BUILD COMPLETE -  build.19
Date of build: 2012-05-15T00:01:33
Time to build: 0 minute(s) 41 second(s)
Last changed: 2012-05-14T23:56:33
Last log entry: upgrading to using servlet api 6 or 7
Build Artifacts

 Modifications since last successful build:  (1)
modified andreas /ava-core/trunk/pom.xml 15543 2012-05-14T23:56:33 upgrading to using servlet api 6 or 7

Initial Messages
[INFO] Scanning for projects...
[INFO] Searching repository for plugin with prefix: 'source'.
[INFO] ------------------------------------------------------------------------
[INFO] Building ava-core
[INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy]
[INFO] ------------------------------------------------------------------------
clean:clean {execution: default-clean}
[INFO] Deleting directory /opt/cruise/projects/ava-core/target
resources:resources {execution: default-resources}
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 0 resource
[INFO] artifact org.apache.tomcat:servlet-api: checking for updates from maven2-repository.dev.java.net
[INFO] artifact org.apache.tomcat:servlet-api: checking for updates from maven-repository.dev.java.net
[INFO] artifact org.apache.tomcat:servlet-api: checking for updates from rcsb-pdb-maven-repo
[INFO] artifact org.apache.tomcat:servlet-api: checking for updates from biojava-maven-repo
[INFO] artifact org.apache.tomcat:servlet-api: checking for updates from central
Downloading: http://download.java.net/maven/2/org/apache/tomcat/servlet-api/6.0.35/servlet-api-6.0.35.pom
[INFO] Unable to find resource 'org.apache.tomcat:servlet-api:pom:6.0.35' in repository maven2-repository.dev.java.net (http://download.java.net/maven/2)
Downloading: http://download.java.net/maven/1/org/apache/tomcat/servlet-api/6.0.35/servlet-api-6.0.35.pom
[INFO] Unable to find resource 'org.apache.tomcat:servlet-api:pom:6.0.35' in repository maven-repository.dev.java.net (http://download.java.net/maven/1)
Downloading: http://source.rcsb.org//maven//org/apache/tomcat/servlet-api/6.0.35/servlet-api-6.0.35.pom
[INFO] Unable to find resource 'org.apache.tomcat:servlet-api:pom:6.0.35' in repository rcsb-pdb-maven-repo (http://source.rcsb.org//maven/)
Downloading: http://www.biojava.org/download/maven//org/apache/tomcat/servlet-api/6.0.35/servlet-api-6.0.35.pom
[INFO] Unable to find resource 'org.apache.tomcat:servlet-api:pom:6.0.35' in repository biojava-maven-repo (http://www.biojava.org/download/maven/)
Downloading: http://repo1.maven.org/maven2/org/apache/tomcat/servlet-api/6.0.35/servlet-api-6.0.35.pom
Downloading: http://repo1.maven.org/maven2/org/apache/tomcat/servlet-api/6.0.35/servlet-api-6.0.35.jar
compiler:compile {execution: default-compile}
[INFO] Compiling 64 source files to /opt/cruise/projects/ava-core/target/classes
resources:testResources {execution: default-testResources}
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /opt/cruise/projects/ava-core/src/test/resources
compiler:testCompile {execution: default-testCompile}
[INFO] Compiling 6 source files to /opt/cruise/projects/ava-core/target/test-classes
surefire:test {execution: default-test}
[INFO] Surefire report directory: /opt/cruise/projects/ava-core/target/surefire-reports
-------------------------------------------------------
 T E S T S
-------------------------------------------------------
Running TestGzipCompression
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec
Running TestDomainAssignments
Could not register RMI.Port already in use: 1099; nested exception is:
java.net.BindException: Address already in use
Init of InitialContext
using developer domainalig...
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.742 sec
Running TestBrokenDomainIDs
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec
Running TestDomainAssignment
Setting ScopDatabase to type: org.biojava.bio.structure.scop.ScopInstallation
Setting ScopDatabase to type: org.biojava.bio.structure.scop.ScopInstallation
Setting ScopDatabase to type: org.biojava.bio.structure.scop.ScopInstallation
Setting ScopDatabase to type: org.biojava.bio.structure.scop.ScopInstallation
Setting ScopDatabase to type: org.biojava.bio.structure.scop.ScopInstallation
Setting ScopDatabase to type: org.biojava.bio.structure.scop.ScopInstallation
Setting ScopDatabase to type: org.biojava.bio.structure.scop.ScopInstallation
Setting ScopDatabase to type: org.biojava.bio.structure.scop.ScopInstallation
Setting ScopDatabase to type: org.biojava.bio.structure.scop.ScopInstallation
Setting ScopDatabase to type: org.biojava.bio.structure.scop.ScopInstallation
>PDP:3LGFAa<
creating new cache /tmp/remotepdpdomaindefs.ser
http://source.rcsb.org/jfatcatserver/domains/getRepresentativePDPDomains
got 22296 domain ranges for PDP domains from server.
http://source.rcsb.org/jfatcatserver/domains/getPDPDomain?pdpId=PDP:3LGFAa
structure PDP:3LGFAa 3LGF Description: sub-range A_1485-1603 of 3LGF subset of 3LGF null Authors: S.ROY,T.G.KUTATELADZE IdCode: 3LGF Classification: CELL CYCLE DepDate: Wed Jan 20 00:00:00 PST 2010 Technique: X-RAY DIFFRACTION Resolution: 1.5 ModDate: Wed May 12 00:00:00 PDT 2010 Title: CRYSTAL STRUCTURE OF THE 53BP1 TANDEM TUDOR DOMAIN IN COMPLEX WITH P53K370ME2
chains:
chain 0: >A<
length SEQRES: 0 length ATOM: 119 aminos: 119 hetatms: 0 nucleotides: 0
DBRefs: 2
DBREF 3LGF A 1484 1603 UNP Q12888 TP53B_HUMAN 1484 1603
DBREF 3LGF B 366 375 PDB 3LGF 3LGF 366 375
Molecules:
>PDP:3LGFB_<
http://source.rcsb.org/jfatcatserver/domains/getPDPDomain?pdpId=PDP:3LGFB_
structure PDP:3LGFB_ 3LGF Description: sub-range B of 3LGF subset of 3LGF null Authors: S.ROY,T.G.KUTATELADZE IdCode: 3LGF Classification: CELL CYCLE DepDate: Wed Jan 20 00:00:00 PST 2010 Technique: X-RAY DIFFRACTION Resolution: 1.5 ModDate: Wed May 12 00:00:00 PDT 2010 Title: CRYSTAL STRUCTURE OF THE 53BP1 TANDEM TUDOR DOMAIN IN COMPLEX WITH P53K370ME2
chains:
chain 0: >B<
length SEQRES: 0 length ATOM: 2 aminos: 0 hetatms: 2 nucleotides: 0
DBRefs: 2
DBREF 3LGF A 1484 1603 UNP Q12888 TP53B_HUMAN 1484 1603
DBREF 3LGF B 366 375 PDB 3LGF 3LGF 366 375
Molecules:
>d1apy.1<
parsed 110800 scop sunid domains.
parsed 143428 scop sunid descriptions.
structure d1apy.1 d1apy.1 Description: d.153.1.5 | (Glycosyl)asparaginase Authors: J.ROUVINEN,C.OINONEN IdCode: 1APY Classification: HYDROLASE DepDate: Wed Jun 14 00:00:00 PDT 1995 Technique: X-RAY DIFFRACTION Resolution: 2.0 ModDate: Wed Jul 13 00:00:00 PDT 2011 Title: HUMAN ASPARTYLGLUCOSAMINIDASE
chains:
chain 0: >A<
length SEQRES: 0 length ATOM: 242 aminos: 161 hetatms: 81 nucleotides: 0
chain 1: >B<
length SEQRES: 0 length ATOM: 189 aminos: 141 hetatms: 48 nucleotides: 0
DBRefs: 4
DBREF 1APY A 1 162 UNP P20933 ASPG_HUMAN 24 185
DBREF 1APY B 183 323 UNP P20933 ASPG_HUMAN 206 346
DBREF 1APY C 1 162 UNP P20933 ASPG_HUMAN 24 185
DBREF 1APY D 183 323 UNP P20933 ASPG_HUMAN 206 346
Molecules:
>d1apy.2<
structure d1apy.2 d1apy.2 Description: d.153.1.5 | (Glycosyl)asparaginase Authors: J.ROUVINEN,C.OINONEN IdCode: 1APY Classification: HYDROLASE DepDate: Wed Jun 14 00:00:00 PDT 1995 Technique: X-RAY DIFFRACTION Resolution: 2.0 ModDate: Wed Jul 13 00:00:00 PDT 2011 Title: HUMAN ASPARTYLGLUCOSAMINIDASE
chains:
chain 0: >C<
length SEQRES: 0 length ATOM: 226 aminos: 161 hetatms: 65 nucleotides: 0
chain 1: >D<
length SEQRES: 0 length ATOM: 190 aminos: 141 hetatms: 49 nucleotides: 0
DBRefs: 4
DBREF 1APY A 1 162 UNP P20933 ASPG_HUMAN 24 185
DBREF 1APY B 183 323 UNP P20933 ASPG_HUMAN 206 346
DBREF 1APY C 1 162 UNP P20933 ASPG_HUMAN 24 185
DBREF 1APY D 183 323 UNP P20933 ASPG_HUMAN 206 346
Molecules:
[DomainFragment [pdbId=1APY, domId=d1apy.1, chainId=A, start=null, end=null, fragmentNr=1], DomainFragment [pdbId=1APY, domId=d1apy.1, chainId=B, start=null, end=null, fragmentNr=2], DomainFragment [pdbId=1APY, domId=d1apy.2, chainId=C, start=null, end=null, fragmentNr=1], DomainFragment [pdbId=1APY, domId=d1apy.2, chainId=D, start=null, end=null, fragmentNr=2]]
[d3bmva1, d3bmva2, d3bmva3, d3bmva4]
[2UV8.A_983-1092,A_1182-1452,A_1505-1701]
d4hhba_
downloading ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/hh/pdb4hhb.ent.gz to /tmp/pdb4hhb7395932239644664812.gz
copying to /tmp/hh/pdb4hhb.ent.gz
d4hhbb_
d4hhbc_
d4hhbd_
4HHB.A
4HHB.B
4HHB.C
4HHB.D
PDP:3LGFAa, PDP:3LGFB_
Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.605 sec
Running TestSequenceCluster
got entityChains: 123164
got chainEntities: 221533
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.015 sec
Running TestDomainFragmentLoading
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 sec
Results :
Tests run: 18, Failures: 0, Errors: 0, Skipped: 0
jar:jar {execution: default-jar}
[INFO] Building jar: /opt/cruise/projects/ava-core/target/ava-core-2012-03-16-SNAPSHOT.jar
install:install {execution: default-install}
[INFO] Installing /opt/cruise/projects/ava-core/target/ava-core-2012-03-16-SNAPSHOT.jar to /home/andreas/.m2/repository/org/rcsb/ava-core/2012-03-16-SNAPSHOT/ava-core-2012-03-16-SNAPSHOT.jar
[INFO] Preparing source:jar
[INFO] No goals needed for project - skipping
source:jar {execution: default-cli}
[INFO] Building jar: /opt/cruise/projects/ava-core/target/ava-core-2012-03-16-SNAPSHOT-sources.jar
javadoc:jar {execution: default-cli}
Loading source files for package org.rcsb.ava.dbsearch.domainassign...
Loading source files for package org.rcsb.ava.util.ftp...
Loading source files for package org.rcsb.fatcat.server.dao...
Loading source files for package org.rcsb.fatcat.server...
Loading source files for package org.rcsb.fatcat.server.threads...
Loading source files for package org.rcsb.fatcat.server.xml...
Loading source files for package org.rcsb.fatcat.server.model...
Loading source files for package org.rcsb.fatcat.server.util...
Loading source files for package flex...
Loading source files for package demo.flex...
Constructing Javadoc information...
Standard Doclet version 1.7.0
Building tree for all the packages and classes...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/ava/dbsearch/domainassign/AssignmentXMLSerializer.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/ava/dbsearch/domainassign/DomainAssigner.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/ava/dbsearch/domainassign/DomainAssignment.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/ava/util/ftp/AbstractFtpSyncedFile.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/ava/util/ftp/FtpSyncedFile.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/ava/util/ftp/RCSBFtpUtils.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/AlignmentIDCache.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/AlignmentXMLResultProvider.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/AVADataWrapper.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/DBAlignment.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/DefaultDBAlignmentProvider.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/DefaultResourceProvider.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/DomainSplitDAO.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/EntityChainMap.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/PdbDAO.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/RCSBLocalDomainProvider.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/RCSBLocalPDPProvider.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/SecondaryDbDao.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/SequenceClusterDAO.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/SplitDatabase.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/SplitDBResourceProvider.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/AVAXmlFileStorage.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/DbUtils.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/LocalFileStorage.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/PdbChainKey.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/ResultSubmitter.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/SimpleSSHFileStorage.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/TarSSHFileStorage.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/threads/CreateRowThread.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/threads/DatabasePoisonCleaner.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/xml/AFPDataWrapper.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/xml/AFPDataWrapperSaxParser.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/model/ClusterEntity.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/model/DomainFragment.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/model/TableName.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/model/TableRow.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/AlignmentCache.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/DumpResultFile.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/MyUserInfo.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/PdbLog.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/PDBLogger.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/PropertyNames.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/ResourceManager.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/ServerAtomCache.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/ServerProperties.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/SetupJNDIDataSource.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/TarTools.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/flex/ClusterFlexibilityData.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/flex/ClusterFlexibilityDataSet.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/flex/FlexibilityAnalysis.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/flex/FlexibilityDemo.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/ClusterDemo.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/ClusterFlexibilityAnalyze.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/ClusterFlexibilityAnalyzeDemo.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/Clusters.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/ClusterStructuralAlignment.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/ClusterStructuralAlignmentDemo.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/CSVReader.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/CSVreaderdemo.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/RMSD.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/RMSDAnalyze.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/RMSDAnalyzeDemo.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/StructuralAlignmentOfAllCluster.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/StructuralAlignmentOfAllClusterDemo.html...
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Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/package-frame.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/package-summary.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/package-tree.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/flex/package-frame.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/flex/package-summary.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/flex/package-tree.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/ava/dbsearch/domainassign/package-frame.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/ava/dbsearch/domainassign/package-summary.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/ava/dbsearch/domainassign/package-tree.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/ava/util/ftp/package-frame.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/ava/util/ftp/package-summary.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/ava/util/ftp/package-tree.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/package-frame.html...
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Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/package-frame.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/package-summary.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/package-tree.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/model/package-frame.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/model/package-summary.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/model/package-tree.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/threads/package-frame.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/threads/package-summary.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/threads/package-tree.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/package-frame.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/package-summary.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/package-tree.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/xml/package-frame.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/xml/package-summary.html...
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Generating /opt/cruise/projects/ava-core/target/apidocs/constant-values.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/serialized-form.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/ava/dbsearch/domainassign/class-use/AssignmentXMLSerializer.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/ava/dbsearch/domainassign/class-use/DomainAssignment.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/ava/dbsearch/domainassign/class-use/DomainAssigner.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/ava/util/ftp/class-use/RCSBFtpUtils.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/ava/util/ftp/class-use/AbstractFtpSyncedFile.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/ava/util/ftp/class-use/FtpSyncedFile.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/class-use/SecondaryDbDao.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/class-use/DefaultDBAlignmentProvider.html...
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Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/class-use/RCSBLocalDomainProvider.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/class-use/DomainSplitDAO.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/class-use/DBAlignment.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/class-use/SequenceClusterDAO.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/class-use/PdbDAO.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/class-use/AlignmentIDCache.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/class-use/RCSBLocalPDPProvider.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/class-use/SplitDatabase.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/class-use/AVADataWrapper.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/class-use/EntityChainMap.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/class-use/DefaultResourceProvider.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/class-use/AlignmentXMLResultProvider.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/class-use/SimpleSSHFileStorage.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/class-use/ResultSubmitter.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/class-use/AVAXmlFileStorage.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/class-use/PdbChainKey.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/class-use/TarSSHFileStorage.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/class-use/LocalFileStorage.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/class-use/DbUtils.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/threads/class-use/CreateRowThread.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/threads/class-use/DatabasePoisonCleaner.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/xml/class-use/AFPDataWrapperSaxParser.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/xml/class-use/AFPDataWrapper.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/model/class-use/ClusterEntity.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/model/class-use/DomainFragment.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/model/class-use/TableName.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/model/class-use/TableRow.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/class-use/SetupJNDIDataSource.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/class-use/AlignmentCache.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/class-use/PropertyNames.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/class-use/PdbLog.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/class-use/ServerProperties.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/class-use/DumpResultFile.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/class-use/ServerAtomCache.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/class-use/PDBLogger.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/class-use/MyUserInfo.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/class-use/ResourceManager.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/class-use/TarTools.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/flex/class-use/ClusterFlexibilityDataSet.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/flex/class-use/ClusterFlexibilityData.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/flex/class-use/FlexibilityAnalysis.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/flex/class-use/FlexibilityDemo.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/class-use/StructuralAlignmentOfAllCluster.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/class-use/ClusterFlexibilityAnalyzeDemo.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/class-use/RMSDAnalyze.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/class-use/ClusterDemo.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/class-use/ClusterStructuralAlignment.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/class-use/Clusters.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/class-use/RMSDAnalyzeDemo.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/class-use/ClusterStructuralAlignmentDemo.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/class-use/RMSD.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/class-use/ClusterFlexibilityAnalyze.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/class-use/CSVReader.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/class-use/CSVreaderdemo.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/class-use/StructuralAlignmentOfAllClusterDemo.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/demo/flex/package-use.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/flex/package-use.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/ava/dbsearch/domainassign/package-use.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/ava/util/ftp/package-use.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/package-use.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/dao/package-use.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/model/package-use.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/threads/package-use.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/util/package-use.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/org/rcsb/fatcat/server/xml/package-use.html...
Building index for all the packages and classes...
Generating /opt/cruise/projects/ava-core/target/apidocs/overview-tree.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/index-all.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /opt/cruise/projects/ava-core/target/apidocs/allclasses-frame.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/allclasses-noframe.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/index.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/overview-summary.html...
Generating /opt/cruise/projects/ava-core/target/apidocs/help-doc.html...
46 warnings
[WARNING] Javadoc Warnings
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/ava/util/ftp/RCSBFtpUtils.java:106: warning - @param argument "pl" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/ava/util/ftp/RCSBFtpUtils.java:164: warning - @param argument "pl" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/ava/util/ftp/RCSBFtpUtils.java:206: warning - @param argument "user" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/ava/util/ftp/RCSBFtpUtils.java:206: warning - @param argument "port" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/ava/util/ftp/RCSBFtpUtils.java:206: warning - @param argument "password" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/ava/util/ftp/RCSBFtpUtils.java:206: warning - @param argument "isBinary" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/ava/util/ftp/RCSBFtpUtils.java:206: warning - @param argument "pl" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/ava/util/ftp/RCSBFtpUtils.java:232: warning - @param argument "pl" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/ava/util/ftp/RCSBFtpUtils.java:382: warning - @param argument "pl" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/ava/util/ftp/RCSBFtpUtils.java:429: warning - @param argument "pl" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/DefaultDBAlignmentProvider.java:173: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SplitDBResourceProvider.java:16: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/EntityChainMap.java:102: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/EntityChainMap.java:111: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/EntityChainMap.java:92: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/PdbDAO.java:41: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SequenceClusterDAO.java:319: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SequenceClusterDAO.java:149: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SequenceClusterDAO.java:37: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SequenceClusterDAO.java:37: warning - @param argument "percentCutoff" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SequenceClusterDAO.java:96: warning - @param argument "percentCutoff" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SequenceClusterDAO.java:149: warning - @param argument "pdbId" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SplitDatabase.java:2245: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SplitDatabase.java:2308: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SplitDatabase.java:2181: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SplitDatabase.java:2339: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SplitDatabase.java:1734: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SplitDatabase.java:2514: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SplitDatabase.java:1384: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SplitDatabase.java:2584: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SplitDatabase.java:2908: warning - @param argument "aligId" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SplitDatabase.java:2994: warning - @param argument "table" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/AVAXmlFileStorage.java:25: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/PdbChainKey.java:118: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/PdbChainKey.java:107: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/PdbChainKey.java:30: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/ResultSubmitter.java:450: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/model/ClusterEntity.java:30: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/model/ClusterEntity.java:60: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/model/ClusterEntity.java:42: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/util/AlignmentCache.java:77: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/util/TarTools.java:34: warning - @param argument "dirPath" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/util/TarTools.java:34: warning - @param argument "archivePath" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/util/TarTools.java:104: warning - @gzip is an unknown tag.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/util/TarTools.java:104: warning - @param argument "fileContent," is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/demo/flex/ClusterStructuralAlignment.java:337: warning - @return tag has no arguments.
[INFO] Building jar: /opt/cruise/projects/ava-core/target/ava-core-2012-03-16-SNAPSHOT-javadoc.jar
resources:resources {execution: default-resources}
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 0 resource
compiler:compile {execution: default-compile}
[INFO] Nothing to compile - all classes are up to date
resources:testResources {execution: default-testResources}
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /opt/cruise/projects/ava-core/src/test/resources
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/ava-core/target/surefire-reports
-------------------------------------------------------
 T E S T S
-------------------------------------------------------
Running TestGzipCompression
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 sec
Running TestDomainAssignments
Could not register RMI.Port already in use: 1099; nested exception is:
java.net.BindException: Address already in use
Init of InitialContext
using developer domainalig...
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.592 sec
Running TestBrokenDomainIDs
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec
Running TestDomainAssignment
Setting ScopDatabase to type: org.biojava.bio.structure.scop.ScopInstallation
Setting ScopDatabase to type: org.biojava.bio.structure.scop.ScopInstallation
Setting ScopDatabase to type: org.biojava.bio.structure.scop.ScopInstallation
Setting ScopDatabase to type: org.biojava.bio.structure.scop.ScopInstallation
Setting ScopDatabase to type: org.biojava.bio.structure.scop.ScopInstallation
Setting ScopDatabase to type: org.biojava.bio.structure.scop.ScopInstallation
Setting ScopDatabase to type: org.biojava.bio.structure.scop.ScopInstallation
Setting ScopDatabase to type: org.biojava.bio.structure.scop.ScopInstallation
Setting ScopDatabase to type: org.biojava.bio.structure.scop.ScopInstallation
Setting ScopDatabase to type: org.biojava.bio.structure.scop.ScopInstallation
d4hhba_
parsed 110800 scop sunid domains.
parsed 143428 scop sunid descriptions.
d4hhbb_
d4hhbc_
d4hhbd_
4HHB.A
4HHB.B
4HHB.C
4HHB.D
PDP:3LGFAa, PDP:3LGFB_
>PDP:3LGFAa<
creating new cache /tmp/remotepdpdomaindefs.ser
http://source.rcsb.org/jfatcatserver/domains/getRepresentativePDPDomains
got 22296 domain ranges for PDP domains from server.
http://source.rcsb.org/jfatcatserver/domains/getPDPDomain?pdpId=PDP:3LGFAa
structure PDP:3LGFAa 3LGF Description: sub-range A_1485-1603 of 3LGF subset of 3LGF null Authors: S.ROY,T.G.KUTATELADZE IdCode: 3LGF Classification: CELL CYCLE DepDate: Wed Jan 20 00:00:00 PST 2010 Technique: X-RAY DIFFRACTION Resolution: 1.5 ModDate: Wed May 12 00:00:00 PDT 2010 Title: CRYSTAL STRUCTURE OF THE 53BP1 TANDEM TUDOR DOMAIN IN COMPLEX WITH P53K370ME2
chains:
chain 0: >A<
length SEQRES: 0 length ATOM: 119 aminos: 119 hetatms: 0 nucleotides: 0
DBRefs: 2
DBREF 3LGF A 1484 1603 UNP Q12888 TP53B_HUMAN 1484 1603
DBREF 3LGF B 366 375 PDB 3LGF 3LGF 366 375
Molecules:
>PDP:3LGFB_<
http://source.rcsb.org/jfatcatserver/domains/getPDPDomain?pdpId=PDP:3LGFB_
structure PDP:3LGFB_ 3LGF Description: sub-range B of 3LGF subset of 3LGF null Authors: S.ROY,T.G.KUTATELADZE IdCode: 3LGF Classification: CELL CYCLE DepDate: Wed Jan 20 00:00:00 PST 2010 Technique: X-RAY DIFFRACTION Resolution: 1.5 ModDate: Wed May 12 00:00:00 PDT 2010 Title: CRYSTAL STRUCTURE OF THE 53BP1 TANDEM TUDOR DOMAIN IN COMPLEX WITH P53K370ME2
chains:
chain 0: >B<
length SEQRES: 0 length ATOM: 2 aminos: 0 hetatms: 2 nucleotides: 0
DBRefs: 2
DBREF 3LGF A 1484 1603 UNP Q12888 TP53B_HUMAN 1484 1603
DBREF 3LGF B 366 375 PDB 3LGF 3LGF 366 375
Molecules:
>d1apy.1<
structure d1apy.1 d1apy.1 Description: d.153.1.5 | (Glycosyl)asparaginase Authors: J.ROUVINEN,C.OINONEN IdCode: 1APY Classification: HYDROLASE DepDate: Wed Jun 14 00:00:00 PDT 1995 Technique: X-RAY DIFFRACTION Resolution: 2.0 ModDate: Wed Jul 13 00:00:00 PDT 2011 Title: HUMAN ASPARTYLGLUCOSAMINIDASE
chains:
chain 0: >A<
length SEQRES: 0 length ATOM: 242 aminos: 161 hetatms: 81 nucleotides: 0
chain 1: >B<
length SEQRES: 0 length ATOM: 189 aminos: 141 hetatms: 48 nucleotides: 0
DBRefs: 4
DBREF 1APY A 1 162 UNP P20933 ASPG_HUMAN 24 185
DBREF 1APY B 183 323 UNP P20933 ASPG_HUMAN 206 346
DBREF 1APY C 1 162 UNP P20933 ASPG_HUMAN 24 185
DBREF 1APY D 183 323 UNP P20933 ASPG_HUMAN 206 346
Molecules:
>d1apy.2<
structure d1apy.2 d1apy.2 Description: d.153.1.5 | (Glycosyl)asparaginase Authors: J.ROUVINEN,C.OINONEN IdCode: 1APY Classification: HYDROLASE DepDate: Wed Jun 14 00:00:00 PDT 1995 Technique: X-RAY DIFFRACTION Resolution: 2.0 ModDate: Wed Jul 13 00:00:00 PDT 2011 Title: HUMAN ASPARTYLGLUCOSAMINIDASE
chains:
chain 0: >C<
length SEQRES: 0 length ATOM: 226 aminos: 161 hetatms: 65 nucleotides: 0
chain 1: >D<
length SEQRES: 0 length ATOM: 190 aminos: 141 hetatms: 49 nucleotides: 0
DBRefs: 4
DBREF 1APY A 1 162 UNP P20933 ASPG_HUMAN 24 185
DBREF 1APY B 183 323 UNP P20933 ASPG_HUMAN 206 346
DBREF 1APY C 1 162 UNP P20933 ASPG_HUMAN 24 185
DBREF 1APY D 183 323 UNP P20933 ASPG_HUMAN 206 346
Molecules:
[DomainFragment [pdbId=1APY, domId=d1apy.1, chainId=A, start=null, end=null, fragmentNr=1], DomainFragment [pdbId=1APY, domId=d1apy.1, chainId=B, start=null, end=null, fragmentNr=2], DomainFragment [pdbId=1APY, domId=d1apy.2, chainId=C, start=null, end=null, fragmentNr=1], DomainFragment [pdbId=1APY, domId=d1apy.2, chainId=D, start=null, end=null, fragmentNr=2]]
[d3bmva1, d3bmva2, d3bmva3, d3bmva4]
[2UV8.A_983-1092,A_1182-1452,A_1505-1701]
Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.435 sec
Running TestSequenceCluster
got entityChains: 123164
got chainEntities: 221533
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.101 sec
Running TestDomainFragmentLoading
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 sec
Results :
Tests run: 18, Failures: 0, Errors: 0, Skipped: 0
jar:jar {execution: default-jar}
install:install {execution: default-install}
[INFO] Installing /opt/cruise/projects/ava-core/target/ava-core-2012-03-16-SNAPSHOT.jar to /home/andreas/.m2/repository/org/rcsb/ava-core/2012-03-16-SNAPSHOT/ava-core-2012-03-16-SNAPSHOT.jar
[INFO] Installing /opt/cruise/projects/ava-core/target/ava-core-2012-03-16-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/rcsb/ava-core/2012-03-16-SNAPSHOT/ava-core-2012-03-16-SNAPSHOT-sources.jar
[INFO] Installing /opt/cruise/projects/ava-core/target/ava-core-2012-03-16-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/rcsb/ava-core/2012-03-16-SNAPSHOT/ava-core-2012-03-16-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/rcsb/ava-core/2012-03-16-SNAPSHOT/ava-core-2012-03-16-SNAPSHOT.jar
193K uploaded (ava-core-2012-03-16-SNAPSHOT.jar)
[INFO] Retrieving previous metadata from rcsb-pdb-maven-repo
[INFO] Uploading repository metadata for: 'snapshot org.rcsb:ava-core:2012-03-16-SNAPSHOT'
[INFO] Uploading project information for ava-core 2012-03-16-SNAPSHOT
[INFO] Retrieving previous metadata from rcsb-pdb-maven-repo
[INFO] Uploading repository metadata for: 'artifact org.rcsb:ava-core'
[INFO] Retrieving previous build number from rcsb-pdb-maven-repo
Uploading: scp://emmy.rcsb.org/opt/maven//org/rcsb/ava-core/2012-03-16-SNAPSHOT/ava-core-2012-03-16-SNAPSHOT-sources.jar
113K uploaded (ava-core-2012-03-16-SNAPSHOT-sources.jar)
[INFO] Retrieving previous build number from rcsb-pdb-maven-repo
Uploading: scp://emmy.rcsb.org/opt/maven//org/rcsb/ava-core/2012-03-16-SNAPSHOT/ava-core-2012-03-16-SNAPSHOT-javadoc.jar
372K uploaded (ava-core-2012-03-16-SNAPSHOT-javadoc.jar)
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[INFO] Building ava-core
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javadoc:aggregate {execution: default-cli}
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Building index for all the packages and classes...
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46 warnings
[WARNING] Javadoc Warnings
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/ava/util/ftp/RCSBFtpUtils.java:106: warning - @param argument "pl" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/ava/util/ftp/RCSBFtpUtils.java:164: warning - @param argument "pl" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/ava/util/ftp/RCSBFtpUtils.java:206: warning - @param argument "user" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/ava/util/ftp/RCSBFtpUtils.java:206: warning - @param argument "port" is not a parameter name.
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[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/ava/util/ftp/RCSBFtpUtils.java:206: warning - @param argument "isBinary" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/ava/util/ftp/RCSBFtpUtils.java:206: warning - @param argument "pl" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/ava/util/ftp/RCSBFtpUtils.java:232: warning - @param argument "pl" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/ava/util/ftp/RCSBFtpUtils.java:382: warning - @param argument "pl" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/ava/util/ftp/RCSBFtpUtils.java:429: warning - @param argument "pl" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/DefaultDBAlignmentProvider.java:173: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SplitDBResourceProvider.java:16: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/EntityChainMap.java:102: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/EntityChainMap.java:111: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/EntityChainMap.java:92: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/PdbDAO.java:41: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SequenceClusterDAO.java:319: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SequenceClusterDAO.java:149: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SequenceClusterDAO.java:37: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SequenceClusterDAO.java:37: warning - @param argument "percentCutoff" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SequenceClusterDAO.java:96: warning - @param argument "percentCutoff" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SequenceClusterDAO.java:149: warning - @param argument "pdbId" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SplitDatabase.java:2245: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SplitDatabase.java:2308: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SplitDatabase.java:2181: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SplitDatabase.java:2339: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SplitDatabase.java:1734: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SplitDatabase.java:2514: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SplitDatabase.java:1384: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SplitDatabase.java:2584: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SplitDatabase.java:2908: warning - @param argument "aligId" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/dao/SplitDatabase.java:2994: warning - @param argument "table" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/AVAXmlFileStorage.java:25: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/PdbChainKey.java:118: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/PdbChainKey.java:107: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/PdbChainKey.java:30: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/ResultSubmitter.java:450: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/model/ClusterEntity.java:30: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/model/ClusterEntity.java:60: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/model/ClusterEntity.java:42: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/util/AlignmentCache.java:77: warning - @return tag has no arguments.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/util/TarTools.java:34: warning - @param argument "dirPath" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/util/TarTools.java:34: warning - @param argument "archivePath" is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/util/TarTools.java:104: warning - @gzip is an unknown tag.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/org/rcsb/fatcat/server/util/TarTools.java:104: warning - @param argument "fileContent," is not a parameter name.
[WARNING] /opt/cruise/projects/ava-core/src/main/java/demo/flex/ClusterStructuralAlignment.java:337: warning - @return tag has no arguments.
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESSFUL
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 40 seconds
[INFO] Finished at: Mon May 14 17:02:15 PDT 2012
[INFO] Final Memory: 51M/870M
[INFO] ------------------------------------------------------------------------

 Unit Tests: (0)
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