[biojava] Log of /biojava-live/trunk/biojava3-ws

Revision 9941 - Directory Listing
Modified Fri Nov 30 18:52:08 2012 UTC (5 months, 2 weeks ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 9939 - Directory Listing
Modified Fri Nov 30 18:52:01 2012 UTC (5 months, 2 weeks ago) by andreas

[maven-release-plugin] prepare release biojava-3.0.5

Revision 9753 - Directory Listing
Modified Tue Jul 31 20:45:40 2012 UTC (9 months, 2 weeks ago) by andreas

workaround for a problem  that seems openjdk specific

Revision 9752 - Directory Listing
Modified Tue Jul 31 19:10:25 2012 UTC (9 months, 2 weeks ago) by andreas

adding javadoc

Revision 9749 - Directory Listing
Modified Mon Jul 23 18:34:21 2012 UTC (9 months, 3 weeks ago) by andreas

PDBWW-4789 entityView is now linked to structure summary page!

Revision 9715 - Directory Listing
Modified Fri Jun 15 17:56:06 2012 UTC (11 months ago) by andreas

now serializable

Revision 9714 - Directory Listing
Modified Fri Jun 15 17:55:55 2012 UTC (11 months ago) by andreas

now serializable

Revision 9666 - Directory Listing
Modified Wed May 30 16:03:27 2012 UTC (11 months, 2 weeks ago) by andreas

switching the json library according to request from Olivier Sallou

Revision 9645 - Directory Listing
Modified Tue May 22 03:42:41 2012 UTC (11 months, 4 weeks ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 9643 - Directory Listing
Modified Tue May 22 03:42:34 2012 UTC (11 months, 4 weeks ago) by andreas

[maven-release-plugin] prepare release biojava-3.0.4

Revision 9590 - Directory Listing
Modified Fri Mar 16 22:28:32 2012 UTC (14 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 9588 - Directory Listing
Modified Fri Mar 16 22:28:24 2012 UTC (14 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0.3

Revision 9533 - Directory Listing
Modified Sat Feb 11 20:33:45 2012 UTC (15 months, 1 week ago) by gediminas

NCBIQBlastService replaced with the new implementation.
(For usage example see NCBIQBlastServiceDemo)

Revision 9500 - Directory Listing
Modified Thu Jan 12 03:11:59 2012 UTC (16 months, 1 week ago) by rthornton

Reversed conditions in if statement so null check was first.  Prevents NPE.

Revision 9490 - Directory Listing
Modified Mon Jan 9 20:56:01 2012 UTC (16 months, 1 week ago) by gediminas

Alternate implementation of NCBIQBlastService

Revision 9484 - Directory Listing
Modified Tue Dec 20 14:02:03 2011 UTC (16 months, 4 weeks ago) by andreas

adding @since 3.0.3 annotations

Revision 9483 - Directory Listing
Modified Tue Dec 20 14:01:38 2011 UTC (16 months, 4 weeks ago) by andreas

now dependent on org.json for the RESTful Hmmer API

Revision 9482 - Directory Listing
Modified Tue Dec 20 13:25:57 2011 UTC (16 months, 4 weeks ago) by andreas

Adding a new client for submitting ProteinSequences to the Hmmer3 web service and retrieving Pfam domain annotations

Revision 9478 - Directory Listing
Modified Mon Dec 12 21:28:06 2011 UTC (17 months, 1 week ago) by foisys

Included some error catching mechanisms into NCBIQBlastService to intercept QBlast's error messages.

Revision 9477 - Directory Listing
Modified Thu Dec 8 17:50:10 2011 UTC (17 months, 1 week ago) by foisys

Fixing PAM250 default values

Revision 9476 - Directory Listing
Modified Thu Dec 8 17:25:17 2011 UTC (17 months, 1 week ago) by foisys

Major mods in NCBIQBlastAlignmentProperties: it is now responsible for basic sanity checks of these properties instead of NCBIQBlastService. Also added get/set methods for blastp matrix selection and associated gap creation/extension costs.

Revision 9473 - Directory Listing
Modified Fri Dec 2 20:42:55 2011 UTC (17 months, 2 weeks ago) by foisys

Adjustments to getBlastFromPOsition and getBlastToPosition

Revision 9472 - Directory Listing
Modified Fri Dec 2 20:13:58 2011 UTC (17 months, 2 weeks ago) by foisys

using MEGABLAST should now work in setBlastProgram

Revision 9471 - Directory Listing
Modified Fri Dec 2 19:49:07 2011 UTC (17 months, 2 weeks ago) by foisys

added getBlastWordSize/setBlastWordSize to use WORD_SIZE values for BLAST requests

Revision 9470 - Directory Listing
Modified Fri Dec 2 19:25:47 2011 UTC (17 months, 2 weeks ago) by foisys

added getBlastExpect/setBlastExpect to use EXPECT values for BLAST requests

Revision 9169 - Directory Listing
Modified Fri Sep 2 15:17:53 2011 UTC (20 months, 2 weeks ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 9167 - Directory Listing
Modified Fri Sep 2 15:17:45 2011 UTC (20 months, 2 weeks ago) by andreas

[maven-release-plugin] prepare release biojava-3.0.2

Revision 9116 - Directory Listing
Modified Tue Aug 30 18:27:32 2011 UTC (20 months, 2 weeks ago) by foisys

Simple comment addition

Revision 9114 - Directory Listing
Modified Tue Aug 30 16:51:42 2011 UTC (20 months, 2 weeks ago) by foisys

Commented out code removed, cleaning the mess...

Revision 8975 - Directory Listing
Modified Thu May 26 18:12:01 2011 UTC (23 months, 3 weeks ago) by foisys

Fix a problem that appeared in the NCBI QBlast service where using the FORMAT_OBJECT=ALIGNMENT tag in the URL would return no results from the getAlignementResults method...

Revision 8876 - Directory Listing
Modified Tue Apr 5 22:00:28 2011 UTC (2 years, 1 month ago) by blivens

Added eclipse hidden files to svn:ignore for subprojects

Revision 8794 - Directory Listing
Modified Mon Feb 21 19:26:05 2011 UTC (2 years, 2 months ago) by foisys

New methods to add getting/setting EXPECT and WORD_SIZE parameters

Revision 8793 - Directory Listing
Modified Mon Feb 21 01:44:08 2011 UTC (2 years, 2 months ago) by foisys

More bug fixes: checking for null program or null database now works with new code

Revision 8792 - Directory Listing
Modified Mon Feb 21 01:31:00 2011 UTC (2 years, 2 months ago) by foisys

Bug fixes

Revision 8752 - Directory Listing
Modified Mon Feb 14 04:49:52 2011 UTC (2 years, 3 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 8750 - Directory Listing
Modified Mon Feb 14 04:49:40 2011 UTC (2 years, 3 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0.1

Revision 8716 - Directory Listing
Modified Thu Feb 3 06:10:28 2011 UTC (2 years, 3 months ago) by andreas

removing dependency on old biojava-core

Revision 8687 - Directory Listing
Modified Tue Jan 25 15:00:02 2011 UTC (2 years, 3 months ago) by foisys

Revision 8686 - Directory Listing
Modified Tue Jan 25 14:59:13 2011 UTC (2 years, 3 months ago) by foisys

Improving the code...

Revision 8685 - Directory Listing
Modified Tue Jan 25 14:54:43 2011 UTC (2 years, 3 months ago) by foisys

Fixing BJ1.7 to BJ3 bugs

Revision 8684 - Directory Listing
Modified Tue Jan 25 14:40:06 2011 UTC (2 years, 3 months ago) by foisys

Fixing bugs generated from BJ1.7 to BJ3 transitions

Revision 8678 - Directory Listing
Modified Mon Jan 24 16:12:26 2011 UTC (2 years, 3 months ago) by foisys

Fixing more BJ1.7 to BJ3.0 bugs

Revision 8663 - Directory Listing
Modified Tue Jan 11 21:05:11 2011 UTC (2 years, 4 months ago) by foisys

Working on removing old legacy BJ dust... Sequence interface used instead of RichSequence. I also included the import requests for DNASequence and ProteinSequence. I need to add the logic related to the matching of molecule class to blast program.

Revision 8662 - Directory Listing
Modified Tue Jan 11 20:54:48 2011 UTC (2 years, 4 months ago) by foisys

Working on removing old legacy BJ dust... Sequence interface used instead of RichSequence

Revision 8648 - Directory Listing
Modified Tue Dec 28 17:33:53 2010 UTC (2 years, 4 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 8646 - Directory Listing
Modified Tue Dec 28 17:33:41 2010 UTC (2 years, 4 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0

Revision 8627 - Directory Listing
Modified Sun Dec 19 10:37:20 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 8625 - Directory Listing
Modified Sun Dec 19 10:37:07 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0-beta4

Revision 8589 - Directory Listing
Modified Fri Dec 17 12:12:02 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 8587 - Directory Listing
Modified Fri Dec 17 12:11:49 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0-beta3

Revision 8500 - Directory Listing
Modified Wed Nov 24 01:51:29 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 8498 - Directory Listing
Modified Wed Nov 24 01:51:21 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0-beta1

Revision 8495 - Directory Listing
Modified Wed Nov 24 01:45:19 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] rollback the release of biojava-3.0-beta1

Revision 8494 - Directory Listing
Modified Wed Nov 24 01:32:29 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 8492 - Directory Listing
Modified Wed Nov 24 01:32:21 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0-beta1

Revision 8489 - Directory Listing
Modified Wed Nov 24 01:26:58 2010 UTC (2 years, 5 months ago) by andreas

setting correct project version

Revision 8450 - Directory Listing
Modified Mon Nov 22 17:38:51 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 8448 - Directory Listing
Modified Mon Nov 22 17:38:42 2010 UTC (2 years, 5 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0-alpha6

Revision 8418 - Directory Listing
Modified Sat Nov 13 18:47:35 2010 UTC (2 years, 6 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 8416 - Directory Listing
Modified Sat Nov 13 18:47:27 2010 UTC (2 years, 6 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0-alpha5

Revision 8388 - Directory Listing
Modified Sat Oct 30 10:46:37 2010 UTC (2 years, 6 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 8386 - Directory Listing
Modified Sat Oct 30 10:46:28 2010 UTC (2 years, 6 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0-alpha4

Revision 8383 - Directory Listing
Modified Fri Oct 29 22:23:15 2010 UTC (2 years, 6 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 8381 - Directory Listing
Modified Fri Oct 29 22:23:07 2010 UTC (2 years, 6 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0-alpha3

Revision 8353 - Directory Listing
Modified Fri Oct 22 17:35:31 2010 UTC (2 years, 6 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 8351 - Directory Listing
Modified Fri Oct 22 17:35:22 2010 UTC (2 years, 6 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0-alpha2

Revision 8340 - Directory Listing
Modified Thu Oct 21 22:28:35 2010 UTC (2 years, 6 months ago) by andreas

now with correct artifact version nr

Revision 8314 - Directory Listing
Modified Sat Oct 16 02:44:51 2010 UTC (2 years, 7 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 8312 - Directory Listing
Modified Sat Oct 16 02:44:43 2010 UTC (2 years, 7 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0-alpha1

Revision 8310 - Directory Listing
Modified Sat Oct 16 02:37:32 2010 UTC (2 years, 7 months ago) by andreas

[maven-release-plugin] rollback the release of biojava-3.0-alpha1

Revision 8308 - Directory Listing
Modified Sat Oct 16 02:07:11 2010 UTC (2 years, 7 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0-alpha1

Revision 8307 - Directory Listing
Modified Sat Oct 16 01:44:19 2010 UTC (2 years, 7 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 8304 - Directory Listing
Modified Sat Oct 16 00:49:02 2010 UTC (2 years, 7 months ago) by andreas

[maven-release-plugin] rollback the release of biojava-3.0-alpha1

Revision 8303 - Directory Listing
Modified Sat Oct 16 00:11:55 2010 UTC (2 years, 7 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 8293 - Directory Listing
Modified Fri Oct 15 22:51:13 2010 UTC (2 years, 7 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0-alpha1

Revision 8272 - Directory Listing
Modified Thu Sep 30 22:07:00 2010 UTC (2 years, 7 months ago) by foisys

Revision 8271 - Directory Listing
Modified Thu Sep 30 22:06:42 2010 UTC (2 years, 7 months ago) by foisys

Revision 8269 - Directory Listing
Modified Thu Sep 30 21:12:24 2010 UTC (2 years, 7 months ago) by foisys

Correcting a "==" inequality, using Arrays' searchBinary() method instead.

Revision 8268 - Directory Listing
Modified Thu Sep 30 21:10:16 2010 UTC (2 years, 7 months ago) by foisys

Various fixing to match biojava3 usage: removing usage of BioException

Revision 8095 - Directory Listing
Modified Thu Jul 15 20:02:45 2010 UTC (2 years, 10 months ago) by foisys

Revision 8087 - Directory Listing
Modified Thu Jul 15 14:24:33 2010 UTC (2 years, 10 months ago) by foisys

Revision 8086 - Directory Listing
Modified Thu Jul 15 14:23:59 2010 UTC (2 years, 10 months ago) by foisys

Revision 8085 - Directory Listing
Modified Thu Jul 15 14:17:43 2010 UTC (2 years, 10 months ago) by foisys

Revision 8081 - Directory Listing
Modified Wed Jul 14 15:27:10 2010 UTC (2 years, 10 months ago) by foisys

Fixing legacy package information

Revision 8070 - Directory Listing
Added Tue Jul 6 15:55:34 2010 UTC (2 years, 10 months ago) by foisys

First commit of basic file/folder structure for the biojava2-ws module, a module to link Biojava objects to various web resources for processing