October 2004 Commit Log

Number of Commits:

11

Number of Active Developers:

2

vloux 2004-10-20 11:00 #11

ca_manager :
Modification in ContigDB and ContigSoreQueryImpl to improve performances.
Modifications in MugenPanel and EditFeature to improve performances.

Biotools :
add a method in Nucleic to get the number of features associated with it.

152 lines of code changed in:

• Agmial2/ca_manager/src/cam/reader: ContigStoreQueryImpl.java (+25 -20), EditFeature.java (+12 -13), MugenPanel.java (+108 -91)
• BioTools/src/biotools/nucleic: Nucleic.java (+3), NucleicFeatureTable.java (+4 -1)

vloux 2004-10-20 10:09 #10

Artemis :
specific urls (link to ContigStore* ; ProteinPanel) and keywords( organization, manager ...) are centralized into the project_properties file. Optionally user name and password can be stored to be prefilled in the authentification dialog.
One has to launch artemis with the following parameters :
./agmial -options project_properties

ca_manager :
Modification in ContigDB and ContigSoreQueryImpl to improve performances.
Modifications in MugenPanel and EditFeature to improve performances.

Biotools :
add a method in Nucleic to get the number of features associated with it.

86 lines of code changed in:

• Agmial2: template_project.properties (+35)
• Agmial2/artemis_client/ARTEMIS/etc: options (+1 -19)
• Agmial2/artemis_client/src/agmial/artemis: AgmialAccessDialog.java (+8 -3), AgmialAuthenticateDialog.java (+5 -3)
• Agmial2/ca_manager/src/cam/contigdb: ContigDB.java (+37 -6)

rbossy 2004-10-12 18:21 #9

On installe a partir de Agmial2/build.xml, les targets sont
start_cam -> ca_manager/build.xml:install
start_pam -> pa_manager/build.xml:install
start_dir -> agmial_directory/build.xml:install
start_all ...
stop_cam -> ca_manager/build.xml:remove
stop_pam -> pa_manager/build.xml:remove
stop_dir -> agmial_directory/build.xml:remove
stop_all ...

Agmial2/build.xml lit les fichiers de config: web_services.properties, organization.properties et project.properties

Les fichiers agmial_directory/build.xml, ca_manager/build.xml, pa_manager/build.xml ne sont plus a configurer puisqu'ils heritent de ces trois fichiers de conf.
Les fichiers ca_manager/web/web.xml, pa_manager/web/web.xml et pa_manager/web/web_public_dir.xml ne sont plus a configurer non plus car les build.xml respectifs effectuent les remplacements appropries.

103 lines of code changed in:

• Agmial2: build.xml (+32 -24), template_project.properties (new 25), web_services.properties (new 4)
• Agmial2/agmial_directory: build.xml (+9 -18), web_services.properties (del)
• Agmial2/ca_manager: build.xml (+22 -21)
• Agmial2/ca_manager/web: web.xml (+11 -11)

rbossy 2004-10-12 13:01 #8

Ajout des target "start" et "stop" dans Agmial2/build.xml qui remontent dans les trois modules pour faire les install.

15 lines of code changed in:

• Agmial2: build.xml (+15 -1)

vloux 2004-10-07 08:26 #7

Bug fix

7 lines of code changed in:

• Agmial2/artemis_client/src/agmial/artemis: AgmialAccessDialog.java (+7 -7)

vloux 2004-10-06 14:51 #6

Externalisation of keywords/Identifier to retriev info from UDDI in ARTEMIS/etc/options

ARTEMIS/diana/components/FeatureDisplay.java : better browser launch (works for windows).

143 lines of code changed in:

• Agmial2/artemis_client/ARTEMIS/diana/components: FeatureDisplay.java (+96 -8)
• Agmial2/artemis_client/ARTEMIS/etc: options (+11 -3)
• Agmial2/artemis_client/src/agmial/artemis: AgmialAccessDialog.java (+7 -7), AgmialInterfaceImpl.java (+29 -14)

vloux 2004-10-05 15:10 #5

Imporvement of the way GenBankEntry are generated. Consumes less memory. Hope to avaoid java.lang.OutOfMemoryError ...

63 lines of code changed in:

• BioTools/src/biotools/nucleic: GenBankEntry.java (+27 -27), NucleicEntry.java (+18 -6), NucleicFeature.java (-5), NucleicFeatureLocation.java (+18 -8)

vloux 2004-10-05 15:09 #4

Improvements of the way contig region are retrieved (No mor java.lang.OutOfMemeory Errors).

29 lines of code changed in:

• Agmial2/ca_manager/src/cam/contigdb: ContigDB.java (+5 -6)
• Agmial2/ca_manager/src/cam/lifecycle: ContextListener.java (+3 -3)
• Agmial2/ca_manager/src/cam/reader: ContigStoreQueryImpl.java (+21 -16)

vloux 2004-10-05 15:08 #3

Better memory footprint.
Added the src_xsdl files (more convenient)

188 lines of code changed in:

• Agmial2/artemis_client/src/agmial/artemis: AgmialAccessDialog.java (+21 -5), AgmialDocument.java (+9 -1), AgmialInterfaceImpl.java (+4 -4)
• Agmial2/artemis_client/src_wsdl: ContigStoreAdmin.wsdl (new 44), ContigStoreQuery.wsdl (new 89), ProfileStoreQuery.wsdl (new 21)

rbossy 2004-10-04 16:38 #2

Ona nettoye startup_agmial et shutdown_agmial
Ca marche jusqu'a un certain point (agmial_directory + pages de gardes des modules).

34 lines of code changed in:

• Agmial2: shutdown_agmial (+5 -65), startup_agmial (+4 -65)
• Agmial2/agmial_directory: build.xml (+1 -1), web_services.properties (+1 -1)
• Agmial2/ca_manager: build.xml (+1 -1), cam_manager.properties (+10 -10)
• Agmial2/common: build.xml (+5)
• Agmial2/pa_manager: build.xml (+1 -1), pam_manager.properties (+5 -5)
• Agmial2/pa_manager/src/pam/reader: ParalogTable.java (+1 -1)

rbossy 2004-10-04 15:03 #1

Ajout de src_wsdl (trop galere de le refire)
Fix des build.xml et des web.xml

248 lines of code changed in:

• Agmial2/agmial_directory: build.xml (+2 -2), web_services.properties (+2 -2)
• Agmial2/ca_manager: build.xml (+5 -5)
• Agmial2/ca_manager/src_wsdl: ProteinSourceAdmin.wsdl (new 86)
• Agmial2/ca_manager/web: web.xml (+11 -11)
• Agmial2/common: build.xml (+1 -1)
• Agmial2/pa_manager: build.xml (+7 -7)
• Agmial2/pa_manager/src_wsdl: ContigStoreAdmin.wsdl (new 121)
• Agmial2/pa_manager/web: web.xml (+13 -13)

September 2004 »