agmial Developers: rbossy

Activity by Clock Time

Activity in Directories

Most Recent Commits

rbossy 2005-04-22 11:53

Nettoyage des fichiers properties vierges

50 lines of code changed in:

• Agmial2: template_project.properties (+45 -71), template_web_services.properties (+5 -10)

rbossy 2005-04-21 18:09

Removage de commentaires en trop

8 lines of code changed in:

• Agmial2/ca_manager/src/cam/contigdb: ContigDB.java (+8 -9)
• Agmial2/ca_manager/src/cam/control: UpdateCDSAction.java (-17)

rbossy 2005-04-21 18:04

Ajout des target: clean_pam, clean_all, redeploy_cam, redeploy_pam, redeploy_dir, redeploy_all

14 lines of code changed in:

• Agmial2: build.xml (+14)

rbossy 2005-04-15 11:13

Vieux trucs que j'avais oublie de commiter... ne me demande pas ce que c'est...

64 lines of code changed in:

• SQL_SCRIPTS: broken_annot.sql (+2 -1)
• SQL_Tools: break_annotation_comments.pl (+62 -19)

rbossy 2005-01-18 17:22

1- Documentation (projets multiples)
2- build.xml un peu plus intelligent (pas fini)

*************** ATTENTION VALENTIN *****************
Voila comment ca marche:
- Agmial2/build.xml a des nouveaux targets (start_pam, start_cam, start_dir, start_all, stop_cam, stop_pam, stop_dir, stop_all). Leus sens me semble ?vident
- Ce meme fichier prend des properties dans organization.properties et dans project.properties, il les transmet aux trois build.xml respectifs
- En consequence, les builds.xml respectifs ne fonctionnent pas tout seuls puisqu'ils ne chargent pas directement les properties des fichiers de configs... a voir...

169 lines of code changed in:

• Agmial2/pa_manager: build.xml (+39 -27)
• Agmial2/pa_manager/web: web.xml (+14 -14), web_public_dir.xml (+4 -4)
• doc: projets_multiples.tex (+112 -2)

rbossy 2004-10-12 18:21

On installe a partir de Agmial2/build.xml, les targets sont
start_cam -> ca_manager/build.xml:install
start_pam -> pa_manager/build.xml:install
start_dir -> agmial_directory/build.xml:install
start_all ...
stop_cam -> ca_manager/build.xml:remove
stop_pam -> pa_manager/build.xml:remove
stop_dir -> agmial_directory/build.xml:remove
stop_all ...

Agmial2/build.xml lit les fichiers de config: web_services.properties, organization.properties et project.properties

Les fichiers agmial_directory/build.xml, ca_manager/build.xml, pa_manager/build.xml ne sont plus a configurer puisqu'ils heritent de ces trois fichiers de conf.
Les fichiers ca_manager/web/web.xml, pa_manager/web/web.xml et pa_manager/web/web_public_dir.xml ne sont plus a configurer non plus car les build.xml respectifs effectuent les remplacements appropries.

103 lines of code changed in:

• Agmial2: build.xml (+32 -24), template_project.properties (new 25), web_services.properties (new 4)
• Agmial2/agmial_directory: build.xml (+9 -18), web_services.properties (del)
• Agmial2/ca_manager: build.xml (+22 -21)
• Agmial2/ca_manager/web: web.xml (+11 -11)

rbossy 2004-10-12 13:01

Ajout des target "start" et "stop" dans Agmial2/build.xml qui remontent dans les trois modules pour faire les install.

15 lines of code changed in:

• Agmial2: build.xml (+15 -1)

rbossy 2004-10-04 16:38

Ona nettoye startup_agmial et shutdown_agmial
Ca marche jusqu'a un certain point (agmial_directory + pages de gardes des modules).

34 lines of code changed in:

• Agmial2: shutdown_agmial (+5 -65), startup_agmial (+4 -65)
• Agmial2/agmial_directory: build.xml (+1 -1), web_services.properties (+1 -1)
• Agmial2/ca_manager: build.xml (+1 -1), cam_manager.properties (+10 -10)
• Agmial2/common: build.xml (+5)
• Agmial2/pa_manager: build.xml (+1 -1), pam_manager.properties (+5 -5)
• Agmial2/pa_manager/src/pam/reader: ParalogTable.java (+1 -1)

rbossy 2004-10-04 15:03

Ajout de src_wsdl (trop galere de le refire)
Fix des build.xml et des web.xml

248 lines of code changed in:

• Agmial2/agmial_directory: build.xml (+2 -2), web_services.properties (+2 -2)
• Agmial2/ca_manager: build.xml (+5 -5)
• Agmial2/ca_manager/src_wsdl: ProteinSourceAdmin.wsdl (new 86)
• Agmial2/ca_manager/web: web.xml (+11 -11)
• Agmial2/common: build.xml (+1 -1)
• Agmial2/pa_manager: build.xml (+7 -7)
• Agmial2/pa_manager/src_wsdl: ContigStoreAdmin.wsdl (new 121)
• Agmial2/pa_manager/web: web.xml (+13 -13)

rbossy 2004-09-29 16:40

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)