April 2005 Commit Log

Number of Commits:

40

Number of Active Developers:

4

vloux 2005-04-29 16:31 #40

Choix des layer a afficher

132 lines of code changed in:

• Agmial2/artemis_client: build.xml (+3 -3)
• Agmial2/artemis_client/src/agmial/artemis: AgmialAccessDialog.java (+87 -28), AgmialAuthenticator.java (+2 -2), AgmialDocument.java (+11 -12), AgmialInterface.java (+3 -4), AgmialInterfaceImpl.java (+19 -11), AgmialProfileDocument.java (+7 -12)

vloux 2005-04-29 11:29 #39

artemis standalone

0 lines of code changed in:

• Agmial2/artemis_client/ARTEMIS/lib: commons-logging.jar (del), jaas.jar (del), jaxb-api.jar (del), jaxb-impl.jar (del), jaxb-libs.jar (del), jaxb-xjc.jar (del), jaxp-api.jar (del), jaxrpc-impl.jar (changed), xalan.jar (changed), xercesImpl.jar (changed)

vloux 2005-04-27 17:48 #38

Aretmis standalone

2 lines of code changed in:

• Agmial2/artemis_client: artemis.bat (+1 -2), artemis.sh (+1 -1)

vloux 2005-04-27 17:37 #37

Artemis standalone

9 lines of code changed in:

• Agmial2/artemis_client: artemis_agmial.bat (del), artemis_agmial.sh (del)
• Agmial2/artemis_client/ARTEMIS: AGMIAL_README (new 9), agmial (del)

vloux 2005-04-27 17:31 #36

Agmial standalone

936 lines of code changed in:

• Agmial2/artemis_client: README (new), artemis.bat (new 3), artemis.sh (new 2), build.xml (-3)
• Agmial2/artemis_client/ARTEMIS: Makefile (+2 -1)
• Agmial2/artemis_client/ARTEMIS/META-INF: MANIFEST.MF (+2 -1)
• Agmial2/artemis_client/ARTEMIS/diana: Options.java (+5 -5)
• Agmial2/artemis_client/ARTEMIS/lib: Agmial-2.0.jar (+73 -88), BioTools-1.0.jar (new), jax-qname.jar (new), jaxrpc-impl.jar (changed), namespace.jar (new), xalan.jar (changed), xercesImpl.jar (+849 -849), xmlParserAPIs.jar (new)

miquenti 2005-04-26 10:54 #35

Modification du readOnly

113 lines of code changed in:

• Agmial2/ca_manager/src/cam/reader: EditFeature.java (+26 -30), MugenPanel.java (+87 -94)

rbossy 2005-04-22 11:53 #34

Nettoyage des fichiers properties vierges

50 lines of code changed in:

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

vloux 2005-04-22 08:38 #33

SequinEntry :
(+) avec/sans generation a la volee du qualifier gene
(+) avec/sans les qualifiers valides

134 lines of code changed in:

• BioTools: build.xml (+18 -5)
• BioTools/src/biotools/nucleic: SequinEntry.java (+67 -8), SequinEntryTest.java (+49 -6)

rbossy 2005-04-21 18:09 #32

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 #31

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)

vloux 2005-04-21 13:49 #30

BugFix:
(-) Use of qualifier /pseudo -> null pointer exception

5 lines of code changed in:

• BioTools/src/biotools/nucleic: SequinEntry.java (+5 -2)

vloux 2005-04-20 13:43 #29

boolean NucleicFeature.existQualifier
Nettoyage du code.

978 lines of code changed in:

• BioTools/src/biotools/calc: BioCalc.java (+35 -12), CalcParams.java (+16 -2), CalcResults.java (+4 -1), FileParameter.java (+25 -3), FileResult.java (+25 -3), FloatResult.java (+40 -5), HomologyMatch.java (+23 -4), HomologyMatchPair.java (+34 -7), HomologyResult.java (+7), MotifSpan.java (+15 -3), NucleicFeaturesResult.java (+35 -6), ProteinFeaturesResult.java (+6), ResultEntry.java (+6 -1), ResultEntryPosn.java (+42 -14), ResultText.java (+19 -4), SingleProfileResult.java (+47 -7), ValuedSpan.java (+30 -4)
• BioTools/src/biotools/general: GeneticCode.java (+21 -7)
• BioTools/src/biotools/nucleic: Nucleic.java (+55 -10), NucleicEntry.java (+7 -1), NucleicEntryPosn.java (+42 -14), NucleicFeature.java (+39 -3), NucleicFeatureLocation.java (+20 -3), NucleicFeatureQualifier.java (+21 -2), NucleicFeatureTable.java (+6), NucleicSource.java (+15 -2), NucleicText.java (+6 -1), SequinEntryTest.java (+13)
• BioTools/src/biotools/protein: AnnotTable.java (+6 -1), EntryDate.java (+30 -3), FloatAnnot.java (+16 -3), Protein.java (+59 -13), ProteinEntry.java (+7 -1), ProteinEntryPosn.java (+42 -14), ProteinFeature.java (+61 -11), ProteinFeatureTable.java (+6), ProteinText.java (+6 -2), TextAnnot.java (+16 -3)
• BioTools/src/biotools/util: BioFileStream.java (+11 -1), PrintfFormat.java (+64 -12)

miquenti 2005-04-18 14:06 #28

Correction bug precision

15 lines of code changed in:

• Agmial2/ca_manager/src/cam/reader: MugenPanel.java (+15 -23)

vloux 2005-04-15 17:59 #27

++ template_web_service.properties

19 lines of code changed in:

• Agmial2: organization.properties (del), template_organization.properties (del), template_web_services.properties (new 19)
• Agmial2/pa_manager: build.xml (-2)

rbossy 2005-04-15 11:13 #26

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)

agmial 2005-04-15 10:50 #25

Homologies structuraales dans la bdd...

9 lines of code changed in:

• Agmial2/pa_manager/sql: protdb_creation.sql (+4)
• Agmial2/pa_manager/src/pam/protdb: PAMHomologyResultSchema.java (+5 -2)

vloux 2005-04-15 10:36 #24

BugFix

2 lines of code changed in:

• Agmial2/pa_manager/src/pam/reader: SearchAnnotationPanel.java (+1 -1)

miquenti 2005-04-14 11:24 #23

(MQuentin) EditFeature + MugenPanel final commit

1366 lines of code changed in:

• Agmial2/ca_manager/src/cam/reader: EditFeature.java (+1093 -96), MugenPanel.java (+273 -232)

vloux 2005-04-14 07:58 #22

Ajout de la gestion des pseudogenes :
- Checkbox pseudo et text input pseudogene number dans ProteinPanel
- Changement des Interfaces de comm PAM/CAM -> wsdl ? regenerer et ? copier dans src_wsdl

7 lines of code changed in:

• Agmial2/pa_manager/src/pam/lifecycle: ContextListener.java (+1 -1)
• Agmial2/pa_manager/src_wsdl: ContigStoreAdmin.wsdl (+6 -4)

vloux 2005-04-14 07:52 #21

Ajout de la gestion des pseudogenes :
- Checkbox pseudo et text input pseudogene number dans ProteinPanel
- Changement des Interfaces de comm PAM/CAM -> wsdl ? regenerer et ? copier dans src_wsdl

261 lines of code changed in:

• Agmial2/artemis_client/src_wsdl: ContigStoreAdmin.wsdl (+6 -4), ContigStoreQuery.wsdl (+16 -2)
• Agmial2/ca_manager: build.xml (+1)
• Agmial2/ca_manager/src/cam/admin: ContigStoreAdminIF.java (+1 -1), ContigStoreAdminImpl.java (+13 -6)
• Agmial2/ca_manager/src/cam/control: CAMControl.java (+12 -14), UpdateCDSAction.java (+11 -1)
• Agmial2/ca_manager/src/cam/reader: MugenPanel.java (+1 -1)
• Agmial2/ca_manager/src_wsdl: ProteinSourceAdmin.wsdl (+6 -4)
• Agmial2/ca_manager/web: web.xml.in (+1 -1)
• Agmial2/pa_manager: build.xml (+3 -1)
• Agmial2/pa_manager/src/pam/admin: ProteinSourceAdminIF.java (+1 -2), ProteinSourceAdminImpl.java (+30 -14), UpdateFunction.java (+16 -5)
• Agmial2/pa_manager/src/pam/control: DetermineFunctionAction.java (+1 -1), NotifyFunctionAction.java (+4 -1), NotifyFunctionMotivation.java (+2 -2), PAMControl.java (+14 -13), ProteinRefActionQueue.java (+1)
• Agmial2/pa_manager/src/pam/protdb: PAMProtein.java (+28 -2), PAMProteinSchema.java (+38 -8), ProteinDB.java (+28 -9)
• Agmial2/pa_manager/src/pam/reader: ProteinPanel.java (+20 -1)
• Agmial2/pa_manager/web: web.xml (+3 -7), web.xml.in (+4 -8)

agmial 2005-04-13 15:30 #20

J'ai enlev? des System.err/out.println qui polluaient les logs...

1 lines of code changed in:

• BioTools/src/biotools/calc: BioCalc.java (+1 -1), FROSTText.java (-2)

agmial 2005-04-13 15:03 #19

Added the FROST_CALC skill.
Added restrictions on motivations of protein calculations:
- setMinProteinSizeRestriction: motivation only for proteins larger than the given threshold
- setMaxProteinSizeRestriction: motivation only for proteins smaller than the given threshold
- setTargetSourceRestriction: motivation only for proteins from the given source
TODO: restriction on datasets

48 lines of code changed in:

• Agmial2/pa_manager/src/pam/control: PAMControl.java (+19), ProteinActionMotivation.java (+29 -1)

vloux 2005-04-12 14:46 #18

Ajout de pseudogene pseudogene_number dans prot_db.
TODO : Passer pseudogene et gene_of_interest de varchar(3) ? booleen

10 lines of code changed in:

• Agmial2/pa_manager/sql: protdb_creation.sql (+10)

vloux 2005-04-12 10:50 #17

Bugfix

10 lines of code changed in:

• Agmial2/agmial_directory: .cvsignore (new 2)
• Agmial2/ca_manager: .cvsignore (new 3)
• Agmial2/ca_manager/web: main_menu.html (+1), web.xml.in (+1 -1)
• Agmial2/pa_manager: .cvsignore (new 3)

vloux 2005-04-12 10:50 #16

BugFix + Menage

38 lines of code changed in:

• Agmial2: .classpath (new 18), .cvsignore (new 1), .project (new 17)
• Agmial2/common: .cvsignore (new 2)

vloux 2005-04-12 09:29 #15

Bugfix

1 lines of code changed in:

• Agmial2/pa_manager: build.xml (+1 -1)

vloux 2005-04-12 08:43 #14

BugFix + Menage

16 lines of code changed in:

• BioTools/src/biotools/nucleic: SequinEntry.java (+15 -10), SequinEntryTest.java (+1 -2)

vloux 2005-04-11 17:45 #13

Suite menage et integration MugenPanel

105 lines of code changed in:

• Agmial2/agmial_directory/web: web.xml (+7 -7)
• Agmial2/ca_manager: build.xml (+7 -3)
• Agmial2/ca_manager/src/cam/reader: EditFeature.java (+17 -13), MugenPanel.java (+37 -26)
• Agmial2/ca_manager/web: web.xml (-5), web.xml.in (+37)

vloux 2005-04-11 16:44 #12

Merge de MugenPanel dans HEAD
Centralisation des chemins utilis?s dans MugenPanel et EditFeature
Modifs de build.xml, template_project.properties

962 lines of code changed in:

• Agmial2: template_project.properties (+12)
• Agmial2/ca_manager/src/cam/reader: EditFeature.java (+31 -990), MugenPanel.java (+918 -6566)
• Agmial2/ca_manager/web: web.xml.in (-5)
• Agmial2/pa_manager: build.xml (+1 -1)

vloux 2005-04-11 15:28 #11

Merge de GlobalPanel dans HEAD

259 lines of code changed in:

• Agmial2/ca_manager/src/cam/contigdb: ContigDB.java (+99 -17)
• Agmial2/ca_manager/src/cam/reader: ContigInfoBean.java (+18), ContigStoreQueryImpl.java (+11 -1), GlobalPanel.java (new 131)

vloux 2005-04-11 15:04 #10

Nettoyage du code : imports, methodes deprecated ...

1288 lines of code changed in:

• Agmial2: web_services.properties (+5 -2)
• Agmial2/ca_manager/src/cam/admin: AddBatch.java (+9 -11), AddProject.java (+6 -9), ContigStoreAdminImpl.java (+29 -14), LockContig.java (+7 -15), MonitorBatchTasks.java (+12 -8), MonitorContigTasks.java (+12 -8), MonitorFeatureTasks.java (+12 -8), MonitorProjectTasks.java (+12 -8), MonitorTasks.java (+12 -8), ProfileStoreAdminImpl.java (+9 -11), ShowAddBatch.java (+12 -10), ShowAddProject.java (+7 -4), ShowAdminBatches.java (+12 -6), ShowUpdateContig.java (+12 -6), ShowUpdateProfile.java (+12 -6), UpdateContig.java (+11 -15), UpdateProfile.java (+10 -16)
• Agmial2/ca_manager/src/cam/contigdb: CAMBatchAction.java (+2 -3), CAMBatchSchema.java (+5 -3), CAMContigAction.java (+2 -3), CAMFeatureSchema.java (+9 -7), CAMFileSchema.java (+6 -6), CAMLockSchema.java (+5 -3), CAMProject.java (-1), CAMProjectAction.java (+2 -3), CAMProjectSchema.java (+5 -3), CAMSingleProfileSchema.java (+7 -8), CAMSkillMeta.java (-1), CAMSkillParam.java (-1), CAMSkillParamSchema.java (+5 -3), ContigDB.java (+18 -10)
• Agmial2/ca_manager/src/cam/control: BatchActionMotivation.java (+7 -11), BatchActionQueue.java (+11 -11), BatchCalcAction.java (+16 -14), CAMActionQueue.java (+2 -10), CAMControl.java (+9 -13), CAMMotivation.java (+4 -8), ContigActionMotivation.java (+7 -11), ContigActionQueue.java (+11 -11), ContigCalcAction.java (+14 -13), FeatureActionQueue.java (+11 -11), ProjectActionQueue.java (+11 -11), ProjectMotivation.java (+7 -11), QueryFeatureMotivation.java (+7 -11), TellCDSRemovedAction.java (+10 -20), TransferFeatureAction.java (+6 -18), UpdateCDSAction.java (+23 -20), UpdateProjectAction.java (+10 -17)
• Agmial2/ca_manager/src/cam/lifecycle: ContextListener.java (+6 -12)
• Agmial2/ca_manager/src/cam/reader: ContigPanel.java (+10 -16), ContigStoreQueryImpl.java (+13 -13), EditFeature.java (+24 -19), GetContigRegion.java (+10 -16), MugenPanel.java (+118 -101), ProfileStoreQueryImpl.java (+6 -13), QueryBatches.java (+8 -15), QueryContigs.java (+14 -22), QueryProjects.java (+10 -16)
• Agmial2/common/src/agmial/control: Action.java (+3 -5), ActionQueue.java (+4 -6), DefaultOrdering.java (+1 -5)
• Agmial2/common/src/agmial/registry: ManagerRegistryInterface.java (+35 -7)
• Agmial2/pa_manager/src/pam/admin: AddProteinSource.java (+6 -11), AddProteins.java (+13 -15), MonitorProteinRefTasks.java (+12 -8), MonitorProteinTasks.java (+12 -8), MonitorTasks.java (+12 -8), ProteinSourceAdminImpl.java (+19 -12), RetireProteins.java (+13 -12), ShowAddProteinSource.java (+6 -5), ShowAddProteins.java (+12 -11), ShowAdminSources.java (+6 -8), ShowRetireProteins.java (+12 -11), UpdateAnnotation.java (+7 -12), UpdateFunction.java (+9 -13)
• Agmial2/pa_manager/src/pam/control: AfterActionMotivation.java (+7 -11), DetermineFunctionAction.java (+8 -20), HomologyResultsMotivation.java (+7 -11), NotifyFunctionAction.java (+11 -21), NotifyFunctionMotivation.java (+7 -11), PAMActionQueue.java (+2 -10), PAMControl.java (+12 -13), PAMMotivation.java (+4 -8), ParalogResultsMotivation.java (+7 -11), ProteinActionMotivation.java (+5 -10), ProteinActionQueue.java (+11 -11), ProteinCalcAction.java (+15 -15), ProteinRefActionQueue.java (+11 -11), SwissAnnotAction.java (+9 -24)
• Agmial2/pa_manager/src/pam/lifecycle: ContextListener.java (+6 -13)
• Agmial2/pa_manager/src/pam/protdb: PAMDatabaseMetaSchema.java (+5 -3), PAMFileSchema.java (+6 -6), PAMFloatValueResultSchema.java (+5 -4), PAMHomologyResultSchema.java (+9 -7), PAMInfoSourceMetaSchema.java (+5 -3), PAMMembraneSpanSchema.java (+7 -7), PAMMethodMetaSchema.java (+5 -3), PAMMotifFeatureSchema.java (+7 -7), PAMProteinAction.java (+2 -3), PAMProteinFeatureSchema.java (+7 -6), PAMProteinRef.java (-2), PAMProteinRefSchema.java (+4 -3), PAMProteinSchema.java (+8 -6), PAMProteinSource.java (-1), PAMProteinSourceSchema.java (+5 -3), PAMSkillMeta.java (-1), PAMSkillParam.java (-1), PAMSkillParamSchema.java (+5 -3), PAMValuedFeatureSchema.java (+7 -7)
• Agmial2/pa_manager/src/pam/reader: AAFeaturesFormatter.java (+8 -8), AlignImage.java (+4 -18), EditingBuffer.java (-7), FeaturesGraphic.java (+5 -13), FeaturesViewer.java (+6 -12), FormattedFeature.java (+1 -8), HomologyAlignPanel.java (+12 -12), HomologyGraphic.java (+3 -12), HomologyImagePanel.java (+16 -18), HomologyPanel.java (+12 -12), ParalogTable.java (+4 -5), ProteinPanel.java (+32 -13), QueryDataSets.java (+14 -13), QueryProteinSources.java (+16 -14), QueryProteins.java (+14 -13), ResidueFormatter.java (+3 -8), SearchAnnotationPanel.java (+11 -12), SearchDataSets.java (+14 -12), SearchPanel.java (+10 -12), SearchProteinSources.java (+16 -14), SearchResults.java (+19 -13), SearchResultsPanel.java (+6 -11), SearchSQLQueryPanel.java (+6 -11), SearchSQLQueryResults.java (+13 -11)

vloux 2005-04-11 14:58 #9

Menage ...

0 lines of code changed in:

• Agmial2/artemis_client/ARTEMIS/jalview: LB#1#Contig109:1->2466 READ ONLY .seq.00001 (del)

vloux 2005-04-11 14:43 #8

Nettoyage du code : imports, methodes deprecated ...

186 lines of code changed in:

• BioTools/src/biotools/calc: Aln2FreqCalc.java (-6), Aln2FreqParams.java (-1), BLASTCalc.java (+2 -6), BLASTParams.java (-1), BLASTText.java (+5 -5), CDDCalc.java (+2 -6), CDDParams.java (-1), CDDText.java (+5 -5), COILCalc.java (+2 -6), COILParams.java (-1), COILText.java (+8 -4), CalcResult.java (-2), DoubleInSingleOut.java (-1), FROSTCalc.java (+2 -6), FROSTParams.java (-1), FROSTText.java (+5 -5), FileParameter.java (-1), FloatResult.java (-1), HomologyMatch.java (+1 -5), HomologyMatchPair.java (-3), HomologyResult.java (+2 -5), INTERPROCalc.java (+10 -7), INTERPROParams.java (-1), INTERPROText.java (+6 -4), MEMSATCalc.java (+6 -5), MEMSATParams.java (-1), MULSATCalc.java (+2 -6), MULSATParams.java (-1), MotifSpan.java (+1 -3), NucleicFeaturesResult.java (+1 -2), PICalc.java (+2 -6), PIParams.java (-1), PIText.java (+3 -4), PetrinCalc.java (+3 -6), PetrinParams.java (-1), PetrinText.java (+4 -4), ProfileFastAText.java (+7 -3), ProteinFeaturesResult.java (+1 -2), RRNAScanCalc.java (+3 -6), RRNAScanParams.java (-1), RRNAScanText.java (+4 -4), ResultEntry.java (+1 -3), ResultEntryPosn.java (-4), SEGCalc.java (+2 -6), SEGParams.java (-1), SEGText.java (+4 -4), SHOWCalc.java (+3 -6), SHOWParams.java (-1), SHOWText.java (+4 -4), SIGSEQCalc.java (+2 -6), SIGSEQParams.java (-1), SIGSEQText.java (+6 -5), SingleInOut.java (-1), TMSpan.java (-3), TRNAScanCalc.java (+3 -6), TRNAScanParams.java (-1), TRNAScanText.java (+4 -4), ValuedSpan.java (+1 -3)
• BioTools/src/biotools/general: GeneticCode.java (+11 -5), Organism.java (-3)
• BioTools/src/biotools/nucleic: Codon.java (+1 -5), GenBankText.java (+5 -3), Nucleic.java (+1 -4), NucleicEntryPosn.java (+2 -4), NucleicFastAEntry.java (+3 -3), NucleicFastAText.java (+5 -4), NucleicFeatureLocation.java (+1 -5), NucleicRes.java (+3 -3), NucleicSource.java (-3), NucleicText.java (+4 -4)
• BioTools/src/biotools/protein: Annot.java (-1), AnnotTable.java (+1 -4), FloatAnnot.java (-3), OrganismAnnot.java (-4), PirText.java (+5 -3), Protein.java (-3), ProteinEntryPosn.java (+2 -4), ProteinFastAText.java (+5 -3), ProteinFeature.java (-3), ProteinFeatureTable.java (+1 -4), ProteinPirText.java (+5 -3), ProteinRes.java (+2 -3), ProteinSource.java (-3), ProteinText.java (+4 -4), SwissText.java (+5 -3), TextAnnot.java (-3)
• BioTools/src/biotools/util: BioFileStream.java (+3 -2), BioStream.java (-2)

vloux 2005-04-11 11:17 #7

Sequin export
Junit test for SequinEntry

335 lines of code changed in:

• BioTools: build.xml (+1 -1)
• BioTools/src/biotools/nucleic: NucleicFeature.java (+12 -3), NucleicFeatureQualifier.java (+1 -3), NucleicFeatureTable.java (+4 -4), SequinEntry.java (+120 -49), SequinEntryTest.java (new 197)

agmial 2005-04-08 17:58 #6

Parametres de FROST ... + petite boulette dans SIGSEQCalc

12 lines of code changed in:

• BioTools: biotools.props (+6)
• BioTools/src/biotools/calc: FROSTCalc.java (+4 -2), FROSTParams.java (+1 -1), SIGSEQCalc.java (+1 -1)

agmial 2005-04-08 13:44 #5

Ajout de FROST dans biotools.calc
J'ai du ajouter quelques membres dans la classe HomologyMatchPair pour mettre les informations sur la structure

RB

265 lines of code changed in:

• BioTools/src/biotools/calc: FROSTCalc.java (new 49), FROSTParams.java (new 38), FROSTText.java (new 125), HomologyMatchPair.java (+53 -14)

vloux 2005-04-06 16:05 #4

Removed files re-added

3028 lines of code changed in:

• BioTools/src/biotools/nucleic: Codon.java (new 60), GenBankEntry.java (new 533), GenBankEntryX.java (new 34), GenBankText.java (new 95), Nucleic.java (new 151), NucleicEntry.java (new 77), NucleicEntryPosn.java (new 45), NucleicFastAEntry.java (new 100), NucleicFastAText.java (new 98), NucleicFeature.java (new 146), NucleicFeatureLocation.java (new 245), NucleicFeatureQualifier.java (new 40), NucleicFeatureTable.java (new 112), NucleicRes.java (new 114), NucleicResIUPAC.java (new 555), NucleicResIUPACX.java (new 554), NucleicSource.java (new 38), NucleicText.java (new 31)

vloux 2005-04-05 09:03 #3

Effac?s par erreur

6914 lines of code changed in:

• BioTools/src/biotools/nucleic: SequinEntry.java (new 191)
• 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), SwissEntry.java (new 209), SwissText.java (new 64), TextAnnot.java (new 36)
• 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)

vloux 2005-04-05 09:02 #2

effac?s par erreur

5508 lines of code changed in:

• BioTools: build.xml (+1 -1)
• 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), 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)

vloux 2005-04-04 15:26 #1

Bugfixes

0 lines of code changed in:

• BioTools/src/biotools/calc: Aln2FreqCalc.java (del), Aln2FreqParams.java (del), BLASTCalc.java (del), BLASTParams.java (del), BLASTText.java (del), BioCalc.java (del), CDDCalc.java (del), CDDParams.java (del), CDDText.java (del), COILCalc.java (del), COILParams.java (del), COILText.java (del), CalcException.java (del), CalcParams.java (del), CalcResult.java (del), CalcResults.java (del), DoubleInSingleOut.java (del), FileParameter.java (del), FileResult.java (del), FloatResult.java (del), HomologyMatch.java (del), HomologyMatchPair.java (del), HomologyResult.java (del), INTERPROCalc.java (del), INTERPROParams.java (del), INTERPROText.java (del), MEMSATCalc.java (del), MEMSATParams.java (del), MEMSATText.java (del), MULSATCalc.java (del), MULSATParams.java (del), MotifSpan.java (del), NucleicFeaturesResult.java (del), PICalc.java (del), PIParams.java (del), PIText.java (del), PetrinCalc.java (del), PetrinEntry.java (del), PetrinParams.java (del), PetrinText.java (del), ProfileFastAText.java (del), ProteinFeaturesResult.java (del), README (del), RRNAScanCalc.java (del), RRNAScanEntry.java (del), RRNAScanParams.java (del), RRNAScanText.java (del), ResultEntry.java (del), ResultEntryPosn.java (del), ResultText.java (del), SEGCalc.java (del), SEGParams.java (del), SEGText.java (del), SHOWCalc.java (del), SHOWEntry.java (del), SHOWParams.java (del), SHOWText.java (del), SIGSEQCalc.java (del), SIGSEQParams.java (del), SIGSEQText.java (del), SingleInOut.java (del), SingleProfileResult.java (del), TMSpan.java (del), TRNAScanCalc.java (del), TRNAScanEntry.java (del), TRNAScanParams.java (del), TRNAScanText.java (del), ValuedSpan.java (del)
• BioTools/src/biotools/general: GeneticCode.java (del), Organism.java (del), README (del)
• BioTools/src/biotools/nucleic: Codon.java (del), GenBankEntry.java (del), GenBankEntryX.java (del), GenBankText.java (del), Nucleic.java (del), NucleicEntry.java (del), NucleicEntryPosn.java (del), NucleicFastAEntry.java (del), NucleicFastAText.java (del), NucleicFeature.java (del), NucleicFeatureLocation.java (del), NucleicFeatureQualifier.java (del), NucleicFeatureTable.java (del), NucleicRes.java (del), NucleicResIUPAC.java (del), NucleicResIUPACX.java (del), NucleicSource.java (del), NucleicText.java (del), SequinEntry.java (del)
• BioTools/src/biotools/protein: Annot.java (del), AnnotTable.java (del), EntryDate.java (del), FloatAnnot.java (del), OrganismAnnot.java (del), PirEntry.java (del), PirText.java (del), Protein.java (del), ProteinEntry.java (del), ProteinEntryPosn.java (del), ProteinFastAEntry.java (del), ProteinFastAText.java (del), ProteinFeature.java (del), ProteinFeatureTable.java (del), ProteinPirEntry.java (del), ProteinPirText.java (del), ProteinRes.java (del), ProteinResCased.java (del), ProteinResStandard.java (del), ProteinResTranslated.java (del), ProteinSource.java (del), ProteinText.java (del), README (del), SwissEntry.java (del), SwissText.java (del), TextAnnot.java (del), errors (del)
• BioTools/src/biotools/util: BioArgumentException.java (del), BioBufferStream.java (del), BioConversionException.java (del), BioException.java (del), BioFileStream.java (del), BioFormatException.java (del), BioParseException.java (del), BioResources.java (del), BioStream.java (del), BioStreamException.java (del), EOSException.java (del), FileLog.java (del), Log.java (del), NestedError.java (del), NestedException.java (del), PrintfFormat.java (del)

March 2005 »