Jim Procter [Sun, 23 Nov 2014 20:10:19 +0000 (20:10 +0000)]
Merge branch 'JAL-1569_wuss_vienna_broke' into develop
Jim Procter [Sun, 23 Nov 2014 16:43:54 +0000 (16:43 +0000)]
employ test and secondary structure character for determining base pairing direction for rendering rna annotation
Jim Procter [Sun, 23 Nov 2014 16:42:55 +0000 (16:42 +0000)]
JAL-1569 formatting
Jim Procter [Sun, 23 Nov 2014 16:42:01 +0000 (16:42 +0000)]
JAL-1593 allow per-sequence shading of RNA helix (stored in each annotation element's value field for a paired base)
Jim Procter [Sun, 23 Nov 2014 16:37:33 +0000 (16:37 +0000)]
JAL-1569 test for open/close RNA parenthesis character
Jim Procter [Sun, 23 Nov 2014 16:35:56 +0000 (16:35 +0000)]
JAL-1569 formatting
Jim Procter [Sun, 23 Nov 2014 16:34:42 +0000 (16:34 +0000)]
JAL-1569 refactoring of stockholm test
Jim Procter [Sun, 23 Nov 2014 16:33:59 +0000 (16:33 +0000)]
JAL-1569 consistent handling of sequence and alignment associated annotation export in stockholm
Jim Procter [Sun, 23 Nov 2014 16:32:37 +0000 (16:32 +0000)]
JAL-1569 revise tests to count number and type of annotation in each file
Jim Procter [Sun, 23 Nov 2014 16:31:26 +0000 (16:31 +0000)]
JAL-1569 formatting
Jim Procter [Sun, 23 Nov 2014 16:29:58 +0000 (16:29 +0000)]
JAL-1569 preserve input ordering for stockholm files (Hashtable implementation changed possibly ?)
Jim Procter [Sun, 23 Nov 2014 16:22:25 +0000 (16:22 +0000)]
JAL-1569 remove stdout on parsing RNA
Jim Procter [Sun, 23 Nov 2014 16:21:34 +0000 (16:21 +0000)]
JAL-1152 avoid NPE on null alignment annotation vector
Jim Procter [Fri, 21 Nov 2014 09:01:03 +0000 (09:01 +0000)]
JAL-674 add RNA sequence associated annotation to alignment as hidden annotation
Jim Procter [Fri, 21 Nov 2014 08:59:49 +0000 (08:59 +0000)]
JAL-1569 formatting
Jim Procter [Fri, 21 Nov 2014 08:56:52 +0000 (08:56 +0000)]
JAL-1140 sensible name for seuqences in RNAML files that have no ID
Jim Procter [Fri, 21 Nov 2014 08:55:38 +0000 (08:55 +0000)]
JAL-1489 change initial value to distinguish non-rna from valid and invalid RNA structure with one call to .isValidStructure()
Jim Procter [Fri, 21 Nov 2014 08:54:11 +0000 (08:54 +0000)]
JAL-1592 JAL-1489 avoid invalid RNA structure and distinguish alignment associated from sequence associated structure lines
Jim Procter [Thu, 20 Nov 2014 14:54:01 +0000 (14:54 +0000)]
JAL-1569 rna pair code in secondary structure character of annotation
Jim Procter [Thu, 20 Nov 2014 14:52:22 +0000 (14:52 +0000)]
JAL-674 JAL-1569 mark RNA helix number in the value field
Jim Procter [Thu, 20 Nov 2014 14:49:36 +0000 (14:49 +0000)]
JAL-1569 remove log output during RNA secondary structure processing
Jim Procter [Tue, 18 Nov 2014 09:57:09 +0000 (09:57 +0000)]
Merge branch 'JAL-1587_promotedisorder' into develop
Jim Procter [Tue, 18 Nov 2014 09:52:35 +0000 (09:52 +0000)]
JAL-674 make temperature factor, local secondary structure and service based secondary structure processing configurable
Jim Procter [Tue, 18 Nov 2014 09:44:36 +0000 (09:44 +0000)]
JAL-674 JAL-1512 JAL-1333 documentation
Jim Procter [Mon, 17 Nov 2014 17:14:23 +0000 (17:14 +0000)]
JAL-1517 JAL-1587 JAL-674 secondary structure and annotation from prediction services documentation
Jim Procter [Mon, 17 Nov 2014 17:12:54 +0000 (17:12 +0000)]
JAL-1517 release notes for 2.8.2
Jim Procter [Mon, 17 Nov 2014 14:47:17 +0000 (14:47 +0000)]
JAL-1587 distinct calc IDs for JPredMSA and Jpred single sequence.
Jim Procter [Mon, 17 Nov 2014 14:43:37 +0000 (14:43 +0000)]
JAL-1587 propagate results of JABA sequence based predictors to dataset
Jim Procter [Mon, 17 Nov 2014 14:42:21 +0000 (14:42 +0000)]
imports and formatting
Jim Procter [Mon, 17 Nov 2014 14:41:56 +0000 (14:41 +0000)]
JAL-1587 propagate JPred annotation from legacy jpred service to the dataset
Jim Procter [Mon, 17 Nov 2014 14:38:37 +0000 (14:38 +0000)]
formatting
Jim Procter [Mon, 17 Nov 2014 14:38:16 +0000 (14:38 +0000)]
JAL-1587 JAL-407 instrument setDataset to add dataset sequences to existing dataset if they aren't already present
Jim Procter [Mon, 17 Nov 2014 11:44:48 +0000 (11:44 +0000)]
Merge branch 'r282_portforward' into develop
Jim Procter [Mon, 17 Nov 2014 11:42:02 +0000 (11:42 +0000)]
JAL-1469 help documentation
Jim Procter [Mon, 17 Nov 2014 11:39:05 +0000 (11:39 +0000)]
JAL-1469 help documentation
Jim Procter [Mon, 17 Nov 2014 11:31:23 +0000 (11:31 +0000)]
Merge branch 'mrg_dev_282' into Release_2_8_2_Branch
Jim Procter [Mon, 17 Nov 2014 11:31:13 +0000 (11:31 +0000)]
Merge branch 'Release_2_8_2_Branch' into mrg_dev_282
Charles Ofoegbu [Mon, 17 Nov 2014 10:01:53 +0000 (10:01 +0000)]
comand line support for svg generation
Release_2_8_2_Branch only for JAL-1469 -removed changes to BioJS importer
code
Conflicts:
.classpath
src/jalview/io/HtmlFile.java
gmungoc [Mon, 17 Nov 2014 11:16:59 +0000 (11:16 +0000)]
JAL-1580 size parameters dialog to height of Desktop
Charles Ofoegbu [Mon, 17 Nov 2014 11:10:08 +0000 (11:10 +0000)]
Merge branch 'bug/JAL-1570_unable-to-add-JABAWS-Server-which-fails-validation' into Release_2_8_2_Branch
Charles Ofoegbu [Mon, 17 Nov 2014 11:04:24 +0000 (11:04 +0000)]
JAL-1570 patch to enable adding a webservice which fails validation
Jim Procter [Mon, 17 Nov 2014 10:40:02 +0000 (10:40 +0000)]
Merge branch 'mrg_dev_282' into Release_2_8_2_Branch
gmungoc [Fri, 14 Nov 2014 12:53:45 +0000 (12:53 +0000)]
JAL-1528 Chimera Help doc + fixes to setting colours
gmungoc [Thu, 13 Nov 2014 12:40:33 +0000 (12:40 +0000)]
JAL-1528 new Preference CHIMERA_PATH (Preferences | Structure)
gmungoc [Thu, 13 Nov 2014 11:15:42 +0000 (11:15 +0000)]
JAL-1528 Chimera tidy errors, focus after align, close option
gmungoc [Wed, 12 Nov 2014 16:55:00 +0000 (16:55 +0000)]
JAL-1528 bug fixes and adjustments to Chimera interface
Jim Procter [Mon, 17 Nov 2014 10:25:33 +0000 (10:25 +0000)]
Charles Ofoegbu [Mon, 17 Nov 2014 10:01:53 +0000 (10:01 +0000)]
comand line support for svg generation
Charles Ofoegbu [Fri, 14 Nov 2014 16:09:51 +0000 (16:09 +0000)]
Merge branch 'feature/JAL-1541_BioJsMSAViewer-export-option' into develop
Charles Ofoegbu [Fri, 14 Nov 2014 16:08:37 +0000 (16:08 +0000)]
git conflict resolution
Charles Ofoegbu [Fri, 14 Nov 2014 16:05:31 +0000 (16:05 +0000)]
updated BioJsTemplate.txt
Charles Ofoegbu [Fri, 14 Nov 2014 15:54:43 +0000 (15:54 +0000)]
house keeping
Charles Ofoegbu [Fri, 14 Nov 2014 15:49:20 +0000 (15:49 +0000)]
Merge branch 'features/JAL-1541_BioJsMSAViewer-export-option' of https://source.jalview.org/git/jalview.git into features/JAL-1541_BioJsMSAViewer-export-option
Conflicts:
src/jalview/gui/AlignViewport.java
gmungoc [Fri, 14 Nov 2014 15:33:20 +0000 (15:33 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
Charles Ofoegbu [Fri, 14 Nov 2014 14:43:56 +0000 (14:43 +0000)]
House keeping
gmungoc [Fri, 14 Nov 2014 12:53:45 +0000 (12:53 +0000)]
JAL-1528 Chimera Help doc + fixes to setting colours
Jim Procter [Thu, 13 Nov 2014 16:46:06 +0000 (16:46 +0000)]
Merge branch 'features/JAL-1469_svg-output-for-figure-export' into develop
Conflicts:
.classpath
.gitignore
src/jalview/gui/AlignmentPanel.java
src/jalview/jbgui/GAlignFrame.java
Jim Procter [Thu, 13 Nov 2014 16:38:00 +0000 (16:38 +0000)]
Merge branch 'features/JAL-1469_svg-output-for-figure-export' into Release_2_8_2_Branch
Conflicts:
.gitignore
src/jalview/gui/AlignmentPanel.java
Jim Procter [Thu, 13 Nov 2014 16:34:59 +0000 (16:34 +0000)]
JAL-1469 added jfreesvg to desktop dependencies
gmungoc [Thu, 13 Nov 2014 16:15:54 +0000 (16:15 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 13 Nov 2014 16:15:23 +0000 (16:15 +0000)]
merge
gmungoc [Thu, 13 Nov 2014 12:40:33 +0000 (12:40 +0000)]
JAL-1528 new Preference CHIMERA_PATH (Preferences | Structure)
gmungoc [Thu, 13 Nov 2014 11:15:42 +0000 (11:15 +0000)]
JAL-1528 Chimera tidy errors, focus after align, close option
Charles Ofoegbu [Wed, 12 Nov 2014 20:07:58 +0000 (20:07 +0000)]
house-keeping
Charles Ofoegbu [Wed, 12 Nov 2014 17:54:32 +0000 (17:54 +0000)]
Added support for SVG Export
gmungoc [Wed, 12 Nov 2014 16:55:00 +0000 (16:55 +0000)]
JAL-1528 bug fixes and adjustments to Chimera interface
Jim Procter [Wed, 12 Nov 2014 15:22:42 +0000 (15:22 +0000)]
Merge branch 'features/JAL-1541_BioJsMSAViewer-export-option' into develop
Jim Procter [Wed, 12 Nov 2014 15:22:34 +0000 (15:22 +0000)]
JAL-1541 exclude all unnecessary jalview.io classes from applet build
Jim Procter [Wed, 12 Nov 2014 15:20:41 +0000 (15:20 +0000)]
Merge branch 'features/JAL-1541_BioJsMSAViewer-export-option' into develop
Jim Procter [Wed, 12 Nov 2014 15:19:19 +0000 (15:19 +0000)]
Merge branch 'develop' into features/JAL-1541_BioJsMSAViewer-export-option
Jim Procter [Wed, 12 Nov 2014 14:56:16 +0000 (14:56 +0000)]
Merge branch 'features/typed_annotations_calcId' into Release_2_8_2_Branch
Jim Procter [Wed, 12 Nov 2014 14:56:03 +0000 (14:56 +0000)]
Merge branch 'features/typed_annotations_calcId' into develop
Jim Procter [Wed, 12 Nov 2014 14:55:45 +0000 (14:55 +0000)]
JAL-974 fix class contamination for jalviewLite build
gmungoc [Wed, 12 Nov 2014 14:30:46 +0000 (14:30 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
Jim Procter [Wed, 12 Nov 2014 12:44:17 +0000 (12:44 +0000)]
Merge branch 'features/typed_annotations_calcId' into Release_2_8_2_Branch
Jim Procter [Wed, 12 Nov 2014 12:41:52 +0000 (12:41 +0000)]
Merge branch 'features/typed_annotations_calcId' into develop
Jim Procter [Wed, 12 Nov 2014 12:40:43 +0000 (12:40 +0000)]
javadoc
Jim Procter [Wed, 12 Nov 2014 12:40:24 +0000 (12:40 +0000)]
JAL-674 use the getMapping/transfer to transfer annotation when creating a mapping to a sequence
Jim Procter [Wed, 12 Nov 2014 12:39:50 +0000 (12:39 +0000)]
JAL-674 patch broken getMapping function
Jim Procter [Wed, 12 Nov 2014 12:39:05 +0000 (12:39 +0000)]
JAL-674 switch from .transfer to .liftOver for transfer of annotation
Jim Procter [Wed, 12 Nov 2014 12:37:12 +0000 (12:37 +0000)]
JAL-674 note about broken .transfer method (expect this to disappear in future!)
Jim Procter [Wed, 12 Nov 2014 12:36:36 +0000 (12:36 +0000)]
JAL-674 javadoc
Jim Procter [Wed, 12 Nov 2014 12:35:40 +0000 (12:35 +0000)]
JAL-674 new tests and deprecated tests for PDB mapping to sequence code
Charles Ofoegbu [Wed, 12 Nov 2014 12:19:55 +0000 (12:19 +0000)]
Excluded HtmlFile.java dependencies from AppletFomatAdapter
Jim Procter [Wed, 12 Nov 2014 10:39:08 +0000 (10:39 +0000)]
JAL-1541 added Jsoup to the InstallAnywhere config
Jim Procter [Wed, 12 Nov 2014 10:29:16 +0000 (10:29 +0000)]
JAL-1541 added Jsoup to the InstallAnywhere config
Jim Procter [Wed, 12 Nov 2014 10:28:25 +0000 (10:28 +0000)]
JAL-1541 added Jsoup to the InstallAnywhere config
Charles Ofoegbu [Wed, 12 Nov 2014 10:23:25 +0000 (10:23 +0000)]
mearge with develop
Jim Procter [Wed, 12 Nov 2014 10:15:59 +0000 (10:15 +0000)]
JAL-1541 added Jsoup to the InstallAnywhere config
Charles Ofoegbu [Wed, 12 Nov 2014 09:30:02 +0000 (09:30 +0000)]
Modified biojs exporter/importer to preserve SequenceFeatures during a write/read operation
gmungoc [Tue, 11 Nov 2014 09:20:40 +0000 (09:20 +0000)]
JAL-1527 opening a project saved with JMol should use JMol (disregard
viewer preference).
Charles Ofoegbu [Fri, 7 Nov 2014 12:08:22 +0000 (12:08 +0000)]
Updated BioJsTemplate to not show the menu by default and implemented a toggle button for the menu, also the LableId was disabled by default
Charles Ofoegbu [Fri, 7 Nov 2014 09:46:37 +0000 (09:46 +0000)]
Modified BioJsHTMLOutput.java to clean up and close used resources properly
Charles Ofoegbu [Fri, 7 Nov 2014 09:31:09 +0000 (09:31 +0000)]
Modified BioJsHTMLOutput.java to use class loader while loading BioJsTemplate file
Charles Ofoegbu [Thu, 6 Nov 2014 18:19:53 +0000 (18:19 +0000)]
Changes from JAL-1541 patch
Charles Ofoegbu [Thu, 6 Nov 2014 17:47:38 +0000 (17:47 +0000)]
Updated BioJs Html to be capable of launching jalivew
Jim Procter [Thu, 6 Nov 2014 17:18:44 +0000 (17:18 +0000)]
Merge branch 'features/JAL-1152annotationSorting' into features/typed_annotations_calcId
Jim Procter [Thu, 6 Nov 2014 16:33:25 +0000 (16:33 +0000)]
Merge branch 'features/JAL-1541_BioJsMSAViewer-export-option' into develop
gmungoc [Thu, 6 Nov 2014 14:33:26 +0000 (14:33 +0000)]
JAL-1152 use a proper RadioButton not a faked one
gmungoc [Wed, 5 Nov 2014 16:04:10 +0000 (16:04 +0000)]
JAL-674 Prefences tweaks incl help documentation for Structure tab
git://source.jalview.org / jalview.git / log