jabaws.git
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

11 years agoAdd a file with the runnig command and environment in each wrok dir
Sasha Sherstnev [Thu, 8 Aug 2013 13:23:35 +0000 (14:23 +0100)]
Add a file with the runnig command and environment in each wrok dir

11 years agoImprove coding style
Sasha Sherstnev [Thu, 8 Aug 2013 13:19:29 +0000 (14:19 +0100)]
Improve coding style

11 years agoChange header
Sasha Sherstnev [Thu, 8 Aug 2013 13:13:52 +0000 (14:13 +0100)]
Change header

change header

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

11 years agoAdd a file with the runnig command and environment in each wrok dir
Sasha Sherstnev [Thu, 8 Aug 2013 13:23:35 +0000 (14:23 +0100)]
Add a file with the runnig command and environment in each wrok dir

11 years agoImprove coding style
Sasha Sherstnev [Thu, 8 Aug 2013 13:19:29 +0000 (14:19 +0100)]
Improve coding style

11 years agochange header
Sasha Sherstnev [Thu, 8 Aug 2013 13:15:19 +0000 (14:15 +0100)]
change header

11 years agoChange header
Sasha Sherstnev [Thu, 8 Aug 2013 13:13:52 +0000 (14:13 +0100)]
Change header

11 years ago1st working Jpred tester
Sasha Sherstnev [Thu, 8 Aug 2013 13:12:52 +0000 (14:12 +0100)]
1st working Jpred tester

11 years agoCheck and correct several runner testers
Sasha Sherstnev [Thu, 8 Aug 2013 13:12:07 +0000 (14:12 +0100)]
Check and correct several runner testers

11 years agoRemove unused global varibles
Sasha Sherstnev [Thu, 8 Aug 2013 12:16:14 +0000 (13:16 +0100)]
Remove unused global varibles

11 years agoAdd test of parser of Jpred output
Sasha Sherstnev [Thu, 8 Aug 2013 12:15:19 +0000 (13:15 +0100)]
Add test of parser of Jpred output

11 years agouncomment limit files in order to make some tests successful
Sasha Sherstnev [Thu, 8 Aug 2013 12:13:30 +0000 (13:13 +0100)]
uncomment limit files in order to make some tests successful

11 years agoAdd results of tests of Jpred
Sasha Sherstnev [Thu, 8 Aug 2013 12:12:04 +0000 (13:12 +0100)]
Add results of tests of Jpred

11 years agoAdd Jpred result files
Sasha Sherstnev [Thu, 8 Aug 2013 12:10:37 +0000 (13:10 +0100)]
Add Jpred result files

11 years agoWebservice works! but only supports some parameters. Replacing RNAstuct
Daniel Barton [Thu, 8 Aug 2013 09:34:34 +0000 (10:34 +0100)]
Webservice works! but only supports some parameters. Replacing RNAstuct
with String.

11 years agoNecessary modifications in JABAWS for Jpred
Sasha Sherstnev [Wed, 7 Aug 2013 16:28:09 +0000 (17:28 +0100)]
Necessary modifications in JABAWS for Jpred

11 years agoDescribe new parameters of Jpred
Sasha Sherstnev [Wed, 7 Aug 2013 16:23:58 +0000 (17:23 +0100)]
Describe new parameters of Jpred

11 years agoModify Jpred for JABAWS
Sasha Sherstnev [Wed, 7 Aug 2013 16:19:16 +0000 (17:19 +0100)]
Modify Jpred for JABAWS

11 years agoSimple datamodel for RNAalifold.exe output and method to convert from
Daniel Barton [Mon, 5 Aug 2013 16:51:47 +0000 (17:51 +0100)]
Simple datamodel for RNAalifold.exe output and method to convert from
fasta to clustal format and write clustal input files.

11 years agoParameters Tester updated. Untested webservice code. generate xsd/wsdl?
Daniel Barton [Sun, 4 Aug 2013 21:05:46 +0000 (22:05 +0100)]
Parameters Tester updated. Untested webservice code. generate xsd/wsdl?

11 years agoBasic Testing Setup, no getResults method yet
Daniel Barton [Sat, 3 Aug 2013 11:18:32 +0000 (12:18 +0100)]
Basic Testing Setup, no getResults method yet

11 years agoAdd Java wrapper class for Jpred
Sasha Sherstnev [Fri, 2 Aug 2013 16:20:05 +0000 (17:20 +0100)]
Add Java wrapper class for Jpred

11 years agoRe-format configuration files
Sasha Sherstnev [Fri, 2 Aug 2013 16:18:28 +0000 (17:18 +0100)]
Re-format configuration files

11 years agoadd results of one Jpred test
Sasha Sherstnev [Fri, 2 Aug 2013 16:17:57 +0000 (17:17 +0100)]
add results of one Jpred test

11 years agoAdd converion Jpred output from align/jnet to fasta
Sasha Sherstnev [Fri, 2 Aug 2013 16:15:25 +0000 (17:15 +0100)]
Add converion Jpred output from align/jnet to fasta

11 years agoChange JABAWS version: 2.0.1 -> 2.5
Sasha Sherstnev [Fri, 2 Aug 2013 13:38:12 +0000 (14:38 +0100)]
Change JABAWS version: 2.0.1 -> 2.5