Directory Agmial2/pa_manager/src/pam/control/

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Most Recent Commits

vloux 2007-01-11 10:50

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

88 lines of code changed in:

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

vloux 2006-11-25 14:35

+ EC transfert : if descript contains (EC x.x.x.x) pattern, tansfer it to EC field

34 lines of code changed in:

• Agmial2/pa_manager/src/pam/control: DetermineFunctionAction.java (+34 -10)

vloux 2006-10-25 11:41

Merge CedricSoubrie branch and HEAD

16 lines of code changed in:

• Agmial2/pa_manager/src/pam/control: PAMActionQueue.java (+1 -1), PAMControl.java (+10 -5), ProteinActionQueue.java (+5 -1)

vloux 2006-04-20 17:33

ConnectionPool :
- clean destroy

14 lines of code changed in:

• Agmial2/pa_manager/src/pam/control: PAMControl.java (+14)

vloux 2006-04-20 16:59

ConnectionPool :
- clean destroy

ActionsQueues/Motivations :
- sleepTime passed in constructor

ProteinDB/DAOs :
- statements not released properly causing locks

74 lines of code changed in:

• Agmial2/pa_manager/src/pam/control: PAMActionQueue.java (+17 -10), PAMControl.java (+20 -7), ProteinActionQueue.java (+18), ProteinRefActionQueue.java (+19)

vloux 2006-03-16 13:01

Chgt wsdl
Pool connection sgbd
BugFix Search
Control

107 lines of code changed in:

• Agmial2/pa_manager/src/pam/control: DetermineFunctionAction.java (+45 -16), PAMControl.java (+21 -21), ProteinCalcAction.java (+35 -20), SwissAnnotAction.java (+6 -4)

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

681 lines of code changed in:

• Agmial2/pa_manager/src/pam/control: AfterActionMotivation.java (+79 -96), DetermineFunctionAction.java (+189 -133), HomologyResultsMotivation.java (+76 -91), NotifyFunctionAction.java (+1 -1), NotifyFunctionMotivation.java (+79 -94), PAMControl.java (+73 -70), ParalogResultsMotivation.java (del), ProteinActionMotivation.java (+15 -25), ProteinActionQueue.java (+70 -125), ProteinCalcAction.java (+2 -4), ProteinRefActionQueue.java (+66 -107), SwissAnnotAction.java (+31 -28)

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

22 lines of code changed in:

• Agmial2/pa_manager/src/pam/control: DetermineFunctionAction.java (+1 -1), NotifyFunctionAction.java (+4 -1), NotifyFunctionMotivation.java (+2 -2), PAMControl.java (+14 -13), ProteinRefActionQueue.java (+1)

agmial 2005-04-13 15:03

Added the FROST_CALC skill.
Added restrictions on motivations of protein calculations:
- setMinProteinSizeRestriction: motivation only for proteins larger than the given threshold
- setMaxProteinSizeRestriction: motivation only for proteins smaller than the given threshold
- setTargetSourceRestriction: motivation only for proteins from the given source
TODO: restriction on datasets

48 lines of code changed in:

• Agmial2/pa_manager/src/pam/control: PAMControl.java (+19), ProteinActionMotivation.java (+29 -1)

vloux 2005-04-11 15:04

Nettoyage du code : imports, methodes deprecated ...

116 lines of code changed in:

• Agmial2/pa_manager/src/pam/control: AfterActionMotivation.java (+7 -11), DetermineFunctionAction.java (+8 -20), HomologyResultsMotivation.java (+7 -11), NotifyFunctionAction.java (+11 -21), NotifyFunctionMotivation.java (+7 -11), PAMActionQueue.java (+2 -10), PAMControl.java (+12 -13), PAMMotivation.java (+4 -8), ParalogResultsMotivation.java (+7 -11), ProteinActionMotivation.java (+5 -10), ProteinActionQueue.java (+11 -11), ProteinCalcAction.java (+15 -15), ProteinRefActionQueue.java (+11 -11), SwissAnnotAction.java (+9 -24)

vloux 2005-03-02 16:25

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

44 lines of code changed in:

• Agmial2/pa_manager/src/pam/control: AfterActionMotivation.java (+1 -1), DetermineFunctionAction.java (+1 -1), HomologyResultsMotivation.java (+1 -1), NotifyFunctionAction.java (+1 -1), NotifyFunctionMotivation.java (+1 -1), PAMActionQueue.java (+1 -1), PAMControl.java (+31 -31), PAMMotivation.java (+1 -1), ParalogResultsMotivation.java (+1 -1), ProteinActionMotivation.java (+1 -1), ProteinActionQueue.java (+1 -1), ProteinCalcAction.java (+1 -1), ProteinRefActionQueue.java (+1 -1), SwissAnnotAction.java (+1 -1)

vloux 2005-02-10 10:27

Preambule GPL

266 lines of code changed in:

• Agmial2/pa_manager/src/pam/control: AfterActionMotivation.java (+19), DetermineFunctionAction.java (+19), HomologyResultsMotivation.java (+19), NotifyFunctionAction.java (+19), NotifyFunctionMotivation.java (+19), PAMActionQueue.java (+19), PAMControl.java (+19), PAMMotivation.java (+19), ParalogResultsMotivation.java (+19), ProteinActionMotivation.java (+19), ProteinActionQueue.java (+19), ProteinCalcAction.java (+19), ProteinRefActionQueue.java (+19), SwissAnnotAction.java (+19)

vloux 2005-02-09 17:26

Static endpoint

23 lines of code changed in:

• Agmial2/pa_manager/src/pam/control: DetermineFunctionAction.java (-3), NotifyFunctionAction.java (+23 -17)

vloux 2005-02-08 14:58

Cassage de pipe (5)

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 ...

2 lines of code changed in:

• Agmial2/pa_manager/src/pam/control: NotifyFunctionAction.java (+2 -2), NotifyFunctionAction.java.in (del), PAMControl.java.in (del)

rbossy 2004-09-29 16:40

Initial revision

1791 lines of code changed in:

• Agmial2/pa_manager/src/pam/control: AfterActionMotivation.java (new 115), DetermineFunctionAction.java (new 147), HomologyResultsMotivation.java (new 107), NotifyFunctionAction.java (new 90), NotifyFunctionAction.java.in (new), NotifyFunctionMotivation.java (new 102), PAMActionQueue.java (new 99), PAMControl.java (new 341), PAMControl.java.in (new), PAMMotivation.java (new 59), ParalogResultsMotivation.java (new), ProteinActionMotivation.java (new 103), ProteinActionQueue.java (new 164), ProteinCalcAction.java (new 133), ProteinRefActionQueue.java (new 149), SwissAnnotAction.java (new 182)