Directory Agmial2/ca_manager/src/cam/control/

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vloux 2007-10-24 11:42

ExtractORFAction :
for each CDS take the surrounding ORF and put it in a specific layer.
OrfAlign : similarity search on ORFs created by ExtractOrfAction

359 lines of code changed in:

• Agmial2/ca_manager/src/cam/control: CAMControl.java (+34 -4), ExtractOrfAction.java (new 105), FeatureCalcAction.java (new 218), UpdateCDSAction.java (+2 -1)

vloux 2006-10-25 11:34

Merge CedricSoubrie branch and HEAD

1 lines of code changed in:

• Agmial2/ca_manager/src/cam/control: BatchCalcAction.java (+1)

vloux 2006-04-20 16:58

ConnectionPool :
- clean destroy

ActionsQueues/Motivations :
- sleepTime passed in constructor

ProteinDB/DAOs :
- statements not released properly causing locks

18 lines of code changed in:

• Agmial2/ca_manager/src/cam/control: CAMActionQueue.java (+4 -7), CAMControl.java (+14)

vloux 2006-03-17 17:32

BugFix

CAM :
contigDB
Gestion DataSource
Prepa release 20060317

209 lines of code changed in:

• Agmial2/ca_manager/src/cam/control: BatchActionMotivation.java (+5 -4), BatchActionQueue.java (+11), BatchCalcAction.java (+5 -3), CAMActionQueue.java (+14 -2), CAMControl.java (+105 -65), CAMMotivation.java (+5), ContigActionMotivation.java (+11 -9), ContigActionQueue.java (+11), ContigCalcAction.java (+4 -3), FeatureActionQueue.java (+13 -1), ProjectActionQueue.java (+15 -2), TellCDSRemovedAction.java (+1 -1), UpdateCDSAction.java (+8 -13), UpdateProjectAction.java (+1 -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).

13 lines of code changed in:

• Agmial2/ca_manager/src/cam/control: TellCDSRemovedAction.java (+2 -2), UpdateCDSAction.java (+10 -7), UpdateProjectAction.java (+1 -1)

vloux 2005-09-28 14:26

BugFixes
Removed generated web.xml from repository

14 lines of code changed in:

• Agmial2/ca_manager/src/cam/control: CAMControl.java (+9 -9), QueryFeatureMotivation.java (+3 -3), UpdateCDSAction.java (+2 -2)

vloux 2005-09-22 17:11

BugFixes

8 lines of code changed in:

• Agmial2/ca_manager/src/cam/control: ProjectActionQueue.java (+1 -1), ProjectMotivation.java (+5 -3), UpdateProjectAction.java (+2 -2)

vloux 2005-08-24 10:54

CAM Summer Cleaning !
Various code cleaning (imports, externalisation of some parameters in properties files).

0 lines of code changed in:

• Agmial2/ca_manager/src/cam/control: BatchActionMotivation.java (-3), ContigActionQueue.java (-2), QueryFeatureMotivation.java (-6), TransferFeatureAction.java (-2)

vloux 2005-08-23 16:59

CAM Summer Cleaning !

+ Database Pooling with apache dbcp (Database Connection Pools <http://jakarta.apache.org/commons/dbcp/>) served via jni to the servlet. Added a context.xmlfile with all the parameters for the connection.

+ Users and Roles are no longer stored in an xml file. Management via a dedicated database, served via jni to the servlets.

CAM refactoring :
moving all select/update/insert statement into contigdb package :

admin/ContigStoreAdminImpl.java OK (2)
admin/MonitorBatchTasks.java OK (1)(2)
admin/MonitorContigTasks.java OK (2)
admin/MonitorFeatureTasks.java OK (2)
admin/MonitorProjectTasks.java OK (2)
admin/MonitorTasks.java OK (2)
admin/ShowAddBatch.java OK (2)
admin/ShowAdminBatches.java OK (2)
admin/ShowUpdateContig.java OK (2)
admin/ShowUpdateProfile.java OK (2)

control/BatchActionMotivation.java OK(2)
control/BatchActionQueue.java OK(2)
control/BatchCalcAction.java OK(2)
control/ContigActionMotivation.java OK(2)
control/ContigActionQueue.java OK(2)
control/FeatureActionQueue.java OK(2)(3)
control/ProjectActionQueue.java OK(2)
control/ProjectMotivation.java OK(2)
control/QueryFeatureMotivation.java OK(2)

reader/ContigStoreQueryImpl.java OK
reader/EditFeature.java OK(2)
reader/MugenPanel.java TODO
reader/ProfileStoreQueryImpl.java OK(2)


(1) CAMActionList creation
(2) new methods in ContigDB
(3) CAMFeature creation

New policy for database accession :
All db accession is made via classes from the contigdb package.

For each object , two classes : CAMObject is the POJO
object.CAMOjectSchema is the Data Transfer Object and make the link
between the database and the POJO.
The CAMObjectSchema has at least two methods : add(CAMObjectSchema)
and update CAMObjectSchema();
ContigDB provide methods to interact with the object, mainly
getters/setters that call the corresponding methods in CAMObjectSchema.


--> reader/MugenPanel.java TODO

568 lines of code changed in:

• Agmial2/ca_manager/src/cam/control: BatchActionMotivation.java (+10 -16), BatchActionQueue.java (+103 -119), BatchCalcAction.java (+11 -33), CAMActionQueue.java (+1 -1), CAMControl.java (+133 -129), CAMMotivation.java (+1 -1), ContigActionMotivation.java (+8 -23), ContigActionQueue.java (+6 -23), ContigCalcAction.java (+3 -2), FeatureActionQueue.java (+103 -120), ProjectActionQueue.java (+87 -106), ProjectMotivation.java (+80 -88), QueryFeatureMotivation.java (+16 -22), TransferFeatureAction.java (+3 -3), UpdateCDSAction.java (+1 -1), UpdateProjectAction.java (+2 -1)

rbossy 2005-04-21 18:09

Removage de commentaires en trop

0 lines of code changed in:

• Agmial2/ca_manager/src/cam/control: UpdateCDSAction.java (-17)

vloux 2005-04-14 07:52

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

23 lines of code changed in:

• Agmial2/ca_manager/src/cam/control: CAMControl.java (+12 -14), UpdateCDSAction.java (+11 -1)

vloux 2005-04-11 15:04

Nettoyage du code : imports, methodes deprecated ...

166 lines of code changed in:

• 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)

vloux 2005-03-02 16:28

Modifs sur en tete GPL
Correction du build.xml
Bugfix contextlistener.java
Ajout lien vers MuGenPanel dans ProteinPanel

42 lines of code changed in:

• Agmial2/ca_manager/src/cam/control: BatchActionMotivation.java (+1 -1), BatchActionQueue.java (+1 -1), BatchCalcAction.java (+1 -1), CAMActionQueue.java (+1 -1), CAMControl.java (+26 -26), CAMMotivation.java (+1 -1), ContigActionMotivation.java (+1 -1), ContigActionQueue.java (+1 -1), ContigCalcAction.java (+1 -1), FeatureActionQueue.java (+1 -1), ProjectActionQueue.java (+1 -1), ProjectMotivation.java (+1 -1), QueryFeatureMotivation.java (+1 -1), TellCDSRemovedAction.java (+1 -1), TransferFeatureAction.java (+1 -1), UpdateCDSAction.java (+1 -1), UpdateProjectAction.java (+1 -1)

vloux 2005-02-10 10:24

Preambule GPL

323 lines of code changed in:

• Agmial2/ca_manager/src/cam/control: BatchActionMotivation.java (+19), BatchActionQueue.java (+19), BatchCalcAction.java (+19), CAMActionQueue.java (+19), CAMControl.java (+19), CAMMotivation.java (+19), ContigActionMotivation.java (+19), ContigActionQueue.java (+19), ContigCalcAction.java (+19), FeatureActionQueue.java (+19), ProjectActionQueue.java (+19), ProjectMotivation.java (+19), QueryFeatureMotivation.java (+19), TellCDSRemovedAction.java (+19), TransferFeatureAction.java (+19), UpdateCDSAction.java (+19), UpdateProjectAction.java (+19)

vloux 2005-02-09 17:26

Static endpoint

88 lines of code changed in:

• Agmial2/ca_manager/src/cam/control: TellCDSRemovedAction.java (+22 -15), UpdateCDSAction.java (+45 -32), UpdateProjectAction.java (+21 -14)

vloux 2005-02-08 14:57

Cassage de pipe (3)

Build.xml OK pour ca_manger et pa_manager.
Propage l'info conteue dans project_properties.
Fin (?) ajustements jwsdp1.5
Plus de startup_agmial/shutdown_agmial car nous deployons la webapp. A la place deploy-agmial/undeploy_agmial. La webapp est deployee -> il suffit de demarrer tomcat pour qu'elle soit dispo ...

13 lines of code changed in:

• Agmial2/ca_manager/src/cam/control: CAMControl.java (+4 -2), CAMControl.java.in (del), TellCDSRemovedAction.java (+3 -2), TellCDSRemovedAction.java.in (del), TransferFeatureAction.java (-1), UpdateCDSAction.java (+4 -2), UpdateProjectAction.java (+2 -2), UpdateProjectAction.java.in (del)

rbossy 2004-09-29 16:40

Initial revision

2267 lines of code changed in:

• Agmial2/ca_manager/src/cam/control: BatchActionMotivation.java (new 101), BatchActionQueue.java (new 145), BatchCalcAction.java (new 153), CAMActionQueue.java (new 85), CAMControl.java (new 197), CAMControl.java.in (new), CAMMotivation.java (new 64), ContigActionMotivation.java (new 102), ContigActionQueue.java (new 145), ContigCalcAction.java (new 134), FeatureActionQueue.java (new 145), ProjectActionQueue.java (new 145), ProjectMotivation.java (new 108), QueryFeatureMotivation.java (new 119), TellCDSRemovedAction.java (new 84), TellCDSRemovedAction.java.in (new), TransferFeatureAction.java (new 88), UpdateCDSAction.java (new 372), UpdateProjectAction.java (new 80), UpdateProjectAction.java.in (new)