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
gmungoc [Wed, 5 Nov 2014 12:21:23 +0000 (12:21 +0000)]
JAL-1152 new Structure tab on Preferences for SS derivation / annotation
gmungoc [Tue, 4 Nov 2014 09:37:50 +0000 (09:37 +0000)]
JAL-1152 help updates for Preferences
gmungoc [Tue, 4 Nov 2014 09:10:14 +0000 (09:10 +0000)]
JAL-1152 annotation sort algorithm optimisation
Jim Procter [Tue, 4 Nov 2014 08:19:19 +0000 (08:19 +0000)]
JAL-1213 normalise sequence extracted from Jmol in same way as MCview
Jim Procter [Tue, 4 Nov 2014 08:11:59 +0000 (08:11 +0000)]
JAL-1213 test to ensure JMol extracted sequences are same as MCView
gmungoc [Mon, 3 Nov 2014 16:59:26 +0000 (16:59 +0000)]
Merge branch 'features/JAL-1152annotationSorting' of https://source.jalview.org/git/jalview.git into features/JAL-1152annotationSorting
gmungoc [Mon, 3 Nov 2014 16:59:04 +0000 (16:59 +0000)]
JAL-1152 annotation sorting preferences and help documentation
Jim Procter [Mon, 3 Nov 2014 16:13:35 +0000 (16:13 +0000)]
Merge branch 'develop' into features/JAL-1152annotationSorting
Jim Procter [Mon, 3 Nov 2014 16:12:44 +0000 (16:12 +0000)]
Merge branch 'bug/JAL-1250_redundance-removal' into develop
Jim Procter [Mon, 3 Nov 2014 16:02:18 +0000 (16:02 +0000)]
Merge branch 'develop' into features/JAL-1152annotationSorting
Jim Procter [Mon, 3 Nov 2014 16:01:56 +0000 (16:01 +0000)]
Merge branch 'features/ssFromPDBEntry' into develop
Jim Procter [Mon, 3 Nov 2014 15:51:04 +0000 (15:51 +0000)]
JAL-795 JAL-674 tweaked logic to avoid black annotation shading and hard-wire secondary structure colours when no custom colours available
Jim Procter [Mon, 3 Nov 2014 13:02:39 +0000 (13:02 +0000)]
fix for JAL-1579 create threshold object for annotation rows that match shading pattern but do not have threshold objects as yet (nb - side effect is that cancel leaves old threshold lines on these annotation)
Jim Procter [Mon, 3 Nov 2014 10:10:09 +0000 (10:10 +0000)]
JAL-1578 test property accessors/copy constructor
Jim Procter [Mon, 3 Nov 2014 10:09:08 +0000 (10:09 +0000)]
JAL-1578 JAL-674 store/restore alignment annotation properties in Jalview 2.8.2 project (allows the Annotated PDB file import/export to project/import test to pass)
Jim Procter [Mon, 3 Nov 2014 10:04:09 +0000 (10:04 +0000)]
JAL-1578 formatting and imports
Jim Procter [Mon, 3 Nov 2014 10:03:22 +0000 (10:03 +0000)]
JAL-674 peptide structure input so test is not dependent on network
Jim Procter [Mon, 3 Nov 2014 10:02:27 +0000 (10:02 +0000)]
JAL-1551 formatting
Jim Procter [Mon, 3 Nov 2014 10:01:43 +0000 (10:01 +0000)]
JAL-674 JAL-961 JAL-1578 accessors and copy constructor for annotation row properties
Jim Procter [Mon, 3 Nov 2014 09:58:29 +0000 (09:58 +0000)]
javadoc
gmungoc [Fri, 31 Oct 2014 16:43:46 +0000 (16:43 +0000)]
JAL-1152 bug fix for 'no sort' case + tests for autocalc placement
gmungoc [Fri, 31 Oct 2014 16:18:33 +0000 (16:18 +0000)]
JAL-1152 menu tweaks plus new option to put Autocalc at top or below.
Jim Procter [Fri, 31 Oct 2014 16:14:27 +0000 (16:14 +0000)]
JAL-674 JAL-961 pass row reference to handler to check calcId and any specific properties (e.g. originating PDB ID for the row data)
Jim Procter [Fri, 31 Oct 2014 16:11:45 +0000 (16:11 +0000)]
JAL-674 JAL-961 properties to stash additional information for an alignment annotation row
Charles Ofoegbu [Fri, 31 Oct 2014 12:57:09 +0000 (12:57 +0000)]
added jsoup lib to class path
Charles Ofoegbu [Fri, 31 Oct 2014 09:56:45 +0000 (09:56 +0000)]
JAL-1541 upadated BioJs emmitter to store alignment data as json
Jim Procter [Thu, 30 Oct 2014 17:05:36 +0000 (17:05 +0000)]
Merge branch 'develop' into features/ssFromPDBEntry
Jim Procter [Thu, 30 Oct 2014 16:53:20 +0000 (16:53 +0000)]
JAL-674 hang on to sequences created by secondary parsiing process to manage transfer of annotation
Jim Procter [Thu, 30 Oct 2014 16:51:10 +0000 (16:51 +0000)]
JAL-674 count number of annotation transferred in test
gmungoc [Thu, 30 Oct 2014 16:29:01 +0000 (16:29 +0000)]
JAL-1152 with sticky annotation sort order that updates as sequences are
moved up or down
Jim Procter [Thu, 30 Oct 2014 15:51:54 +0000 (15:51 +0000)]
JAL-674 propagate annotation onto mapped sequence and its dataset sequence
Jim Procter [Thu, 30 Oct 2014 15:50:30 +0000 (15:50 +0000)]
JAL-674 register PDB IDs when ever they are resolved on file IO
git://source.jalview.org / jalview.git / log