Module BioTools/src/biotools/nucleic/

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Summary Period: 2004-09-29 to 2006-05-09

Modules

[root]/BioTools/src/biotools/nucleic

Lines of Code

Total Lines Of Code: 4270 (2006-12-21 16:51)

Authors

Most Recent Commits

vloux 2006-05-09 15:56

BugFix:
Pb in CGView Entry format when function equals ""

5 lines of code changed in:

• BioTools/src/biotools/nucleic: CGViewEntry.java (+5)

vloux 2006-02-28 16:02

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

4 lines of code changed in:

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

vloux 2006-02-28 10:37

[#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

180 lines of code changed in:

• BioTools/src/biotools/nucleic: CGViewEntry.java (new 180), SequinEntry.java (-2)

vloux 2006-02-01 09:30

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

27 lines of code changed in:

• BioTools/src/biotools/nucleic: Location.java (+5), NucleicFeatureLocation.java (+22 -5)

vloux 2005-10-20 17:01

BugFixes :
#130 Bug Parsing CDD
#132 Passage ? Interpro V4

Ajouts de tests (en cours):
CDD
Interpro
memsat
psort

0 lines of code changed in:

• BioTools/src/biotools/nucleic: GenBankTextTest.java (del)

vloux 2005-09-14 15:41

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

0 lines of code changed in:

• BioTools/src/biotools/nucleic: NucleicFeatureLocationTest.java (del), NucleicPackageTest.java (del), NucleicTest.java (del), SequinEntryTest.java (del)

vloux 2005-09-01 17:00

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

19 lines of code changed in:

• BioTools/src/biotools/nucleic: GenBankTextTest.java (+7 -9), NucleicPackageTest.java (+12 -5), nucleic-aid.ucd (changed)

vloux 2005-08-09 11:22

Formatage code

2619 lines of code changed in:

• BioTools/src/biotools/nucleic: Codon.java (+22 -24), GenBankEntry.java (+386 -378), GenBankEntryX.java (+9 -11), GenBankText.java (+70 -66), GenBankTextTest.java (+5 -5), Location.java (+51 -44), Nucleic.java (+40 -48), NucleicEntry.java (+42 -38), NucleicEntryPosn.java (+16 -15), NucleicFastAEntry.java (+60 -65), NucleicFastAText.java (+72 -68), NucleicFeature.java (+63 -67), NucleicFeatureLocation.java (+75 -73), NucleicFeatureLocationTest.java (+380 -314), NucleicFeatureQualifier.java (+6 -10), NucleicFeatureTable.java (+51 -60), NucleicPackageTest.java (+4 -5), NucleicRes.java (+58 -49), NucleicResIUPAC.java (+266 -288), NucleicResIUPACX.java (+271 -285), NucleicSource.java (+7 -12), NucleicTest.java (+16 -17), NucleicText.java (+18 -12), SequinEntry.java (+310 -285), SequinEntryTest.java (+321 -252)

vloux 2005-08-09 11:09

BioTools :
+ ClustalWCalc
Modifications Location

Tests :
SingleInOutTest
NucleicPackageTest
NucleicTest

112 lines of code changed in:

• BioTools/src/biotools/nucleic: Location.java (+75 -5), NucleicEntry.java (+4 -1), NucleicPackageTest.java (+1 -1), NucleicTest.java (new 17), SequinEntry.java (+15 -4)

vloux 2005-06-15 15:42

BioTools :
+ NucleicFeatureLocation gere les localisations de type join(www..xxx,yy..zzz)
+ Test unitaires :
- GenBankTextTest
- SequinEntryTest
- NucleicFeatureLocationTest
regroup?s sous la classe NucleicPackageTest qui est une suite des test precedents.

947 lines of code changed in:

• BioTools/src/biotools/nucleic: GenBankTextTest.java (new 9), Location.java (new 160), NucleicFeatureLocation.java (+458 -159), NucleicFeatureLocationTest.java (new 314), NucleicPackageTest.java (new 6)

vloux 2005-04-22 08:38

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

116 lines of code changed in:

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

vloux 2005-04-21 13:49

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

boolean NucleicFeature.existQualifier
Nettoyage du code.

224 lines of code changed in:

• 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)

vloux 2005-04-12 08:43

BugFix + Menage

16 lines of code changed in:

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

vloux 2005-04-11 14:43

Nettoyage du code : imports, methodes deprecated ...

25 lines of code changed in:

• 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)

vloux 2005-04-11 11:17

Sequin export
Junit test for SequinEntry

334 lines of code changed in:

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

vloux 2005-04-06 16:05

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 09:06

Effac?s par erreur

191 lines of code changed in:

• BioTools/src/biotools/nucleic: SequinEntry.java (new 191)

vloux 2005-04-04 15:26

Bugfixes

0 lines of code changed in:

• 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)

vloux 2005-02-02 16:43

Export in sequin feature table format <http://www.ncbi.nlm.nih.gov/Genbank/genomesubmit.html#fig2>

223 lines of code changed in:

• BioTools/src/biotools/nucleic: NucleicFeatureLocation.java (+34 -1), SequinEntry.java (new 189)

(3 more)