February 2006 Commit Log

Number of Commits:

9

Number of Active Developers:

1

vloux 2006-02-28 16:32 #9

EdtFeature :
changement start
Affichage start putatifs a la demande et uniquement si CDS

38 lines of code changed in:

• Agmial2/ca_manager/src/cam/reader: EditFeature.java (+38 -30)

vloux 2006-02-28 16:10 #8

[#200] Export donn?es format tabul? CGView
Ajout properties pour affichage Lien CGView (cgview.enabled)
Creation CGViewPanel
+ Nettoyage (template)_project_properties
+ Generation auto liens du main_menu.html par build.xml

393 lines of code changed in:

• Agmial2: template_project.properties (+39 -31)
• Agmial2/ca_manager: build.xml (+31 -14)
• Agmial2/ca_manager/src/cam/admin: GlobalAdmin.java (+10 -10)
• Agmial2/ca_manager/src/cam/contigdb: ContigDB.java (+7 -2)
• Agmial2/ca_manager/src/cam/reader: CGViewPanel.java (new 79), ContigPanel.java (+98 -75), ContigStoreQueryImpl.java (+57 -1), QueryContigs.java (+10 -2)
• Agmial2/ca_manager/web: cam.css (+6), main_intro.html (+1 -1), main_intro.html.in (new), main_menu.html (+6 -7), main_menu.html.in (new), web.xml (+27 -7), web.xml.in (+22 -2)
• Agmial2/ca_manager/web/applets: CGView.jar (new)

vloux 2006-02-28 16:02 #7

[#200] Export donn?es format tabul? CGView
Prise en compte hyperlien

6 lines of code changed in:

• BioTools/src/biotools/nucleic: CGViewEntry.java (+4 -3)
• BioTools/src/test/biotools/nucleic: CGViewEntryTest.java (+2 -4)

vloux 2006-02-28 10:37 #6

[#200] Export donn?es format tabul? CGView
Permettre l'export des donn?es au format CGView (http://wishart.biology.ualberta.ca/cgview/tab_input.html).
CGViewEntry + tests (basiques) associ?s

560 lines of code changed in:

• BioTools: build.xml (+15 -4)
• BioTools/src/biotools/nucleic: CGViewEntry.java (new 180), SequinEntry.java (-2)
• BioTools/src/test/biotools: log4j.properties (new 33)
• BioTools/src/test/biotools/nucleic: CGViewEntryTest.java (new 331), NucleicPackageTest.java (+1)

vloux 2006-02-27 14:41 #5

AGMIAL Feature #197
Gestion liste : sauvegarde d'un resultat de recherche comme une nouvelle liste.

1933 lines of code changed in:

• Agmial2/agmial_directory/web: web.xml (new 78)
• Agmial2/ca_manager/web: web.xml (new 633)
• Agmial2/pa_manager/src/pam/admin: ProteinSourceAdminImpl.java (+394 -324), UpdateLists.java (+66 -2)
• Agmial2/pa_manager/src/pam/protdb: PAMProteinListSchema.java (+23 -1), ProteinDB.java (+28)
• Agmial2/pa_manager/src/pam/reader: QueryDataSets.java (+42 -35), SearchResults.java (+669 -462)

vloux 2006-02-24 15:58 #4

AGMIAL Feature #197
Gestion liste

1471 lines of code changed in:

• Agmial2: build.xml (+1 -1)
• Agmial2/pa_manager/sql: protdb_creation.sql (+17)
• Agmial2/pa_manager/src/pam/admin: ProteinSourceAdminImpl.java (+493 -412), ShowAdminSources.java (+5 -1), UpdateAnnotation.java (+1 -1), UpdateFunction.java (+2 -2), UpdateLists.java (new 192)
• Agmial2/pa_manager/src/pam/protdb: PAMProtein.java (+27 -4), PAMProteinList.java (new 102), PAMProteinListSchema.java (new 200), ProteinDB.java (+201 -1)
• Agmial2/pa_manager/src/pam/reader: ProteinPanel.java (+68 -9), QueryDataSets.java (+89 -62), QueryProteins.java (+61 -43), SearchResults.java (+1 -4)
• Agmial2/pa_manager/web: web.xml.in (+11)

vloux 2006-02-03 17:43 #3

[#189]

Tests Biotools (encore du chemin ...)
Ajout fichiers input
Extension tests

Logging avec log4j

768 lines of code changed in:

• BioTools/libs: log4j-1.2.11.jar (new)
• BioTools/src/biotools: log4j.properties (new 33)
• BioTools/src/biotools/calc: BioCalc.java (+2 -2), PSORTCalc.java (new 55), PSORTParams.java (new 58), SingleInOutTest.java (del)
• BioTools/src/biotools/general: GeneticCode.java (+1)
• BioTools/src/test/biotools: BioToolsTestSuite.java (new 58)
• BioTools/src/test/biotools/calc: BLASTTest.java (+6), CDDTest.java (+14 -3), CalcPackageTest.java (new 53), FROSTTest.java (+12 -6), INTERPROCalcTest.java (+43 -34), INTERPROTest.java (+13 -4), PSORTTest.java (+4 -2), SingleInOutTest.java (new 157), TMHMMTest.java (+16 -5)
• BioTools/src/test/biotools/general: GeneralPackageTest.java (new 38), GeneticCodeTest.java (+61 -61)
• BioTools/src/test/biotools/nucleic: GenBankTextTest.java (+13)
• BioTools/test_input: 1.fas.txt (new 7), export.xml (new 124), myco1.faa (new), myco_complete.faa (new), myco_complete.faa.phr (new), myco_complete.faa.pin (new), myco_complete.faa.psq (new), seq_input.fasta (new)

vloux 2006-02-01 16:39 #2

Ajout Psort (Feature Request #188).
Modifs BioTools
Test basique sur sortie "long" Gram+ et Gram-

635 lines of code changed in:

• BioTools/src/biotools/calc: PSORTText.java (+357 -37)
• BioTools/src/biotools/general: GeneticCode.java (+10 -5)
• BioTools/src/test/biotools/calc: MEMSATTest.java (+5 -2), PSORTTest.java (+21)
• BioTools/src/test/biotools/general: GeneticCodeTest.java (new 172)
• BioTools/src/test/biotools/nucleic: GenBankTextTest.java (+10 -10)
• BioTools/src/test/biotools/protein: ProteinTest.java (new 60)
• BioTools/test_input: biotools.props (changed)

vloux 2006-02-01 09:30 #1

Correction Bug [#187] NucleicFeatureLocation.createShifted() does not work -> consequences on artemis browsing

180 lines of code changed in:

• BioTools/src/biotools/nucleic: Location.java (+5), NucleicFeatureLocation.java (+22 -5)
• BioTools/src/test/biotools/nucleic: NucleicFeatureLocationTest.java (+24), NucleicFeatureTest.java (new 77), NucleicPackageTest.java (+1 -5), NucleicTest.java (+51)

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