Lines of Code
[root]/Agmial2/ca_manager/src/cam/reader
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 127 (100.0%) | 19232 (100.0%) | 151.4 |
| rbossy | 14 (11.0%) | 11509 (59.8%) | 822.0 |
| vloux | 107 (84.3%) | 6228 (32.4%) | 58.2 |
| miquenti | 5 (3.9%) | 1494 (7.8%) | 298.8 |
| agmial | 1 (0.8%) | 1 (0.0%) | 1.0 |
ExtractORFAction :
for each CDS take the surrounding ORF and put it in a specific layer.
OrfAlign : similarity search on ORFs created by ExtractOrfAction
5 lines of code changed in:
Merge CedricSoubrie branch and HEAD
5 lines of code changed in:
BugFix
CAM :
contigDB
Gestion DataSource
Prepa release 20060317
107 lines of code changed in:
Fin nettoyage properties cam/pam
Fin nettoyage url en dur
Ajouts page par defaut erreurs 404,401,500 dans agmial_directory,pam,cam
[#213] Filtrer quote et retours chariots dans les formulaires
Filtre cot? client par javascript
7 lines of code changed in:
EdtFeature :
changement start
Affichage start putatifs a la demande et uniquement si CDS
38 lines of code changed in:
[#200] Export donn?es format tabul? CGView
Ajout properties pour affichage Lien CGView (cgview.enabled)
Creation CGViewPanel
+ Nettoyage (template)_project_properties
+ Generation auto liens du main_menu.html par build.xml
244 lines of code changed in:
Changement de start ? la vol?e (Affichage dans editFeature de tous les starts putatifs de l'ORF, transmission des annotations existantes).
168 lines of code changed in:
BugFixes
Removed generated web.xml from repository
1 lines of code changed in:
BugFixes
5 lines of code changed in:
CAM Summer Cleaning !
Various code cleaning (imports, externalisation of some parameters in properties files).
39 lines of code changed in:
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
328 lines of code changed in:
Move project-specific paths to web.xml
5 lines of code changed in:
Fasta protein & gene export
+ FastaCreator : Create (multi) fasta (nucleic or proteic) from agmial_id and contig_accession.
41 lines of code changed in:
+ ClustalLauncher : launch clustal to produce alignement for jalview
+ FastaCreator : Create (multi) fasta (nucleic or proteic) from agmial_id and contig_accession.
+ ContigDB : refactoring.
154 lines of code changed in:
GlobalPanel
MugenPanel Interface (admin & readOnly) Improved
Multiple bugfixes
3116 lines of code changed in:
Int?gration de Jalview
HomologyPanel : construction de tableaux de r?sum? avec boite ? cocher
ProteinPanel : bouton de soumission "Jalview checked sequences"
+ JalviewLauncher : page de lancement de Jalview
+ FastaCreator : cr?e un fichier fasta regroupant les sequences des prots pass?es en parametre
1 lines of code changed in:
Modification du readOnly
113 lines of code changed in:
Correction bug precision
15 lines of code changed in:
(MQuentin) EditFeature + MugenPanel final commit
1366 lines of code changed in:
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
1 lines of code changed in:
(13 more)