September 2005 Commit Log

Number of Commits:

6

Number of Active Developers:

1

vloux 2005-09-28 14:26 #6

BugFixes
Removed generated web.xml from repository

34 lines of code changed in:

• Agmial2/agmial_directory/web: web.xml (del)
• Agmial2/ca_manager/src/cam/contigdb: ContigDB.java (+5 -2)
• Agmial2/ca_manager/src/cam/control: CAMControl.java (+9 -9), QueryFeatureMotivation.java (+3 -3), UpdateCDSAction.java (+2 -2)
• Agmial2/ca_manager/src/cam/lifecycle: ContextListener.java (+14 -12)
• Agmial2/ca_manager/src/cam/reader: MugenPanel.java (+1 -1)
• Agmial2/ca_manager/web: web.xml (del)
• Agmial2/pa_manager/web: web.xml (del)

vloux 2005-09-22 17:11 #5

BugFixes

746 lines of code changed in:

• Agmial2/ca_manager: build.xml (+1 -2)
• Agmial2/ca_manager/sql: contigdb_creation.sql (+1)
• Agmial2/ca_manager/src/cam/admin: AddBatch.java (+93 -92), AddProject.java (+7 -1), ContigStoreAdminImpl.java (+479 -455), GlobalAdmin.java (+48 -53), MonitorProjectTasks.java (+7 -2), ShowAddBatch.java (+4 -3), ShowAddProject.java (+1)
• Agmial2/ca_manager/src/cam/contigdb: CAMProject.java (+15 -1), CAMProjectSchema.java (+16 -3), ContigDB.java (+49 -32)
• Agmial2/ca_manager/src/cam/control: ProjectActionQueue.java (+1 -1), ProjectMotivation.java (+5 -3), UpdateProjectAction.java (+2 -2)
• Agmial2/ca_manager/src/cam/reader: MugenPanel.java (+5)
• Agmial2/ca_manager/web: web.xml.in (+5)
• Agmial2/pa_manager/src/pam/protdb: PAMHomologyResultSchema.java (+1 -1), PAMProteinRef.java (+2 -1), PAMProteinRefAction.java (+1), ProteinDB.java (+3 -3)

vloux 2005-09-14 15:41 #4

Package Reorganisation :
Tests in a separate folder but still belong to the same package.

1177 lines of code changed in:

• BioTools/src/biotools/calc: BLASTTest.java (del)
• BioTools/src/biotools/nucleic: NucleicFeatureLocationTest.java (del), NucleicPackageTest.java (del), NucleicTest.java (del), SequinEntryTest.java (del)
• BioTools/src/biotools/protein: protein-a.ucd (new)
• BioTools/src/test/biotools/calc: BLASTTest.java (new 150)
• BioTools/src/test/biotools/nucleic: NucleicFeatureLocationTest.java (new 474), NucleicPackageTest.java (new 31), NucleicTest.java (new 40), SequinEntryTest.java (new 482)

vloux 2005-09-14 11:50 #3

ProtDB code improvments

396 lines of code changed in:

• Agmial2/pa_manager/src/pam/protdb: ProteinDB.java (+396 -31)

vloux 2005-09-08 11:05 #2

contigDB code improvments

537 lines of code changed in:

• Agmial2/ca_manager/src/cam/contigdb: ContigDB.java (+537 -48)

vloux 2005-09-01 17:00 #1

PAM Summer cleaning

DBPooling with apache dbpc and jni.

PAM refactoring :
moving all select/update/insert statement into proteindb package :

reader/HomologyAlignPanel.java OK(1)(2)
reader/HomologyImagePanel.java OK(1)(2)
reader/HomologyPanel.java OK(1)(2)

reader/ProteinPanel.java OK (1),(2)

reader/QueryDataSets.java OK(1)
reader/QueryProteins.java OK(1)
reader/QueryProteinSources.java OK(1)

reader/SearchDataSets.java OK
reader/SearchProteinSources.javaOK
reader/SearchResults.java TODO (Need to reorganize the search ->
will be done at that moment)


admin/MonitorProteinRefTasks.java OK(1),(3)
admin/MonitorProteinTasks.java OK(1)
admin/MonitorTasks.java OK(1)
admin/RetireProteins.java OK(1)
admin/ShowAddProteins.java OK
admin/ShowRetireProteins.java OK

control/AfterActionMotivation.java OK
control/DetermineFunctionAction.java OK(1)
control/HomologyResultsMotivation.java OK(1)
control/NotifyFunctionMotivation.java OK
control/ParalogResultsMotivation.java DELETED
control/ProteinActionMotivation.java OK
control/ProteinActionQueue.java OK
control/ProteinRefActionQueue.java OK
control/SwissAnnotAction.java OK

(1)new methods in ProteinDB
(2) new DTO classes
(3) new classes in proteinDB

28044 lines of code changed in:

• Agmial2/agmial_directory/web: web.xml (+2 -2)
• Agmial2/ca_manager/src/cam/contigdb: CAMActionList.java (-7), ContigDB.java (+27 -26)
• Agmial2/ca_manager/src/cam/lifecycle: ContextListener.java (+2 -1)
• Agmial2/ca_manager/web: context.xml.in (changed), web.xml (new 617)
• Agmial2/pa_manager: build.xml (+32 -17), build.xml.in (del)
• Agmial2/pa_manager/sql: protdb_creation.sql (+3 -1)
• Agmial2/pa_manager/src/pam/admin: AddProteinSource.java (+5), AddProteins.java (+5), GlobalAdmin.java (+12 -18), MonitorProteinRefTasks.java (+33 -45), MonitorProteinTasks.java (+34 -46), MonitorTasks.java (+19 -23), ProteinSourceAdminImpl.java (+10 -4), RetireProteins.java (+21 -17), ShowAddProteinSource.java (+5), ShowAddProteins.java (+84 -89), ShowAdminSources.java (+5), ShowRetireProteins.java (+70 -75), UpdateAnnotation.java (+5), UpdateFunction.java (+7 -5)
• Agmial2/pa_manager/src/pam/control: AfterActionMotivation.java (+79 -96), DetermineFunctionAction.java (+189 -133), HomologyResultsMotivation.java (+76 -91), NotifyFunctionAction.java (+1 -1), NotifyFunctionMotivation.java (+79 -94), PAMControl.java (+73 -70), ParalogResultsMotivation.java (del), ProteinActionMotivation.java (+15 -25), ProteinActionQueue.java (+70 -125), ProteinCalcAction.java (+2 -4), ProteinRefActionQueue.java (+66 -107), SwissAnnotAction.java (+31 -28)
• Agmial2/pa_manager/src/pam/lifecycle: ContextListener.java (+19 -17)
• Agmial2/pa_manager/src/pam/protdb: PAMActionList.java (new 137), PAMFileResult.java (new 80), PAMFileSchema.java (+4 -8), PAMFloatValueResult.java (new 93), PAMFloatValueResultSchema.java (+21), PAMHomologyResult.java (new 107), PAMHomologyResultSchema.java (+56 -4), PAMMembraneSpan.java (new 94), PAMMembraneSpanSchema.java (+78 -57), PAMMotifFeature.java (new 97), PAMMotifFeatureSchema.java (+32), PAMProteinAction.java (+42 -7), PAMProteinActionSchema.java (+14), PAMProteinFeature.java (new 112), PAMProteinFeatureSchema.java (+41 -4), PAMProteinRef.java (+66 -4), PAMProteinRefAction.java (+35 -1), PAMProteinRefActionSchema.java (+95 -76), PAMSkillParam.java (+12), PAMValuedFeature.java (new 104), PAMValuedFeatureSchema.java (+40 -1), ProteinDB.java (+1802 -1118)
• Agmial2/pa_manager/src/pam/reader: CDDTable.java (+187 -64), FastaCreator.java (+14 -9), HomologyAlignPanel.java (+11 -2), HomologyImagePanel.java (+13 -3), HomologyPanel.java (+4), HomologyTable.java (+217 -103), JalviewLauncher.java (+16 -2), ProteinPanel.java (+375 -458), QueryDataSets.java (+11 -22), QueryProteinSources.java (+105 -108), QueryProteins.java (+83 -105), SearchAnnotationPanel.java (+5), SearchDataSets.java (+64 -77), SearchPanel.java (+5), SearchProteinSources.java (+113 -113), SearchResults.java (+695 -691), SearchResultsPanel.java (+5), SearchSQLQueryPanel.java (+5), SearchSQLQueryResults.java (+4)
• Agmial2/pa_manager/src/pam/util: PAMException.java (+6 -1)
• Agmial2/pa_manager/web: context.xml.in (new), web.xml (+93 -38), web.xml.in (+19 -12)
• BioTools/src/biotools/calc: BLASTTest.java (new), CalcException.java (+18 -13), HomologyMatch.java (+84 -30), HomologyMatchPair.java (+72 -65), HomologyResult.java (+29 -25)
• BioTools/src/biotools/nucleic: GenBankTextTest.java (+7 -9), NucleicPackageTest.java (+12 -5), nucleic-aid.ucd (new)
• BioTools/src/biotools/util: BioArgumentException.java (+13 -8), BioConversionException.java (+17 -12), BioException.java (+18 -13), BioFormatException.java (+18 -12), BioParseException.java (+16 -11), BioStreamException.java (+13 -8), EOSException.java (+10 -5), NestedError.java (+49 -44), NestedException.java (+42 -35)
• BioTools/test_input: blast_myco.raw (new), mycoplasmaGenitalium.gbk (new 20716)

August 2005 »