January 2007 Commit Log

Number of Commits:

6

Number of Active Developers:

1

vloux 2007-01-25 18:10 #6

Origin,goterms and Keyword display for homology result
Externalisation into HomologyPanel of HomologyResults display (from ProteinPanel)

476 lines of code changed in:

• Agmial2/pa_manager/src/pam/admin: UpdateAnnotation.java (+1 -32), UpdateFunction.java (+3 -37), UpdateLists.java (+1 -1)
• Agmial2/pa_manager/src/pam/protdb: GoListSchema.java (+1 -1)
• Agmial2/pa_manager/src/pam/reader: HomologyAlignPanel.java (del), HomologyGraphic.java (+32 -15), HomologyImagePanel.java (del), HomologyPanel.java (+321 -146), HomologyTable.java (+90 -34), ProteinPanel.java (+27 -220)

vloux 2007-01-25 18:02 #5

Tests
GOTermTable & AnnotTable implements Iteratable to permits "foreach" loop
HomologyMatchPair.Ontology enum comes with abbreviation and definition
Various fixes

49 lines of code changed in:

• BioTools/src/biotools/protein: AnnotTable.java (+6 -1), GOTerm.java (+15 -7), GOTermTable.java (+7 -1), PirText.java (+1 -1), ProteinFastAEntry.java (+2), ProteinFastAText.java (+2 -2), ProteinPirText.java (+1 -1)
• BioTools/src/test/biotools: BioToolsTest.java (+1 -1)
• BioTools/src/test/biotools/calc: BLASTTest.java (+3 -2), FROSTTest.java (+2 -2)
• BioTools/src/test/biotools/protein: GOTermTest.java (+7 -7), ProteinTest.java (+2 -3)

vloux 2007-01-24 18:15 #4

Added classes to manage goterms, keywords and origin of a match.
Display of origin in table and graphics

604 lines of code changed in:

• Agmial2/pa_manager/src/pam/protdb: GoListSchema.java (new 96), KwListSchema.java (new 94), MatchOriginSchema.java (new 80), PAMHomologyResult.java (+3), PAMHomologyResultSchema.java (+3), ProteinDB.java (+87 -2)
• Agmial2/pa_manager/src/pam/reader: CDDTable.java (+15 -1), HomologyGraphic.java (+112 -32), HomologyTable.java (+47 -6), ProteinPanel.java (+67 -60)
• Agmial2/pa_manager/web: context.xml.in (changed)
• Agmial2/pa_manager/web/images: go-down.png (new), go-jump.png (new), go-up.png (new)

vloux 2007-01-24 18:09 #3

Added classes to manage goterms, keywords and origin of a match.
Display of origin in table and graphics

238 lines of code changed in:

• BioTools/src/biotools/calc: HomologyMatch.java (+93 -1), HomologyMatchPair.java (+6 -1), HomologyResult.java (+1 -1)
• BioTools/src/biotools/protein: AnnotTable.java (+6 -1), GOTerm.java (+27 -5), GOTermTable.java (new 64), TextAnnot.java (+11)
• BioTools/src/test/biotools/protein: GOTermTest.java (+29 -10), ProteinPackageTest.java (+1)

vloux 2007-01-11 17:49 #2

GOterm encapsulation class with real pieces of java1.5 inside

323 lines of code changed in:

• BioTools/src/biotools/protein: GOTerm.java (new 196)
• BioTools/src/test/biotools/protein: GOTermTest.java (new 127)

vloux 2007-01-11 10:50 #1

Changed DetrmineFunctionAction to trace where automartic annotation come from.
Authorized Manager to change status from Automatic down gto Original

139 lines of code changed in:

• Agmial2/pa_manager/src/pam/admin: ProteinSourceAdminImpl.java (+51 -28)
• Agmial2/pa_manager/src/pam/control: DetermineFunctionAction.java (+88 -47)

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