jabaws.git
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 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 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 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 agoMerge branch 'develop' of https://source.jalview.org/git/jabaws into develop
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

11 years agoRNAalifold.java runner and RNAalifoldTester incomplete
Daniel Barton [Thu, 1 Aug 2013 16:29:20 +0000 (17:29 +0100)]
RNAalifold.java runner and RNAalifoldTester incomplete

11 years agoFix problem in a clean target
Sasha Sherstnev [Thu, 1 Aug 2013 15:41:40 +0000 (16:41 +0100)]
Fix problem in a clean target

11 years agoAn attempt to sort out a warning in tomcat in Eclipse
Sasha Sherstnev [Thu, 1 Aug 2013 14:53:41 +0000 (15:53 +0100)]
An attempt to sort out a warning in tomcat in Eclipse

11 years agoReplace jar with GA sources: 1.0 -> 1.1
Sasha Sherstnev [Tue, 30 Jul 2013 10:32:01 +0000 (11:32 +0100)]
Replace jar with GA sources: 1.0 -> 1.1

11 years agoadd list of ant targets
Sasha Sherstnev [Tue, 30 Jul 2013 10:03:24 +0000 (11:03 +0100)]
add list of ant targets

11 years agochange code style
Sasha Sherstnev [Tue, 30 Jul 2013 10:03:08 +0000 (11:03 +0100)]
change code style

11 years ago1. git rid of jaba (now jabaws is everywhere)
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

11 years agoReplace jabaws-2.0.1 logo with jabaws-3.alpha logo
Sasha Sherstnev [Mon, 29 Jul 2013 16:54:14 +0000 (17:54 +0100)]
Replace jabaws-2.0.1 logo with jabaws-3.alpha logo

11 years agoUpdate GoogleAnalytics jar.
Sasha Sherstnev [Mon, 29 Jul 2013 16:53:05 +0000 (17:53 +0100)]
Update GoogleAnalytics jar.
bug fixed: tomcat did not stop after shutdown due to problem in the jar

11 years agomerge JABAWS_Release_2_1 into develop
Sasha Sherstnev [Mon, 29 Jul 2013 12:58:12 +0000 (13:58 +0100)]
merge JABAWS_Release_2_1 into develop

11 years agoCorrect log4j file
Sasha [Mon, 29 Jul 2013 12:18:17 +0000 (13:18 +0100)]
Correct log4j file

11 years agoupdate derby.jar and add version number to the library
Sasha [Mon, 29 Jul 2013 11:53:27 +0000 (12:53 +0100)]
update derby.jar and add version number to the library

11 years agoImprove shutdown of JABAWS and some code style improvements
Sasha [Mon, 29 Jul 2013 11:57:42 +0000 (12:57 +0100)]
Improve shutdown of JABAWS and some code style improvements

11 years agoimprove logging system
Sasha [Mon, 29 Jul 2013 11:55:54 +0000 (12:55 +0100)]
improve logging system

11 years agoRefactoring and code style improving
Sasha [Mon, 29 Jul 2013 11:55:21 +0000 (12:55 +0100)]
Refactoring and code style improving

11 years agoupdate derby.jar and add version number to the library
Sasha [Mon, 29 Jul 2013 11:53:27 +0000 (12:53 +0100)]
update derby.jar and add version number to the library

11 years agochange a jsp page (make a link a real link)
Sasha [Mon, 29 Jul 2013 09:54:07 +0000 (10:54 +0100)]
change a jsp page (make a link a real link)

11 years agochange Eclipse configuration
Sasha [Mon, 29 Jul 2013 09:53:34 +0000 (10:53 +0100)]
change Eclipse configuration

11 years agore-configure log4j location in order to allow log4j using both in Eclipse and ant
Sasha [Mon, 29 Jul 2013 09:50:35 +0000 (10:50 +0100)]
re-configure log4j location in order to allow log4j using both in Eclipse and ant

11 years agoRemove jar/zip files from git
Sasha [Mon, 29 Jul 2013 09:47:50 +0000 (10:47 +0100)]
Remove jar/zip files from git

11 years agoModify Eclipse configuration for log4j
Sasha [Fri, 26 Jul 2013 10:14:14 +0000 (11:14 +0100)]
Modify Eclipse configuration for log4j

11 years agoImprove building process: log4j.properties is in a right place both in
Sasha [Fri, 26 Jul 2013 10:13:12 +0000 (11:13 +0100)]
Improve building process: log4j.properties is in a right place both in
jabaw.war and Eclipse building

11 years agoAdd SVG version of some logos
Sasha [Tue, 2 Jul 2013 11:59:51 +0000 (12:59 +0100)]
Add SVG version of some logos

11 years agoAdd release date
Sasha [Tue, 2 Jul 2013 11:57:25 +0000 (12:57 +0100)]
Add release date

11 years agoAdd funding page
Sasha [Tue, 2 Jul 2013 10:37:21 +0000 (11:37 +0100)]
Add funding page

11 years agoMisprint correction
Sasha [Mon, 1 Jul 2013 15:16:29 +0000 (16:16 +0100)]
Misprint correction

11 years agoMerge branches 'JABAWS_Release_2_1', 'JABAWS_Release_2_1' and 'JABAWS_Release_2_1...
Jim Procter [Mon, 1 Jul 2013 14:16:01 +0000 (15:16 +0100)]
Merge branches 'JABAWS_Release_2_1', 'JABAWS_Release_2_1' and 'JABAWS_Release_2_1' of https://source.jalview.org/git/jabaws into JABAWS_Release_2_1

11 years agoMerge branches 'JABAWS_Release_2_1' and 'JABAWS_Release_2_1' of https://source.jalvie...
Jim Procter [Mon, 1 Jul 2013 14:14:16 +0000 (15:14 +0100)]
Merge branches 'JABAWS_Release_2_1' and 'JABAWS_Release_2_1' of https://source.jalview.org/git/jabaws into JABAWS_Release_2_1

Conflicts:
website/man_about.html
Tweaked the wording a bit more - introduced standard man_about.html#jabaX.Y.Z style name anchor for update history

11 years agoChange version number: 2.0 -> 2.0.1
Sasha [Mon, 1 Jul 2013 13:47:59 +0000 (14:47 +0100)]
Change version number: 2.0 -> 2.0.1
add building min-client without log4j

11 years agoSome small changes on web pages
Sasha [Mon, 1 Jul 2013 13:46:51 +0000 (14:46 +0100)]
Some small changes on web pages

11 years agotypo
Jim Procter [Mon, 1 Jul 2013 13:37:26 +0000 (14:37 +0100)]
typo

11 years agogrammar
Jim Procter [Mon, 1 Jul 2013 13:30:34 +0000 (14:30 +0100)]
grammar

11 years agogrammar
Jim Procter [Mon, 1 Jul 2013 13:30:07 +0000 (14:30 +0100)]
grammar

11 years agotweaked opening paragraph for sense and to avoid parentheses
Jim Procter [Mon, 1 Jul 2013 12:57:56 +0000 (13:57 +0100)]
tweaked opening paragraph for sense and to avoid parentheses

11 years agogrammar tweak
Jim Procter [Mon, 1 Jul 2013 12:56:47 +0000 (13:56 +0100)]
grammar tweak

11 years agogrammar tweak
Jim Procter [Mon, 1 Jul 2013 12:56:26 +0000 (13:56 +0100)]
grammar tweak

11 years agoadd Sasha S to list of authors
Jim Procter [Mon, 1 Jul 2013 12:55:55 +0000 (13:55 +0100)]
add Sasha S to list of authors

11 years agoinvalid XML document header
Jim Procter [Mon, 1 Jul 2013 12:53:37 +0000 (13:53 +0100)]
invalid XML document header

11 years agoJWS-50 refactored the valid AACon method parameters as a series of options in the...
Sasha [Fri, 28 Jun 2013 16:18:36 +0000 (17:18 +0100)]
JWS-50 refactored the valid AACon method parameters as a series of options in the JABAWS config (cont.)

11 years agoUpdate manual and other static html page for JABAWS 2.0.1
Sasha [Fri, 28 Jun 2013 14:20:32 +0000 (15:20 +0100)]
Update manual and other static html page for JABAWS 2.0.1

11 years agoUpdate manual and other static html page for JABAWS 2.0.1
Sasha [Fri, 28 Jun 2013 14:19:33 +0000 (15:19 +0100)]
Update manual and other static html page for JABAWS 2.0.1

11 years agoUpdate manual and other static html page for JABAWS 2.0.1
Sasha [Fri, 28 Jun 2013 13:55:40 +0000 (14:55 +0100)]
Update manual and other static html page for JABAWS 2.0.1

11 years agoJWS-50 patch AAConWS test for refactoring of calculation parameters to a series of...
Jim Procter [Wed, 19 Jun 2013 14:42:50 +0000 (15:42 +0100)]
JWS-50 patch AAConWS test for refactoring of calculation parameters to a series of options

11 years agoWorkaround for JWS-61 that resolves JAL-1127
Jim Procter [Wed, 19 Jun 2013 14:33:37 +0000 (15:33 +0100)]
Workaround for JWS-61 that resolves JAL-1127

11 years agoJWS-61 test demonstrating compound option value problem with JABAWS client
Jim Procter [Wed, 19 Jun 2013 14:28:03 +0000 (15:28 +0100)]
JWS-61 test demonstrating compound option value problem with JABAWS client

11 years agoJWS-50 refactored the valid AACon method parameters as a series of options in the...
Jim Procter [Mon, 17 Jun 2013 15:41:44 +0000 (16:41 +0100)]
JWS-50 refactored the valid AACon method parameters as a series of options in the JABAWS config

11 years agoNew target: full-clean
Sasha [Tue, 18 Jun 2013 15:41:42 +0000 (16:41 +0100)]
New target: full-clean
re-formatted file

11 years agoremove war/jar files from git
Sasha [Mon, 17 Jun 2013 16:21:40 +0000 (17:21 +0100)]
remove war/jar files from git

11 years agoMake configuration file clearer and add new parameters to dundee-conf
Sasha [Mon, 17 Jun 2013 16:00:34 +0000 (17:00 +0100)]
Make configuration file clearer and add new parameters to dundee-conf

11 years agoJWS-50 refactored the valid AACon method parameters as a series of options in the...
Jim Procter [Mon, 17 Jun 2013 15:41:44 +0000 (16:41 +0100)]
JWS-50 refactored the valid AACon method parameters as a series of options in the JABAWS config

11 years agoJWS-60 removed unused logger reference
Jim Procter [Mon, 17 Jun 2013 15:38:49 +0000 (16:38 +0100)]
JWS-60 removed unused logger reference

11 years agoChange jar/war file for jabaws-2.1
Sasha [Mon, 17 Jun 2013 15:20:19 +0000 (16:20 +0100)]
Change jar/war file for jabaws-2.1

11 years agoChange jar/war file for jabaws-2.1
Sasha [Mon, 17 Jun 2013 15:02:31 +0000 (16:02 +0100)]
Change jar/war file for jabaws-2.1

11 years agoNecessary changes in website for jabaws-2.1
Sasha [Fri, 14 Jun 2013 14:13:37 +0000 (15:13 +0100)]
Necessary changes in website for jabaws-2.1

11 years agoNecessary changes in website for jabaws-2.1
Sasha [Fri, 14 Jun 2013 14:12:08 +0000 (15:12 +0100)]
Necessary changes in website for jabaws-2.1

11 years agoadd some additional configuration lines
Sasha [Fri, 14 Jun 2013 11:59:12 +0000 (12:59 +0100)]
add some additional configuration lines

11 years agoNew project name for developemnt jabaws
Sasha [Fri, 14 Jun 2013 11:57:24 +0000 (12:57 +0100)]
New project name for developemnt jabaws

11 years agoCode for cleaning up old job directories
Sasha [Fri, 14 Jun 2013 11:49:32 +0000 (12:49 +0100)]
Code for cleaning up old job directories

11 years agoCode for cleaning up old job directories
Sasha [Fri, 14 Jun 2013 11:03:42 +0000 (12:03 +0100)]
Code for cleaning up old job directories

11 years agoDelete old job directory automatically
Sasha [Fri, 26 Apr 2013 17:26:47 +0000 (18:26 +0100)]
Delete old job directory automatically

11 years agoAdd new methods
Sasha [Fri, 26 Apr 2013 17:24:44 +0000 (18:24 +0100)]
Add new methods

11 years agore-formatting code
Sasha [Fri, 26 Apr 2013 17:23:54 +0000 (18:23 +0100)]
re-formatting code

11 years agocopy log4j.properties to WEB-INF/classes
Sasha [Fri, 26 Apr 2013 17:21:49 +0000 (18:21 +0100)]
copy log4j.properties to WEB-INF/classes

11 years agoRe-formatting files
Sasha [Fri, 26 Apr 2013 17:19:05 +0000 (18:19 +0100)]
Re-formatting files

11 years agoNew build of JABAWS
Sasha [Wed, 24 Apr 2013 16:37:43 +0000 (17:37 +0100)]
New build of JABAWS

11 years agodebug version of /log4j.properties
Sasha [Wed, 24 Apr 2013 16:35:39 +0000 (17:35 +0100)]
debug version of /log4j.properties

11 years agodelete wronigly located log4j.properties
Sasha [Wed, 24 Apr 2013 16:35:11 +0000 (17:35 +0100)]
delete wronigly located log4j.properties