[MOBY-guts] biomoby commit
Dmitry Repchevski
drepchevski at dev.open-bio.org
Fri Dec 18 11:20:57 UTC 2009
drepchevski
Fri Dec 18 06:20:57 EST 2009
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/ontology
In directory dev.open-bio.org:/tmp/cvs-serv21923
Added Files:
AminoAcidSequence.java AnnotatedAASequence.java
AnnotatedDomain.java AnnotatedNASequence.java
AnnotatedStructure.java Annotation.java AnnotationHits.java
AntigenicAnnotatedAASequence.java AntigenicAnnotation.java
AntigenicReport.java Array.java ArrayFloat.java
ArrayInteger.java ArrayString.java ArrayXYData.java
BL2GAnnotation.java BLAST_XML.java BLAST__Text.java
BLOCKAnnotation.java BasicAnnotation.java
BlocksAnnotatedAASequence.java ByoDynInput.java
ByoDynOEDParameter.java ByoDynTarget.java CATHDomain.java
CathDomainDescription_XML.java Clustalw_Evaluated_Text.java
Clustalw_Text.java ClusterProfile_Text.java Clustering.java
CodcmpReport_Text.java CodonUsageTable_Text.java
CommentedAASequence.java CommentedAASubsequence.java
CommentedDNASequence.java CommentedNASequence.java
CommentedObject.java CommentedRNASequence.java
CommentedWeightedObject.java Consensus_Sequence_Text.java
CpGAnnotatedNASequence.java CpGAnnotation.java CpGReport.java
DASGFF.java DCCP_Text.java DGPI_Report.java DNASequence.java
DSSP_Text.java DTA_Text.java
DifferentialExpressionTest_Text.java
DifferentialExpressionTest__Text.java DigestReport.java
Distance_Matrix.java Domain.java DomainAnnotatedSequence.java
EMBL_Text.java ENSEMBLHomolog.java Element.java
ElementFloat.java ElementInteger.java ElementString.java
ElementXYData.java EmowseAnnotatedAASequence.java
Enzymatic_Text.java EquicktandemAnnotatedNASequence.java
EquicktandemAnnotation.java EquicktandemReport.java
ExpressionCore.java ExpressionStatistics.java FASTA.java
FASTA_AA.java FASTA_AA_multi.java FASTA_NA.java
FASTA_NA_multi.java FASTA_Text.java FASTA_pep.java
FSOLV_Text.java FSSP_Text.java FamilyBLOCKAnnotation.java
FatiGO_Text.java FatiGO__XML.java FatiScan_Text.java
FatiScan__XML.java FeatureAASequence.java
FeatureAnnotatedAASequence.java FeatureAnnotation.java
FunCUT_Annotation_XML.java GFF.java GFF2.java GFF3.java
GOGraph.java GOTerm.java GenBank_Text.java
GenericSequence.java HMMPfam_Report.java HMMSearch_Report.java
HMM_Text.java HSSP_Text.java HierarchicalClustering.java
ISS_Annotation_XML.java ISS_Report.java Image_Encoded.java
IntAct_XML.java InterProMotifAnnotatedAASequence.java
InterProMotifAnnotation.java Interaction.java
InteractionMethod.java Interactor.java List_Text.java
List__Text.java LutefiskAnnotatedAASequence.java
LutefiskAnnotation.java LutefiskReport.java MEME_Text.java
MSF.java MatchingPattern.java Matrix.java MatrixFloat.java
MatrixInteger.java MatrixString.java Meta_Alignment_Text.java
MicroArrayData_Text.java MicroArrayData__Text.java
MmCIF_Text.java MmCIF__Text.java MolWeightAnnotation.java
MolWeightsAnnotatedAASequence.java MolWeightsArray.java
MotifAnnotatedAASequence.java MotifAnnotation.java
MotifMatrix.java MultiParameter.java NAMD_Conf_Text.java
NAMD_Output.java NAMD_Structure.java NCBI_BLAST_Text.java
NCut_Clusters.java NCut_Matrix.java NCut_Text.java
NDB__Text.java Newick_Text.java Newick__Text.java
NucleotideSequence.java OMIM.java PDB_Enriched.java
PDB__Text.java PHD_Text.java PIR_Text.java PMUT_Text.java
PPSearchReport.java PSF_Text.java Parameter.java
Parameters4Values.java ParametersToVary.java
PatmatdbReport.java PatmatmotifsReport.java Pattern.java
PepNovoReport.java Pepcoil_Text.java PepinfoReport.java
Pepstats_Text.java Phylip_Interleaved_Text.java
Phylip_Text.java Phylip_tree_Text.java
Phylip_treefile_Text.java PredictionModel__XML.java
Prediction__Text.java PredictorTraining_Text.java
ProbMolWeightAnnotation.java
ProbMolWeightsAnnotatedAASequence.java ProdomMotif.java
PropertySequence.java PrositeDoc_Text.java PrositeMotif.java
RNASequence.java RefSeq_Text.java
RestrictAnnotatedNASequence.java RestrictAnnotation.java
RestrictReport.java Rules.java SCOPDomain.java
SCOPLayerNode.java SIAM_Annotation_XML.java
ScoredMotifAnnotatedAASequence.java ScoredMotifAnnotation.java
SequenceDescription_Text.java Sequence_alignment_report.java
SigcleaveAnnotatedAASequence.java SigcleaveAnnotation.java
SigcleaveReport.java Stockholm_Text.java
StructureBoundaries.java StructureDomain.java
StructureFragment.java Structure_Alignment_Report.java
SwissProt_Text.java TFscan_Text.java TTS.java Target.java
TargetArgument.java Text__formatted.java Text__html.java
Text__plain.java Text__xhtml.java Text__xml.java
TransmembraneAnnotatedAASequence.java
TransmembraneAnnotation.java TransmembraneReport.java
TreeDet_Annotation_HTML.java TreeDet_Annotation_XML.java
TreeDet_Report.java Typed_Image.java URL__Text.java
VirtualSequence.java WeightedAminoAcidSequences.java
WeightedList_Text.java WeightedList__Text.java
WeightedObject.java Zip_Encoded.java jaxb.index
package-info.java
Log Message:
added generated by MobyGenerator java ontology classes...
moby-live/Java/src/main/org/inb/biomoby/shared/ontology AminoAcidSequence.java,NONE,1.1 AnnotatedAASequence.java,NONE,1.1 AnnotatedDomain.java,NONE,1.1 AnnotatedNASequence.java,NONE,1.1 AnnotatedStructure.java,NONE,1.1 Annotation.java,NONE,1.1 AnnotationHits.java,NONE,1.1 AntigenicAnnotatedAASequence.java,NONE,1.1 AntigenicAnnotation.java,NONE,1.1 AntigenicReport.java,NONE,1.1 Array.java,NONE,1.1 ArrayFloat.java,NONE,1.1 ArrayInteger.java,NONE,1.1 ArrayString.java,NONE,1.1 ArrayXYData.java,NONE,1.1 BL2GAnnotation.java,NONE,1.1 BLAST_XML.java,NONE,1.1 BLAST__Text.java,NONE,1.1 BLOCKAnnotation.java,NONE,1.1 BasicAnnotation.java,NONE,1.1 BlocksAnnotatedAASequence.java,NONE,1.1 ByoDynInput.java,NONE,1.1 ByoDynOEDParameter.java,NONE,1.1 ByoDynTarget.java,NONE,1.1 CATHDomain.java,NONE,1.1 CathDomainDescription_XML.java,NONE,1.1 Clustalw_Evaluated_Text.java,NONE,1.1 Clustalw_Text.java,NONE,1.1 ClusterProfile_Text.java,NONE,1.1 Clustering.java,NONE,1.1 CodcmpReport_Text.java,NONE,1.!
1 CodonUsageTable_Text.java,NONE,1.1 CommentedAASequence.java,NONE,1.1 CommentedAASubsequence.java,NONE,1.1 CommentedDNASequence.java,NONE,1.1 CommentedNASequence.java,NONE,1.1 CommentedObject.java,NONE,1.1 CommentedRNASequence.java,NONE,1.1 CommentedWeightedObject.java,NONE,1.1 Consensus_Sequence_Text.java,NONE,1.1 CpGAnnotatedNASequence.java,NONE,1.1 CpGAnnotation.java,NONE,1.1 CpGReport.java,NONE,1.1 DASGFF.java,NONE,1.1 DCCP_Text.java,NONE,1.1 DGPI_Report.java,NONE,1.1 DNASequence.java,NONE,1.1 DSSP_Text.java,NONE,1.1 DTA_Text.java,NONE,1.1 DifferentialExpressionTest_Text.java,NONE,1.1 DifferentialExpressionTest__Text.java,NONE,1.1 DigestReport.java,NONE,1.1 Distance_Matrix.java,NONE,1.1 Domain.java,NONE,1.1 DomainAnnotatedSequence.java,NONE,1.1 EMBL_Text.java,NONE,1.1 ENSEMBLHomolog.java,NONE,1.1 Element.java,NONE,1.1 ElementFloat.java,NONE,1.1 ElementInteger.java,NONE,1.1 ElementString.java,NONE,1.1 ElementXYData.java,NONE,1.1 EmowseAnnotatedAASequence.java,NONE,1.1 E!
nzymatic_Text.java,NONE,1.1 EquicktandemAnnotatedNASequence.ja!
va,NONE,
1.1 EquicktandemAnnotation.java,NONE,1.1 EquicktandemReport.java,NONE,1.1 ExpressionCore.java,NONE,1.1 ExpressionStatistics.java,NONE,1.1 FASTA.java,NONE,1.1 FASTA_AA.java,NONE,1.1 FASTA_AA_multi.java,NONE,1.1 FASTA_NA.java,NONE,1.1 FASTA_NA_multi.java,NONE,1.1 FASTA_Text.java,NONE,1.1 FASTA_pep.java,NONE,1.1 FSOLV_Text.java,NONE,1.1 FSSP_Text.java,NONE,1.1 FamilyBLOCKAnnotation.java,NONE,1.1 FatiGO_Text.java,NONE,1.1 FatiGO__XML.java,NONE,1.1 FatiScan_Text.java,NONE,1.1 FatiScan__XML.java,NONE,1.1 FeatureAASequence.java,NONE,1.1 FeatureAnnotatedAASequence.java,NONE,1.1 FeatureAnnotation.java,NONE,1.1 FunCUT_Annotation_XML.java,NONE,1.1 GFF.java,NONE,1.1 GFF2.java,NONE,1.1 GFF3.java,NONE,1.1 GOGraph.java,NONE,1.1 GOTerm.java,NONE,1.1 GenBank_Text.java,NONE,1.1 GenericSequence.java,NONE,1.1 HMMPfam_Report.java,NONE,1.1 HMMSearch_Report.java,NONE,1.1 HMM_Text.java,NONE,1.1 HSSP_Text.java,NONE,1.1 HierarchicalClustering.java,NONE,1.1 ISS_Annotation_XML.java,NONE,1.1 ISS_Report.!
java,NONE,1.1 Image_Encoded.java,NONE,1.1 IntAct_XML.java,NONE,1.1 InterProMotifAnnotatedAASequence.java,NONE,1.1 InterProMotifAnnotation.java,NONE,1.1 Interaction.java,NONE,1.1 InteractionMethod.java,NONE,1.1 Interactor.java,NONE,1.1 List_Text.java,NONE,1.1 List__Text.java,NONE,1.1 LutefiskAnnotatedAASequence.java,NONE,1.1 LutefiskAnnotation.java,NONE,1.1 LutefiskReport.java,NONE,1.1 MEME_Text.java,NONE,1.1 MSF.java,NONE,1.1 MatchingPattern.java,NONE,1.1 Matrix.java,NONE,1.1 MatrixFloat.java,NONE,1.1 MatrixInteger.java,NONE,1.1 MatrixString.java,NONE,1.1 Meta_Alignment_Text.java,NONE,1.1 MicroArrayData_Text.java,NONE,1.1 MicroArrayData__Text.java,NONE,1.1 MmCIF_Text.java,NONE,1.1 MmCIF__Text.java,NONE,1.1 MolWeightAnnotation.java,NONE,1.1 MolWeightsAnnotatedAASequence.java,NONE,1.1 MolWeightsArray.java,NONE,1.1 MotifAnnotatedAASequence.java,NONE,1.1 MotifAnnotation.java,NONE,1.1 MotifMatrix.java,NONE,1.1 MultiParameter.java,NONE,1.1 NAMD_Conf_Text.java,NONE,1.1 NAMD_Output!
.java,NONE,1.1 NAMD_Structure.java,NONE,1.1 NCBI_BLAST_Text.ja!
va,NONE,
1.1 NCut_Clusters.java,NONE,1.1 NCut_Matrix.java,NONE,1.1 NCut_Text.java,NONE,1.1 NDB__Text.java,NONE,1.1 Newick_Text.java,NONE,1.1 Newick__Text.java,NONE,1.1 NucleotideSequence.java,NONE,1.1 OMIM.java,NONE,1.1 PDB_Enriched.java,NONE,1.1 PDB__Text.java,NONE,1.1 PHD_Text.java,NONE,1.1 PIR_Text.java,NONE,1.1 PMUT_Text.java,NONE,1.1 PPSearchReport.java,NONE,1.1 PSF_Text.java,NONE,1.1 Parameter.java,NONE,1.1 Parameters4Values.java,NONE,1.1 ParametersToVary.java,NONE,1.1 PatmatdbReport.java,NONE,1.1 PatmatmotifsReport.java,NONE,1.1 Pattern.java,NONE,1.1 PepNovoReport.java,NONE,1.1 Pepcoil_Text.java,NONE,1.1 PepinfoReport.java,NONE,1.1 Pepstats_Text.java,NONE,1.1 Phylip_Interleaved_Text.java,NONE,1.1 Phylip_Text.java,NONE,1.1 Phylip_tree_Text.java,NONE,1.1 Phylip_treefile_Text.java,NONE,1.1 PredictionModel__XML.java,NONE,1.1 Prediction__Text.java,NONE,1.1 PredictorTraining_Text.java,NONE,1.1 ProbMolWeightAnnotation.java,NONE,1.1 ProbMolWeightsAnnotatedAASequence.java,NONE,1.1 Prod!
omMotif.java,NONE,1.1 PropertySequence.java,NONE,1.1 PrositeDoc_Text.java,NONE,1.1 PrositeMotif.java,NONE,1.1 RNASequence.java,NONE,1.1 RefSeq_Text.java,NONE,1.1 RestrictAnnotatedNASequence.java,NONE,1.1 RestrictAnnotation.java,NONE,1.1 RestrictReport.java,NONE,1.1 Rules.java,NONE,1.1 SCOPDomain.java,NONE,1.1 SCOPLayerNode.java,NONE,1.1 SIAM_Annotation_XML.java,NONE,1.1 ScoredMotifAnnotatedAASequence.java,NONE,1.1 ScoredMotifAnnotation.java,NONE,1.1 SequenceDescription_Text.java,NONE,1.1 Sequence_alignment_report.java,NONE,1.1 SigcleaveAnnotatedAASequence.java,NONE,1.1 SigcleaveAnnotation.java,NONE,1.1 SigcleaveReport.java,NONE,1.1 Stockholm_Text.java,NONE,1.1 StructureBoundaries.java,NONE,1.1 StructureDomain.java,NONE,1.1 StructureFragment.java,NONE,1.1 Structure_Alignment_Report.java,NONE,1.1 SwissProt_Text.java,NONE,1.1 TFscan_Text.java,NONE,1.1 TTS.java,NONE,1.1 Target.java,NONE,1.1 TargetArgument.java,NONE,1.1 Text__formatted.java,NONE,1.1 Text__html.java,NONE,1.1 Text!
__plain.java,NONE,1.1 Text__xhtml.java,NONE,1.1 Text__xml.java!
,NONE,1.
1 TransmembraneAnnotatedAASequence.java,NONE,1.1 TransmembraneAnnotation.java,NONE,1.1 TransmembraneReport.java,NONE,1.1 TreeDet_Annotation_HTML.java,NONE,1.1 TreeDet_Annotation_XML.java,NONE,1.1 TreeDet_Report.java,NONE,1.1 Typed_Image.java,NONE,1.1 URL__Text.java,NONE,1.1 VirtualSequence.java,NONE,1.1 WeightedAminoAcidSequences.java,NONE,1.1 WeightedList_Text.java,NONE,1.1 WeightedList__Text.java,NONE,1.1 WeightedObject.java,NONE,1.1 Zip_Encoded.java,NONE,1.1 jaxb.index,NONE,1.1 package-info.java,NONE,1.1
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