September 2004 Commit Log

Number of Commits:

1

Number of Active Developers:

1

rbossy 2004-09-29 16:40 #1

Initial revision

57000 lines of code changed in:

• crontab.master (new 16)
• Agmial2: TODO (new 4), build.xml (new 97), organization.properties (new 2), shutdown_agmial (new 71), startup_agmial (new 69)
• Agmial2/agmial_directory: build.xml (new 95), build.xml.in (new), web_services.properties (new 2)
• Agmial2/agmial_directory/src/agmial/directory: InfoPoint.java (new 119), InfoPoint.java.in (new)
• Agmial2/agmial_directory/web: agmial_directory.css (new 90), inra_logo.gif (new), mig_logo.jpg (new), web.xml (new 37)
• Agmial2/agmial_directory/web/agmial_user_guide: agmial_user_guide.html (new 80), index.html (new 80)
• Agmial2/artemis_client: agmial (new), build.xml (new 11), build.xml.in (new), client_ContigStoreAdmin_Config.xml (new), client_ContigStoreQuery_Config.xml (new), client_ProfileStoreQuery_Config.xml (new)
• Agmial2/artemis_client/ARTEMIS: BRYSON_README (new), COPYING (new), COPYING.JacORB (new), CorbaApplet.java (new), INSTALL (new), MAKEFILE_OUT (new), MAKEFILE_RESULT (new), Makefile (new 1), README (new), agmial (new), art (new), art.bat (new), art2 (new), mart (new), results_to_netscape (new), run_blast (new), run_blastn (new), run_blastp (new), run_blastx (new), run_fasta (new), run_hth (new), run_jalview (new), run_sigcleave (new), run_tblastn (new), run_tblastx (new), stylesheet.css (new)
• Agmial2/artemis_client/ARTEMIS/META-INF: MANIFEST.MF (new 1)
• Agmial2/artemis_client/ARTEMIS/collections: ArrayEnumeration.java (new), Assertable.java (new), Bag.java (new), BinaryFunction.java (new), CEImpl.java (new), CLCell.java (new), CLEnumeration.java (new), Cell.java (new), CheckedBag.java (new), CheckedCollection.java (new), CheckedMap.java (new), CheckedSeq.java (new), CheckedSet.java (new), CircularList.java (new), Collection.java (new), CollectionEnumeration.java (new), Comparator.java (new), CorruptedEnumerationException.java (new), DAEnumeration.java (new), DefaultComparator.java (new), DefaultImplementations.java (new), Dynarray.java (new), ElementSortedCollection.java (new), FilteringEnumeration.java (new), Function.java (new), HTEnumeration.java (new), HTPairEnumeration.java (new), HashTableParams.java (new), HashedMap.java (new), HashedSet.java (new), IllegalElementException.java (new), Immutable.java (new), ImplementationCheckable.java (new), ImplementationError.java (new), IncrBag.java (new), IncrCollectionEnumeration.java (new), IncrImpl.java (new), IncrMap.java (new), IncrSeq.java (new), IncrSet.java (new), InterleavingEnumeration.java (new), KeySortedCollection.java (new), Keyed.java (new), LBEnumeration.java (new), LLCell.java (new), LLCellEnumeration.java (new), LLMap.java (new), LLPair.java (new), LLPairEnumeration.java (new), LinkedBuffer.java (new), LinkedList.java (new), Map.java (new), MappingEnumeration.java (new), Pair.java (new), Predicate.java (new), Procedure.java (new), RBCell.java (new), RBCellEnumeration.java (new), RBMap.java (new), RBPair.java (new), RBPairEnumeration.java (new), RBTree.java (new), Seq.java (new), Set.java (new), SimpleTest.java (new), SortableCollection.java (new), UpdatableBag.java (new), UpdatableBagImpl.java (new), UpdatableCollection.java (new), UpdatableImpl.java (new), UpdatableMap.java (new), UpdatableMapImpl.java (new), UpdatableSeq.java (new), UpdatableSeqImpl.java (new), UpdatableSet.java (new), UpdatableSetImpl.java (new), collections_Dynarray.h (new), javaMake (new)
• Agmial2/artemis_client/ARTEMIS/corba: apollo.idl (new), ensembl.idl (new), nsdb.idl (new), nsdb_write.idl (new), seqdb.idl (new), types.idl (new)
• Agmial2/artemis_client/ARTEMIS/diana: AlignMatch.java (new), AlignMatchVector.java (new), AppGlobal.java (new), ChangeEvent.html (new), ChangeEvent.java (new), ChangeListener.html (new), ChangeListener.java (new), ClipBoard.java (new), ComparisonData.java (new), ComparisonDataFactory.java (new), ComparisonDataParseException.java (new), Diana.java (new), Entry.FeatureEnumerator.html (new), Entry.html (new), Entry.java (new), EntryChangeEvent.html (new), EntryChangeEvent.java (new), EntryChangeListener.html (new), EntryChangeListener.java (new), EntryGroup.html (new), EntryGroup.java (new), EntryGroupChangeEvent.html (new), EntryGroupChangeEvent.java (new), EntryGroupChangeListener.html (new), EntryGroupChangeListener.java (new), EntrySource.html (new), EntrySource.java (new), EntrySourceVector.html (new), EntrySourceVector.java (new), EntryVector.html (new), EntryVector.java (new), ExternalApplication.html (new), ExternalApplication.java (new), ExternalProgram.html (new), ExternalProgram.java (new), ExternalProgramException.html (new), ExternalProgramException.java (new), ExternalProgramVector.html (new), ExternalProgramVector.java (new), ExternalSearchProgram.html (new), ExternalSearchProgram.java (new), Feature.html (new), Feature.java (new), FeatureChangeEvent.html (new), FeatureChangeEvent.java (new), FeatureChangeListener.html (new), FeatureChangeListener.java (new), FeatureEnumeration.html (new), FeatureEnumeration.java (new), FeatureFromVectorPredicate.html (new), FeatureFromVectorPredicate.java (new), FeatureKeyPredicate.html (new), FeatureKeyPredicate.java (new), FeatureKeyQualifierPredicate.html (new), FeatureKeyQualifierPredicate.java (new), FeaturePredicate.html (new), FeaturePredicate.java (new), FeatureSegment.html (new), FeatureSegment.java (new), FeatureSegmentVector.html (new), FeatureSegmentVector.java (new), FeatureVector.html (new), FeatureVector.java (new), FilteredEntryGroup.FeatureEnumerator.html (new), FilteredEntryGroup.html (new), FilteredEntryGroup.java (new), GotoEvent.html (new), GotoEvent.java (new), GotoEventSource.html (new), GotoEventSource.java (new), GotoListener.html (new), GotoListener.java (new), LastSegmentException.html (new), LastSegmentException.java (new), Logger.html (new), Logger.java (new), MSPcrunchComparisonData.java (new), MUMmerComparisonData.java (new), Options.html (new), Options.java (new 5), Selectable.html (new), Selectable.java (new), Selection.html (new), Selection.java (new), SelectionChangeEvent.html (new), SelectionChangeEvent.java (new), SelectionChangeListener.html (new), SelectionChangeListener.java (new), SimpleComparisonData.java (new), SimpleEntryGroup.FeatureEnumerator.html (new), SimpleEntryGroup.html (new), SimpleEntryGroup.java (new), SimpleGotoEventSource.html (new), SimpleGotoEventSource.java (new), helix.gif (new), sanger-centre.gif (new)
• Agmial2/artemis_client/ARTEMIS/diana/components: ActMain.java (new), AddMenu.html (new), AddMenu.java (new), AlignmentViewer.java (new), ArtemisMain.html (new), ArtemisMain.java (new), BasePlot.html (new), BasePlot.java (new), BasePlotGroup.html (new), BasePlotGroup.java (new), BasicArrow.html (new), BasicArrow.java (new), CanvasPanel.java (new), Comparator.java (new), ComparatorDialog.java (new), CorbaEntrySource.html (new), CorbaEntrySource.java (new), DisplayAdjustmentEvent.html (new), DisplayAdjustmentEvent.java (new), DisplayAdjustmentListener.html (new), DisplayAdjustmentListener.java (new), DisplayComponent.html (new), DisplayComponent.java (new), EMBLCorbaEntrySource.html (new), EMBLCorbaEntrySource.java (new), EditMenu.html (new), EditMenu.java (new), EnsemblEntrySource.java (new), EntryActionListener.html (new), EntryActionListener.java (new), EntryEdit.html (new), EntryEdit.java (new), EntryEditVector.html (new), EntryEditVector.java (new), EntryFileDialog.html (new), EntryFileDialog.java (new), EntryGroupDisplay.html (new), EntryGroupDisplay.java (new), EntryGroupInfoDisplay.html (new), EntryGroupInfoDisplay.java (new), EntryGroupMenu.html (new), EntryGroupMenu.java (new), EntryGroupPanel.html (new), EntryGroupPanel.java (new), EntryHeaderEdit.html (new), EntryHeaderEdit.java (new), ExternalProgramOptions.html (new), ExternalProgramOptions.java (new), FeatureAminoAcidViewer.html (new), FeatureAminoAcidViewer.java (new), FeatureBaseViewer.html (new), FeatureBaseViewer.java (new), FeatureDisplay.html (new), FeatureDisplay.java (new 8), FeatureDisplayOwner.html (new), FeatureDisplayOwner.java (new), FeatureEdit.html (new), FeatureEdit.java (new), FeatureInfo.html (new), FeatureInfo.java (new), FeatureList.html (new), FeatureList.java (new), FeatureListFrame.html (new), FeatureListFrame.java (new), FeaturePlot.html (new), FeaturePlot.java (new), FeaturePlotGroup.html (new), FeaturePlotGroup.java (new), FeaturePopup.html (new), FeaturePopup.java (new), FeatureShape.html (new), FeatureShape.java (new), FeatureViewer.html (new), FeatureViewer.java (new), FileDialogEntrySource.html (new), FileDialogEntrySource.java (new), FileViewer.html (new), FileViewer.java (new), GotoMenu.html (new), GotoMenu.java (new), KeyChoice.html (new), KeyChoice.java (new), KeyChooser.html (new), KeyChooser.java (new), ListDialog.html (new), ListDialog.java (new), LogViewer.html (new), LogViewer.java (new), MarkerRangeRequester.html (new), MarkerRangeRequester.java (new), MarkerRangeRequesterEvent.html (new), MarkerRangeRequesterEvent.java (new), MarkerRangeRequesterListener.html (new), MarkerRangeRequesterListener.java (new), MessageDialog.html (new), MessageDialog.java (new), MessageFrame.html (new), MessageFrame.java (new), Navigator.html (new), Navigator.java (new), Plot.html (new), Plot.java (new), PlotMouseListener.html (new), PlotMouseListener.java (new), ProcessWatcher.html (new), ProcessWatcher.java (new), ProcessWatcherEvent.html (new), ProcessWatcherEvent.java (new), ProcessWatcherListener.html (new), ProcessWatcherListener.java (new), Promoter.html (new), Promoter.java (new), QualifierChoice.html (new), QualifierChoice.java (new), RawFeatureEdit.java (new), ReadFeaturesActionListener.html (new), Rectangle.html (new), Rectangle.java (new), RunMenu.html (new), RunMenu.java (new), SaveEntryActionListener.html (new), SaveEntryAsActionListener.html (new), SaveEntryAsEMBLActionListener.html (new), SaveEntryAsGFFActionListener.html (new), SaveEntryAsGenbankActionListener.html (new), SaveEntryAsSubmissionActionListener.html (new), ScoreChangeEvent.html (new), ScoreChangeEvent.java (new), ScoreChangeListener.html (new), ScoreChangeListener.java (new), ScoreChanger.html (new), ScoreChanger.java (new), ScoreScrollbar.html (new), ScoreScrollbar.java (new), SearchResultViewer.html (new), SearchResultViewer.java (new), SelectMenu.html (new), SelectMenu.java (new), SelectionInfoDisplay.html (new), SelectionInfoDisplay.java (new), SelectionMenu.html (new), SelectionMenu.java (new), SelectionViewer.html (new), SelectionViewer.java (new), Selector.html (new), Selector.java (new), SequenceViewer.html (new), SequenceViewer.java (new), Splash.html (new), Splash.java (new), Terminator.html (new), Terminator.java (new), TextDialog.html (new), TextDialog.java (new), TextRequester.html (new), TextRequester.java (new), TextRequesterEvent.html (new), TextRequesterEvent.java (new), TextRequesterListener.html (new), TextRequesterListener.java (new), ViewMenu.html (new), ViewMenu.java (new), WideArrow.html (new), WideArrow.java (new), WindowAdjustmentEvent.java (new), WindowAdjustmentListener.java (new), WritableEMBLCorbaEntrySource.html (new), WritableEMBLCorbaEntrySource.java (new), WriteMenu.html (new), WriteMenu.java (new), YesNoDialog.html (new), YesNoDialog.java (new)
• Agmial2/artemis_client/ARTEMIS/diana/plot: AGWindowAlgorithm.html (new), AGWindowAlgorithm.java (new), ATDeviationAlgorithm.html (new), ATDeviationAlgorithm.java (new), Algorithm.html (new), Algorithm.java (new), BaseAlgorithm.html (new), BaseAlgorithm.java (new), Codon12CorrelationAlgorithm.html (new), Codon12CorrelationAlgorithm.java (new), CodonUsageAlgorithm.html (new), CodonUsageAlgorithm.java (new), CodonUsageFormatException.html (new), CodonUsageFormatException.java (new), CodonUsageWeight.html (new), CodonUsageWeight.java (new), CodonWeight.html (new), CodonWeight.java (new), CoilFeatureAlgorithm.html (new), CoilFeatureAlgorithm.java (new), FeatureAlgorithm.html (new), FeatureAlgorithm.java (new), GCDeviationAlgorithm.html (new), GCDeviationAlgorithm.java (new), GCFrameAlgorithm.html (new), GCFrameAlgorithm.java (new), GCSDWindowAlgorithm.html (new), GCSDWindowAlgorithm.java (new), GCWindowAlgorithm.html (new), GCWindowAlgorithm.java (new), HydroAlgorithm.html (new), HydroAlgorithm.java (new), HydrophilicityAlgorithm.html (new), HydrophilicityAlgorithm.java (new), HydrophobicityAlgorithm.html (new), HydrophobicityAlgorithm.java (new), UserDataAlgorithm.html (new), UserDataAlgorithm.java (new)
• Agmial2/artemis_client/ARTEMIS/diana/sequence: AminoAcidSequence.html (new), AminoAcidSequence.java (new), BasePattern.html (new), BasePattern.java (new), BasePatternFormatException.html (new), BasePatternFormatException.java (new), Bases.html (new), Bases.java (new), Marker.html (new), Marker.java (new), MarkerChangeEvent.html (new), MarkerChangeEvent.java (new), MarkerChangeListener.html (new), MarkerChangeListener.java (new), MarkerInternal.html (new), MarkerRange.html (new), MarkerRange.java (new), MarkerRangeVector.html (new), MarkerRangeVector.java (new), NoSequenceException.html (new), NoSequenceException.java (new), SequenceChangeEvent.html (new), SequenceChangeEvent.java (new), SequenceChangeListener.html (new), SequenceChangeListener.java (new), Strand.html (new), Strand.java (new)
• Agmial2/artemis_client/ARTEMIS/docs: Makefile (new), acknowledgements.sgml (new), act_display_menus.sgml (new), act_file_menu.sgml (new), act_intro_chapter.sgml (new), act_main_window.sgml (new), act_main_window_1.gif (new), act_main_window_2.gif (new), act_main_window_3.gif (new), act_main_window_4.gif (new), act_main_window_5.gif (new), act_manual.sgml (new), act_start_chapter.sgml (new), act_user_manual_screen_shot.gif (new), artemis.dsl (new), concepts.sgml (new), copyright.sgml (new), display_common.sgml (new), display_menu.sgml (new), feature_list.sgml (new), file_menu.sgml (new), getting_java.sgml (new), intro_chapter.sgml (new), main_window_1.gif (new), main_window_2.gif (new), main_window_3.gif (new), main_window_4.gif (new), main_window_5.gif (new), main_window_6.gif (new), main_window_chapter.sgml (new), manual.sgml (new), menus.sgml (new), mousebuttons.sgml (new), options.sgml (new), requirements.sgml (new), run_menu.sgml (new), start_chapter.sgml (new), unix_args.sgml (new), user_manual_screen_shot.gif (new), views_popup.sgml (new), views_scale.sgml (new), views_scrolling.sgml (new), views_selection.sgml (new)
• Agmial2/artemis_client/ARTEMIS/etc: feature_keys (new), options (new 11), pombe.usage (new), qualifier_types (new)
• Agmial2/artemis_client/ARTEMIS/jalview: LB#1#Contig109:1->2466 READ ONLY .seq.00001 (new), file_number_counter (new), file_of_filenames.1 (new)
• Agmial2/artemis_client/ARTEMIS/lib: JacORB.jar (new)
• Agmial2/artemis_client/ARTEMIS/uk/ac/sanger/pathogens: Document.html (new), Document.java (new), FastVector.html (new), FastVector.java (new), FileDocument.html (new), FileDocument.java (new), FileProgressDocument.html (new), FileProgressDocument.java (new), InputStreamProgressEvent.html (new), InputStreamProgressEvent.java (new), InputStreamProgressListener.html (new), InputStreamProgressListener.java (new), OutOfRangeException.html (new), OutOfRangeException.java (new), ProgressInputStream.html (new), ProgressInputStream.java (new), ReadOnlyException.html (new), ReadOnlyException.java (new), StringVector.html (new), StringVector.java (new), URLDocument.html (new), URLDocument.java (new)
• Agmial2/artemis_client/ARTEMIS/uk/ac/sanger/pathogens/embl: BetweenRange.html (new), BetweenRange.java (new), ComparableFeature.html (new), ComparableFeature.java (new), CorbaEntry.html (new), CorbaEntry.java (new), CorbaFeature.html (new), CorbaFeature.java (new), CorbaSequence.html (new), CorbaSequence.java (new), DateStampFeature.html (new), DateStampFeature.java (new), DocumentEntry.html (new), DocumentEntry.java (new), DocumentEntryAutosaveThread.html (new), DocumentEntryAutosaveThread.java (new), DocumentEntryFactory.html (new), DocumentEntryFactory.java (new), DocumentFeature.html (new), DocumentFeature.java (new), EMBLObject.html (new), EMBLObject.java (new), EmblDocumentEntry.html (new), EmblDocumentEntry.java (new), EmblMisc.html (new), EmblMisc.java (new), EmblStreamFeature.html (new), EmblStreamFeature.java (new), EmblStreamSequence.html (new), EmblStreamSequence.java (new), EnsemblCorbaEntry.html (new), EnsemblCorbaEntry.java (new), EnsemblCorbaFeature.html (new), EnsemblCorbaFeature.java (new), EnsemblCorbaSequence.html (new), EnsemblCorbaSequence.java (new), Entry.html (new), Entry.java (new), EntryInformation.html (new), EntryInformation.java (new), EntryInformationException.html (new), EntryInformationException.java (new), FastaStreamSequence.html (new), FastaStreamSequence.java (new), Feature.html (new), Feature.java (new), FeatureComparator.html (new), FeatureComparator.java (new), FeatureEnumeration.html (new), FeatureEnumeration.java (new), FeatureHeader.html (new), FeatureHeader.java (new), FeatureTable.html (new), FeatureTable.java (new), FeatureTree.FeatureEnumerator.html (new), FeatureTree.html (new), FeatureTree.java (new), FeatureVector.html (new), FeatureVector.java (new), FuzzyRange.html (new), FuzzyRange.java (new), GFFDocumentEntry.html (new), GFFDocumentEntry.java (new), GFFEntryInformation.html (new), GFFEntryInformation.java (new), GFFMisc.html (new), GFFMisc.java (new), GFFStreamFeature.html (new), GFFStreamFeature.java (new), GenbankDocumentEntry.html (new), GenbankDocumentEntry.java (new), GenbankMisc.html (new), GenbankMisc.java (new), GenbankStreamFeature.html (new), GenbankStreamFeature.java (new), GenbankStreamSequence.html (new), GenbankStreamSequence.java (new), InvalidKeyException.html (new), InvalidKeyException.java (new), InvalidQualifierException.html (new), InvalidQualifierException.java (new), InvalidRelationException.html (new), InvalidRelationException.java (new), Key.html (new), Key.java (new), KeyVector.html (new), KeyVector.java (new), LineGroup.html (new), LineGroup.java (new), LineGroupVector.html (new), LineGroupVector.java (new), LinePushBackReader.html (new), LinePushBackReader.java (new), Location.html (new), Location.java (new), LocationLexer.TokenEnumeration.html (new), LocationLexer.html (new), LocationLexer.java (new), LocationParseException.html (new), LocationParseException.java (new), LocationParseNode.html (new), LocationParseNode.java (new), LocationParseNodeVector.html (new), LocationParseNodeVector.java (new), LowerInteger.html (new), LowerInteger.java (new), MSPcrunchDocumentEntry.html (new), MSPcrunchDocumentEntry.java (new), MSPcrunchEntryInformation.html (new), MSPcrunchEntryInformation.java (new), MSPcrunchStreamFeature.html (new), MSPcrunchStreamFeature.java (new), MiscLineGroup.html (new), MiscLineGroup.java (new), NucFeatureHasher.html (new), OutOfDateException.html (new), OutOfDateException.java (new), PublicDBDocumentEntry.html (new), PublicDBDocumentEntry.java (new), PublicDBStreamFeature.html (new), PublicDBStreamFeature.java (new), PushBackException.html (new), PushBackException.java (new), Qualifier.html (new), Qualifier.java (new), QualifierInfo.html (new), QualifierInfo.java (new), QualifierInfoException.html (new), QualifierInfoException.java (new), QualifierInfoVector.html (new), QualifierInfoVector.java (new), QualifierParseException.html (new), QualifierParseException.java (new), QualifierVector.html (new), QualifierVector.java (new), RWCorbaEntry.html (new), RWCorbaEntry.java (new), RWCorbaFeature.html (new), RWCorbaFeature.java (new), Range.html (new), Range.java (new), RangeVector.html (new), RangeVector.java (new), RawStreamSequence.html (new), RawStreamSequence.java (new), ReadFormatException.html (new), ReadFormatException.java (new), ReadOnlyEntry.html (new), ReadOnlyEntry.java (new), Sequence.html (new), Sequence.java (new), SimpleDocumentEntry.html (new), SimpleDocumentEntry.java (new), SimpleDocumentFeature.html (new), SimpleDocumentFeature.java (new), SimpleEntryInformation.html (new), SimpleEntryInformation.java (new), StreamFeature.html (new), StreamFeature.java (new), StreamFeatureTable.html (new), StreamFeatureTable.java (new), StreamQualifier.html (new), StreamQualifier.java (new), StreamSequence.html (new), StreamSequence.java (new), StreamSequenceFactory.html (new), StreamSequenceFactory.java (new), UpperInteger.html (new), UpperInteger.java (new), embl.example (new)
• Agmial2/artemis_client/src: build.xml (new), cam_manager.properties (new)
• Agmial2/artemis_client/src/agmial/artemis: AgmialAccessDialog.java (new 5), AgmialAuthenticateDialog.java (new 3), AgmialAuthenticator.java (new), AgmialDocument.java (new 1), AgmialInterface.java (new), AgmialInterfaceFactory.java (new), AgmialInterfaceImpl.java (new 60), AgmialInterfaceImpl.java.in (new), AgmialProfileDocument.java (new), README (new)
• Agmial2/ca_manager: build.xml (new 203), build.xml.in (new), cam_manager.properties (new 49), cam_manager.properties.in (new 49), client_ProteinSourceAdmin_Config.xml (new 3), server_ContigStoreAdmin_Config.xml (new), server_ContigStoreQuery_Config.xml (new), server_ProfileStoreAdmin_Config.xml (new), server_ProfileStoreQuery_Config.xml (new)
• Agmial2/ca_manager/sql: contigdb_creation.sql (new 391)
• Agmial2/ca_manager/src/cam/admin: AddBatch.java (new 102), AddProject.java (new 79), ContigStoreAdminIF.java (new 20), ContigStoreAdminImpl.java (new 521), LockContig.java (new 72), MonitorBatchTasks.java (new 192), MonitorContigTasks.java (new 191), MonitorFeatureTasks.java (new 195), MonitorProjectTasks.java (new 191), MonitorTasks.java (new 153), ProfileStoreAdminIF.java (new 15), ProfileStoreAdminImpl.java (new 90), ShowAddBatch.java (new 98), ShowAddProject.java (new 54), ShowAdminBatches.java (new 107), ShowUpdateContig.java (new 106), ShowUpdateProfile.java (new 145), UpdateContig.java (new 154), UpdateProfile.java (new 119)
• Agmial2/ca_manager/src/cam/contigdb: CAMBatch.java (new 50), CAMBatchAction.java (new 84), CAMBatchActionSchema.java (new 82), CAMBatchSchema.java (new 40), CAMContigAction.java (new 73), CAMContigActionSchema.java (new 79), CAMContigSchema.java (new 72), CAMFeatureAction.java (new 105), CAMFeatureActionSchema.java (new 89), CAMFeatureSchema.java (new 630), CAMFileSchema.java (new 69), CAMLock.java (new 76), CAMLockSchema.java (new 45), CAMProject.java (new 34), CAMProjectAction.java (new 74), CAMProjectActionSchema.java (new 79), CAMProjectSchema.java (new 35), CAMSingleProfileSchema.java (new 52), CAMSkillMeta.java (new 56), CAMSkillMetaSchema.java (new 73), CAMSkillParam.java (new 66), CAMSkillParamSchema.java (new 76), ContigDB.java (new 1305), README (new 5)
• Agmial2/ca_manager/src/cam/control: BatchActionMotivation.java (new 101), BatchActionQueue.java (new 145), BatchCalcAction.java (new 153), CAMActionQueue.java (new 85), CAMControl.java (new 197), CAMControl.java.in (new), CAMMotivation.java (new 64), ContigActionMotivation.java (new 102), ContigActionQueue.java (new 145), ContigCalcAction.java (new 134), FeatureActionQueue.java (new 145), ProjectActionQueue.java (new 145), ProjectMotivation.java (new 108), QueryFeatureMotivation.java (new 119), TellCDSRemovedAction.java (new 84), TellCDSRemovedAction.java.in (new), TransferFeatureAction.java (new 88), UpdateCDSAction.java (new 372), UpdateProjectAction.java (new 80), UpdateProjectAction.java.in (new)
• Agmial2/ca_manager/src/cam/lifecycle: ContextListener.java (new 120)
• Agmial2/ca_manager/src/cam/reader: ContigInfoBean.java (new 35), ContigLockInfoBean.java (new), ContigPanel.java (new 96), ContigStoreQueryIF.java (new 28), ContigStoreQueryImpl.java (new 402), EditFeature.java (new 2452), GenomeProjectBean.java (new 35), GetContigRegion.java (new 104), MugenPanel.java (new 7971), ProfileStoreQueryIF.java (new 15), ProfileStoreQueryImpl.java (new 112), QueryBatches.java (new 81), QueryContigs.java (new 100), QueryProjects.java (new 78)
• Agmial2/ca_manager/src/cam/util: CAMException.java (new 18)
• Agmial2/ca_manager/web: ContigStoreAdmin_Config.patch (new 3), ContigStoreQuery_Config.patch (new 3), ProfileStoreAdmin_Config.patch (new 3), ProfileStoreQuery_Config.patch (new 3), cam.css (new 65), index.html (new 18), main_intro.html (new 50), main_menu.html (new 20), sidebar_intro.html (new 13), web.xml (new 547), web.xml.in (new 547)
• Agmial2/ca_manager/web/images: inra_logo.gif (new 188), mig_logo.jpg (new 58)
• Agmial2/common: build.xml (new 32)
• Agmial2/common/src/agmial/control: Action.java (new 270), ActionEventHandler.java (new 18), ActionException.java (new 21), ActionQueue.java (new 198), DefaultOrdering.java (new 42)
• Agmial2/common/src/agmial/registry: ManagerRegistryInterface.java (new 917)
• Agmial2/common/src/agmial/util: AgmialDataException.java (new 18), AgmialException.java (new 18), MultiPartParser.java (new 155), NestedException.java (new 74), ServletLog.java (new 35)
• Agmial2/pa_manager: build.xml (new 182), build.xml.in (new), client_ContigStoreAdmin_Config.xml (new 3), pam_manager.properties (new 6), pam_manager.properties.in (new), server_ProteinSourceAdmin_Config.xml (new)
• Agmial2/pa_manager/sql: protdb_creation.sql (new 507), update_database.sql (new 15)
• Agmial2/pa_manager/src/pam/admin: AddProteinSource.java (new 104), AddProteins.java (new 128), MonitorProteinRefTasks.java (new 194), MonitorProteinTasks.java (new 193), MonitorTasks.java (new 120), ProteinSourceAdminIF.java (new 14), ProteinSourceAdminImpl.java (new 419), RetireProteins.java (new 122), ShowAddProteinSource.java (new 58), ShowAddProteins.java (new 110), ShowAdminSources.java (new 63), ShowRetireProteins.java (new 94), UpdateAnnotation.java (new 102), UpdateFunction.java (new 101)
• Agmial2/pa_manager/src/pam/control: AfterActionMotivation.java (new 115), DetermineFunctionAction.java (new 147), HomologyResultsMotivation.java (new 107), NotifyFunctionAction.java (new 90), NotifyFunctionAction.java.in (new), NotifyFunctionMotivation.java (new 102), PAMActionQueue.java (new 99), PAMControl.java (new 341), PAMControl.java.in (new), PAMMotivation.java (new 59), ParalogResultsMotivation.java (new), ProteinActionMotivation.java (new 103), ProteinActionQueue.java (new 164), ProteinCalcAction.java (new 133), ProteinRefActionQueue.java (new 149), SwissAnnotAction.java (new 182)
• Agmial2/pa_manager/src/pam/lifecycle: ContextListener.java (new 111)
• Agmial2/pa_manager/src/pam/protdb: PAMDatabaseMeta.java (new 33), PAMDatabaseMetaSchema.java (new 65), PAMFileSchema.java (new 69), PAMFloatValueResultSchema.java (new 67), PAMHomologyResultSchema.java (new 86), PAMInfoSourceMeta.java (new 69), PAMInfoSourceMetaSchema.java (new 78), PAMMembraneSpanSchema.java (new 65), PAMMethodMeta.java (new 61), PAMMethodMetaSchema.java (new 75), PAMMotifFeatureSchema.java (new 79), PAMProtein.java (new 192), PAMProteinAction.java (new 85), PAMProteinActionSchema.java (new 80), PAMProteinFeatureSchema.java (new 65), PAMProteinRef.java (new 70), PAMProteinRefAction.java (new 114), PAMProteinRefActionSchema.java (new 87), PAMProteinRefSchema.java (new 80), PAMProteinSchema.java (new 138), PAMProteinSource.java (new 30), PAMProteinSourceSchema.java (new 35), PAMSkillMeta.java (new 56), PAMSkillMetaSchema.java (new 74), PAMSkillParam.java (new 75), PAMSkillParamSchema.java (new 81), PAMValuedFeatureSchema.java (new 70), ProteinDB.java (new 1313)
• Agmial2/pa_manager/src/pam/reader: AAFeaturesFormatter.java (new 139), AlignImage.java (new 278), CDDTable.java (new 109), EditingBuffer.java (new 172), FeaturesGraphic.java (new 280), FeaturesViewer.java (new 438), FormattedFeature.java (new 118), HomologyAlignPanel.java (new 142), HomologyGraphic.java (new 260), HomologyImagePanel.java (new), HomologyPanel.java (new 146), HomologyTable.java (new 112), ParalogTable.java (new 1), ProteinPanel.java (new 828), QueryDataSets.java (new 95), QueryProteinSources.java (new 127), QueryProteins.java (new 124), ResidueFormatter.java (new 55), SearchAnnotationPanel.java (new 243), SearchDataSets.java (new 94), SearchPanel.java (new 59), SearchProteinSources.java (new 130), SearchResults.java (new 613), SearchResultsPanel.java (new 139), SearchSQLQueryPanel.java (new 75), SearchSQLQueryResults.java (new 141)
• Agmial2/pa_manager/src/pam/util: PAMException.java (new 18)
• Agmial2/pa_manager/web: ProteinSourceAdmin_Config.patch (new), admin_intro.html (new), browse_intro.html (new), index.html (new 19), main_intro.html (new 31), main_menu.html (new 8), pam.css (new 65), sidebar_intro.html (new), web.xml (new 46), web.xml.in (new 577), web_public_dir.xml (new 4), web_public_dir.xml.in (new)
• Agmial2/pa_manager/web/images: black1.gif (new 1), black5.gif (new 1), blue5.gif (new 1), green5.gif (new 1), inra_logo.gif (new 188), mig_logo.jpg (new 58), orange1.gif (new 1), orange5.gif (new 1), red1.gif (new 1), red5.gif (new 1), red_larrow.gif (new 4), red_rarrow.gif (new 4), white7.gif (new 1), yellow1.gif (new 1), yellow5.gif (new 1)
• BioTools: README (new 15), biotools.props (new 104), build.xml (new 29)
• BioTools/src/biotools: README (new 86)
• BioTools/src/biotools/calc: Aln2FreqCalc.java (new 32), Aln2FreqParams.java (new 50), BLASTCalc.java (new 50), BLASTParams.java (new 37), BLASTText.java (new 301), BioCalc.java (new 386), CDDCalc.java (new 50), CDDParams.java (new 37), CDDText.java (new 286), COILCalc.java (new 46), COILParams.java (new 46), COILText.java (new 89), CalcException.java (new 26), CalcParams.java (new 172), CalcResult.java (new 14), CalcResults.java (new 59), DoubleInSingleOut.java (new 26), FileParameter.java (new 39), FileResult.java (new 37), FloatResult.java (new 42), HomologyMatch.java (new 102), HomologyMatchPair.java (new 163), HomologyResult.java (new 70), INTERPROCalc.java (new 144), INTERPROParams.java (new 57), INTERPROText.java (new 177), MEMSATCalc.java (new 107), MEMSATParams.java (new 41), MEMSATText.java (new 123), MULSATCalc.java (new 46), MULSATParams.java (new 41), MotifSpan.java (new 97), NucleicFeaturesResult.java (new 64), PICalc.java (new 46), PIParams.java (new 37), PIText.java (new 46), PetrinCalc.java (new 56), PetrinEntry.java (new 54), PetrinParams.java (new 45), PetrinText.java (new 109), ProfileFastAText.java (new 123), ProteinFeaturesResult.java (new 42), README (new), RRNAScanCalc.java (new 57), RRNAScanEntry.java (new 54), RRNAScanParams.java (new 45), RRNAScanText.java (new 108), ResultEntry.java (new 52), ResultEntryPosn.java (new 42), ResultText.java (new 70), SEGCalc.java (new 51), SEGParams.java (new 46), SEGText.java (new 81), SHOWCalc.java (new 53), SHOWEntry.java (new 56), SHOWParams.java (new 42), SHOWText.java (new 108), SIGSEQCalc.java (new 45), SIGSEQParams.java (new 41), SIGSEQText.java (new 98), SingleInOut.java (new 27), SingleProfileResult.java (new 109), TMSpan.java (new 44), TRNAScanCalc.java (new 56), TRNAScanEntry.java (new 54), TRNAScanParams.java (new 45), TRNAScanText.java (new 109), ValuedSpan.java (new 52)
• BioTools/src/biotools/general: GeneticCode.java (new 302), Organism.java (new 45), README (new)
• BioTools/src/biotools/nucleic: Codon.java (new 60), GenBankEntry.java (new 533), GenBankEntryX.java (new 34), GenBankText.java (new 95), Nucleic.java (new 148), NucleicEntry.java (new 65), NucleicEntryPosn.java (new 45), NucleicFastAEntry.java (new 100), NucleicFastAText.java (new 98), NucleicFeature.java (new 151), NucleicFeatureLocation.java (new 202), NucleicFeatureQualifier.java (new 40), NucleicFeatureTable.java (new 109), NucleicRes.java (new 114), NucleicResIUPAC.java (new 555), NucleicResIUPACX.java (new 554), NucleicSource.java (new 38), NucleicText.java (new 31)
• BioTools/src/biotools/protein: Annot.java (new 68), AnnotTable.java (new 40), EntryDate.java (new 46), FloatAnnot.java (new 36), OrganismAnnot.java (new 41), PirEntry.java (new 96), PirText.java (new 95), Protein.java (new 126), ProteinEntry.java (new 62), ProteinEntryPosn.java (new 45), ProteinFastAEntry.java (new 134), ProteinFastAText.java (new 106), ProteinFeature.java (new 142), ProteinFeatureTable.java (new 62), ProteinPirEntry.java (new 121), ProteinPirText.java (new 96), ProteinRes.java (new 85), ProteinResCased.java (new 295), ProteinResStandard.java (new 259), ProteinResTranslated.java (new 581), ProteinSource.java (new 39), ProteinText.java (new 30), README (new), SwissEntry.java (new 209), SwissText.java (new 64), TextAnnot.java (new 36), errors (new)
• BioTools/src/biotools/util: BioArgumentException.java (new 18), BioBufferStream.java (new 83), BioConversionException.java (new 21), BioException.java (new 24), BioFileStream.java (new 171), BioFormatException.java (new 22), BioParseException.java (new 20), BioResources.java (new 104), BioStream.java (new 21), BioStreamException.java (new 18), EOSException.java (new 14), FileLog.java (new 45), Log.java (new 12), NestedError.java (new 69), NestedException.java (new 75), PrintfFormat.java (new 3092)
• SQL_SCRIPTS: README (new 7), annotKeyword.sql (new 7), blast1.sql (new 5), blast5.sql (new 5), blast_all.sql (new 5), broken_annot.sql (new 11), coil.sql (new 1), coil_all.sql (new 1), exploration.sql (new 65), features.sql (new 7), features_interpro.sql (new 2), features_interpro_all.sql (new 2), genes.sql (new 2), genes_150.sql (new 2), keywordPTS.sql (new 5), keyword_blast.sql (new 6), keywordtransport_ALL.sql (new 8), keywordtransport_ALL5.sql (new 7), la_totale.sql (new 79), memsat.sql (new 2), memsat_all.sql (new 2), noFeaturesResults.sql (new 16), noHomologs.sql (new 40), paralogs_positions.sql (new 32), residues.sql (new 2), residues_all.sql (new 2), seg_sigseq.sql (new 3), seg_sigseq_all.sql (new 3), small_orfs.sql (new 1)
• SQL_Tools: Queryer.java (new 466), README (new 19), alter_type.pl (new 184), break_annotation_comments.pl (new 300), exploration.pl (new 216), fastout.pl (new 172), gene_sequence.pl (new 303), small_genes_fasta.pl (new 259), small_genes_list.pl (new 158), transferts_feat.pl (new 262)
• bin: agmial (new 64), clean.sh (new 29), dump_postgresql.sh (new 25)
• bin/agmialdaemon: shutdown_agmial (new 46), startup_agmial (new 43)
• doc: Makefile (new 44), agmial_faq.tex (new 38), agmial_install.tex (new), projets_multiples.tex (new 80)