tcofoegbu [Fri, 17 Mar 2017 15:41:01 +0000 (15:41 +0000)]
JAL-2136 JAL-2137 Improvements: enable STRUCTMODEL annotation statement to be less stringent and backwards compatible, Link query and template sequences, transfer annotation from model to template sequence
tcofoegbu [Tue, 14 Mar 2017 15:35:50 +0000 (15:35 +0000)]
JAL-2136 JAL-2137 Improved STRUCTMODEL annotation syntax to reinstated fasta file specification, improved implementation to link the Fasta mapping file to Phyre2 model entry, and moved Phyre2 model info from sequence detail to PDBEntry properties
tcofoegbu [Fri, 10 Mar 2017 14:29:21 +0000 (14:29 +0000)]
JAL-2136 JAL-2137 Modified STRUCTMODEL annotation format and added implementation to register Phyre2 model file from AnnotationFile such that it could be properly processed Phyre2 client on structure viewing.
tcofoegbu [Tue, 28 Feb 2017 12:49:20 +0000 (12:49 +0000)]
JAL-2136 added improvement to parse crudelist file instead of scrapping 'summary.html' and renamed testfiles accordingly
tcofoegbu [Mon, 20 Feb 2017 12:25:32 +0000 (12:25 +0000)]
JAL-2136 merged and resolved conflicts with
80edaa84d6d9beac9f0d2c71b50b7b56fd393427
tcofoegbu [Mon, 20 Feb 2017 10:17:44 +0000 (10:17 +0000)]
Merge branch 'reviews/features/JAL-2136_phyre2_integration_withJims' into merge/JAL-2136_phyre2_integration
Jim Procter [Wed, 8 Feb 2017 15:01:21 +0000 (15:01 +0000)]
JAL-2136 update merged code for JAL-2040 for new FileFormat/Protocol interface (JAL-2344)
tcofoegbu [Mon, 30 Jan 2017 11:37:55 +0000 (11:37 +0000)]
Merge branch 'reviews/features/JAL-2136_phyre2_integration_withJims' into merge/JAL-2136_phyre2_integration
Jim Procter [Mon, 23 Jan 2017 15:13:33 +0000 (15:13 +0000)]
Merge branch 'features/JAL-2040_JAL-2137_phyre2' into reviews/features/JAL-2136_phyre2_integration_withJims
tcofoegbu [Fri, 20 Jan 2017 19:43:20 +0000 (19:43 +0000)]
JAL-2375 JAL-2376 First commit of implementation for Phyre2 result browsing, template parsing and structure mapping. Added fix for failing tests in SiftsClientTest, added improvement to un-offer cached option when cached data is unavailable, added improvement to include horizontal separator between structure filter options and manual input options, and other minor refactoring
Jim Procter [Thu, 19 Jan 2017 17:08:41 +0000 (17:08 +0000)]
Merge branch 'spike/JAL-2040_JAL-2137_phyre2' into features/JAL-2040_JAL-2137_phyre2
gmungoc [Fri, 16 Dec 2016 16:04:52 +0000 (16:04 +0000)]
JAL-2356 enhanced unit test to verify reuse (or not) of file from cache
Jim Procter [Wed, 14 Dec 2016 15:08:14 +0000 (15:08 +0000)]
Merge branch 'patch/JAL-2197_jpredforjnets' into develop
merge was missed for 2.10.1 release!
gmungoc [Fri, 9 Dec 2016 11:52:52 +0000 (11:52 +0000)]
JAL-2105 updated for reviewed REST version 4.8
gmungoc [Fri, 9 Dec 2016 09:23:55 +0000 (09:23 +0000)]
JAL-1895 suppress RNA interaction colour option
gmungoc [Thu, 8 Dec 2016 09:20:08 +0000 (09:20 +0000)]
JAL-2359 add Window menu entry only after all danger of error is passed
gmungoc [Wed, 7 Dec 2016 16:58:46 +0000 (16:58 +0000)]
JAL-2356 use cached Sifts file if not expired
gmungoc [Wed, 7 Dec 2016 13:13:46 +0000 (13:13 +0000)]
JAL-2354 handle error response when fetching features
gmungoc [Wed, 7 Dec 2016 12:10:00 +0000 (12:10 +0000)]
JAL-2344 handle null format, simplify JalviewFileChooser constructor
Jim Procter [Wed, 30 Nov 2016 16:04:57 +0000 (16:04 +0000)]
Merge branch 'features/JAL-2320_closeChimeraAction' into develop
also tidied up javadoc
gmungoc [Wed, 30 Nov 2016 12:38:29 +0000 (12:38 +0000)]
JAL-2344 use ".cif" for saved mmCIF file (and refactor fetch as file)
gmungoc [Tue, 29 Nov 2016 16:20:42 +0000 (16:20 +0000)]
JAL-2329 tests to confirm behaviour of Java extended for loops
gmungoc [Tue, 29 Nov 2016 13:25:45 +0000 (13:25 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Tue, 29 Nov 2016 10:57:10 +0000 (10:57 +0000)]
JAL-2344 corrected conversion of Type enum to FileFormat
Jim Procter [Tue, 29 Nov 2016 09:18:59 +0000 (09:18 +0000)]
Merge branch 'documentation/JAL-2325_release2101' into develop
Jim Procter [Tue, 29 Nov 2016 09:18:14 +0000 (09:18 +0000)]
JAL-2325 update release date in whatsNew
gmungoc [Tue, 29 Nov 2016 09:07:25 +0000 (09:07 +0000)]
JAL-2344 FileFormat.isStructureFile replaces
StructureFile.isStructureFile
Jim Procter [Tue, 29 Nov 2016 07:43:23 +0000 (07:43 +0000)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Tue, 29 Nov 2016 07:42:02 +0000 (07:42 +0000)]
Merge branch 'documentation/JAL-2325_release2101' into develop
gmungoc [Mon, 28 Nov 2016 17:31:30 +0000 (17:31 +0000)]
Merge branch 'develop' into trialMerge
Conflicts:
src/jalview/gui/CutAndPasteTransfer.java
test/MCview/PDBfileTest.java
test/jalview/analysis/AlignmentAnnotationUtilsTest.java
test/jalview/analysis/DnaTest.java
test/jalview/analysis/FinderTest.java
test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
test/jalview/controller/AlignViewControllerTest.java
test/jalview/datamodel/AlignmentTest.java
test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
test/jalview/ext/jmol/JmolParserTest.java
test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java
test/jalview/ext/paradise/TestAnnotate3D.java
test/jalview/io/gff/ExonerateHelperTest.java
test/jalview/io/gff/GffTests.java
test/jalview/structure/Mapping.java
test/jalview/structure/StructureSelectionManagerTest.java
test/jalview/structures/models/AAStructureBindingModelTest.java
test/jalview/util/MappingUtilsTest.java
test/jalview/ws/sifts/SiftsClientTest.java
Jim Procter [Mon, 28 Nov 2016 17:12:16 +0000 (17:12 +0000)]
JAL-2325 JAL-1878 update minimum versions of JRE for running/installing on windows and OSX
tcofoegbu [Mon, 28 Nov 2016 16:02:32 +0000 (16:02 +0000)]
Merge branch 'features/JAL-2326_JOptionPane-refactoring' into develop
gmungoc [Mon, 28 Nov 2016 14:35:59 +0000 (14:35 +0000)]
JAL-2344 added FileFormatI.isStructureFile()
gmungoc [Mon, 28 Nov 2016 14:24:37 +0000 (14:24 +0000)]
JAL-2345 cache generated ImageIcon per file path
Jim Procter [Mon, 28 Nov 2016 14:16:52 +0000 (14:16 +0000)]
Merge branch 'documentation/JAL-2325_release2101' into develop
Jim Procter [Mon, 28 Nov 2016 14:16:39 +0000 (14:16 +0000)]
JAL-2325 finalise release notes
gmungoc [Fri, 25 Nov 2016 15:35:53 +0000 (15:35 +0000)]
JAL-2344 dynamically determine recognised extensions for file browser
Jim Procter [Fri, 25 Nov 2016 15:16:55 +0000 (15:16 +0000)]
Merge branch 'documentation/JAL-2325_release2101' into develop
Jim Procter [Fri, 25 Nov 2016 14:58:27 +0000 (14:58 +0000)]
JAL-2325 JAL-2273 update vms bound to different installers
Jim Procter [Fri, 25 Nov 2016 14:58:08 +0000 (14:58 +0000)]
JAL-2325 more ignores on sourcedist build
gmungoc [Fri, 25 Nov 2016 14:21:34 +0000 (14:21 +0000)]
Merge branch 'develop' into trialMerge
Conflicts:
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AppletJmol.java
src/jalview/appletgui/AppletJmolBinding.java
src/jalview/appletgui/ExtJmol.java
src/jalview/datamodel/PDBEntry.java
src/jalview/ext/ensembl/EnsemblRestClient.java
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/ext/jmol/JmolParser.java
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AppJmolBinding.java
src/jalview/gui/Desktop.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/JalviewChimeraBindingModel.java
src/jalview/gui/StructureChooser.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/BioJsHTMLOutput.java
src/jalview/io/HTMLOutput.java
src/jalview/io/HtmlSvgOutput.java
src/jalview/io/StructureFile.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/structures/models/AAStructureBindingModel.java
src/jalview/ws/dbsources/Pdb.java
src/jalview/ws/dbsources/Xfam.java
test/MCview/PDBfileTest.java
test/jalview/datamodel/AlignmentTest.java
test/jalview/ext/jmol/JmolParserTest.java
test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java
test/jalview/gui/AlignViewportTest.java
test/jalview/io/FeaturesFileTest.java
test/jalview/io/Jalview2xmlTests.java
test/jalview/io/PfamFormatInputTest.java
test/jalview/io/gff/ExonerateHelperTest.java
test/jalview/structure/Mapping.java
test/jalview/structures/models/AAStructureBindingModelTest.java
gmungoc [Fri, 25 Nov 2016 09:43:04 +0000 (09:43 +0000)]
JAL-2344 override to ignore (obsolete?) JalviewFileView
gmungoc [Fri, 25 Nov 2016 09:01:54 +0000 (09:01 +0000)]
JAL-2344 use .equals() to compare FileFormatI objects
gmungoc [Fri, 25 Nov 2016 09:01:23 +0000 (09:01 +0000)]
JAL-2344 correct roundtrip test to exclude Jalview project format
tcofoegbu [Thu, 24 Nov 2016 17:35:50 +0000 (17:35 +0000)]
JAL-2326 added setup method for JvOptionPane in all Jalveiw test classes to enable JvOptionPane to run non-interactively
gmungoc [Thu, 24 Nov 2016 16:43:06 +0000 (16:43 +0000)]
Distinguish text-only output formats and others (.jar/.jvp)
tcofoegbu [Thu, 24 Nov 2016 16:18:54 +0000 (16:18 +0000)]
JAL-2326 updated references of JOptionPane to JvOptionPane
Jim Procter [Thu, 24 Nov 2016 16:16:35 +0000 (16:16 +0000)]
Merge branch 'documentation/JAL-2325_release2101' into develop
Jim Procter [Thu, 24 Nov 2016 16:16:13 +0000 (16:16 +0000)]
JAL-2325 exclude .class and .* files (install anywhere build files) from source distribution
Jim Procter [Thu, 24 Nov 2016 15:49:16 +0000 (15:49 +0000)]
Merge branch 'documentation/JAL-2325_release2101' into develop
Jim Procter [Thu, 24 Nov 2016 15:48:30 +0000 (15:48 +0000)]
JAL-2325 applied BSD license for chimera/StrucViz2 code
gmungoc [Thu, 24 Nov 2016 15:42:52 +0000 (15:42 +0000)]
Further tweaks to get tests passing
tcofoegbu [Thu, 24 Nov 2016 15:40:05 +0000 (15:40 +0000)]
JAL-2326 added layer of abstraction between Jalview and JOptionPane to provide better control for running unattended test non-interactively
Jim Procter [Thu, 24 Nov 2016 15:35:39 +0000 (15:35 +0000)]
JAL-2325 apply license to new source files
Jim Procter [Thu, 24 Nov 2016 15:35:17 +0000 (15:35 +0000)]
JAL-2325 update release date to next Tuesday
gmungoc [Thu, 24 Nov 2016 13:06:38 +0000 (13:06 +0000)]
FileFormatI further tweaks, clean compile
Jim Procter [Thu, 24 Nov 2016 10:06:03 +0000 (10:06 +0000)]
JAL-2325 tidy up release notes
Jim Procter [Wed, 23 Nov 2016 18:51:01 +0000 (18:51 +0000)]
JAL-2325 remove 2.10.0 what’s new
Jim Procter [Wed, 23 Nov 2016 18:50:49 +0000 (18:50 +0000)]
JAL-2325 latest release to 2.10
Jim Procter [Wed, 23 Nov 2016 17:44:12 +0000 (17:44 +0000)]
JAL-1738 Ctrl/Cmd/Alt modifiers and mention that B and Alt-B by default add columns to selection
Jim Procter [Wed, 23 Nov 2016 17:43:24 +0000 (17:43 +0000)]
JAL-1738 hint about using the task switching key combination to quickly mark highlighted regions in Jalview from selections in Chimera.
Jim Procter [Wed, 23 Nov 2016 17:41:56 +0000 (17:41 +0000)]
JAL-1738 mention Ctrl/Cmd/Alt modifiers and mention that B by default adds columns to selection
Jim Procter [Wed, 23 Nov 2016 17:40:59 +0000 (17:40 +0000)]
JAL-1738 mention Ctrl or Cmd for toggle behaviour in tooltip
Jim Procter [Wed, 23 Nov 2016 17:14:12 +0000 (17:14 +0000)]
JAL-2325 updated what’s new for 2.10.1
Jim Procter [Wed, 23 Nov 2016 17:13:59 +0000 (17:13 +0000)]
JAL-2325 reword ‘tame tooltip’ JAL-1723 release note
Jim Procter [Wed, 23 Nov 2016 17:13:15 +0000 (17:13 +0000)]
JAL-2325 rejig authors and add Kira
Jim Procter [Wed, 23 Nov 2016 15:36:39 +0000 (15:36 +0000)]
JAL-2282 JAL-2325 added link to help text from release notes
Jim Procter [Wed, 23 Nov 2016 15:36:31 +0000 (15:36 +0000)]
JAL-2325 updated what’s new for 2.10.1
Jim Procter [Wed, 23 Nov 2016 15:22:50 +0000 (15:22 +0000)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Wed, 23 Nov 2016 15:22:44 +0000 (15:22 +0000)]
JAL-2282 revised docs about warning message.
gmungoc [Wed, 23 Nov 2016 15:07:31 +0000 (15:07 +0000)]
JAL-1738 Spanish versions added
Jim Procter [Wed, 23 Nov 2016 14:36:43 +0000 (14:36 +0000)]
Merge branch 'documentation/JAL-2325_release2101' into develop
Jim Procter [Wed, 23 Nov 2016 14:36:17 +0000 (14:36 +0000)]
JAL-2325 JAL-2332 release notes
Jim Procter [Wed, 23 Nov 2016 14:02:29 +0000 (14:02 +0000)]
Merge branch 'documentation/JAL-2325_release2101' into develop
Jim Procter [Wed, 23 Nov 2016 14:02:19 +0000 (14:02 +0000)]
Merge branch 'bug/JAL-2323disulfideOverview' into develop
Jim Procter [Wed, 23 Nov 2016 13:43:14 +0000 (13:43 +0000)]
JAL-2325 moved disulphide/contact bug fixes (JAL-2323,JAL-2333,JAL-2335,JAL-2327) to ‘General’ section of release notes
Jim Procter [Wed, 23 Nov 2016 12:25:32 +0000 (12:25 +0000)]
JAL-2325 release notes formatting
Jim Procter [Wed, 23 Nov 2016 12:24:43 +0000 (12:24 +0000)]
JAL-2325 release notes
Jim Procter [Wed, 23 Nov 2016 11:45:33 +0000 (11:45 +0000)]
Merge branch 'documentation/JAL-2325_release2101' into develop
Jim Procter [Wed, 23 Nov 2016 11:44:40 +0000 (11:44 +0000)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Wed, 23 Nov 2016 11:43:42 +0000 (11:43 +0000)]
JAL-2325 release notes
Jim Procter [Tue, 22 Nov 2016 18:21:34 +0000 (18:21 +0000)]
JAL-2197 changed tooltip for Jnet annotation rows to “Jpred Output”
tcofoegbu [Tue, 22 Nov 2016 17:21:16 +0000 (17:21 +0000)]
Merge branch 'bug/JAL-2277_refactorPrintUnwrapped' into develop
Jim Procter [Tue, 22 Nov 2016 17:14:38 +0000 (17:14 +0000)]
Merge branch 'features/JAL-2177_update_jmol_to_14.6.4_2016.10.26' into develop
Jim Procter [Tue, 22 Nov 2016 17:10:08 +0000 (17:10 +0000)]
JAL-2325 update release date for 2.10.1
Jim Procter [Tue, 22 Nov 2016 17:07:36 +0000 (17:07 +0000)]
Merge branch 'develop' into documentation/JAL-2325_release2101
gmungoc [Tue, 22 Nov 2016 16:41:36 +0000 (16:41 +0000)]
JAL-2337 fix: only adjust once for scroll offset
gmungoc [Tue, 22 Nov 2016 15:52:32 +0000 (15:52 +0000)]
JAL-1919 JAL-2177 handle empty pdbentries list correctly
Jim Procter [Tue, 22 Nov 2016 13:34:17 +0000 (13:34 +0000)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
tcofoegbu [Tue, 22 Nov 2016 12:48:30 +0000 (12:48 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Tue, 22 Nov 2016 12:48:20 +0000 (12:48 +0000)]
JAL-2322 added runnable interface to HTMLOutput class, abstracted anonymous threads in child classes to the overriding run methods, and then other minor housekeeping
Jim Procter [Tue, 22 Nov 2016 12:45:31 +0000 (12:45 +0000)]
Merge branch 'features/JAL-1738_JAL-345_selectionfromhighlight' into develop
Jim Procter [Tue, 22 Nov 2016 12:42:25 +0000 (12:42 +0000)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Tue, 22 Nov 2016 12:41:33 +0000 (12:41 +0000)]
JAL-1738 JAL-345 changed keystroke to ‘B’ (with modifiers) and added documentation
gmungoc [Tue, 22 Nov 2016 12:22:46 +0000 (12:22 +0000)]
JAL-2277 refactored AlignmentPanel.printUnwrapped to simplify
tcofoegbu [Mon, 21 Nov 2016 17:47:27 +0000 (17:47 +0000)]
JAL-2277 bug fix for mis-alligned graphics output for scrolled annotations
Jim Procter [Mon, 21 Nov 2016 17:05:56 +0000 (17:05 +0000)]
JAL-2325 JAL-2118 2.10.0 patch in release note
Jim Procter [Mon, 21 Nov 2016 16:31:45 +0000 (16:31 +0000)]
JAL-2335 patched FeatureRendererModel.findFeaturesAtRes to honour isContactFeature
Jim Procter [Mon, 21 Nov 2016 16:22:19 +0000 (16:22 +0000)]
JAL-2335 failing test for FeatureRendererModel.findFeaturesAt and contact features
Jim Procter [Mon, 21 Nov 2016 15:40:46 +0000 (15:40 +0000)]
Merge branch 'documentation/JAL-2325_release2101' into develop
git://source.jalview.org / jalview.git / log