jabaws.git
11 years agoChange default formatting
Sasha Sherstnev [Thu, 26 Sep 2013 13:33:00 +0000 (14:33 +0100)]
Change default formatting

11 years agoRefactoring (renaming) 2 classes: AsyncJobRunner.java -> AsyncClusterRunner.java...
Sasha Sherstnev [Thu, 26 Sep 2013 13:30:04 +0000 (14:30 +0100)]
Refactoring (renaming) 2 classes: AsyncJobRunner.java -> AsyncClusterRunner.java and JobRunner.java -> ClusterRunner.java

11 years agoAssign JABAService.V2_SERVICE_NAMESPACE to all new services: JpredWS, RNAalifoldWS...
Sasha Sherstnev [Tue, 24 Sep 2013 16:35:06 +0000 (17:35 +0100)]
Assign JABAService.V2_SERVICE_NAMESPACE to all new services: JpredWS, RNAalifoldWS, MSAprobsWS, GLprobsWS

11 years agoFix a problem with JSP page
Sasha Sherstnev [Tue, 24 Sep 2013 14:36:34 +0000 (15:36 +0100)]
Fix a problem with JSP page

11 years agoReplace binaries with one compatible with the dundee cluster
Sasha Sherstnev [Tue, 24 Sep 2013 14:32:06 +0000 (15:32 +0100)]
Replace binaries with one compatible with the dundee cluster

11 years agoAdd all needed infrastructure for MSAprobs and GLprobs
Sasha Sherstnev [Tue, 24 Sep 2013 14:11:53 +0000 (15:11 +0100)]
Add all needed infrastructure for MSAprobs and GLprobs

11 years agoAdd measurement of execution time for servlets
Sasha Sherstnev [Tue, 24 Sep 2013 14:10:38 +0000 (15:10 +0100)]
Add measurement of execution time for servlets

11 years agoAdd GLprobs and MSAprobs to binaries
Sasha Sherstnev [Tue, 24 Sep 2013 14:08:57 +0000 (15:08 +0100)]
Add GLprobs and MSAprobs to binaries

11 years agoRefactoring: rename duplicated Util classes
Sasha Sherstnev [Fri, 20 Sep 2013 14:32:07 +0000 (15:32 +0100)]
Refactoring: rename duplicated Util classes

11 years agoadd lost exception
Sasha Sherstnev [Fri, 20 Sep 2013 13:35:23 +0000 (14:35 +0100)]
add lost exception

11 years agoFix problems with tests
Sasha Sherstnev [Fri, 20 Sep 2013 12:48:19 +0000 (13:48 +0100)]
Fix problems with tests

11 years agoJWS-17 re-design behaviour of Option.toString
Sasha Sherstnev [Thu, 19 Sep 2013 13:44:57 +0000 (14:44 +0100)]
JWS-17 re-design behaviour of Option.toString

11 years agoRe-generate WS artefacts: option.furtherDetails is xs:string now
Sasha Sherstnev [Thu, 19 Sep 2013 12:47:25 +0000 (13:47 +0100)]
Re-generate WS artefacts: option.furtherDetails is xs:string now

11 years agoJWS-17: fix problem with undefined URL for the furtherDetails tag
Sasha Sherstnev [Thu, 19 Sep 2013 12:46:16 +0000 (13:46 +0100)]
JWS-17: fix problem with undefined URL for the furtherDetails tag

11 years agoAdd reference on Jronn
Sasha Sherstnev [Tue, 17 Sep 2013 16:12:56 +0000 (17:12 +0100)]
Add reference on Jronn

11 years agoFinal fixing of Jpred problem with casting
Sasha Sherstnev [Tue, 17 Sep 2013 14:35:24 +0000 (15:35 +0100)]
Final fixing of Jpred problem with casting

11 years agoFix probem with metadata
Sasha Sherstnev [Tue, 17 Sep 2013 14:20:15 +0000 (15:20 +0100)]
Fix probem with metadata

11 years agoRemove unused imports
Sasha Sherstnev [Tue, 17 Sep 2013 10:46:10 +0000 (11:46 +0100)]
Remove unused imports

11 years agoClean up logging system
Sasha Sherstnev [Tue, 17 Sep 2013 10:22:48 +0000 (11:22 +0100)]
Clean up logging system

11 years agoNew Linux binaries for ViennaRNA
Sasha Sherstnev [Mon, 16 Sep 2013 16:22:00 +0000 (17:22 +0100)]
New Linux binaries for ViennaRNA

11 years agoFix bug with fail WS tests
Sasha Sherstnev [Mon, 16 Sep 2013 16:21:35 +0000 (17:21 +0100)]
Fix bug with fail WS tests

11 years agoAdd info on new programs
Sasha Sherstnev [Mon, 16 Sep 2013 15:06:57 +0000 (16:06 +0100)]
Add info on new programs

11 years agoChange JABAWS version at the website
Sasha Sherstnev [Mon, 16 Sep 2013 14:57:00 +0000 (15:57 +0100)]
Change JABAWS version at the website

11 years agoSet right path to UNIREF at ningal
Sasha Sherstnev [Mon, 16 Sep 2013 14:28:52 +0000 (15:28 +0100)]
Set right path to UNIREF at ningal

11 years agoRe-design the ServiceStatus JSP page
Sasha Sherstnev [Mon, 16 Sep 2013 14:17:02 +0000 (15:17 +0100)]
Re-design the ServiceStatus JSP page

11 years agoDefine proper test for JpredWS
Sasha Sherstnev [Mon, 16 Sep 2013 14:16:35 +0000 (15:16 +0100)]
Define proper test for JpredWS

11 years agoSet right permissions for Jpred binaries
Sasha Sherstnev [Mon, 16 Sep 2013 14:15:46 +0000 (15:15 +0100)]
Set right permissions for Jpred binaries

11 years agoMade the binary executable at ningal
Sasha Sherstnev [Mon, 16 Sep 2013 14:15:10 +0000 (15:15 +0100)]
Made the binary executable at ningal

11 years agoNew set of presets for Jpred
Sasha Sherstnev [Fri, 13 Sep 2013 15:45:35 +0000 (16:45 +0100)]
New set of presets for Jpred

11 years agoNew Jpred parameters and new set of Jpred presets
Sasha Sherstnev [Fri, 13 Sep 2013 15:44:21 +0000 (16:44 +0100)]
New Jpred parameters and new set of Jpred presets

11 years agoFix problem with wrong casting Alignment -> JpredAlignment
Sasha Sherstnev [Fri, 13 Sep 2013 15:43:32 +0000 (16:43 +0100)]
Fix problem with wrong casting Alignment -> JpredAlignment

11 years agoAdd SS prediction for multiple aligment into jpred.pl. Before this was a part of...
Sasha Sherstnev [Fri, 13 Sep 2013 14:47:42 +0000 (15:47 +0100)]
Add SS prediction for multiple aligment into jpred.pl. Before this was a part of another script

11 years agoRemove un-necessary Axis servlets
Sasha Sherstnev [Thu, 12 Sep 2013 08:43:50 +0000 (09:43 +0100)]
Remove un-necessary Axis servlets

11 years agoMore commands...
Sasha Sherstnev [Wed, 11 Sep 2013 16:17:31 +0000 (17:17 +0100)]
More commands...

11 years agoFix problem with the JpredWS service. Now Jws2Client is able to test the service
Sasha Sherstnev [Wed, 11 Sep 2013 16:13:02 +0000 (17:13 +0100)]
Fix problem with the JpredWS service. Now Jws2Client is able to test the service

11 years agoLog file for preparing of new version of wsdl and xsd files for all services
Sasha Sherstnev [Tue, 10 Sep 2013 15:10:56 +0000 (16:10 +0100)]
Log file for preparing of new version of wsdl and xsd files for all services

11 years agoImproved Bld file
Sasha Sherstnev [Tue, 10 Sep 2013 15:10:37 +0000 (16:10 +0100)]
Improved Bld file

11 years agoNew version of wsdl and xsd files for all services
Sasha Sherstnev [Tue, 10 Sep 2013 15:09:58 +0000 (16:09 +0100)]
New version of wsdl and xsd files for all services

11 years agoRe-formatting the file
Sasha Sherstnev [Tue, 10 Sep 2013 15:08:09 +0000 (16:08 +0100)]
Re-formatting the file

11 years agoFile with main building commands
Sasha Sherstnev [Tue, 10 Sep 2013 15:07:12 +0000 (16:07 +0100)]
File with main building commands

11 years agoAdd "safe type casting" warnings
Sasha Sherstnev [Tue, 10 Sep 2013 15:06:14 +0000 (16:06 +0100)]
Add "safe type casting" warnings

11 years agoFix problem with unknown services ("forward" compatibility)
Sasha Sherstnev [Tue, 10 Sep 2013 15:05:08 +0000 (16:05 +0100)]
Fix problem with unknown services ("forward" compatibility)

11 years agoAdd "safe type cast" warnings
Sasha Sherstnev [Tue, 10 Sep 2013 15:02:58 +0000 (16:02 +0100)]
Add "safe type cast" warnings

11 years agoAdd lost description of RNAalifold from ViennaRNA
Sasha Sherstnev [Mon, 9 Sep 2013 09:39:33 +0000 (10:39 +0100)]
Add lost description of RNAalifold from ViennaRNA

11 years agoMerge branch 'JABAWS_Release_2_5' into develop
Sasha Sherstnev [Fri, 6 Sep 2013 16:23:22 +0000 (17:23 +0100)]
Merge branch 'JABAWS_Release_2_5' into develop

Conflicts:
.project
WEB-INF/sun-jaxws.xml
conf/Executable.properties
testsrc/compbio/data/sequence/SequenceUtilTester.java
webservices/compbio/data/msa/Category.java
webservices/compbio/ws/client/Jws2Client.java
webservices/compbio/ws/client/Services.java
webservices/compbio/ws/client/WSTester.java
webservices/compbio/ws/server/WSUtil.java
webservices/compbio/ws/server/resource/AAConWS.wsdl
webservices/compbio/ws/server/resource/AAConWS_schema1.xsd
webservices/compbio/ws/server/resource/ClustalWS.wsdl
webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd
webservices/compbio/ws/server/resource/DisemblWS.wsdl
webservices/compbio/ws/server/resource/DisemblWS_schema1.xsd
webservices/compbio/ws/server/resource/GlobPlotWS.wsdl
webservices/compbio/ws/server/resource/GlobPlotWS_schema1.xsd
webservices/compbio/ws/server/resource/IUPredWS.wsdl
webservices/compbio/ws/server/resource/IUPredWS_schema1.xsd
webservices/compbio/ws/server/resource/JronnWS.wsdl
webservices/compbio/ws/server/resource/JronnWS_schema1.xsd
webservices/compbio/ws/server/resource/MafftWS.wsdl
webservices/compbio/ws/server/resource/MafftWS_schema1.xsd
webservices/compbio/ws/server/resource/MuscleWS.wsdl
webservices/compbio/ws/server/resource/MuscleWS_schema1.xsd
webservices/compbio/ws/server/resource/RegistryWS.wsdl
webservices/compbio/ws/server/resource/RegistryWS_schema1.xsd
webservices/compbio/ws/server/resource/TcoffeeWS.wsdl
webservices/compbio/ws/server/resource/TcoffeeWS_schema1.xsd
wsbuild.xml

11 years agoMerge branch 'JABAWS_Release_2_5' of https://source.jalview.org/git/jabaws into JABAW...
Sasha Sherstnev [Fri, 6 Sep 2013 15:33:09 +0000 (16:33 +0100)]
Merge branch 'JABAWS_Release_2_5' of https://source.jalview.org/git/jabaws into JABAWS_Release_2_5

11 years agoRegenerate wsdl-s
Sasha Sherstnev [Fri, 6 Sep 2013 15:26:24 +0000 (16:26 +0100)]
Regenerate wsdl-s

11 years agoSwitch to olde namespace
Sasha Sherstnev [Fri, 6 Sep 2013 15:25:57 +0000 (16:25 +0100)]
Switch to olde namespace

11 years agoDifferent code style
Sasha Sherstnev [Fri, 6 Sep 2013 15:25:23 +0000 (16:25 +0100)]
Different code style

11 years agoSwitch JpredWS from SequenceAnnotation to MsaWS
Sasha Sherstnev [Fri, 6 Sep 2013 14:29:24 +0000 (15:29 +0100)]
Switch JpredWS from SequenceAnnotation to MsaWS

11 years agoFix problem with path to the UNIREF database
Sasha Sherstnev [Fri, 6 Sep 2013 14:13:54 +0000 (15:13 +0100)]
Fix problem with path to the UNIREF database

11 years agoChange project name
Sasha Sherstnev [Fri, 6 Sep 2013 09:45:37 +0000 (10:45 +0100)]
Change project name

11 years agoFix problem with test data for RNAalifold RNAalifold
Sasha Sherstnev [Fri, 6 Sep 2013 09:29:59 +0000 (10:29 +0100)]
Fix problem with test data for RNAalifold

11 years agoReplace logo files
Sasha Sherstnev [Fri, 6 Sep 2013 09:29:42 +0000 (10:29 +0100)]
Replace logo files

11 years agoChange version: 2.0.1 -> 2.5
Sasha Sherstnev [Thu, 5 Sep 2013 11:10:20 +0000 (12:10 +0100)]
Change version: 2.0.1 -> 2.5

11 years agoFix logging problem
Sasha Sherstnev [Thu, 5 Sep 2013 11:04:06 +0000 (12:04 +0100)]
Fix logging problem

11 years agoAdd missing binaty and statis library
Sasha Sherstnev [Thu, 5 Sep 2013 11:03:37 +0000 (12:03 +0100)]
Add missing binaty and statis library

11 years agoAdd missing doc files
Sasha Sherstnev [Thu, 5 Sep 2013 11:03:18 +0000 (12:03 +0100)]
Add missing doc files

11 years agoReplace Progs/RNAalifold with x64 binary and add all other programs
Sasha Sherstnev [Thu, 5 Sep 2013 10:57:22 +0000 (11:57 +0100)]
Replace Progs/RNAalifold with x64 binary and add all other programs

11 years agoRoll back JpredWS JABAWS namespace: from V3 to V2. V3 will be a Matrix
Sasha Sherstnev [Thu, 5 Sep 2013 10:20:49 +0000 (11:20 +0100)]
Roll back JpredWS JABAWS namespace: from V3 to V2. V3 will be a Matrix

11 years agoFix a bug with wrong namespace
Sasha Sherstnev [Thu, 5 Sep 2013 10:19:18 +0000 (11:19 +0100)]
Fix a bug with wrong namespace

11 years agoUse "right" namespace, i.e. the name from JABAService
Sasha Sherstnev [Thu, 5 Sep 2013 10:18:26 +0000 (11:18 +0100)]
Use "right" namespace, i.e. the name from JABAService

11 years agoChange JAXWS java code and wsdl for changed methods in RegistryWS
Sasha Sherstnev [Thu, 5 Sep 2013 10:07:15 +0000 (11:07 +0100)]
Change JAXWS java code and wsdl for changed methods in RegistryWS

11 years agoOther necessary changes
Sasha Sherstnev [Thu, 5 Sep 2013 09:52:55 +0000 (10:52 +0100)]
Other necessary changes

11 years agoNew version of the JABAWS client
Sasha Sherstnev [Thu, 5 Sep 2013 09:52:28 +0000 (10:52 +0100)]
New version of the JABAWS client

11 years agoAdd new method
Sasha Sherstnev [Thu, 5 Sep 2013 09:50:39 +0000 (10:50 +0100)]
Add new method

11 years agoAdd new V3 namespace
Sasha Sherstnev [Thu, 5 Sep 2013 09:49:57 +0000 (10:49 +0100)]
Add new V3 namespace

11 years agoAdd method for reporting JABAWS namespace
Sasha Sherstnev [Thu, 5 Sep 2013 09:48:54 +0000 (10:48 +0100)]
Add method for reporting JABAWS namespace

11 years agoreport both operating and non-operating services
Sasha Sherstnev [Thu, 5 Sep 2013 09:47:56 +0000 (10:47 +0100)]
report both operating and non-operating services

11 years agoChanges which allow JpredWS test
Sasha Sherstnev [Thu, 5 Sep 2013 09:46:52 +0000 (10:46 +0100)]
Changes which allow JpredWS test

11 years agoImproved help message
Sasha Sherstnev [Thu, 5 Sep 2013 09:45:29 +0000 (10:45 +0100)]
Improved help message

11 years agomerged conf/Executable.properties
Daniel Barton [Sat, 31 Aug 2013 11:04:35 +0000 (12:04 +0100)]
merged conf/Executable.properties

11 years agoParameter bug fixed, Jalview will now run some parameters
Daniel Barton [Sat, 31 Aug 2013 10:54:03 +0000 (11:54 +0100)]
Parameter bug fixed, Jalview will now run some parameters

11 years agoA secondary parameters file with some Jalview friendly parameters
Daniel Barton [Fri, 30 Aug 2013 16:35:00 +0000 (17:35 +0100)]
A secondary parameters file with some Jalview friendly parameters

11 years agoJWS-71 - nominal Limits for RNAFold service - necessary so 'drmaa
Jim Procter [Fri, 30 Aug 2013 14:53:59 +0000 (15:53 +0100)]
JWS-71 - nominal Limits for RNAFold service - necessary so 'drmaa
library not found' exception isn't raised when submitting to cluster

11 years agoClean-up, refactoring, commenting. Parameters file containts only options since Jalvi...
Daniel Barton [Fri, 30 Aug 2013 09:57:53 +0000 (10:57 +0100)]
Clean-up, refactoring, commenting. Parameters file containts only options since Jalview still can't deal with them

11 years agoJWS-69 RNAalifold Linux Binary
Daniel [Thu, 29 Aug 2013 19:47:05 +0000 (20:47 +0100)]
JWS-69 RNAalifold Linux Binary

11 years agoMerge branch 'RNAalifold' of https://source.jalview.org/git/jabaws into RNAalifold
Daniel Luke Barton [Thu, 29 Aug 2013 15:35:22 +0000 (16:35 +0100)]
Merge branch 'RNAalifold' of https://source.jalview.org/git/jabaws into RNAalifold

11 years agoconf/Executable.properties and compilebin.sh updated for linux.
Daniel Luke Barton [Thu, 29 Aug 2013 15:33:46 +0000 (16:33 +0100)]
conf/Executable.properties and compilebin.sh updated for linux.

11 years agoCategory.java updated to include new category for RNA folding. RNAalifoldParameters...
Daniel Barton [Wed, 28 Aug 2013 21:17:49 +0000 (22:17 +0100)]
Category.java updated to include new category for RNA folding. RNAalifoldParameters.xml cut down to a number of parameters which I think are needed and which work easily with Jalview

11 years agoWSTester updated to work plus hopefully all the other changes that need to go into...
Daniel Barton [Thu, 22 Aug 2013 17:03:17 +0000 (18:03 +0100)]
WSTester updated to work plus hopefully all the other changes that need to go into the remote.

11 years agoImport RNAalifold removed from RNAStructReader. @XmlSeeAlso line added
Daniel Barton [Thu, 22 Aug 2013 13:00:35 +0000 (14:00 +0100)]
Import RNAalifold removed from RNAStructReader. @XmlSeeAlso line added
to ScoreManager.

11 years agoReverted some testing changes in TestRNAalifoldWS so that it will run
Daniel Barton [Wed, 21 Aug 2013 11:27:03 +0000 (12:27 +0100)]
Reverted some testing changes in TestRNAalifoldWS so that it will run
successfully.

11 years agoReverted some changes I made for testing back to their original states.
Daniel Barton [Wed, 21 Aug 2013 11:13:40 +0000 (12:13 +0100)]
Reverted some changes I made for testing back to their original states.

11 years agoA third commit where there should have been one.... Everything is here
Daniel Barton [Wed, 21 Aug 2013 10:57:21 +0000 (11:57 +0100)]
A third commit where there should have been one.... Everything is here
now I hope.

11 years agoUpdate the last commit which missed some files. RNAStructScoreManager
Daniel Barton [Wed, 21 Aug 2013 10:55:21 +0000 (11:55 +0100)]
Update the last commit which missed some files. RNAStructScoreManager
replacing RNAStruct. Webservices returns ScoreManager!?!-

11 years agoRNAStruct replaced by RNAStructScoreManager. Why does webservice
Daniel Barton [Wed, 21 Aug 2013 10:49:43 +0000 (11:49 +0100)]
RNAStruct replaced by RNAStructScoreManager. Why does webservice
getAnnotation method still return a ScoreManager Not an
RNAStructScoreManager?!?

11 years agoWebservices Actually working with ScoreManager
Daniel Barton [Fri, 16 Aug 2013 15:26:42 +0000 (16:26 +0100)]
Webservices Actually working with ScoreManager

11 years agoWebservice working with ScoreManager
Daniel Barton [Fri, 16 Aug 2013 15:25:31 +0000 (16:25 +0100)]
Webservice working with ScoreManager

11 years agoWebservice Updated for scoremanager but I think I broke something on the way.
Daniel Barton [Thu, 15 Aug 2013 21:19:34 +0000 (22:19 +0100)]
Webservice Updated for scoremanager but I think I broke something on the way.

11 years agoAlifold results are now parsed and stored in a ScoreManager object
Daniel Barton [Thu, 15 Aug 2013 17:13:25 +0000 (18:13 +0100)]
Alifold results are now parsed and stored in a ScoreManager object

11 years agoWebservice which implements FoldWS and returns String. Parameters.xml file
Daniel Barton [Mon, 12 Aug 2013 14:24:23 +0000 (15:24 +0100)]
Webservice which implements FoldWS and returns String. Parameters.xml file
updated in line with the RunnerConfig schema.

11 years agoMerge branch 'JABAWS_Release_2_5' of https://source.jalview.org/git/jabaws into JABAW...
Sasha Sherstnev [Fri, 9 Aug 2013 09:19:23 +0000 (10:19 +0100)]
Merge branch 'JABAWS_Release_2_5' of https://source.jalview.org/git/jabaws into JABAWS_Release_2_5

11 years agoimprove instruction for new web services
Sasha Sherstnev [Fri, 9 Aug 2013 09:15:35 +0000 (10:15 +0100)]
improve instruction for new web services

11 years agoFix problem with unknown global constants
Sasha Sherstnev [Fri, 9 Aug 2013 09:15:03 +0000 (10:15 +0100)]
Fix problem with unknown global constants

11 years agoRe-generated wsdl for old web services
Sasha Sherstnev [Fri, 9 Aug 2013 09:14:19 +0000 (10:14 +0100)]
Re-generated wsdl for old web services

11 years agoJpredWS code and codes which provide support for JpredWS
Sasha Sherstnev [Fri, 9 Aug 2013 09:13:33 +0000 (10:13 +0100)]
JpredWS code and codes which provide support for JpredWS

11 years agoRegenerated classes. No significant changes
Sasha Sherstnev [Fri, 9 Aug 2013 09:09:34 +0000 (10:09 +0100)]
Regenerated classes. No significant changes

11 years agoPrepare JABAWS for generation of wsdl for Jpred
Sasha Sherstnev [Fri, 9 Aug 2013 08:35:14 +0000 (09:35 +0100)]
Prepare JABAWS for generation of wsdl for Jpred

11 years agoAdd untracked dir
Sasha Sherstnev [Thu, 8 Aug 2013 13:25:13 +0000 (14:25 +0100)]
Add untracked dir