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)
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
Jim Procter [Mon, 21 Nov 2016 15:40:08 +0000 (15:40 +0000)]
Merge branch 'develop' into documentation/JAL-2325_release2101
Jim Procter [Mon, 21 Nov 2016 13:24:10 +0000 (13:24 +0000)]
JAL-2284 documentation for the new command-line option
Jim Procter [Mon, 21 Nov 2016 13:09:37 +0000 (13:09 +0000)]
JAL-2325 post-document JAL-2284 released in 2.10.0
Jim Procter [Mon, 21 Nov 2016 13:04:13 +0000 (13:04 +0000)]
JAL-2325 release notes for JAL-2317
tcofoegbu [Mon, 21 Nov 2016 13:03:50 +0000 (13:03 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Mon, 21 Nov 2016 13:03:40 +0000 (13:03 +0000)]
JAL-2332 bugfix to enable structure chooser opening for hen lysozyme
gmungoc [Mon, 21 Nov 2016 11:58:49 +0000 (11:58 +0000)]
JAL-2333 test beefed up with gaps
git://source.jalview.org / jalview.git / log