Module Agmial2/pa_manager/src/pam/protdb/

back to main page

Summary Period: 2004-09-29 to 2006-11-22

Modules

[root]/Agmial2/pa_manager/src/pam/protdb

Lines of Code

Total Lines Of Code: 7424 (2006-12-21 16:51)

Authors

Most Recent Commits

vloux 2006-11-22 17:30

ProteinDB : getPAMotifFeature : added paramId filter.

1 lines of code changed in:

• Agmial2/pa_manager/src/pam/protdb: ProteinDB.java (+1 -1)

vloux 2006-11-18 16:21

ProteinDB : getPAMotifFeature : added paramId filter.

2 lines of code changed in:

• Agmial2/pa_manager/src/pam/protdb: ProteinDB.java (+2 -2)

vloux 2006-11-16 16:46

Addition of a statistics page with pie charts (Function, Status, EC) made with JFreeChart.

206 lines of code changed in:

• Agmial2/pa_manager/src/pam/protdb: PAMProtein.java (+1), ProteinDB.java (+205 -5)

vloux 2006-10-25 11:41

Merge CedricSoubrie branch and HEAD

4 lines of code changed in:

• Agmial2/pa_manager/src/pam/protdb: MetaDataRetriever.java (del), ProteinDB.java (+4 -2), QueryBuilder.java (del)

vloux 2006-05-03 17:42

#BugFix :
Paralog display (ParalogyTable // HomologyGraphic)
SerachAnnotationPanel : serach by gene of interest fixed.

66 lines of code changed in:

• Agmial2/pa_manager/src/pam/protdb: ProteinDB.java (+66)

csoubrie 2006-04-24 15:06

Class added for the new searchPanel (first Version)

0 lines of code changed in:

• Agmial2/pa_manager/src/pam/protdb: MetaDataRetriever.java (new), QueryBuilder.java (new)

vloux 2006-04-20 16:59

ConnectionPool :
- clean destroy

ActionsQueues/Motivations :
- sleepTime passed in constructor

ProteinDB/DAOs :
- statements not released properly causing locks

14 lines of code changed in:

• Agmial2/pa_manager/src/pam/protdb: PAMHomologyResultSchema.java (-1), PAMProteinActionSchema.java (-1), PAMProteinRefActionSchema.java (-1), ProteinDB.java (+14 -2)

vloux 2006-04-04 15:04

Browse by Locus Tag

49 lines of code changed in:

• Agmial2/pa_manager/src/pam/protdb: PAMProteinRef.java (+25 -1), PAMProteinRefSchema.java (+1 -1), ProteinDB.java (+23 -7)

vloux 2006-03-17 17:13

Bugfixes

11 lines of code changed in:

• Agmial2/pa_manager/src/pam/protdb: ProteinDB.java (+11 -7)

vloux 2006-03-16 13:01

Chgt wsdl
Pool connection sgbd
BugFix Search
Control

1704 lines of code changed in:

• Agmial2/pa_manager/src/pam/protdb: PAMHomologyResultSchema.java (+14 -10), PAMProtein.java (+7 -4), PAMProteinSchema.java (+160 -161), ProteinDB.java (+1523 -1395)

vloux 2006-03-07 15:27

[#197] Listes proteines
BugFix

57 lines of code changed in:

• Agmial2/pa_manager/src/pam/protdb: PAMProteinListSchema.java (+35), ProteinDB.java (+22)

vloux 2006-03-06 10:31

[#203] S?curit? : Single SignOn +Form based Login
PAM
[#213] Filtrer quote et retours chariots dans les formulaires
PAM

15 lines of code changed in:

• Agmial2/pa_manager/src/pam/protdb: ProteinDB.java (+15)

vloux 2006-02-27 14:41

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

51 lines of code changed in:

• Agmial2/pa_manager/src/pam/protdb: PAMProteinListSchema.java (+23 -1), ProteinDB.java (+28)

vloux 2006-02-24 15:58

AGMIAL Feature #197
Gestion liste

530 lines of code changed in:

• Agmial2/pa_manager/src/pam/protdb: PAMProtein.java (+27 -4), PAMProteinList.java (new 102), PAMProteinListSchema.java (new 200), ProteinDB.java (+201 -1)

vloux 2006-01-16 08:58

Changement de start ? la vol?e (Affichage dans editFeature de tous les starts putatifs de l'ORF, transmission des annotations existantes).

65 lines of code changed in:

• Agmial2/pa_manager/src/pam/protdb: PAMProteinRefActionSchema.java (+8), PAMProteinSchema.java (+8 -1), ProteinDB.java (+49 -4)

vloux 2005-09-22 17:11

BugFixes

7 lines of code changed in:

• 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 11:50

ProtDB code improvments

396 lines of code changed in:

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

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

3162 lines of code changed in:

• 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)

agmial 2005-04-15 10:50

Homologies structuraales dans la bdd...

5 lines of code changed in:

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

vloux 2005-04-14 07:53

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

94 lines of code changed in:

• Agmial2/pa_manager/src/pam/protdb: PAMProtein.java (+28 -2), PAMProteinSchema.java (+38 -8), ProteinDB.java (+28 -9)

(5 more)