<br/></span><span class="compile-data">testGetOntology<br/></span><span class="compile-data">testGetObsolete<br/></span><span class="compile-data">testSetObsolete<br/></span><span class="compile-data">Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec<br/></span><span class="compile-data">Running org.biojava.utils.ListToolsTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.HashSequenceDBTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.TranslationTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleNamespaceTest<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetDescription<br/></span><span class="compile-data">testSetDescription<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testSetAcronym<br/></span><span class="compile-data">testSetAuthority<br/></span><span class="compile-data">testSetURI<br/></span><span class="compile-data">testGetAcronym<br/></span><span class="compile-data">testGetAuthority<br/></span><span class="compile-data">testGetURI<br/></span><span class="compile-data">Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Running org.biojavax.DummyCrossReferenceResolverTest<br/></span><span class="compile-data">testGetRemoteSymbolList<br/></span><span class="compile-data">testGetRemoteBioEntry<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.AnnotationTypeTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.RNAToolsTest<br/></span><span class="compile-data">Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec<br/></span><span class="compile-data">Running org.biojava.directory.SystemRegistryTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.243 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.SeqSerializationTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 sec<br/></span><span class="compile-data">Running org.biojavax.ga.functions.AbstractCrossOverFunctionTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.NewSimpleAssemblyTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec<br/></span><span class="compile-data">Running org.biojava.bio.search.MaxMismatchPatternTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.io.filterxml.FilterXMLTest<br/></span><span class="compile-data">Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.CompoundLocationTest<br/></span><span class="compile-data">Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec<br/></span><span class="compile-data">Running org.biojavax.ga.functions.ProportionalSelectionTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.CircularLocationTest<br/></span><span class="compile-data">Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.FeatureHolderUtilsTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.proteomics.IsoelectricPointCalcTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.AlphabetManagerTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.CompoundRichLocationTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.CrossProductTokenizationTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.AlphabetSerializationTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 sec<br/></span><span class="compile-data">Running org.biojava.naming.ObdaUriParserTest<br/></span><span class="compile-data">oneName<br/></span><span class="compile-data">:trail<br/></span><span class="compile-data">lead:<br/></span><span class="compile-data">urn:obda.org:format:embl/ac<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.naming.ObdaInitialContextFactoryTest<br/></span><span class="compile-data">lookup: 'urn:open-bio.org:format:embl' for {urn=org.biojava.naming.ObdaContext@5197d20c}<br/></span><span class="compile-data">My component is urn:open-bio.org:format:embl<br/></span><span class="compile-data">lookup: 'open-bio.org:format:embl' for {open-bio.org=org.biojava.naming.ObdaContext@1646fef3}<br/></span><span class="compile-data">My component is open-bio.org:format:embl<br/></span><span class="compile-data">lookup: 'format:embl' for {type=org.biojava.naming.ObdaContext@f0c0ef2, format=org.biojava.naming.ObdaContext@60a93995, alphabet=org.biojava.naming.ObdaContext@60396c7}<br/></span><span class="compile-data">My component is format:embl<br/></span><span class="compile-data">lookup: 'embl' for {enzyme=org.biojava.naming.ObdaContext@559fe5e6, genbank=org.biojava.naming.ObdaContext@74ae8af4, swissprot=org.biojava.naming.ObdaContext@6f24d504,
embl=org.biojava.naming.ObdaContext@5b1d329d}<br/></span><span class="compile-data">My component is embl<br/></span><span class="compile-data">Reached <br/></span><span class="compile-data"> Attributes: No attributes<br/></span><span class="compile-data">Binding: urn -> org.biojava.naming.ObdaContext@55f4c4a3<br/></span><span class="compile-data">Reached urn<br/></span><span class="compile-data"> Attributes: No attributes<br/></span><span class="compile-data">Binding: open-bio.org -> org.biojava.naming.ObdaContext@3899d56b<br/></span><span class="compile-data">Reached urn:open-bio.org<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">This is the root namespace for all OBDA URNs. All OBDA URNs should be prefixed<br/></span><span class="compile-data">by urn:open-bio.org as described in the file naming/open-bio_urns.txt in the<br/></span><span class="compile-data">module obda-specs in the cvs repository located at<br/></span><span class="compile-data">pub.open-bio.org:/home/repository/obf-common.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: type -> org.biojava.naming.ObdaContext@42101da9<br/></span><span class="compile-data">Reached urn:open-bio.org:type<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The namespace for URNs that identify data types. It is expected that the types<br/></span><span class="compile-data">that are given IDs will be very general in nature, such as Sequence and<br/></span><span class="compile-data">File Format. All types are of type urn:open-bio.org:type:type. Any URN in the<br/></span><span class="compile-data">type namespace that is not of this type is not conforming to the OBDA<br/></span><span class="compile-data">specification for this namespace.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: type -> org.biojava.naming.ObdaContext@300b6421<br/></span><span class="compile-data">Reached urn:open-bio.org:type:type<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The OBDA URN that identifies the concept of 'type'. In a given language, this<br/></span><span class="compile-data">may map to the types of data structures, or objects. Alternativel, it may<br/></span><span class="compile-data">map to a particular set of keys being present in a map, or a term in an<br/></span><span class="compile-data">ontology. This is not important. The important thing is that we have unique<br/></span><span class="compile-data">identifiers for common types that all projects use and interact with.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: format -> org.biojava.naming.ObdaContext@3bdacb2b<br/></span><span class="compile-data">Reached urn:open-bio.org:type:format<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">A file format. Many file formats are used in bioinformatics. Entities of this<br/></span><span class="compile-data">type identify a format. The format can be used to choose how to treat a file.<br/></span><span class="compile-data">The format is not expected to be resolvable to a formal deffinition of the<br/></span><span class="compile-data">file structure using OBDA-supplied functionality. Different applications may<br/></span><span class="compile-data">chose to process a stream with the same format URN in different ways. This<br/></span><span class="compile-data">type of URN is purely there to identify the format of the stream, not the<br/></span><span class="compile-data">manner in which it should be processed.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: alphabet -> org.biojava.naming.ObdaContext@195092c0<br/></span><span class="compile-data">Reached urn:open-bio.org:type:alphabet<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">A biological sequence alphabet. Biological sequences are often represented as<br/></span><span class="compile-data">strings of characters. However, in differnt circumstances, the same characters<br/></span><span class="compile-data">can represent different things. For example, in DNA, the 't' character<br/></span><span class="compile-data">represents tyrosine. In Protein, this same character represents tryptophan.<br/></span><span class="compile-data">Associating alphabets with these sequences disambiguates their interpretation.<br/></span><span class="compile-data">Alphabets do not define a mapping to or from strings, but should be used<br/></span><span class="compile-data">wherever the type of the content of a sequence needs to be stated.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: format -> org.biojava.naming.ObdaContext@78d2883b<br/></span><span class="compile-data">Reached urn:open-bio.org:format<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">A namespace for OBDA URNs that define formats. All URNs within this namespace<br/></span><span class="compile-data">must be of the type urn:open-bio.org:type:format. Any URN in this namespace that<br/></span><span class="compile-data">is not of that type is not a valid OBDA URN.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: enzyme -> org.biojava.naming.ObdaContext@45ee1775<br/></span><span class="compile-data">Reached urn:open-bio.org:format:enzyme<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The Enzyme database entry format. The enzyme database can be downloaded from<br/></span><span class="compile-data">the ebi at:<br/></span><span class="compile-data"> ftp://ftp.ebi.ac.uk/pub/databases/enzyme/<br/></span><span class="compile-data">For an example of a file in this format, see:<br/></span><span class="compile-data"> ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyme.dat<br/></span><span class="compile-data">The format is described more fully in<br/></span><span class="compile-data"> ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyser.txt<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: genbank -> org.biojava.naming.ObdaContext@12462631<br/></span><span class="compile-data">Reached urn:open-bio.org:format:genbank<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The GENBANK file format associated with the GENBANK sequence database.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: swissprot -> org.biojava.naming.ObdaContext@3b756456<br/></span><span class="compile-data">Reached urn:open-bio.org:format:swissprot<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The SWISSPROT file format as used in the SWISSPROT sequence database.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: embl -> org.biojava.naming.ObdaContext@180e6899<br/></span><span class="compile-data">Reached urn:open-bio.org:format:embl<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The EMBL file format associated with entries in the EMBL sequence database.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: alphabet -> org.biojava.naming.ObdaContext@59f52125<br/></span><span class="compile-data">Reached urn:open-bio.org:alphabet<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">A namespace within which to store alphabet identifiers. Alphabets should<br/></span><span class="compile-data">represent URNs that represent objects of the type identified by<br/></span><span class="compile-data">urn:open-bio.org:type:alphabet, and any useage outside of this is not supported.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: rna -> org.biojava.naming.ObdaContext@6c533246<br/></span><span class="compile-data">Reached urn:open-bio.org:alphabet:rna<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The RNA alphabet. RNA is composed from four nucleotides. Read a biochemistry<br/></span><span class="compile-data">or genetics introductory textbook to find out more. Commonly, the nucleotides<br/></span><span class="compile-data">are reprsented by the four letters a, g, c and u. However, this is not a<br/></span><span class="compile-data">formal requirement for a resource to declare this alphabet as its type.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: protein -> org.biojava.naming.ObdaContext@4a09c939<br/></span><span class="compile-data">Reached urn:open-bio.org:alphabet:protein<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The protein alphabet. Proteins are composed from amino-acids. To find out more,<br/></span><span class="compile-data">read a biochemistry or genetics text book. It is common for protein sequences<br/></span><span class="compile-data">to be represented by characters, but this is not a formal requirement for<br/></span><span class="compile-data">a resource to publish an alphabet equal to this identifier.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: dna -> org.biojava.naming.ObdaContext@4879e328<br/></span><span class="compile-data">Reached urn:open-bio.org:alphabet:dna<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The DNA alphabet. DNA is composed from four nucleotides. Read a biochemistry<br/></span><span class="compile-data">or genetics introductory textbook to find out more. Commonly, the nucleotides<br/></span><span class="compile-data">are reprsented by the four letters a, g, c and t. However, this is not a<br/></span><span class="compile-data">formal requirement for a resource to declare this alphabet as its type.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.SimpleAssemblyTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.GappedSymbolListTest<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.UkkonenSuffixTreeTest<br/></span><span class="compile-data">Adding symbol list taccaccagga$<br/></span><span class="compile-data">Adding symbol list taccaccagga$<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.116 sec<br/></span><span class="compile-data">Running org.biojavax.ga.util.WeightedSetTest<br/></span><span class="compile-data">Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SimpleWobbleDistributionTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleNoteTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testSetRank<br/></span><span class="compile-data">testGetRank<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetTerm<br/></span><span class="compile-data">testSetTerm<br/></span><span class="compile-data">testGetValue<br/></span><span class="compile-data">testSetValue<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.utils.SmallMapTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SimpleAtomicSymbolEventTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.dist.TranslatedDistributionTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.SimpleRichFeatureTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.RangeLocationTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.directory.OBDARegistryParserTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.179 sec<br/></span><span class="compile-data">Running org.biojava.ontology.TripleImplTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.MotifToolsTest<br/></span><span class="compile-data">Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Running org.biojava.utils.regex.RegexTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.CircularSequenceTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.DNAToolsTest<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SymbolSerializationTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.TestHashSequenceDB<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.GenbankFormatTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 sec<br/></span><span class="compile-data">Running org.biojava.bio.proteomics.MassCalcTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.dp.MarkovModelEventTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.dist.DistributionToolsTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.LinearAlphabetIndexTest<br/></span><span class="compile-data">getAlphabet<br/></span><span class="compile-data">symbolForIndex<br/></span><span class="compile-data">indexForSymbol<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SimpleCodonPrefTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojavax.ontology.SimpleComparableTripleTest<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testGetAnnotation<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetDescription<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testAddSynonym<br/></span><span class="compile-data">testRemoveSynonym<br/></span><span class="compile-data">testGetSynonyms<br/></span><span class="compile-data">testGetOntology<br/></span><span class="compile-data">testGetSubject<br/></span><span class="compile-data">testGetObject<br/></span><span class="compile-data">testGetPredicate<br/></span><span class="compile-data">testAddDescriptor<br/></span><span class="compile-data">testRemoveDescriptor<br/></span><span class="compile-data">testGetDescriptors<br/></span><span class="compile-data">testSetDescriptors<br/></span><span class="compile-data">Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.INSDseqFormatTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.phred.PhredToolsTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.UniProtFormatTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.impl.SubSequenceTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest<br/></span><span class="compile-data">Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.NameTokenizationTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojavax.bio.taxa.SimpleNCBITaxonNameTest<br/></span><span class="compile-data">testSetName<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testSetNameClass<br/></span><span class="compile-data">testGetNameClass<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleCommentTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetComment<br/></span><span class="compile-data">testSetComment<br/></span><span class="compile-data">testSetRank<br/></span><span class="compile-data">testGetRank<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.GenbankLocationParserTest<br/></span><span class="compile-data">Location 467: 467<br/></span><span class="compile-data">Location 340..565: 340..565<br/></span><span class="compile-data">Location <345..500: <345..500<br/></span><span class="compile-data">Location <1..888: <1..888<br/></span><span class="compile-data">Location (102.110): (102.110)<br/></span><span class="compile-data">Location (23.45)..600: (23.45)..600<br/></span><span class="compile-data">Location (122.133)..(204.221): (122.133)..(204.221)<br/></span><span class="compile-data">Location 123^124: 123^124<br/></span><span class="compile-data">Location 145^177: 145^177<br/></span><span class="compile-data">Location join(12..78,134..202): join(12..78,134..202)<br/></span><span class="compile-data">Location complement(1..23): complement(1..23)<br/></span><span class="compile-data">Location complement(join(2691..4571,4918..5163): complement(join(2691..4571,4918..5163))<br/></span><span class="compile-data">Location join(complement(4918..5163),complement(2691..4571)): complement(join(2691..4571,4918..5163))<br/></span><span class="compile-data">Location complement(34..(122.126)): complement(34..(122.126))<br/></span><span class="compile-data">Location complement((122.126)..34): complement((122.126)..34)<br/></span><span class="compile-data">Location J00194:100..202: J00194:100..202<br/></span><span class="compile-data">Location (8298.8300)..10206: (8298.8300)..10206<br/></span><span class="compile-data">Location join((8298.8300)..10206,1..855): join((8298.8300)..10206,1..855)<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.MergeFeatureHolderTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.utils.process.ExternalProcessTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.222 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleRankedCrossRefTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetCrossRef<br/></span><span class="compile-data">testSetRank<br/></span><span class="compile-data">testGetRank<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.io.SeqIOToolsTest<br/></span><span class="compile-data">idb length: 79<br/></span><span class="compile-data">Testing SP read<br/></span><span class="compile-data">Testing SP read<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.598 sec<br/></span><span class="compile-data">Running org.biojava.bio.dist.DistSerTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.impl.GappedSequenceTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.Bug2250_2256Test<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.143 sec<br/></span><span class="compile-data">Running org.biojavax.CrossReferenceResolutionExceptionTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.ontology.ParseOBOFileTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.34 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.BetweenLocationTest<br/></span><span class="compile-data">Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec<br/></span><span class="compile-data">Running org.biojava.ontology.TermImplTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojavax.ga.impl.SimplePopulationTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.IndexedNoAmbPackTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SimpleBasisSymbolEventTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.molbio.RestrictionEnzymeTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.ontology.OntologyTest<br/></span><span class="compile-data">Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec<br/></span><span class="compile-data">Running org.biojava.utils.automata.NfaTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.directory.RegistryConfigurationTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojavax.ga.impl.SimpleOrganismTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojavax.ga.util.GAToolsTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.proteomics.aaindex.AAindexTest<br/></span><span class="compile-data">org.biojava.bio.symbol.IllegalSymbolException: Symbol adenine not found in alphabet PROTEIN<br/></span><span class="compile-data"> at org.biojava.bio.symbol.AbstractAlphabet.validate(AbstractAlphabet.java:326)<br/></span><span class="compile-data"> at org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper.validate(AlphabetManager.java:1601)<br/></span><span class="compile-data"> at org.biojava.bio.symbol.SimpleSymbolPropertyTable.getDoubleValue(SimpleSymbolPropertyTable.java:67)<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.AAindexTest.testDoubleValue(AAindexTest.java:189)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:168)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:134)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:110)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:128)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:113)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:124)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:232)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:227)<br/></span><span class="compile-data"> at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.io.MSFAlignmentFormatTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 878, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/core/target/core-1.8.1-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/core/target/core-1.8.1-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/core/1.8.1-SNAPSHOT/core-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/core/target/core-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">3 warnings<br/></span><span class="compile-data">[WARNING] Javadoc Warnings<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/core/src/main/java/org/biojava/bio/alignment/SimpleAlignment.java:303: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/core/src/main/java/org/biojavax/RichObjectFactory.java:74: warning - Tag @see:
reference not found: org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/core/src/main/java/org/biojavax/bio/seq/io/GenbankLocationParser.java:52: warning
- @authour is an unknown tag.<br/></span><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/core/target/core-1.8.1-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 29 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 51 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/core/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.utils.lsid.LifeScienceIdentifierTest<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SymbolListTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.051 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleDocRefAuthorTest<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetExtendedName<br/></span><span class="compile-data">testIsConsortium<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec<br/></span><span class="compile-data">Running org.biojavax.ga.functions.SimpleMutationFunctionTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec<br/></span><span class="compile-data">Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.267 sec<br/></span><span class="compile-data">Running org.biojava.bio.dp.EmissionStateEventTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.SimpleRichLocationTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec<br/></span><span class="compile-data">Running org.biojava.bio.search.SeqContentPatternTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Running org.biojavax.EmptyRichAnnotationTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testContains<br/></span><span class="compile-data">testKeys<br/></span><span class="compile-data">testAsMap<br/></span><span class="compile-data">testClear<br/></span><span class="compile-data">testGetNoteSet<br/></span><span class="compile-data">testSetNoteSet<br/></span><span class="compile-data">testGetProperty<br/></span><span class="compile-data">testGetNote<br/></span><span class="compile-data">testSetProperty<br/></span><span class="compile-data">testAddNote<br/></span><span class="compile-data">testRemoveProperty<br/></span><span class="compile-data">testRemoveNote<br/></span><span class="compile-data">testContainsProperty<br/></span><span class="compile-data">Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.FeatureFilterTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.Bug2255Test<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 sec<br/></span><span class="compile-data">Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.073 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleDocRefTest<br/></span><span class="compile-data">testGetLocation<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testSetRemark<br/></span><span class="compile-data">testSetCrossref<br/></span><span class="compile-data">testGetAuthors<br/></span><span class="compile-data">testGetAuthorList<br/></span><span class="compile-data">testGetCRC<br/></span><span class="compile-data">testGetRemark<br/></span><span class="compile-data">testGetCrossref<br/></span><span class="compile-data">testGetTitle<br/></span><span class="compile-data">Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.io.SmartSequenceBuilderTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.407 sec<br/></span><span class="compile-data">Running org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest<br/></span><span class="compile-data">java.lang.NullPointerException: table is null.<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.addTable(SimpleSymbolPropertyTableDB.java:145)<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testAddTable(SimpleSymbolPropertyTableDBTest.java:113)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:168)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:134)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:110)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:128)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:113)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:124)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:232)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:227)<br/></span><span class="compile-data"> at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">java.lang.NullPointerException: name is null.<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:172)<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:126)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:168)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:134)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:110)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:128)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:113)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:124)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:232)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:227)<br/></span><span class="compile-data"> at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">org.biojava.bio.seq.db.IllegalIDException: No table found with name test.<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:175)<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:134)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:168)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:134)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:110)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:128)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:113)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:124)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:232)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:227)<br/></span><span class="compile-data"> at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec<br/></span><span class="compile-data">Running org.biojava.bio.dist.DistributionTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.filter.FilterTransformerTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 sec<br/></span><span class="compile-data">Running org.biojavax.ontology.SimpleComparableOntologyTest<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetDescription<br/></span><span class="compile-data">testSetDescription<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetTerm<br/></span><span class="compile-data">testContainsTerm<br/></span><span class="compile-data">testGetOrCreateTerm<br/></span><span class="compile-data">testGetOrImportTerm<br/></span><span class="compile-data">testCreateTerm<br/></span><span class="compile-data">testImportTerm<br/></span><span class="compile-data">testCreateTriple<br/></span><span class="compile-data">testDeleteTerm<br/></span><span class="compile-data">testGetTriples<br/></span><span class="compile-data">testSetTripleSet<br/></span><span class="compile-data">testGetTripleSet<br/></span><span class="compile-data">testGetTerms<br/></span><span class="compile-data">testSetTermSet<br/></span><span class="compile-data">testGetTermSet<br/></span><span class="compile-data">testContainsTriple<br/></span><span class="compile-data">testCreateVariable<br/></span><span class="compile-data">testGetOps<br/></span><span class="compile-data">Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.indexdb.IndexToolsTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.097 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.ProteinToolsTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojavax.bio.SimpleBioEntryTest<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testGetAnnotation<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetDescription<br/></span><span class="compile-data">testSetDescription<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetRankedCrossRefs<br/></span><span class="compile-data">testSetTaxon<br/></span><span class="compile-data">testGetNoteSet<br/></span><span class="compile-data">testSetNoteSet<br/></span><span class="compile-data">testGetComments<br/></span><span class="compile-data">testGetRankedDocRefs<br/></span><span class="compile-data">testGetRelationships<br/></span><span class="compile-data">testSetIdentifier<br/></span><span class="compile-data">testSetDivision<br/></span><span class="compile-data">testGetAccession<br/></span><span class="compile-data">testGetDivision<br/></span><span class="compile-data">testGetIdentifier<br/></span><span class="compile-data">testGetNamespace<br/></span><span class="compile-data">testGetTaxon<br/></span><span class="compile-data">testGetVersion<br/></span><span class="compile-data">testAddRankedCrossRef<br/></span><span class="compile-data">testRemoveRankedCrossRef<br/></span><span class="compile-data">testAddRankedDocRef<br/></span><span class="compile-data">testRemoveRankedDocRef<br/></span><span class="compile-data">testAddComment<br/></span><span class="compile-data">testRemoveComment<br/></span><span class="compile-data">testAddRelationship<br/></span><span class="compile-data">testRemoveRelationship<br/></span><span class="compile-data">testSetRankedCrossRefs<br/></span><span class="compile-data">Tests run: 32, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleRichAnnotationTest<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testContains<br/></span><span class="compile-data">testKeys<br/></span><span class="compile-data">testAsMap<br/></span><span class="compile-data">testClear<br/></span><span class="compile-data">testGetNoteSet<br/></span><span class="compile-data">testSetNoteSet<br/></span><span class="compile-data">testGetProperty<br/></span><span class="compile-data">testGetNote<br/></span><span class="compile-data">testSetProperty<br/></span><span class="compile-data">testAddNote<br/></span><span class="compile-data">testRemoveProperty<br/></span><span class="compile-data">testRemoveNote<br/></span><span class="compile-data">testContainsProperty<br/></span><span class="compile-data">testGetPropertys<br/></span><span class="compile-data">testRemoveProperty2<br/></span><span class="compile-data">Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.PointLocationTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.MergeAnnotationTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec<br/></span><span class="compile-data">Running org.biojava.bio.dp.DPSerializationTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.io.SymbolListCharSequenceTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.CodonPrefToolsTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.124 sec<br/></span><span class="compile-data">Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.io.LocationFormatterTest<br/></span><span class="compile-data">Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.178 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.Bug2249_2248Test<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojava.utils.walker.WalkerFactoryTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec<br/></span><span class="compile-data">Running org.biojavax.ga.functions.SimpleCrossOverFunctionTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleCrossRefTest<br/></span><span class="compile-data">testGetAnnotation<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetNoteSet<br/></span><span class="compile-data">testSetNoteSet<br/></span><span class="compile-data">testGetAccession<br/></span><span class="compile-data">testGetVersion<br/></span><span class="compile-data">testGetDbname<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojavax.ga.functions.AbstractMutationFunctionTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.DoubleAlphabetTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.impl.ViewSequenceTest<br/></span><span class="compile-data">template: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any
annotation={geneID=braca1}<br/></span><span class="compile-data">orignal: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any
annotation={geneID=braca1}<br/></span><span class="compile-data">copy: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any
annotation={geneID=braca1}<br/></span><span class="compile-data">template: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any
annotation={geneID=braca1}<br/></span><span class="compile-data">orignal: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any
annotation={geneID=braca1}<br/></span><span class="compile-data">copy: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any
annotation={geneID=braca1}<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.TestSoftMaskedAlphabet<br/></span><span class="compile-data">Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.IntegerAlphabetTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SimpleSymbolListTest<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.EMBLFormatTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SimpleSymbolEventTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.utils.walker.WalkerTest<br/></span><span class="compile-data">Increasing counter: Overlaps([20,50])<br/></span><span class="compile-data">Increasing counter: Overlaps([20,50])<br/></span><span class="compile-data">Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature)<br/></span><span class="compile-data">Increasing counter: And(Overlaps([20,50]) , ByClass(org.biojava.bio.seq.StrandedFeature))<br/></span><span class="compile-data">Increasing counter: Overlaps([20,50])<br/></span><span class="compile-data">Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature)<br/></span><span class="compile-data">Increasing counter: ByClass(org.biojava.bio.seq.ComponentFeature)<br/></span><span class="compile-data">Increasing counter: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))<br/></span><span class="compile-data">Increasing counter: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)))<br/></span><span class="compile-data">OverlapsLocation: Overlaps([20,50])<br/></span><span class="compile-data">Feature: ByClass(org.biojava.bio.seq.StrandedFeature)<br/></span><span class="compile-data">OverlapsLocation: Overlaps([20,50])<br/></span><span class="compile-data">Feature: ByClass(org.biojava.bio.seq.StrandedFeature)<br/></span><span class="compile-data">Feature: ByClass(org.biojava.bio.seq.ComponentFeature)<br/></span><span class="compile-data">Feature: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))<br/></span><span class="compile-data">Feature: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)))<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec<br/></span><span class="compile-data">Running org.biojava.utils.RepeatedCharSequenceTest<br/></span><span class="compile-data">JAM<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.FilterUtilsTest<br/></span><span class="compile-data">Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleRankedDocRefTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testSetRank<br/></span><span class="compile-data">testGetRank<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetDocumentReference<br/></span><span class="compile-data">testGetStart<br/></span><span class="compile-data">testGetEnd<br/></span><span class="compile-data">testSetLocation<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.RichLocationToolsTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.impl.ViewSeqSerializationTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 sec<br/></span><span class="compile-data">Running org.biojava.utils.regex.PatternCheckerTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.MergeLocationTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojavax.ontology.SimpleComparableTermTest<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testGetAnnotation<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetDescription<br/></span><span class="compile-data">testSetDescription<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetRankedCrossRefs<br/></span><span class="compile-data">testSetIdentifier<br/></span><span class="compile-data">testGetIdentifier<br/></span><span class="compile-data">testAddRankedCrossRef<br/></span><span class="compile-data">testRemoveRankedCrossRef<br/></span><span class="compile-data">testSetRankedCrossRefs<br/></span><span class="compile-data">testAddSynonym<br/></span><span class="compile-data">testRemoveSynonym<br/></span><span class="compile-data">testGetSynonyms<br/></span><span class="compile-data">testGetOntology<br/></span><span class="compile-data">testGetObsolete<br/></span><span class="compile-data">testSetObsolete<br/></span><span class="compile-data">Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec<br/></span><span class="compile-data">Running org.biojava.utils.ListToolsTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.HashSequenceDBTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.TranslationTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleNamespaceTest<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetDescription<br/></span><span class="compile-data">testSetDescription<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testSetAcronym<br/></span><span class="compile-data">testSetAuthority<br/></span><span class="compile-data">testSetURI<br/></span><span class="compile-data">testGetAcronym<br/></span><span class="compile-data">testGetAuthority<br/></span><span class="compile-data">testGetURI<br/></span><span class="compile-data">Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojavax.DummyCrossReferenceResolverTest<br/></span><span class="compile-data">testGetRemoteSymbolList<br/></span><span class="compile-data">testGetRemoteBioEntry<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.AnnotationTypeTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.RNAToolsTest<br/></span><span class="compile-data">Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec<br/></span><span class="compile-data">Running org.biojava.directory.SystemRegistryTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.223 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.SeqSerializationTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 sec<br/></span><span class="compile-data">Running org.biojavax.ga.functions.AbstractCrossOverFunctionTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.NewSimpleAssemblyTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec<br/></span><span class="compile-data">Running org.biojava.bio.search.MaxMismatchPatternTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.io.filterxml.FilterXMLTest<br/></span><span class="compile-data">Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.082 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.CompoundLocationTest<br/></span><span class="compile-data">Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec<br/></span><span class="compile-data">Running org.biojavax.ga.functions.ProportionalSelectionTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.CircularLocationTest<br/></span><span class="compile-data">Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.FeatureHolderUtilsTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.proteomics.IsoelectricPointCalcTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.AlphabetManagerTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.CompoundRichLocationTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.CrossProductTokenizationTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.AlphabetSerializationTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 sec<br/></span><span class="compile-data">Running org.biojava.naming.ObdaUriParserTest<br/></span><span class="compile-data">oneName<br/></span><span class="compile-data">:trail<br/></span><span class="compile-data">lead:<br/></span><span class="compile-data">urn:obda.org:format:embl/ac<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.naming.ObdaInitialContextFactoryTest<br/></span><span class="compile-data">lookup: 'urn:open-bio.org:format:embl' for {urn=org.biojava.naming.ObdaContext@638e8fbd}<br/></span><span class="compile-data">My component is urn:open-bio.org:format:embl<br/></span><span class="compile-data">lookup: 'open-bio.org:format:embl' for {open-bio.org=org.biojava.naming.ObdaContext@adc9515}<br/></span><span class="compile-data">My component is open-bio.org:format:embl<br/></span><span class="compile-data">lookup: 'format:embl' for {type=org.biojava.naming.ObdaContext@17bf9b45, format=org.biojava.naming.ObdaContext@246adb31, alphabet=org.biojava.naming.ObdaContext@635c80a4}<br/></span><span class="compile-data">My component is format:embl<br/></span><span class="compile-data">lookup: 'embl' for {enzyme=org.biojava.naming.ObdaContext@4e01c1f2, genbank=org.biojava.naming.ObdaContext@55641ee0, swissprot=org.biojava.naming.ObdaContext@20272fec,
embl=org.biojava.naming.ObdaContext@6cbb3f71}<br/></span><span class="compile-data">My component is embl<br/></span><span class="compile-data">Reached <br/></span><span class="compile-data"> Attributes: No attributes<br/></span><span class="compile-data">Binding: urn -> org.biojava.naming.ObdaContext@44755866<br/></span><span class="compile-data">Reached urn<br/></span><span class="compile-data"> Attributes: No attributes<br/></span><span class="compile-data">Binding: open-bio.org -> org.biojava.naming.ObdaContext@73feb3a6<br/></span><span class="compile-data">Reached urn:open-bio.org<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">This is the root namespace for all OBDA URNs. All OBDA URNs should be prefixed<br/></span><span class="compile-data">by urn:open-bio.org as described in the file naming/open-bio_urns.txt in the<br/></span><span class="compile-data">module obda-specs in the cvs repository located at<br/></span><span class="compile-data">pub.open-bio.org:/home/repository/obf-common.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: type -> org.biojava.naming.ObdaContext@380b4f9<br/></span><span class="compile-data">Reached urn:open-bio.org:type<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The namespace for URNs that identify data types. It is expected that the types<br/></span><span class="compile-data">that are given IDs will be very general in nature, such as Sequence and<br/></span><span class="compile-data">File Format. All types are of type urn:open-bio.org:type:type. Any URN in the<br/></span><span class="compile-data">type namespace that is not of this type is not conforming to the OBDA<br/></span><span class="compile-data">specification for this namespace.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: type -> org.biojava.naming.ObdaContext@76e9493a<br/></span><span class="compile-data">Reached urn:open-bio.org:type:type<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The OBDA URN that identifies the concept of 'type'. In a given language, this<br/></span><span class="compile-data">may map to the types of data structures, or objects. Alternativel, it may<br/></span><span class="compile-data">map to a particular set of keys being present in a map, or a term in an<br/></span><span class="compile-data">ontology. This is not important. The important thing is that we have unique<br/></span><span class="compile-data">identifiers for common types that all projects use and interact with.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: format -> org.biojava.naming.ObdaContext@4dc6bbd3<br/></span><span class="compile-data">Reached urn:open-bio.org:type:format<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">A file format. Many file formats are used in bioinformatics. Entities of this<br/></span><span class="compile-data">type identify a format. The format can be used to choose how to treat a file.<br/></span><span class="compile-data">The format is not expected to be resolvable to a formal deffinition of the<br/></span><span class="compile-data">file structure using OBDA-supplied functionality. Different applications may<br/></span><span class="compile-data">chose to process a stream with the same format URN in different ways. This<br/></span><span class="compile-data">type of URN is purely there to identify the format of the stream, not the<br/></span><span class="compile-data">manner in which it should be processed.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: alphabet -> org.biojava.naming.ObdaContext@32554189<br/></span><span class="compile-data">Reached urn:open-bio.org:type:alphabet<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">A biological sequence alphabet. Biological sequences are often represented as<br/></span><span class="compile-data">strings of characters. However, in differnt circumstances, the same characters<br/></span><span class="compile-data">can represent different things. For example, in DNA, the 't' character<br/></span><span class="compile-data">represents tyrosine. In Protein, this same character represents tryptophan.<br/></span><span class="compile-data">Associating alphabets with these sequences disambiguates their interpretation.<br/></span><span class="compile-data">Alphabets do not define a mapping to or from strings, but should be used<br/></span><span class="compile-data">wherever the type of the content of a sequence needs to be stated.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: format -> org.biojava.naming.ObdaContext@7b41a32f<br/></span><span class="compile-data">Reached urn:open-bio.org:format<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">A namespace for OBDA URNs that define formats. All URNs within this namespace<br/></span><span class="compile-data">must be of the type urn:open-bio.org:type:format. Any URN in this namespace that<br/></span><span class="compile-data">is not of that type is not a valid OBDA URN.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: enzyme -> org.biojava.naming.ObdaContext@1240a1e1<br/></span><span class="compile-data">Reached urn:open-bio.org:format:enzyme<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The Enzyme database entry format. The enzyme database can be downloaded from<br/></span><span class="compile-data">the ebi at:<br/></span><span class="compile-data"> ftp://ftp.ebi.ac.uk/pub/databases/enzyme/<br/></span><span class="compile-data">For an example of a file in this format, see:<br/></span><span class="compile-data"> ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyme.dat<br/></span><span class="compile-data">The format is described more fully in<br/></span><span class="compile-data"> ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyser.txt<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: genbank -> org.biojava.naming.ObdaContext@5143c423<br/></span><span class="compile-data">Reached urn:open-bio.org:format:genbank<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The GENBANK file format associated with the GENBANK sequence database.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: swissprot -> org.biojava.naming.ObdaContext@3801ff83<br/></span><span class="compile-data">Reached urn:open-bio.org:format:swissprot<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The SWISSPROT file format as used in the SWISSPROT sequence database.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: embl -> org.biojava.naming.ObdaContext@b2e0e2f<br/></span><span class="compile-data">Reached urn:open-bio.org:format:embl<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The EMBL file format associated with entries in the EMBL sequence database.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: alphabet -> org.biojava.naming.ObdaContext@7ca53564<br/></span><span class="compile-data">Reached urn:open-bio.org:alphabet<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">A namespace within which to store alphabet identifiers. Alphabets should<br/></span><span class="compile-data">represent URNs that represent objects of the type identified by<br/></span><span class="compile-data">urn:open-bio.org:type:alphabet, and any useage outside of this is not supported.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: rna -> org.biojava.naming.ObdaContext@4254782a<br/></span><span class="compile-data">Reached urn:open-bio.org:alphabet:rna<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The RNA alphabet. RNA is composed from four nucleotides. Read a biochemistry<br/></span><span class="compile-data">or genetics introductory textbook to find out more. Commonly, the nucleotides<br/></span><span class="compile-data">are reprsented by the four letters a, g, c and u. However, this is not a<br/></span><span class="compile-data">formal requirement for a resource to declare this alphabet as its type.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: protein -> org.biojava.naming.ObdaContext@379d2f6b<br/></span><span class="compile-data">Reached urn:open-bio.org:alphabet:protein<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The protein alphabet. Proteins are composed from amino-acids. To find out more,<br/></span><span class="compile-data">read a biochemistry or genetics text book. It is common for protein sequences<br/></span><span class="compile-data">to be represented by characters, but this is not a formal requirement for<br/></span><span class="compile-data">a resource to publish an alphabet equal to this identifier.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Binding: dna -> org.biojava.naming.ObdaContext@30943653<br/></span><span class="compile-data">Reached urn:open-bio.org:alphabet:dna<br/></span><span class="compile-data"> Attributes: {description=description: <br/></span><span class="compile-data">The DNA alphabet. DNA is composed from four nucleotides. Read a biochemistry<br/></span><span class="compile-data">or genetics introductory textbook to find out more. Commonly, the nucleotides<br/></span><span class="compile-data">are reprsented by the four letters a, g, c and t. However, this is not a<br/></span><span class="compile-data">formal requirement for a resource to declare this alphabet as its type.<br/></span><span class="compile-data"> }<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.SimpleAssemblyTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.GappedSymbolListTest<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.UkkonenSuffixTreeTest<br/></span><span class="compile-data">Adding symbol list taccaccagga$<br/></span><span class="compile-data">Adding symbol list taccaccagga$<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.119 sec<br/></span><span class="compile-data">Running org.biojavax.ga.util.WeightedSetTest<br/></span><span class="compile-data">Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SimpleWobbleDistributionTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleNoteTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testSetRank<br/></span><span class="compile-data">testGetRank<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testGetTerm<br/></span><span class="compile-data">testSetTerm<br/></span><span class="compile-data">testGetValue<br/></span><span class="compile-data">testSetValue<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.utils.SmallMapTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SimpleAtomicSymbolEventTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.dist.TranslatedDistributionTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.SimpleRichFeatureTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.RangeLocationTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.directory.OBDARegistryParserTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.182 sec<br/></span><span class="compile-data">Running org.biojava.ontology.TripleImplTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.MotifToolsTest<br/></span><span class="compile-data">Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Running org.biojava.utils.regex.RegexTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.CircularSequenceTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.DNAToolsTest<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SymbolSerializationTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.TestHashSequenceDB<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.GenbankFormatTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec<br/></span><span class="compile-data">Running org.biojava.bio.proteomics.MassCalcTest<br/></span><span class="compile-data">Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.bio.dp.MarkovModelEventTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.dist.DistributionToolsTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.LinearAlphabetIndexTest<br/></span><span class="compile-data">getAlphabet<br/></span><span class="compile-data">symbolForIndex<br/></span><span class="compile-data">indexForSymbol<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SimpleCodonPrefTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojavax.ontology.SimpleComparableTripleTest<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testGetAnnotation<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetDescription<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testAddSynonym<br/></span><span class="compile-data">testRemoveSynonym<br/></span><span class="compile-data">testGetSynonyms<br/></span><span class="compile-data">testGetOntology<br/></span><span class="compile-data">testGetSubject<br/></span><span class="compile-data">testGetObject<br/></span><span class="compile-data">testGetPredicate<br/></span><span class="compile-data">testAddDescriptor<br/></span><span class="compile-data">testRemoveDescriptor<br/></span><span class="compile-data">testGetDescriptors<br/></span><span class="compile-data">testSetDescriptors<br/></span><span class="compile-data">Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.INSDseqFormatTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.phred.PhredToolsTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.UniProtFormatTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.impl.SubSequenceTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest<br/></span><span class="compile-data">Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.NameTokenizationTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojavax.bio.taxa.SimpleNCBITaxonNameTest<br/></span><span class="compile-data">testSetName<br/></span><span class="compile-data">testGetName<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">testSetNameClass<br/></span><span class="compile-data">testGetNameClass<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleCommentTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetComment<br/></span><span class="compile-data">testSetComment<br/></span><span class="compile-data">testSetRank<br/></span><span class="compile-data">testGetRank<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.GenbankLocationParserTest<br/></span><span class="compile-data">Location 467: 467<br/></span><span class="compile-data">Location 340..565: 340..565<br/></span><span class="compile-data">Location <345..500: <345..500<br/></span><span class="compile-data">Location <1..888: <1..888<br/></span><span class="compile-data">Location (102.110): (102.110)<br/></span><span class="compile-data">Location (23.45)..600: (23.45)..600<br/></span><span class="compile-data">Location (122.133)..(204.221): (122.133)..(204.221)<br/></span><span class="compile-data">Location 123^124: 123^124<br/></span><span class="compile-data">Location 145^177: 145^177<br/></span><span class="compile-data">Location join(12..78,134..202): join(12..78,134..202)<br/></span><span class="compile-data">Location complement(1..23): complement(1..23)<br/></span><span class="compile-data">Location complement(join(2691..4571,4918..5163): complement(join(2691..4571,4918..5163))<br/></span><span class="compile-data">Location join(complement(4918..5163),complement(2691..4571)): complement(join(2691..4571,4918..5163))<br/></span><span class="compile-data">Location complement(34..(122.126)): complement(34..(122.126))<br/></span><span class="compile-data">Location complement((122.126)..34): complement((122.126)..34)<br/></span><span class="compile-data">Location J00194:100..202: J00194:100..202<br/></span><span class="compile-data">Location (8298.8300)..10206: (8298.8300)..10206<br/></span><span class="compile-data">Location join((8298.8300)..10206,1..855): join((8298.8300)..10206,1..855)<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.MergeFeatureHolderTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.utils.process.ExternalProcessTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.23 sec<br/></span><span class="compile-data">Running org.biojavax.SimpleRankedCrossRefTest<br/></span><span class="compile-data">testEquals<br/></span><span class="compile-data">testToString<br/></span><span class="compile-data">testGetCrossRef<br/></span><span class="compile-data">testSetRank<br/></span><span class="compile-data">testGetRank<br/></span><span class="compile-data">testCompareTo<br/></span><span class="compile-data">testHashCode<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.io.SeqIOToolsTest<br/></span><span class="compile-data">idb length: 79<br/></span><span class="compile-data">Testing SP read<br/></span><span class="compile-data">Testing SP read<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.446 sec<br/></span><span class="compile-data">Running org.biojava.bio.dist.DistSerTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.impl.GappedSequenceTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Running org.biojavax.bio.seq.io.Bug2250_2256Test<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 sec<br/></span><span class="compile-data">Running org.biojavax.CrossReferenceResolutionExceptionTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.ontology.ParseOBOFileTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.361 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.BetweenLocationTest<br/></span><span class="compile-data">Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec<br/></span><span class="compile-data">Running org.biojava.ontology.TermImplTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojavax.ga.impl.SimplePopulationTest<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.IndexedNoAmbPackTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojava.bio.symbol.SimpleBasisSymbolEventTest<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.molbio.RestrictionEnzymeTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Running org.biojava.ontology.OntologyTest<br/></span><span class="compile-data">Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec<br/></span><span class="compile-data">Running org.biojava.utils.automata.NfaTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.directory.RegistryConfigurationTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec<br/></span><span class="compile-data">Running org.biojavax.ga.impl.SimpleOrganismTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec<br/></span><span class="compile-data">Running org.biojavax.ga.util.GAToolsTest<br/></span><span class="compile-data">Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec<br/></span><span class="compile-data">Running org.biojava.bio.proteomics.aaindex.AAindexTest<br/></span><span class="compile-data">org.biojava.bio.symbol.IllegalSymbolException: Symbol adenine not found in alphabet PROTEIN<br/></span><span class="compile-data"> at org.biojava.bio.symbol.AbstractAlphabet.validate(AbstractAlphabet.java:326)<br/></span><span class="compile-data"> at org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper.validate(AlphabetManager.java:1601)<br/></span><span class="compile-data"> at org.biojava.bio.symbol.SimpleSymbolPropertyTable.getDoubleValue(SimpleSymbolPropertyTable.java:67)<br/></span><span class="compile-data"> at org.biojava.bio.proteomics.aaindex.AAindexTest.testDoubleValue(AAindexTest.java:189)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at junit.framework.TestCase.runTest(TestCase.java:168)<br/></span><span class="compile-data"> at junit.framework.TestCase.runBare(TestCase.java:134)<br/></span><span class="compile-data"> at junit.framework.TestResult$1.protect(TestResult.java:110)<br/></span><span class="compile-data"> at junit.framework.TestResult.runProtected(TestResult.java:128)<br/></span><span class="compile-data"> at junit.framework.TestResult.run(TestResult.java:113)<br/></span><span class="compile-data"> at junit.framework.TestCase.run(TestCase.java:124)<br/></span><span class="compile-data"> at junit.framework.TestSuite.runTest(TestSuite.java:232)<br/></span><span class="compile-data"> at junit.framework.TestSuite.run(TestSuite.java:227)<br/></span><span class="compile-data"> at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83)<br/></span><span class="compile-data"> at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115)<br/></span><span class="compile-data"> at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102)<br/></span><span class="compile-data"> at org.apache.maven.surefire.Surefire.run(Surefire.java:180)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br/></span><span class="compile-data"> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br/></span><span class="compile-data"> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br/></span><span class="compile-data"> at java.lang.reflect.Method.invoke(Method.java:616)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350)<br/></span><span class="compile-data"> at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021)<br/></span><span class="compile-data">Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec<br/></span><span class="compile-data">Running org.biojava.bio.seq.io.MSFAlignmentFormatTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 878, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/core/target/core-1.8.1-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/core/1.8.1-SNAPSHOT/core-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/core/target/core-1.8.1-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/core/1.8.1-SNAPSHOT/core-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/core/target/core-1.8.1-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/core/1.8.1-SNAPSHOT/core-1.8.1-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/core/1.8.1-SNAPSHOT/core-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">2408K uploaded (core-1.8.1-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:core:1.8.1-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:core'<br/></span><span class="compile-data">[INFO] Uploading project information for core 1.8.1-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/core/1.8.1-SNAPSHOT/core-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">2034K uploaded (core-1.8.1-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/core/1.8.1-SNAPSHOT/core-1.8.1-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">13140K uploaded (core-1.8.1-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building alignment<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-legacy/alignment/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/alignment/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 14 source files to /opt/cruise/projects/biojava-legacy/alignment/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 1 resource<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 4 source files to /opt/cruise/projects/biojava-legacy/alignment/target/test-classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/alignment/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.bio.alignment.SubstitutionMatrixTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.216 sec<br/></span><span class="compile-data">Running org.biojava.bio.alignment.FlexibleAlignmentTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.283 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/alignment/target/alignment-1.8.1-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/alignment/target/alignment-1.8.1-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/alignment/1.8.1-SNAPSHOT/alignment-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/alignment/target/alignment-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">13 warnings<br/></span><span class="compile-data">[WARNING] Javadoc Warnings<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/AbstractULAlignment.java:207:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:57: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:392: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:532: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:524: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:327: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:335: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:343: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:351: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:359: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:367: warning
- @return tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:226: warning
- @param argument "queryLength" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/FlexibleAlignment.java:270:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/alignment/target/alignment-1.8.1-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/alignment/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 1 resource<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/alignment/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.bio.alignment.SubstitutionMatrixTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.216 sec<br/></span><span class="compile-data">Running org.biojava.bio.alignment.FlexibleAlignmentTest<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.283 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 3, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/alignment/target/alignment-1.8.1-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/alignment/1.8.1-SNAPSHOT/alignment-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/alignment/target/alignment-1.8.1-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/alignment/1.8.1-SNAPSHOT/alignment-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/alignment/target/alignment-1.8.1-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/alignment/1.8.1-SNAPSHOT/alignment-1.8.1-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/alignment/1.8.1-SNAPSHOT/alignment-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">36K uploaded (alignment-1.8.1-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:alignment'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:alignment:1.8.1-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Uploading project information for alignment 1.8.1-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/alignment/1.8.1-SNAPSHOT/alignment-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">33K uploaded (alignment-1.8.1-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/alignment/1.8.1-SNAPSHOT/alignment-1.8.1-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">198K uploaded (alignment-1.8.1-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building biosql<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-legacy/biosql/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/biosql/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 35 source files to /opt/cruise/projects/biojava-legacy/biosql/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/biosql/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 2 source files to /opt/cruise/projects/biojava-legacy/biosql/target/test-classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/biosql/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest<br/></span><span class="compile-data">No hsqldb driver found.<br/></span><span class="compile-data">Tests run: 0, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 0, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/biosql/target/biosql-1.8.1-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/biosql/target/biosql-1.8.1-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biosql/1.8.1-SNAPSHOT/biosql-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/biosql/target/biosql-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/biosql/target/biosql-1.8.1-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/biosql/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/biosql/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/biosql/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest<br/></span><span class="compile-data">No hsqldb driver found.<br/></span><span class="compile-data">Tests run: 0, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 0, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/biosql/target/biosql-1.8.1-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biosql/1.8.1-SNAPSHOT/biosql-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/biosql/target/biosql-1.8.1-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/biosql/1.8.1-SNAPSHOT/biosql-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/biosql/target/biosql-1.8.1-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/biosql/1.8.1-SNAPSHOT/biosql-1.8.1-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biosql/1.8.1-SNAPSHOT/biosql-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">164K uploaded (biosql-1.8.1-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:biosql'<br/></span><span class="compile-data">[INFO] Uploading project information for biosql 1.8.1-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:biosql:1.8.1-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biosql/1.8.1-SNAPSHOT/biosql-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">135K uploaded (biosql-1.8.1-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biosql/1.8.1-SNAPSHOT/biosql-1.8.1-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">670K uploaded (biosql-1.8.1-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building blast<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-legacy/blast/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 3 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 56 source files to /opt/cruise/projects/biojava-legacy/blast/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 22 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 19 source files to /opt/cruise/projects/biojava-legacy/blast/target/test-classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/blast/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.507 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.171 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.244 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.33 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.5 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.35 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.795 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.303 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.645 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.107 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.33 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.sax.BlastTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.082 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.77 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.sax.blastxml.BlastXMLTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.067 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.72 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.672 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.314 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.77 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 118, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/blast/target/blast-1.8.1-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/blast/target/blast-1.8.1-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/blast/1.8.1-SNAPSHOT/blast-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/blast/target/blast-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/blast/target/blast-1.8.1-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 3 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 22 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/blast/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.508 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.173 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.266 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.33 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.496 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.344 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.8 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.306 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.645 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.106 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.325 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.sax.BlastTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.766 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.sax.blastxml.BlastXMLTest<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.067 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.722 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.665 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.315 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test<br/></span><span class="compile-data">Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.772 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 118, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/blast/target/blast-1.8.1-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/blast/1.8.1-SNAPSHOT/blast-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/blast/target/blast-1.8.1-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/blast/1.8.1-SNAPSHOT/blast-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/blast/target/blast-1.8.1-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/blast/1.8.1-SNAPSHOT/blast-1.8.1-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/blast/1.8.1-SNAPSHOT/blast-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">181K uploaded (blast-1.8.1-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Uploading project information for blast 1.8.1-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:blast:1.8.1-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:blast'<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/blast/1.8.1-SNAPSHOT/blast-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">128K uploaded (blast-1.8.1-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/blast/1.8.1-SNAPSHOT/blast-1.8.1-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">300K uploaded (blast-1.8.1-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building das<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-legacy/das/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/das/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 91 source files to /opt/cruise/projects/biojava-legacy/das/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 5 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 9 source files to /opt/cruise/projects/biojava-legacy/das/target/test-classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/das/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.dasobert.TestRegistry<br/></span><span class="compile-data">unsupported capability: das1:cors<br/></span><span class="compile-data">unsupported capability: das1:cors<br/></span><span class="compile-data">unsupported capability: das1:cors<br/></span><span class="compile-data">Das2SourceHandler: source size: 1317<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.551 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestInteractionParse<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestExternalSource<br/></span><span class="compile-data">Das2SourceHandler: source size: 46<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.275 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestSisyphusServer<br/></span><span class="compile-data">Jan 25, 2011 1:02:09 AM org.biojava.dasobert.das.AlignmentThread retrieveAlignments<br/></span><span class="compile-data">INFO: requesting alignment http://sisyphus.mrc-cpe.cam.ac.uk/sisyphus/das/alignments/alignment?query%3DAL10057468<br/></span><span class="compile-data">object: CONSTRUCT:35<br/></span><span class="compile-data">object: CONSTRUCT:36<br/></span><span class="compile-data">object: CONSTRUCT:37<br/></span><span class="compile-data">object: CONSTRUCT:38<br/></span><span class="compile-data">object: CONSTRUCT:39<br/></span><span class="compile-data">object: CONSTRUCT:40<br/></span><span class="compile-data">object: CONSTRUCT:41<br/></span><span class="compile-data">object: CONSTRUCT:42<br/></span><span class="compile-data">object: CONSTRUCT:43<br/></span><span class="compile-data">object: CONSTRUCT:44<br/></span><span class="compile-data">object: CONSTRUCT:45<br/></span><span class="compile-data">object: CONSTRUCT:46<br/></span><span class="compile-data">object: CONSTRUCT:47<br/></span><span class="compile-data">object: CONSTRUCT:48<br/></span><span class="compile-data">object: CONSTRUCT:49<br/></span><span class="compile-data">object: CONSTRUCT:50<br/></span><span class="compile-data">object: CONSTRUCT:51<br/></span><span class="compile-data">object: CONSTRUCT:52<br/></span><span class="compile-data">object: CONSTRUCT:53<br/></span><span class="compile-data">object: CONSTRUCT:54<br/></span><span class="compile-data">object: CONSTRUCT:55<br/></span><span class="compile-data">number of blocks: 4<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.024 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestSequenceParse<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestSourcesParse<br/></span><span class="compile-data">unsupported capability: das1:dna<br/></span><span class="compile-data">Das2SourceHandler: source size: 267<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestUCSCFeatures<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.server.TestServers<br/></span><span class="compile-data">Jan 25, 2011 1:02:10 AM org.biojava.dasobert.das.SequenceThread retrieveSequence<br/></span><span class="compile-data">INFO: requesting sequence from http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/sequence?segment=P50225<br/></span><span class="compile-data">MELIQDTSRPPLEYVKGVPLIKYFAEALGPLQSFQARPDDLLISTYPKSGTTWVSQILDMIYQGGDLEKCHRAPIFMRVPFLEFKAPGIPSGMETLKDTPAPRLLKTHLPLALLPQTLLDQKVKVVYVARNAKDVAVSYYHFYHMAKVHPEPGTWDSFLEKFMVGEVSYGSWYQHVQEWWELSRTHPVLYLFYEDMKENPKREIQKILEFVGRSLPEETVDFVVQHTSFKEMKKNPMTNYTTVPQEFMDHSISPFMRKGMAGDWKTTFTVAQNERFDADYAEKMAGCSLSFRSEL<br/></span><span class="compile-data">started getInteractions method<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.355 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestFeatureParse<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/das/target/das-1.8.1-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/das/target/das-1.8.1-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/das/1.8.1-SNAPSHOT/das-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/das/target/das-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">6 warnings<br/></span><span class="compile-data">[WARNING] Javadoc Warnings<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/das/src/main/java/de/mpg/mpiinf/ag3/dasmi/model/Detail.java:143: warning - @return
tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/das/src/main/java/de/mpg/mpiinf/ag3/dasmi/model/Interaction.java:178: warning
- @param argument "interactors" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/das/src/main/java/de/mpg/mpiinf/ag3/dasmi/model/Interaction.java:187: warning
- @param argument "ref" is not a parameter name.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/das/src/main/java/de/mpg/mpiinf/ag3/dasmi/model/Interactor.java:237: warning
- @returntrue is an unknown tag.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/das/src/main/java/org/biojava/dasobert/das/Capabilities.java:58: warning - @return
tag has no arguments.<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/das/src/main/java/org/biojava/dasobert/das2/io/DASRegistryCoordinatesReaderXML.java:56:
warning - @return tag has no arguments.<br/></span><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/das/target/das-1.8.1-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/das/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 5 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/das/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.dasobert.TestRegistry<br/></span><span class="compile-data">unsupported capability: das1:cors<br/></span><span class="compile-data">unsupported capability: das1:cors<br/></span><span class="compile-data">unsupported capability: das1:cors<br/></span><span class="compile-data">Das2SourceHandler: source size: 1317<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.852 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestInteractionParse<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestExternalSource<br/></span><span class="compile-data">Das2SourceHandler: source size: 46<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.916 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestSisyphusServer<br/></span><span class="compile-data">Jan 25, 2011 1:02:26 AM org.biojava.dasobert.das.AlignmentThread retrieveAlignments<br/></span><span class="compile-data">INFO: requesting alignment http://sisyphus.mrc-cpe.cam.ac.uk/sisyphus/das/alignments/alignment?query%3DAL10057468<br/></span><span class="compile-data">object: CONSTRUCT:35<br/></span><span class="compile-data">object: CONSTRUCT:36<br/></span><span class="compile-data">object: CONSTRUCT:37<br/></span><span class="compile-data">object: CONSTRUCT:38<br/></span><span class="compile-data">object: CONSTRUCT:39<br/></span><span class="compile-data">object: CONSTRUCT:40<br/></span><span class="compile-data">object: CONSTRUCT:41<br/></span><span class="compile-data">object: CONSTRUCT:42<br/></span><span class="compile-data">object: CONSTRUCT:43<br/></span><span class="compile-data">object: CONSTRUCT:44<br/></span><span class="compile-data">object: CONSTRUCT:45<br/></span><span class="compile-data">object: CONSTRUCT:46<br/></span><span class="compile-data">object: CONSTRUCT:47<br/></span><span class="compile-data">object: CONSTRUCT:48<br/></span><span class="compile-data">object: CONSTRUCT:49<br/></span><span class="compile-data">object: CONSTRUCT:50<br/></span><span class="compile-data">object: CONSTRUCT:51<br/></span><span class="compile-data">object: CONSTRUCT:52<br/></span><span class="compile-data">object: CONSTRUCT:53<br/></span><span class="compile-data">object: CONSTRUCT:54<br/></span><span class="compile-data">object: CONSTRUCT:55<br/></span><span class="compile-data">number of blocks: 4<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.802 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestSequenceParse<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestSourcesParse<br/></span><span class="compile-data">unsupported capability: das1:dna<br/></span><span class="compile-data">Das2SourceHandler: source size: 267<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestUCSCFeatures<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.server.TestServers<br/></span><span class="compile-data">Jan 25, 2011 1:02:27 AM org.biojava.dasobert.das.SequenceThread retrieveSequence<br/></span><span class="compile-data">INFO: requesting sequence from http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/sequence?segment=P50225<br/></span><span class="compile-data">MELIQDTSRPPLEYVKGVPLIKYFAEALGPLQSFQARPDDLLISTYPKSGTTWVSQILDMIYQGGDLEKCHRAPIFMRVPFLEFKAPGIPSGMETLKDTPAPRLLKTHLPLALLPQTLLDQKVKVVYVARNAKDVAVSYYHFYHMAKVHPEPGTWDSFLEKFMVGEVSYGSWYQHVQEWWELSRTHPVLYLFYEDMKENPKREIQKILEFVGRSLPEETVDFVVQHTSFKEMKKNPMTNYTTVPQEFMDHSISPFMRKGMAGDWKTTFTVAQNERFDADYAEKMAGCSLSFRSEL<br/></span><span class="compile-data">started getInteractions method<br/></span><span class="compile-data">Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.107 sec<br/></span><span class="compile-data">Running org.biojava.dasobert.TestFeatureParse<br/></span><span class="compile-data">Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 10, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/das/target/das-1.8.1-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/das/1.8.1-SNAPSHOT/das-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/das/target/das-1.8.1-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/das/1.8.1-SNAPSHOT/das-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/das/target/das-1.8.1-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/das/1.8.1-SNAPSHOT/das-1.8.1-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/das/1.8.1-SNAPSHOT/das-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">175K uploaded (das-1.8.1-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:das:1.8.1-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:das'<br/></span><span class="compile-data">[INFO] Uploading project information for das 1.8.1-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/das/1.8.1-SNAPSHOT/das-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">142K uploaded (das-1.8.1-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/das/1.8.1-SNAPSHOT/das-1.8.1-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">809K uploaded (das-1.8.1-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building sequencing<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-legacy/sequencing/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/sequencing/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 28 source files to /opt/cruise/projects/biojava-legacy/sequencing/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 74 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 11 source files to /opt/cruise/projects/biojava-legacy/sequencing/target/test-classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/sequencing/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.SolexaFastqWriterTest<br/></span><span class="compile-data">Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest<br/></span><span class="compile-data">Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.FastqBuilderTest<br/></span><span class="compile-data">Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest<br/></span><span class="compile-data">Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.SangerFastqWriterTest<br/></span><span class="compile-data">Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.SangerFastqReaderTest<br/></span><span class="compile-data">Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.SolexaFastqReaderTest<br/></span><span class="compile-data">Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.FastqVariantTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.FastqTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 129, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/sequencing/target/sequencing-1.8.1-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/sequencing/target/sequencing-1.8.1-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/sequencing/1.8.1-SNAPSHOT/sequencing-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/sequencing/target/sequencing-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/sequencing/target/sequencing-1.8.1-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/sequencing/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 1 source file to /opt/cruise/projects/biojava-legacy/sequencing/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 74 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/sequencing/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.SolexaFastqWriterTest<br/></span><span class="compile-data">Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest<br/></span><span class="compile-data">Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.FastqBuilderTest<br/></span><span class="compile-data">Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest<br/></span><span class="compile-data">Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.SangerFastqWriterTest<br/></span><span class="compile-data">Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.SangerFastqReaderTest<br/></span><span class="compile-data">Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.SolexaFastqReaderTest<br/></span><span class="compile-data">Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.FastqVariantTest<br/></span><span class="compile-data">Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec<br/></span><span class="compile-data">Running org.biojava.bio.program.fastq.FastqTest<br/></span><span class="compile-data">Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 129, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/sequencing/target/sequencing-1.8.1-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/sequencing/1.8.1-SNAPSHOT/sequencing-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/sequencing/target/sequencing-1.8.1-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/sequencing/1.8.1-SNAPSHOT/sequencing-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/sequencing/target/sequencing-1.8.1-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/sequencing/1.8.1-SNAPSHOT/sequencing-1.8.1-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/sequencing/1.8.1-SNAPSHOT/sequencing-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">76K uploaded (sequencing-1.8.1-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:sequencing'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:sequencing:1.8.1-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Uploading project information for sequencing 1.8.1-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/sequencing/1.8.1-SNAPSHOT/sequencing-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">63K uploaded (sequencing-1.8.1-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/sequencing/1.8.1-SNAPSHOT/sequencing-1.8.1-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">372K uploaded (sequencing-1.8.1-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building gui<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-legacy/gui/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/gui/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 99 source files to /opt/cruise/projects/biojava-legacy/gui/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/gui/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] No tests to run.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/gui/target/gui-1.8.1-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/gui/target/gui-1.8.1-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/gui/1.8.1-SNAPSHOT/gui-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/gui/target/gui-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/gui/target/gui-1.8.1-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/gui/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/gui/src/test/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] No tests to run.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/gui/target/gui-1.8.1-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/gui/1.8.1-SNAPSHOT/gui-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/gui/target/gui-1.8.1-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/gui/1.8.1-SNAPSHOT/gui-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/gui/target/gui-1.8.1-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/gui/1.8.1-SNAPSHOT/gui-1.8.1-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/gui/1.8.1-SNAPSHOT/gui-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">232K uploaded (gui-1.8.1-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:gui:1.8.1-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:gui'<br/></span><span class="compile-data">[INFO] Uploading project information for gui 1.8.1-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/gui/1.8.1-SNAPSHOT/gui-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">170K uploaded (gui-1.8.1-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/gui/1.8.1-SNAPSHOT/gui-1.8.1-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">1110K uploaded (gui-1.8.1-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Building phylo<br/></span><span class="compile-data">[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>clean:clean {execution: default-clean}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Deleting /opt/cruise/projects/biojava-legacy/phylo/target<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/phylo/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 37 source files to /opt/cruise/projects/biojava-legacy/phylo/target/classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 3 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Compiling 1 source file to /opt/cruise/projects/biojava-legacy/phylo/target/test-classes<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/phylo/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojavax.bio.phylo.io.nexus.TreesBlockTest<br/></span><span class="compile-data">Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.19 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 12, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/phylo/target/phylo-1.8.1-SNAPSHOT.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/phylo/target/phylo-1.8.1-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/phylo/1.8.1-SNAPSHOT/phylo-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Preparing source:jar<br/></span><span class="compile-data">[INFO] No goals needed for project - skipping<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>source:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/phylo/target/phylo-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[WARNING] DEPRECATED [aggregate]: As of version 2.5, use the goals <code>javadoc:aggregate</code> and<br/></span><span class="compile-data"><code>javadoc:test-aggregate</code> instead.<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>javadoc:jar {execution: default-cli}</td>
</tr>
<tr>
<td><span class="compile-data">1 warning<br/></span><span class="compile-data">[WARNING] Javadoc Warnings<br/></span><span class="compile-data">[WARNING] /opt/cruise/projects/biojava-legacy/phylo/src/main/java/org/biojavax/bio/phylo/io/nexus/TreesBlock.java:640: warning
- Tag @link: can't find getTreeAsJGraphT(java.lang.String) in org.biojavax.bio.phylo.io.nexus.TreesBlock<br/></span><span class="compile-data">[INFO] Building jar: /opt/cruise/projects/biojava-legacy/phylo/target/phylo-1.8.1-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:resources {execution: default-resources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/phylo/src/main/resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:compile {execution: default-compile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>resources:testResources {execution: default-testResources}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Using 'UTF-8' encoding to copy filtered resources.<br/></span><span class="compile-data">[INFO] Copying 3 resources<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>compiler:testCompile {execution: default-testCompile}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Nothing to compile - all classes are up to date<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>surefire:test {execution: default-test}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/phylo/target/surefire-reports<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data"> T E S T S<br/></span><span class="compile-data">-------------------------------------------------------<br/></span><span class="compile-data">Running org.biojavax.bio.phylo.io.nexus.TreesBlockTest<br/></span><span class="compile-data">Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.192 sec<br/></span><span class="compile-data">Results :<br/></span><span class="compile-data">Tests run: 12, Failures: 0, Errors: 0, Skipped: 0<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>jar:jar {execution: default-jar}</td>
</tr>
<tr>
<td></td>
</tr>
<tr class="compile-sectionheader">
<td>install:install {execution: default-install}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/phylo/target/phylo-1.8.1-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/phylo/1.8.1-SNAPSHOT/phylo-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/phylo/target/phylo-1.8.1-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/phylo/1.8.1-SNAPSHOT/phylo-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">[INFO] Installing /opt/cruise/projects/biojava-legacy/phylo/target/phylo-1.8.1-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/phylo/1.8.1-SNAPSHOT/phylo-1.8.1-SNAPSHOT-javadoc.jar<br/></span></td>
</tr>
<tr class="compile-sectionheader">
<td>deploy:deploy {execution: default-deploy}</td>
</tr>
<tr>
<td><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/phylo/1.8.1-SNAPSHOT/phylo-1.8.1-SNAPSHOT.jar<br/></span><span class="compile-data">78K uploaded (phylo-1.8.1-SNAPSHOT.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'snapshot org.biojava:phylo:1.8.1-SNAPSHOT'<br/></span><span class="compile-data">[INFO] Uploading project information for phylo 1.8.1-SNAPSHOT<br/></span><span class="compile-data">[INFO] Retrieving previous metadata from biojava-maven-repo<br/></span><span class="compile-data">[INFO] Uploading repository metadata for: 'artifact org.biojava:phylo'<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/phylo/1.8.1-SNAPSHOT/phylo-1.8.1-SNAPSHOT-sources.jar<br/></span><span class="compile-data">60K uploaded (phylo-1.8.1-SNAPSHOT-sources.jar)<br/></span><span class="compile-data">[INFO] Retrieving previous build number from biojava-maven-repo<br/></span><span class="compile-data">Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/phylo/1.8.1-SNAPSHOT/phylo-1.8.1-SNAPSHOT-javadoc.jar<br/></span><span class="compile-data">404K uploaded (phylo-1.8.1-SNAPSHOT-javadoc.jar)<br/></span><span class="compile-data">[INFO] <br/></span><span class="compile-data">[INFO] <br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Reactor Summary:<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] biojava-legacy ........................................ SUCCESS [24.468s]<br/></span><span class="compile-data">[INFO] bytecode .............................................. SUCCESS [51.519s]<br/></span><span class="compile-data">[INFO] core .................................................. SUCCESS [4:21.041s]<br/></span><span class="compile-data">[INFO] alignment ............................................. SUCCESS [51.270s]<br/></span><span class="compile-data">[INFO] biosql ................................................ SUCCESS [1:08.928s]<br/></span><span class="compile-data">[INFO] blast ................................................. SUCCESS [1:28.752s]<br/></span><span class="compile-data">[INFO] das ................................................... SUCCESS [1:22.475s]<br/></span><span class="compile-data">[INFO] sequencing ............................................ SUCCESS [1:09.134s]<br/></span><span class="compile-data">[INFO] gui ................................................... SUCCESS [1:07.992s]<br/></span><span class="compile-data">[INFO] phylo ................................................. SUCCESS [1:02.182s]<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] BUILD SUCCESSFUL<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span><span class="compile-data">[INFO] Total time: 13 minutes 48 seconds<br/></span><span class="compile-data">[INFO] Finished at: Tue Jan 25 01:06:43 PST 2011<br/></span><span class="compile-data">[INFO] Final Memory: 133M/1199M<br/></span><span class="compile-data">[INFO] ------------------------------------------------------------------------<br/></span></td>
</tr>
</table>
</p>
<p></p>
<p></p>
<p></p>
<p></p>
<p></p>
<p>
<table xmlns:lxslt="http://xml.apache.org/xslt" align="center" cellpadding="2" cellspacing="0" border="0" width="98%">
<tr>
<td class="unittests-sectionheader" colspan="4">
Unit Tests: (0)
</td>
</tr>
<tr>
<td colspan="2" class="unittests-data">
No Tests Run
</td>
</tr>
<tr>
<td colspan="2" class="unittests-error">
This project doesn't have any tests
</td>
</tr>
<tr>
<td>
<table align="center" cellpadding="2" cellspacing="0" border="0" width="98%"></table>
</td>
</tr>
<tr></tr>
<tr>
<td colspan="2"> </td>
</tr>
</table>
</p>
<p></p>
<p>
<table align="center" cellpadding="2" cellspacing="1" border="0" width="98%">
<tr>
<td class="modifications-sectionheader" colspan="6">
Modifications since last successful build:
(1)
</td>
</tr>
<tr class="modifications-evenrow">
<td class="modifications-data">modified</td>
<td class="modifications-data">gwaldon</td>
<td class="modifications-data">/biojava-legacy/trunk/core/src/main/java/org/biojavax/bio/seq/SimpleRichLocation.java</td>
<td class="modifications-data">8682</td>
<td class="modifications-data">2011-01-25T05:42:33</td>
<td class="modifications-data">Fix unexpected throwing of exception when invoking symbols(SymbolList seq) on circular locations</td>
</tr>
</table>
</p>
<p></p>
<p>
<table xmlns:lxslt="http://xml.apache.org/xslt" align="center" cellpadding="2" cellspacing="0" border="0" width="98%"></table>
</p>
</body></html>