Sasha Sherstnev [Mon, 9 Sep 2013 09:39:33 +0000 (10:39 +0100)]
Add lost description of RNAalifold from ViennaRNA
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
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
Sasha Sherstnev [Fri, 6 Sep 2013 15:26:24 +0000 (16:26 +0100)]
Regenerate wsdl-s
Sasha Sherstnev [Fri, 6 Sep 2013 15:25:57 +0000 (16:25 +0100)]
Switch to olde namespace
Sasha Sherstnev [Fri, 6 Sep 2013 15:25:23 +0000 (16:25 +0100)]
Different code style
Sasha Sherstnev [Fri, 6 Sep 2013 14:29:24 +0000 (15:29 +0100)]
Switch JpredWS from SequenceAnnotation to MsaWS
Sasha Sherstnev [Fri, 6 Sep 2013 14:13:54 +0000 (15:13 +0100)]
Fix problem with path to the UNIREF database
Sasha Sherstnev [Fri, 6 Sep 2013 09:45:37 +0000 (10:45 +0100)]
Change project name
Sasha Sherstnev [Fri, 6 Sep 2013 09:29:59 +0000 (10:29 +0100)]
Fix problem with test data for RNAalifold
Sasha Sherstnev [Fri, 6 Sep 2013 09:29:42 +0000 (10:29 +0100)]
Replace logo files
Sasha Sherstnev [Thu, 5 Sep 2013 11:10:20 +0000 (12:10 +0100)]
Change version: 2.0.1 -> 2.5
Sasha Sherstnev [Thu, 5 Sep 2013 11:04:06 +0000 (12:04 +0100)]
Fix logging problem
Sasha Sherstnev [Thu, 5 Sep 2013 11:03:37 +0000 (12:03 +0100)]
Add missing binaty and statis library
Sasha Sherstnev [Thu, 5 Sep 2013 11:03:18 +0000 (12:03 +0100)]
Add missing doc files
Sasha Sherstnev [Thu, 5 Sep 2013 10:57:22 +0000 (11:57 +0100)]
Replace Progs/RNAalifold with x64 binary and add all other programs
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
Sasha Sherstnev [Thu, 5 Sep 2013 10:19:18 +0000 (11:19 +0100)]
Fix a bug with wrong namespace
Sasha Sherstnev [Thu, 5 Sep 2013 10:18:26 +0000 (11:18 +0100)]
Use "right" namespace, i.e. the name from JABAService
Sasha Sherstnev [Thu, 5 Sep 2013 10:07:15 +0000 (11:07 +0100)]
Change JAXWS java code and wsdl for changed methods in RegistryWS
Sasha Sherstnev [Thu, 5 Sep 2013 09:52:55 +0000 (10:52 +0100)]
Other necessary changes
Sasha Sherstnev [Thu, 5 Sep 2013 09:52:28 +0000 (10:52 +0100)]
New version of the JABAWS client
Sasha Sherstnev [Thu, 5 Sep 2013 09:50:39 +0000 (10:50 +0100)]
Add new method
Sasha Sherstnev [Thu, 5 Sep 2013 09:49:57 +0000 (10:49 +0100)]
Add new V3 namespace
Sasha Sherstnev [Thu, 5 Sep 2013 09:48:54 +0000 (10:48 +0100)]
Add method for reporting JABAWS namespace
Sasha Sherstnev [Thu, 5 Sep 2013 09:47:56 +0000 (10:47 +0100)]
report both operating and non-operating services
Sasha Sherstnev [Thu, 5 Sep 2013 09:46:52 +0000 (10:46 +0100)]
Changes which allow JpredWS test
Sasha Sherstnev [Thu, 5 Sep 2013 09:45:29 +0000 (10:45 +0100)]
Improved help message
Daniel Barton [Sat, 31 Aug 2013 11:04:35 +0000 (12:04 +0100)]
merged conf/Executable.properties
Daniel Barton [Sat, 31 Aug 2013 10:54:03 +0000 (11:54 +0100)]
Parameter bug fixed, Jalview will now run some parameters
Daniel Barton [Fri, 30 Aug 2013 16:35:00 +0000 (17:35 +0100)]
A secondary parameters file with some Jalview friendly parameters
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
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
Daniel [Thu, 29 Aug 2013 19:47:05 +0000 (20:47 +0100)]
JWS-69 RNAalifold Linux Binary
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
Daniel Luke Barton [Thu, 29 Aug 2013 15:33:46 +0000 (16:33 +0100)]
conf/Executable.properties and compilebin.sh updated for linux.
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
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.
Daniel Barton [Thu, 22 Aug 2013 13:00:35 +0000 (14:00 +0100)]
Import RNAalifold removed from RNAStructReader. @XmlSeeAlso line added
to ScoreManager.
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.
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.
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.
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!?!-
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?!?
Daniel Barton [Fri, 16 Aug 2013 15:26:42 +0000 (16:26 +0100)]
Webservices Actually working with ScoreManager
Daniel Barton [Fri, 16 Aug 2013 15:25:31 +0000 (16:25 +0100)]
Webservice working with ScoreManager
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.
Daniel Barton [Thu, 15 Aug 2013 17:13:25 +0000 (18:13 +0100)]
Alifold results are now parsed and stored in a ScoreManager object
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.
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
Sasha Sherstnev [Fri, 9 Aug 2013 09:15:35 +0000 (10:15 +0100)]
improve instruction for new web services
Sasha Sherstnev [Fri, 9 Aug 2013 09:15:03 +0000 (10:15 +0100)]
Fix problem with unknown global constants
Sasha Sherstnev [Fri, 9 Aug 2013 09:14:19 +0000 (10:14 +0100)]
Re-generated wsdl for old web services
Sasha Sherstnev [Fri, 9 Aug 2013 09:13:33 +0000 (10:13 +0100)]
JpredWS code and codes which provide support for JpredWS
Sasha Sherstnev [Fri, 9 Aug 2013 09:09:34 +0000 (10:09 +0100)]
Regenerated classes. No significant changes
Sasha Sherstnev [Fri, 9 Aug 2013 08:35:14 +0000 (09:35 +0100)]
Prepare JABAWS for generation of wsdl for Jpred
Sasha Sherstnev [Thu, 8 Aug 2013 13:25:13 +0000 (14:25 +0100)]
Add untracked 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
Sasha Sherstnev [Thu, 8 Aug 2013 13:19:29 +0000 (14:19 +0100)]
Improve coding style
Sasha Sherstnev [Thu, 8 Aug 2013 13:13:52 +0000 (14:13 +0100)]
Change header
change header
Sasha Sherstnev [Thu, 8 Aug 2013 13:25:13 +0000 (14:25 +0100)]
Add untracked 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
Sasha Sherstnev [Thu, 8 Aug 2013 13:19:29 +0000 (14:19 +0100)]
Improve coding style
Sasha Sherstnev [Thu, 8 Aug 2013 13:15:19 +0000 (14:15 +0100)]
change header
Sasha Sherstnev [Thu, 8 Aug 2013 13:13:52 +0000 (14:13 +0100)]
Change header
Sasha Sherstnev [Thu, 8 Aug 2013 13:12:52 +0000 (14:12 +0100)]
1st working Jpred tester
Sasha Sherstnev [Thu, 8 Aug 2013 13:12:07 +0000 (14:12 +0100)]
Check and correct several runner testers
Sasha Sherstnev [Thu, 8 Aug 2013 12:16:14 +0000 (13:16 +0100)]
Remove unused global varibles
Sasha Sherstnev [Thu, 8 Aug 2013 12:15:19 +0000 (13:15 +0100)]
Add test of parser of Jpred output
Sasha Sherstnev [Thu, 8 Aug 2013 12:13:30 +0000 (13:13 +0100)]
uncomment limit files in order to make some tests successful
Sasha Sherstnev [Thu, 8 Aug 2013 12:12:04 +0000 (13:12 +0100)]
Add results of tests of Jpred
Sasha Sherstnev [Thu, 8 Aug 2013 12:10:37 +0000 (13:10 +0100)]
Add Jpred result files
Daniel Barton [Thu, 8 Aug 2013 09:34:34 +0000 (10:34 +0100)]
Webservice works! but only supports some parameters. Replacing RNAstuct
with String.
Sasha Sherstnev [Wed, 7 Aug 2013 16:28:09 +0000 (17:28 +0100)]
Necessary modifications in JABAWS for Jpred
Sasha Sherstnev [Wed, 7 Aug 2013 16:23:58 +0000 (17:23 +0100)]
Describe new parameters of Jpred
Sasha Sherstnev [Wed, 7 Aug 2013 16:19:16 +0000 (17:19 +0100)]
Modify Jpred for JABAWS
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.
Daniel Barton [Sun, 4 Aug 2013 21:05:46 +0000 (22:05 +0100)]
Parameters Tester updated. Untested webservice code. generate xsd/wsdl?
Daniel Barton [Sat, 3 Aug 2013 11:18:32 +0000 (12:18 +0100)]
Basic Testing Setup, no getResults method yet
Sasha Sherstnev [Fri, 2 Aug 2013 16:20:05 +0000 (17:20 +0100)]
Add Java wrapper class for Jpred
Sasha Sherstnev [Fri, 2 Aug 2013 16:18:28 +0000 (17:18 +0100)]
Re-format configuration files
Sasha Sherstnev [Fri, 2 Aug 2013 16:17:57 +0000 (17:17 +0100)]
add results of one Jpred test
Sasha Sherstnev [Fri, 2 Aug 2013 16:15:25 +0000 (17:15 +0100)]
Add converion Jpred output from align/jnet to fasta
Sasha Sherstnev [Fri, 2 Aug 2013 13:38:12 +0000 (14:38 +0100)]
Change JABAWS version: 2.0.1 -> 2.5
Sasha Sherstnev [Fri, 2 Aug 2013 13:33:26 +0000 (14:33 +0100)]
Add new artwork
Sasha Sherstnev [Fri, 2 Aug 2013 10:41:08 +0000 (11:41 +0100)]
Impove coding style
Sasha Sherstnev [Fri, 2 Aug 2013 10:38:20 +0000 (11:38 +0100)]
Re-format the config files in order to get more readable files
Sasha Sherstnev [Fri, 2 Aug 2013 10:32:09 +0000 (11:32 +0100)]
JWS-67 configuration and manual file for jpred 3.0.1
Sasha Sherstnev [Fri, 2 Aug 2013 10:28:30 +0000 (11:28 +0100)]
JWS-67 Update internal man for jpred.pl
Sasha Sherstnev [Thu, 1 Aug 2013 17:18:13 +0000 (18:18 +0100)]
JWS-67 Add Jpred to configuration files
Daniel Barton [Thu, 1 Aug 2013 16:49:09 +0000 (17:49 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jabaws into develop
Daniel Barton [Thu, 1 Aug 2013 16:29:20 +0000 (17:29 +0100)]
RNAalifold.java runner and RNAalifoldTester incomplete
Sasha Sherstnev [Thu, 1 Aug 2013 15:41:40 +0000 (16:41 +0100)]
Fix problem in a clean target
Sasha Sherstnev [Thu, 1 Aug 2013 15:39:00 +0000 (16:39 +0100)]
JWS-67 insert Jpred 3.0.1 sources into JABAWS
Sasha Sherstnev [Thu, 1 Aug 2013 14:53:41 +0000 (15:53 +0100)]
An attempt to sort out a warning in tomcat in Eclipse
Sasha Sherstnev [Tue, 30 Jul 2013 10:32:01 +0000 (11:32 +0100)]
Replace jar with GA sources: 1.0 -> 1.1
Sasha Sherstnev [Tue, 30 Jul 2013 10:03:24 +0000 (11:03 +0100)]
add list of ant targets
Sasha Sherstnev [Tue, 30 Jul 2013 10:03:08 +0000 (11:03 +0100)]
change code style
Sasha Sherstnev [Tue, 30 Jul 2013 10:00:46 +0000 (11:00 +0100)]
1. git rid of jaba (now jabaws is everywhere)
2. fix problem with the clearStatDB target
Sasha Sherstnev [Mon, 29 Jul 2013 16:54:14 +0000 (17:54 +0100)]
Replace jabaws-2.0.1 logo with jabaws-3.alpha logo
git://source.jalview.org / jabaws.git / log