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 11:42:02 +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)]
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
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
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 14:55:45 +0000 (14:55 +0000)]
JAL-974 fix class contamination for jalviewLite build
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 12:40:43 +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
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).
Jim Procter [Thu, 6 Nov 2014 17:18:44 +0000 (17:18 +0000)]
Merge branch 'features/JAL-1152annotationSorting' into features/typed_annotations_calcId
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
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
Jim Procter [Thu, 30 Oct 2014 15:47:07 +0000 (15:47 +0000)]
JAL-674 use PDB ID<>File registry to look up correct ID for PDB file derived annotation on a mapped sequence
Jim Procter [Thu, 30 Oct 2014 15:44:50 +0000 (15:44 +0000)]
JAL-674 return original and replacement sequences and the alignment to allow more processing if needed
Jim Procter [Thu, 30 Oct 2014 15:40:31 +0000 (15:40 +0000)]
JAL-674 helpful javadoc for remap method
Jim Procter [Thu, 30 Oct 2014 15:39:53 +0000 (15:39 +0000)]
JAL-674 flag and proxy method to distinguish setMapping calls which create a mapping for a displayed structure and those which transfer annotation
Jim Procter [Thu, 30 Oct 2014 15:30:50 +0000 (15:30 +0000)]
JAL-674 map on StructureSelectionManager to record PDB IDs extracted/assigned to PDB files
Jim Procter [Thu, 30 Oct 2014 15:26:11 +0000 (15:26 +0000)]
patch for JAL-795 - use base secondary structure colour if no colour defined on annotation row element
Jim Procter [Thu, 30 Oct 2014 15:24:00 +0000 (15:24 +0000)]
JAL-674 patch test to verify presence of annotation on the sequence associated with the PDB file
Jim Procter [Thu, 30 Oct 2014 15:21:31 +0000 (15:21 +0000)]
JAL-1551 format and tidy
gmungoc [Thu, 30 Oct 2014 14:18:42 +0000 (14:18 +0000)]
JAL-1152 prototype of new Annotations menu with sort options
Charles Ofoegbu [Thu, 30 Oct 2014 12:27:40 +0000 (12:27 +0000)]
JAL-353 updated patch for undo successive remove redundant sequence
Charles Ofoegbu [Wed, 29 Oct 2014 19:05:37 +0000 (19:05 +0000)]
JAL-353 updated patch for undo successive remove redundant sequences
Jim Procter [Wed, 29 Oct 2014 10:47:13 +0000 (10:47 +0000)]
JAL-1264 JAL-674 test to exercise the AlignmentAnnotation.remap method via
the jalview.structure.StructureMapping.transfer method
Jim Procter [Wed, 29 Oct 2014 10:44:33 +0000 (10:44 +0000)]
JAL-1264 JAL-674 method to copy annotation on structure positions to associated sequence positions
Jim Procter [Wed, 29 Oct 2014 10:41:32 +0000 (10:41 +0000)]
JAL-674 JAL-1264 remap method to allow annotation positions to be updated from simple int-pair arrays (like those used in the StructureManager mappings)
gmungoc [Tue, 28 Oct 2014 15:52:53 +0000 (15:52 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Tue, 28 Oct 2014 15:51:46 +0000 (15:51 +0000)]
JAL-1264 refactor to add menu options to _both_ sequence and selection
pop-ups, plus unit tests.
Charles Ofoegbu [Tue, 28 Oct 2014 11:03:09 +0000 (11:03 +0000)]
2_8_2_Branch merge
Charles Ofoegbu [Tue, 28 Oct 2014 10:35:44 +0000 (10:35 +0000)]
JAL-353 undo for successive removal of redundant sequence - bugfix
Charles Ofoegbu [Tue, 28 Oct 2014 10:32:23 +0000 (10:32 +0000)]
JAL-1250 Redundancy removal bug fix for Applet version
Jim Procter [Mon, 27 Oct 2014 13:40:20 +0000 (13:40 +0000)]
Merge branch 'develop' into Release_2_8_2_Branch
Jim Procter [Mon, 27 Oct 2014 13:39:38 +0000 (13:39 +0000)]
Merge branch 'Release_2_8_2_Branch' into merge_r282_dev
normalised HTML messages and line endings for JAL-1420 JAL-1428 JAL-1355
(darolmar commits)
Conflicts:
resources/lang/Messages.properties
resources/lang/Messages_es.properties
Charles Ofoegbu [Mon, 27 Oct 2014 13:06:19 +0000 (13:06 +0000)]
Updated RedundancyPanel.java to referesh the tree view when reduncancy is applied/unapplied
Charles Ofoegbu [Mon, 27 Oct 2014 11:51:29 +0000 (11:51 +0000)]
Patch for redundancy removal
Jim Procter [Thu, 23 Oct 2014 22:08:56 +0000 (23:08 +0100)]
Merge branch 'hotfix/JAL-1521' into Release_2_8_2_Branch
Conflicts:
.classpath
RELEASE
src/castor.properties
Jim Procter [Thu, 23 Oct 2014 22:02:54 +0000 (23:02 +0100)]
Merge branch 'hotfix/JAL-1521' into develop
Conflicts:
.classpath
RELEASE
unknown [Thu, 23 Oct 2014 21:28:31 +0000 (22:28 +0100)]
JAL-1521 updated xerces to 2.11 along with xml-apis
Jim Procter [Thu, 23 Oct 2014 16:24:12 +0000 (17:24 +0100)]
JAL-1521 patch is to remove xerces from classpath. This may cause problems for java 1.6 builds
Jim Procter [Thu, 23 Oct 2014 16:23:16 +0000 (17:23 +0100)]
JAL-1521 test to check registry is returning sources