BUILD COMPLETE -  build.18
Date of build: 2012-05-07T23:06:16
Time to build: 1 minute(s) 41 second(s)
Last changed: 2012-05-07T22:47:02
Last log entry: now can also align PDP domains and a new script to scan all representative domains used by PDB all vs. all
Build Artifacts

 Modifications since last successful build:  (4)
added andreas /StructCompPlayground/trunk/src/main/java/org/biojava3/structure/align/symm/census/ScanRepresentativesForSymmetry.java 15416 2012-05-07T22:47:02 now can also align PDP domains and a new script to scan all representative domains used by PDB all vs. all
modified andreas /StructCompPlayground/trunk/src/main/java/org/biojava3/structure/align/symm/census/ScanSCOPForSymmetry.java 15416 2012-05-07T22:47:02 now can also align PDP domains and a new script to scan all representative domains used by PDB all vs. all
added andreas /StructCompPlayground/trunk/src/main/java/org/biojava3/structure/align/symm/census/ScopSymmetryCalculation.java 15416 2012-05-07T22:47:02 now can also align PDP domains and a new script to scan all representative domains used by PDB all vs. all
added andreas /StructCompPlayground/trunk/src/main/java/org/biojava3/structure/align/symm/census/SymmetryCalculationJob.java 15416 2012-05-07T22:47:02 now can also align PDP domains and a new script to scan all representative domains used by PDB all vs. all

Initial Messages
[INFO] Scanning for projects...
[INFO] Searching repository for plugin with prefix: 'source'.
[INFO] ------------------------------------------------------------------------
[INFO] Building StructCompPlayground
[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]
[INFO] ------------------------------------------------------------------------
clean:clean {execution: default-clean}
[INFO] Deleting directory /opt/cruise/projects/playground/target
resources:resources {execution: default-resources}
[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent!
[INFO] Copying 2 resources
[INFO] snapshot org.biojava:biojava3-alignment:3.0.4-SNAPSHOT: checking for updates from rcsb-pdb-maven-repo
[INFO] snapshot org.biojava:biojava3-alignment:3.0.4-SNAPSHOT: checking for updates from geotoolkit
[INFO] snapshot org.biojava:biojava3-phylo:3.0.4-SNAPSHOT: checking for updates from rcsb-pdb-maven-repo
[INFO] snapshot org.biojava:biojava3-phylo:3.0.4-SNAPSHOT: checking for updates from geotoolkit
[INFO] snapshot org.biojava:biojava3-structure:3.0.3-SNAPSHOT: checking for updates from geotoolkit
[INFO] snapshot org.biojava:biojava:3.0.3-SNAPSHOT: checking for updates from geotoolkit
[INFO] snapshot org.biojava:biojava3-alignment:3.0.3-SNAPSHOT: checking for updates from geotoolkit
[INFO] snapshot org.biojava:biojava3-core:3.0.3-SNAPSHOT: checking for updates from geotoolkit
Downloading: http://source.rcsb.org//maven//org/rcsb/ava-core/2010.11-SNAPSHOT/ava-core-2010.11-SNAPSHOT.jar
compiler:compile {execution: default-compile}
[INFO] Compiling 91 source files to /opt/cruise/projects/playground/target/classes
[WARNING] /opt/cruise/projects/playground/src/main/java/org/biojava3/structure/align/symm/quaternary/ScanPDBSeqClustersForQuarternarySymmetry.java:[39,23] GroupImpl is internal proprietary API and may be removed in a future release
resources:testResources {execution: default-testResources}
[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent!
[INFO] Copying 0 resource
compiler:testCompile {execution: default-testCompile}
[INFO] Compiling 2 source files to /opt/cruise/projects/playground/target/test-classes
surefire:test {execution: default-test}
[INFO] Surefire report directory: /opt/cruise/projects/playground/target/surefire-reports
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.biojava3.structure.align.symm.CeSymmTest
http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1p9ha_
http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=101968
http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1p9ha_
http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=101968
http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1jlya1
http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=50383
http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1jlya1
http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=50383
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 35.589 sec
Running org.biojava3.benchmark.TestFisherBenchmark
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec
Results :
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0
jar:jar {execution: default-jar}
[INFO] Building jar: /opt/cruise/projects/playground/target/structcomplayground-0.0.2-SNAPSHOT.jar
install:install {execution: default-install}
[INFO] Installing /opt/cruise/projects/playground/target/structcomplayground-0.0.2-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/structcomplayground/0.0.2-SNAPSHOT/structcomplayground-0.0.2-SNAPSHOT.jar
[INFO] Preparing source:jar
[INFO] No goals needed for project - skipping
source:jar {execution: default-cli}
[INFO] Building jar: /opt/cruise/projects/playground/target/structcomplayground-0.0.2-SNAPSHOT-sources.jar
javadoc:jar {execution: default-cli}
[WARNING] Source files encoding has not been set, using platform encoding ANSI_X3.4-1968, i.e. build is platform dependent!
Loading source file /opt/cruise/projects/playground/src/main/java/ShowMirrorSymmetry.java...
Loading source file /opt/cruise/projects/playground/src/main/java/ShowRotationSymmetry.java...
Loading source file /opt/cruise/projects/playground/src/main/java/TestDk.java...
Loading source file /opt/cruise/projects/playground/src/main/java/DemoCeSymmSeqConserv.java...
Loading source file /opt/cruise/projects/playground/src/main/java/MomentsOfInertia.java...
Loading source file /opt/cruise/projects/playground/src/main/java/DemoCeSymm.java...
Loading source files for package org.biojava3.changeux...
Loading source files for package org.biojava3.benchmark...
Loading source files for package org.biojava3.structure.utils...
Loading source files for package org.biojava3.structure.dbscan...
Loading source files for package org.biojava3.structure.align.symm.gui...
Loading source files for package org.biojava3.structure.align.symm...
Loading source files for package org.biojava3.structure.align.symm.quaternary...
Loading source files for package org.biojava3.structure.align.symm.census...
Loading source files for package org.biojava3.structure.sequenceui...
Loading source files for package org.rcsb.remediation2011...
Loading source files for package script...
Loading source files for package results...
Loading source files for package demo...
Constructing Javadoc information...
Standard Doclet version 1.7.0
Building tree for all the packages and classes...
Generating /opt/cruise/projects/playground/target/apidocs/DemoCeSymm.html...
Generating /opt/cruise/projects/playground/target/apidocs/DemoCeSymmSeqConserv.html...
Generating /opt/cruise/projects/playground/target/apidocs/MomentsOfInertia.html...
Generating /opt/cruise/projects/playground/target/apidocs/ShowMirrorSymmetry.html...
Generating /opt/cruise/projects/playground/target/apidocs/ShowRotationSymmetry.html...
Generating /opt/cruise/projects/playground/target/apidocs/TestDk.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/changeux/AlignQuaternaryStructures.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/changeux/IdentifyAllSymmetries.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/changeux/ProgressBar.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/changeux/TestPairwiseBiolUnit.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/benchmark/Benchmark.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/benchmark/FisherBenchmark.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/utils/FileUtils.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/utils/SimpleLog.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/utils/SymmetryTools.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/dbscan/FindMirrorSymmetries.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/dbscan/FindRotationSymmetries.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/dbscan/GetRepresentatives.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/dbscan/ScanDBForSymmetry.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/gui/CEsymmGUI.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/CEMirrorSymm.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/CeSymm.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/CESymmCalculator.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/CeSymmUserArgumentProcessor.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/SymmRefiner.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/AlignTest.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/AligQuaternaryStructure.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/BAFileReaderTest.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/BlastClustReader.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/C2RotationSolver.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/ChainSignature.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/CircleSampler.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/ClusterAlignment.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/DistanceBox.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/FindEvolutionaryRelationships.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/FindQuarternarySymmetry.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/GlobalSequenceGrouper.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/GlobalSequenceGrouperNew.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/IcosahedralSampler.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/InteractingLigand.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/LigandInteractions.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/MomentsOfInertia.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/MomentsOfInertia.SymmetryClass.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/MsaTest.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/PermutationGenerator.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/PermutationGroup.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/ProteinChainExtractor.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/ProteinComplexSignature.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/QuatSuperpositionScorer.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/QuatSymmetryPerceptor.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/QuatSymmetryScreener.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/QuatSymmetrySolver.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/QuatSymmetryWriter.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/Rotation.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/RotationGroup.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/RotationSolver.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/ScanPDBForQuarternarySymmetry.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/ScanPDBSeqClustersForQuarternarySymmetry.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/SequenceAlignmentCluster.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/SequenceClusterer.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/SequenceGrouperObsolete.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/SphereCovering1992.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/SphereSampler.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/SubunitGraph.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/SubunitMapper.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/Subunits.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/SuperPosition.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/SystematicSolver.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/UniqueSequenceList.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/BeanComparator.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/CallableProtodomainComparison.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/CensusResult.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/CensusResults.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/ProtoDomainDBSearchResult.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/ProtoDomainDBSearchResults.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/ResultConverter.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/ResultSorter.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/ScanRepresentativesForSymmetry.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/ScanSCOPForSymmetry.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/ScopSymmetryCalculation.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/SymmetryCalculation.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/SymmetryCalculationJob.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/sequenceui/TestAllChains.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/rcsb/remediation2011/CompareOldvsNew.html...
Generating /opt/cruise/projects/playground/target/apidocs/script/RunDataBaseSearch.html...
Generating /opt/cruise/projects/playground/target/apidocs/results/PlotRMSDvsProbability.html...
Generating /opt/cruise/projects/playground/target/apidocs/results/PlotScorevsProbability.html...
Generating /opt/cruise/projects/playground/target/apidocs/results/SymmetryInSCOPSuperfamilies.html...
Generating /opt/cruise/projects/playground/target/apidocs/demo/AlignProtodomains.html...
Generating /opt/cruise/projects/playground/target/apidocs/demo/BBFtpWrapper.html...
Generating /opt/cruise/projects/playground/target/apidocs/demo/RunFisherBenchmark.html...
Generating /opt/cruise/projects/playground/target/apidocs/demo/ScanProtodomainsDB.html...
Generating /opt/cruise/projects/playground/target/apidocs/overview-frame.html...
Generating /opt/cruise/projects/playground/target/apidocs/package-frame.html...
Generating /opt/cruise/projects/playground/target/apidocs/package-summary.html...
Generating /opt/cruise/projects/playground/target/apidocs/package-tree.html...
Generating /opt/cruise/projects/playground/target/apidocs/demo/package-frame.html...
Generating /opt/cruise/projects/playground/target/apidocs/demo/package-summary.html...
Generating /opt/cruise/projects/playground/target/apidocs/demo/package-tree.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/benchmark/package-frame.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/benchmark/package-summary.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/benchmark/package-tree.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/changeux/package-frame.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/changeux/package-summary.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/changeux/package-tree.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/package-frame.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/package-summary.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/package-tree.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/package-frame.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/package-summary.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/package-tree.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/gui/package-frame.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/gui/package-summary.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/gui/package-tree.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/package-frame.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/package-summary.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/package-tree.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/dbscan/package-frame.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/dbscan/package-summary.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/dbscan/package-tree.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/sequenceui/package-frame.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/sequenceui/package-summary.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/sequenceui/package-tree.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/utils/package-frame.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/utils/package-summary.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/utils/package-tree.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/rcsb/remediation2011/package-frame.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/rcsb/remediation2011/package-summary.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/rcsb/remediation2011/package-tree.html...
Generating /opt/cruise/projects/playground/target/apidocs/results/package-frame.html...
Generating /opt/cruise/projects/playground/target/apidocs/results/package-summary.html...
Generating /opt/cruise/projects/playground/target/apidocs/results/package-tree.html...
Generating /opt/cruise/projects/playground/target/apidocs/script/package-frame.html...
Generating /opt/cruise/projects/playground/target/apidocs/script/package-summary.html...
Generating /opt/cruise/projects/playground/target/apidocs/script/package-tree.html...
Generating /opt/cruise/projects/playground/target/apidocs/constant-values.html...
Generating /opt/cruise/projects/playground/target/apidocs/serialized-form.html...
Generating /opt/cruise/projects/playground/target/apidocs/class-use/ShowMirrorSymmetry.html...
Generating /opt/cruise/projects/playground/target/apidocs/class-use/ShowRotationSymmetry.html...
Generating /opt/cruise/projects/playground/target/apidocs/class-use/TestDk.html...
Generating /opt/cruise/projects/playground/target/apidocs/class-use/DemoCeSymmSeqConserv.html...
Generating /opt/cruise/projects/playground/target/apidocs/class-use/MomentsOfInertia.html...
Generating /opt/cruise/projects/playground/target/apidocs/class-use/DemoCeSymm.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/changeux/class-use/IdentifyAllSymmetries.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/changeux/class-use/ProgressBar.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/changeux/class-use/AlignQuaternaryStructures.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/changeux/class-use/TestPairwiseBiolUnit.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/benchmark/class-use/FisherBenchmark.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/benchmark/class-use/Benchmark.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/utils/class-use/SymmetryTools.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/utils/class-use/FileUtils.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/utils/class-use/SimpleLog.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/dbscan/class-use/FindRotationSymmetries.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/dbscan/class-use/FindMirrorSymmetries.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/dbscan/class-use/ScanDBForSymmetry.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/dbscan/class-use/GetRepresentatives.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/gui/class-use/CEsymmGUI.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/class-use/CeSymmUserArgumentProcessor.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/class-use/CESymmCalculator.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/class-use/CeSymm.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/class-use/SymmRefiner.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/class-use/CEMirrorSymm.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/GlobalSequenceGrouperNew.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/InteractingLigand.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/SequenceClusterer.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/Subunits.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/Rotation.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/PermutationGroup.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/UniqueSequenceList.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/BlastClustReader.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/DistanceBox.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/RotationSolver.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/FindEvolutionaryRelationships.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/MomentsOfInertia.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/MomentsOfInertia.SymmetryClass.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/ScanPDBForQuarternarySymmetry.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/ProteinComplexSignature.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/IcosahedralSampler.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/ProteinChainExtractor.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/SequenceAlignmentCluster.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/QuatSymmetryScreener.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/PermutationGenerator.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/ClusterAlignment.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/SuperPosition.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/QuatSymmetryPerceptor.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/FindQuarternarySymmetry.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/AligQuaternaryStructure.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/ChainSignature.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/AlignTest.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/BAFileReaderTest.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/SequenceGrouperObsolete.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/SubunitGraph.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/MsaTest.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/LigandInteractions.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/SubunitMapper.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/RotationGroup.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/SystematicSolver.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/QuatSymmetrySolver.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/QuatSuperpositionScorer.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/C2RotationSolver.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/CircleSampler.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/GlobalSequenceGrouper.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/SphereSampler.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/QuatSymmetryWriter.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/SphereCovering1992.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/ScanPDBSeqClustersForQuarternarySymmetry.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/class-use/ProtoDomainDBSearchResult.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/class-use/ScanSCOPForSymmetry.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/class-use/ProtoDomainDBSearchResults.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/class-use/BeanComparator.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/class-use/CensusResults.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/class-use/ResultSorter.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/class-use/CensusResult.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/class-use/SymmetryCalculation.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/class-use/SymmetryCalculationJob.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/class-use/CallableProtodomainComparison.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/class-use/ResultConverter.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/class-use/ScanRepresentativesForSymmetry.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/class-use/ScopSymmetryCalculation.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/sequenceui/class-use/TestAllChains.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/rcsb/remediation2011/class-use/CompareOldvsNew.html...
Generating /opt/cruise/projects/playground/target/apidocs/script/class-use/RunDataBaseSearch.html...
Generating /opt/cruise/projects/playground/target/apidocs/results/class-use/PlotRMSDvsProbability.html...
Generating /opt/cruise/projects/playground/target/apidocs/results/class-use/PlotScorevsProbability.html...
Generating /opt/cruise/projects/playground/target/apidocs/results/class-use/SymmetryInSCOPSuperfamilies.html...
Generating /opt/cruise/projects/playground/target/apidocs/demo/class-use/RunFisherBenchmark.html...
Generating /opt/cruise/projects/playground/target/apidocs/demo/class-use/BBFtpWrapper.html...
Generating /opt/cruise/projects/playground/target/apidocs/demo/class-use/ScanProtodomainsDB.html...
Generating /opt/cruise/projects/playground/target/apidocs/demo/class-use/AlignProtodomains.html...
Generating /opt/cruise/projects/playground/target/apidocs/package-use.html...
Generating /opt/cruise/projects/playground/target/apidocs/demo/package-use.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/benchmark/package-use.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/changeux/package-use.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/package-use.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/census/package-use.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/gui/package-use.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/align/symm/quaternary/package-use.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/dbscan/package-use.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/sequenceui/package-use.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/biojava3/structure/utils/package-use.html...
Generating /opt/cruise/projects/playground/target/apidocs/org/rcsb/remediation2011/package-use.html...
Generating /opt/cruise/projects/playground/target/apidocs/results/package-use.html...
Generating /opt/cruise/projects/playground/target/apidocs/script/package-use.html...
Building index for all the packages and classes...
Generating /opt/cruise/projects/playground/target/apidocs/overview-tree.html...
Generating /opt/cruise/projects/playground/target/apidocs/index-all.html...
Generating /opt/cruise/projects/playground/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /opt/cruise/projects/playground/target/apidocs/allclasses-frame.html...
Generating /opt/cruise/projects/playground/target/apidocs/allclasses-noframe.html...
Generating /opt/cruise/projects/playground/target/apidocs/index.html...
Generating /opt/cruise/projects/playground/target/apidocs/overview-summary.html...
Generating /opt/cruise/projects/playground/target/apidocs/help-doc.html...
12 warnings
[WARNING] Javadoc Warnings
[WARNING] /opt/cruise/projects/playground/src/main/java/org/biojava3/structure/align/symm/quaternary/ScanPDBSeqClustersForQuarternarySymmetry.java:39: warning: GroupImpl is internal proprietary API and may be removed in a future release
[WARNING] import sun.security.acl.GroupImpl;
[WARNING] ^
[WARNING] /opt/cruise/projects/playground/src/main/java/org/biojava3/structure/utils/SymmetryTools.java:305: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/playground/src/main/java/org/biojava3/structure/dbscan/FindMirrorSymmetries.java:89: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/playground/src/main/java/org/biojava3/structure/dbscan/FindRotationSymmetries.java:68: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/playground/src/main/java/org/biojava3/structure/dbscan/GetRepresentatives.java:38: warning - @param argument "sequenceIdentity" is not a parameter name.
[WARNING] /opt/cruise/projects/playground/src/main/java/org/biojava3/structure/align/symm/SymmRefiner.java:33: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/playground/src/main/java/org/biojava3/structure/align/symm/quaternary/QuatSuperpositionScorer.java:158: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/playground/src/main/java/org/biojava3/structure/align/symm/quaternary/QuatSuperpositionScorer.java:158: warning - @param argument "solution" is not a parameter name.
[WARNING] /opt/cruise/projects/playground/src/main/java/org/biojava3/structure/align/symm/quaternary/QuatSuperpositionScorer.java:192: warning - @param argument "y" is not a parameter name.
[WARNING] /opt/cruise/projects/playground/src/main/java/org/biojava3/structure/align/symm/quaternary/Rotation.java:117: warning - @param argument "direction" is not a parameter name.
[WARNING] /opt/cruise/projects/playground/src/main/java/org/biojava3/structure/align/symm/quaternary/UniqueSequenceList.java:34: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/playground/src/main/java/results/SymmetryInSCOPSuperfamilies.java:45: warning - @param argument "title" is not a parameter name.
[INFO] Building jar: /opt/cruise/projects/playground/target/structcomplayground-0.0.2-SNAPSHOT-javadoc.jar
resources:resources {execution: default-resources}
[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent!
[INFO] Copying 2 resources
compiler:compile {execution: default-compile}
[INFO] Nothing to compile - all classes are up to date
resources:testResources {execution: default-testResources}
[WARNING] Using platform encoding (ANSI_X3.4-1968 actually) to copy filtered resources, i.e. build is platform dependent!
[INFO] Copying 0 resource
compiler:testCompile {execution: default-testCompile}
[INFO] Nothing to compile - all classes are up to date
surefire:test {execution: default-test}
[INFO] Surefire report directory: /opt/cruise/projects/playground/target/surefire-reports
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.biojava3.structure.align.symm.CeSymmTest
http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1p9ha_
http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=101968
http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1p9ha_
http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=101968
http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1jlya1
http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=50383
http://source.rcsb.org/jfatcatserver/domains/getDomainByScopID?scopId=d1jlya1
http://source.rcsb.org/jfatcatserver/domains/getScopDescriptionBySunid?sunid=50383
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 35.721 sec
Running org.biojava3.benchmark.TestFisherBenchmark
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec
Results :
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0
jar:jar {execution: default-jar}
install:install {execution: default-install}
[INFO] Installing /opt/cruise/projects/playground/target/structcomplayground-0.0.2-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/structcomplayground/0.0.2-SNAPSHOT/structcomplayground-0.0.2-SNAPSHOT.jar
[INFO] Installing /opt/cruise/projects/playground/target/structcomplayground-0.0.2-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/structcomplayground/0.0.2-SNAPSHOT/structcomplayground-0.0.2-SNAPSHOT-sources.jar
[INFO] Installing /opt/cruise/projects/playground/target/structcomplayground-0.0.2-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/structcomplayground/0.0.2-SNAPSHOT/structcomplayground-0.0.2-SNAPSHOT-javadoc.jar
deploy:deploy {execution: default-deploy}
[INFO] Retrieving previous build number from rcsb-pdb-maven-repo
Uploading: scp://emmy.rcsb.org/opt/maven//org/biojava/structcomplayground/0.0.2-SNAPSHOT/structcomplayground-0.0.2-SNAPSHOT.jar
283K uploaded (structcomplayground-0.0.2-SNAPSHOT.jar)
[INFO] Uploading project information for structcomplayground 0.0.2-SNAPSHOT
[INFO] Retrieving previous metadata from rcsb-pdb-maven-repo
[INFO] Uploading repository metadata for: 'snapshot org.biojava:structcomplayground:0.0.2-SNAPSHOT'
[INFO] Retrieving previous metadata from rcsb-pdb-maven-repo
[INFO] Uploading repository metadata for: 'artifact org.biojava:structcomplayground'
[INFO] Retrieving previous build number from rcsb-pdb-maven-repo
Uploading: scp://emmy.rcsb.org/opt/maven//org/biojava/structcomplayground/0.0.2-SNAPSHOT/structcomplayground-0.0.2-SNAPSHOT-sources.jar
168K uploaded (structcomplayground-0.0.2-SNAPSHOT-sources.jar)
[INFO] Retrieving previous build number from rcsb-pdb-maven-repo
Uploading: scp://emmy.rcsb.org/opt/maven//org/biojava/structcomplayground/0.0.2-SNAPSHOT/structcomplayground-0.0.2-SNAPSHOT-javadoc.jar
488K uploaded (structcomplayground-0.0.2-SNAPSHOT-javadoc.jar)
[INFO] ------------------------------------------------------------------------
[INFO] Building StructCompPlayground
[INFO] task-segment: [javadoc:aggregate] (aggregator-style)
[INFO] ------------------------------------------------------------------------
[INFO] Preparing javadoc:aggregate
[INFO] ------------------------------------------------------------------------
[INFO] Building StructCompPlayground
[INFO] ------------------------------------------------------------------------
[INFO] No goals needed for project - skipping
javadoc:aggregate {execution: default-cli}
[WARNING] Source files encoding has not been set, using platform encoding ANSI_X3.4-1968, i.e. build is platform dependent!
Loading source file /opt/cruise/projects/playground/src/main/java/ShowMirrorSymmetry.java...
Loading source file /opt/cruise/projects/playground/src/main/java/ShowRotationSymmetry.java...
Loading source file /opt/cruise/projects/playground/src/main/java/TestDk.java...
Loading source file /opt/cruise/projects/playground/src/main/java/DemoCeSymmSeqConserv.java...
Loading source file /opt/cruise/projects/playground/src/main/java/MomentsOfInertia.java...
Loading source file /opt/cruise/projects/playground/src/main/java/DemoCeSymm.java...
Loading source files for package org.biojava3.changeux...
Loading source files for package org.biojava3.benchmark...
Loading source files for package org.biojava3.structure.utils...
Loading source files for package org.biojava3.structure.dbscan...
Loading source files for package org.biojava3.structure.align.symm.gui...
Loading source files for package org.biojava3.structure.align.symm...
Loading source files for package org.biojava3.structure.align.symm.quaternary...
Loading source files for package org.biojava3.structure.align.symm.census...
Loading source files for package org.biojava3.structure.sequenceui...
Loading source files for package org.rcsb.remediation2011...
Loading source files for package script...
Loading source files for package results...
Loading source files for package demo...
Constructing Javadoc information...
Standard Doclet version 1.7.0
Building tree for all the packages and classes...
Generating /opt/cruise/projects/playground/target/site/apidocs/DemoCeSymm.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/DemoCeSymmSeqConserv.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/MomentsOfInertia.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/ShowMirrorSymmetry.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/ShowRotationSymmetry.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/TestDk.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/changeux/AlignQuaternaryStructures.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/changeux/IdentifyAllSymmetries.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/changeux/ProgressBar.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/changeux/TestPairwiseBiolUnit.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/benchmark/Benchmark.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/benchmark/FisherBenchmark.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/utils/FileUtils.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/utils/SimpleLog.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/utils/SymmetryTools.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/dbscan/FindMirrorSymmetries.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/dbscan/FindRotationSymmetries.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/dbscan/GetRepresentatives.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/dbscan/ScanDBForSymmetry.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/gui/CEsymmGUI.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/CEMirrorSymm.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/CeSymm.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/CESymmCalculator.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/CeSymmUserArgumentProcessor.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/SymmRefiner.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/AlignTest.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/AligQuaternaryStructure.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/BAFileReaderTest.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/BlastClustReader.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/C2RotationSolver.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/ChainSignature.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/CircleSampler.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/ClusterAlignment.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/DistanceBox.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/FindEvolutionaryRelationships.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/FindQuarternarySymmetry.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/GlobalSequenceGrouper.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/GlobalSequenceGrouperNew.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/IcosahedralSampler.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/InteractingLigand.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/LigandInteractions.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/MomentsOfInertia.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/MomentsOfInertia.SymmetryClass.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/MsaTest.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/PermutationGenerator.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/PermutationGroup.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/ProteinChainExtractor.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/ProteinComplexSignature.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/QuatSuperpositionScorer.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/QuatSymmetryPerceptor.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/QuatSymmetryScreener.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/QuatSymmetrySolver.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/QuatSymmetryWriter.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/Rotation.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/RotationGroup.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/RotationSolver.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/ScanPDBForQuarternarySymmetry.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/ScanPDBSeqClustersForQuarternarySymmetry.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/SequenceAlignmentCluster.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/SequenceClusterer.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/SequenceGrouperObsolete.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/SphereCovering1992.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/SphereSampler.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/SubunitGraph.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/SubunitMapper.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/Subunits.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/SuperPosition.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/SystematicSolver.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/UniqueSequenceList.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/BeanComparator.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/CallableProtodomainComparison.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/CensusResult.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/CensusResults.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/ProtoDomainDBSearchResult.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/ProtoDomainDBSearchResults.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/ResultConverter.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/ResultSorter.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/ScanRepresentativesForSymmetry.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/ScanSCOPForSymmetry.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/ScopSymmetryCalculation.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/SymmetryCalculation.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/SymmetryCalculationJob.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/sequenceui/TestAllChains.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/rcsb/remediation2011/CompareOldvsNew.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/script/RunDataBaseSearch.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/results/PlotRMSDvsProbability.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/results/PlotScorevsProbability.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/results/SymmetryInSCOPSuperfamilies.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/demo/AlignProtodomains.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/demo/BBFtpWrapper.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/demo/RunFisherBenchmark.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/demo/ScanProtodomainsDB.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/overview-frame.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/package-frame.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/package-summary.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/package-tree.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/demo/package-frame.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/demo/package-summary.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/demo/package-tree.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/benchmark/package-frame.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/benchmark/package-summary.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/benchmark/package-tree.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/changeux/package-frame.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/changeux/package-summary.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/changeux/package-tree.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/package-frame.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/package-summary.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/package-tree.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/package-frame.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/package-summary.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/package-tree.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/gui/package-frame.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/gui/package-summary.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/gui/package-tree.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/package-frame.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/package-summary.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/package-tree.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/dbscan/package-frame.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/dbscan/package-summary.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/dbscan/package-tree.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/sequenceui/package-frame.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/sequenceui/package-summary.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/sequenceui/package-tree.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/utils/package-frame.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/utils/package-summary.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/utils/package-tree.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/rcsb/remediation2011/package-frame.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/rcsb/remediation2011/package-summary.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/rcsb/remediation2011/package-tree.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/results/package-frame.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/results/package-summary.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/results/package-tree.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/script/package-frame.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/script/package-summary.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/script/package-tree.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/constant-values.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/serialized-form.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/class-use/ShowMirrorSymmetry.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/class-use/ShowRotationSymmetry.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/class-use/TestDk.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/class-use/DemoCeSymmSeqConserv.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/class-use/MomentsOfInertia.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/class-use/DemoCeSymm.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/changeux/class-use/IdentifyAllSymmetries.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/changeux/class-use/ProgressBar.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/changeux/class-use/AlignQuaternaryStructures.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/changeux/class-use/TestPairwiseBiolUnit.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/benchmark/class-use/FisherBenchmark.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/benchmark/class-use/Benchmark.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/utils/class-use/SymmetryTools.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/utils/class-use/FileUtils.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/utils/class-use/SimpleLog.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/dbscan/class-use/FindRotationSymmetries.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/dbscan/class-use/FindMirrorSymmetries.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/dbscan/class-use/ScanDBForSymmetry.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/dbscan/class-use/GetRepresentatives.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/gui/class-use/CEsymmGUI.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/class-use/CeSymmUserArgumentProcessor.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/class-use/CESymmCalculator.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/class-use/CeSymm.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/class-use/SymmRefiner.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/class-use/CEMirrorSymm.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/GlobalSequenceGrouperNew.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/InteractingLigand.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/SequenceClusterer.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/Subunits.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/Rotation.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/PermutationGroup.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/UniqueSequenceList.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/BlastClustReader.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/DistanceBox.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/RotationSolver.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/FindEvolutionaryRelationships.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/MomentsOfInertia.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/MomentsOfInertia.SymmetryClass.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/ScanPDBForQuarternarySymmetry.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/ProteinComplexSignature.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/IcosahedralSampler.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/ProteinChainExtractor.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/SequenceAlignmentCluster.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/QuatSymmetryScreener.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/PermutationGenerator.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/ClusterAlignment.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/SuperPosition.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/QuatSymmetryPerceptor.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/FindQuarternarySymmetry.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/AligQuaternaryStructure.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/ChainSignature.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/AlignTest.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/BAFileReaderTest.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/SequenceGrouperObsolete.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/SubunitGraph.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/MsaTest.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/LigandInteractions.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/SubunitMapper.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/RotationGroup.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/SystematicSolver.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/QuatSymmetrySolver.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/QuatSuperpositionScorer.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/C2RotationSolver.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/CircleSampler.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/GlobalSequenceGrouper.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/SphereSampler.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/QuatSymmetryWriter.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/SphereCovering1992.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/class-use/ScanPDBSeqClustersForQuarternarySymmetry.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/class-use/ProtoDomainDBSearchResult.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/class-use/ScanSCOPForSymmetry.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/class-use/ProtoDomainDBSearchResults.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/class-use/BeanComparator.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/class-use/CensusResults.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/class-use/ResultSorter.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/class-use/CensusResult.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/class-use/SymmetryCalculation.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/class-use/SymmetryCalculationJob.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/class-use/CallableProtodomainComparison.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/class-use/ResultConverter.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/class-use/ScanRepresentativesForSymmetry.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/class-use/ScopSymmetryCalculation.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/sequenceui/class-use/TestAllChains.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/rcsb/remediation2011/class-use/CompareOldvsNew.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/script/class-use/RunDataBaseSearch.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/results/class-use/PlotRMSDvsProbability.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/results/class-use/PlotScorevsProbability.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/results/class-use/SymmetryInSCOPSuperfamilies.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/demo/class-use/RunFisherBenchmark.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/demo/class-use/BBFtpWrapper.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/demo/class-use/ScanProtodomainsDB.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/demo/class-use/AlignProtodomains.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/package-use.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/demo/package-use.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/benchmark/package-use.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/changeux/package-use.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/package-use.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/census/package-use.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/gui/package-use.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/align/symm/quaternary/package-use.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/dbscan/package-use.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/sequenceui/package-use.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/biojava3/structure/utils/package-use.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/org/rcsb/remediation2011/package-use.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/results/package-use.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/script/package-use.html...
Building index for all the packages and classes...
Generating /opt/cruise/projects/playground/target/site/apidocs/overview-tree.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/index-all.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/deprecated-list.html...
Building index for all classes...
Generating /opt/cruise/projects/playground/target/site/apidocs/allclasses-frame.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/allclasses-noframe.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/index.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/overview-summary.html...
Generating /opt/cruise/projects/playground/target/site/apidocs/help-doc.html...
12 warnings
[WARNING] Javadoc Warnings
[WARNING] /opt/cruise/projects/playground/src/main/java/org/biojava3/structure/align/symm/quaternary/ScanPDBSeqClustersForQuarternarySymmetry.java:39: warning: GroupImpl is internal proprietary API and may be removed in a future release
[WARNING] import sun.security.acl.GroupImpl;
[WARNING] ^
[WARNING] /opt/cruise/projects/playground/src/main/java/org/biojava3/structure/utils/SymmetryTools.java:305: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/playground/src/main/java/org/biojava3/structure/dbscan/FindMirrorSymmetries.java:89: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/playground/src/main/java/org/biojava3/structure/dbscan/FindRotationSymmetries.java:68: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/playground/src/main/java/org/biojava3/structure/dbscan/GetRepresentatives.java:38: warning - @param argument "sequenceIdentity" is not a parameter name.
[WARNING] /opt/cruise/projects/playground/src/main/java/org/biojava3/structure/align/symm/SymmRefiner.java:33: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/playground/src/main/java/org/biojava3/structure/align/symm/quaternary/QuatSuperpositionScorer.java:158: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/playground/src/main/java/org/biojava3/structure/align/symm/quaternary/QuatSuperpositionScorer.java:158: warning - @param argument "solution" is not a parameter name.
[WARNING] /opt/cruise/projects/playground/src/main/java/org/biojava3/structure/align/symm/quaternary/QuatSuperpositionScorer.java:192: warning - @param argument "y" is not a parameter name.
[WARNING] /opt/cruise/projects/playground/src/main/java/org/biojava3/structure/align/symm/quaternary/Rotation.java:117: warning - @param argument "direction" is not a parameter name.
[WARNING] /opt/cruise/projects/playground/src/main/java/org/biojava3/structure/align/symm/quaternary/UniqueSequenceList.java:34: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/playground/src/main/java/results/SymmetryInSCOPSuperfamilies.java:45: warning - @param argument "title" is not a parameter name.
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESSFUL
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1 minute 40 seconds
[INFO] Finished at: Mon May 07 16:07:57 PDT 2012
[INFO] Final Memory: 49M/869M
[INFO] ------------------------------------------------------------------------

 Unit Tests: (0)
No Tests Run
This project doesn't have any tests