gmungoc [Fri, 20 Jan 2017 12:03:39 +0000 (12:03 +0000)]
JAL-2383 fixup from last merge
gmungoc [Fri, 20 Jan 2017 11:56:07 +0000 (11:56 +0000)]
Merge branch 'develop' into features/JAL-2360colourSchemeApplicability
Conflicts:
src/jalview/appletgui/APopupMenu.java
src/jalview/appletgui/SliderPanel.java
src/jalview/gui/PopupMenu.java
gmungoc [Fri, 20 Jan 2017 10:55:50 +0000 (10:55 +0000)]
JAL-2383 check for null, spelling
gmungoc [Fri, 20 Jan 2017 10:55:24 +0000 (10:55 +0000)]
JAL-2383 make popup colour menu order and wording consistent
gmungoc [Fri, 20 Jan 2017 10:52:29 +0000 (10:52 +0000)]
JAL-2383 restore group conservation slider setting from project
gmungoc [Fri, 20 Jan 2017 09:47:20 +0000 (09:47 +0000)]
Merge branch 'develop' into features/JAL-2360colourSchemeApplicability
Conflicts:
src/jalview/appletgui/APopupMenu.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/PopupMenu.java
src/jalview/jbgui/GAlignFrame.java
gmungoc [Thu, 19 Jan 2017 16:37:02 +0000 (16:37 +0000)]
JAL-2383 restore PID colour threshold from project; enable/disable
modify PID/Conservation (and add to popup menus)
gmungoc [Thu, 19 Jan 2017 10:29:04 +0000 (10:29 +0000)]
JAL-2370 unit tests for extracted ColumnSelection.stretchGroup()
gmungoc [Thu, 19 Jan 2017 09:40:06 +0000 (09:40 +0000)]
JAL-2370 corrected applet mouse drag, refactored into ColumnSelection
gmungoc [Tue, 17 Jan 2017 15:01:01 +0000 (15:01 +0000)]
JAL-2370 fix bug when hiding a range including two or more hidden ranges
gmungoc [Tue, 17 Jan 2017 13:31:55 +0000 (13:31 +0000)]
Merge branch 'develop' into features/JAL-2360colourSchemeApplicability
Conflicts:
src/jalview/gui/PopupMenu.java
src/jalview/jbgui/GAlignFrame.java
gmungoc [Mon, 16 Jan 2017 09:02:52 +0000 (09:02 +0000)]
JAL-1270 class renamed
gmungoc [Mon, 16 Jan 2017 09:02:34 +0000 (09:02 +0000)]
JAL-2380 fix Matrix.postMultiply()
gmungoc [Mon, 16 Jan 2017 08:52:20 +0000 (08:52 +0000)]
JAL-1270 tweaks to AlignmentGenerator / client class
gmungoc [Thu, 12 Jan 2017 17:10:00 +0000 (17:10 +0000)]
JAL-1270 renamed AlignmentGenerator, and added peptide option
gmungoc [Thu, 12 Jan 2017 16:44:09 +0000 (16:44 +0000)]
JAL-2379 null references to PCA model when panel is closed
gmungoc [Thu, 12 Jan 2017 09:05:56 +0000 (09:05 +0000)]
JAL-2344 now flagging formats as 'identifiable' instead of 'dynamic'
gmungoc [Wed, 11 Jan 2017 16:48:28 +0000 (16:48 +0000)]
JAL-2344 separated AlignmentFileI into AlignmentFileReaderI,
AlignmentFileWriterI
gmungoc [Wed, 11 Jan 2017 16:06:01 +0000 (16:06 +0000)]
JAL-2344 groovy script that registers a new file format
gmungoc [Wed, 11 Jan 2017 16:05:41 +0000 (16:05 +0000)]
JAL-2344 FileFormats singleton for formats, FileFormatI simplified
gmungoc [Wed, 11 Jan 2017 15:38:34 +0000 (15:38 +0000)]
JAL-2344 addSequence() method added to support Groovy parser
gmungoc [Tue, 10 Jan 2017 14:38:48 +0000 (14:38 +0000)]
JAL-2377 avoid infinite loop formatting 1.0E-310
gmungoc [Fri, 6 Jan 2017 14:10:44 +0000 (14:10 +0000)]
JAL-2360 findColour() with no args removed from ColourSchemeI
gmungoc [Fri, 6 Jan 2017 09:03:27 +0000 (09:03 +0000)]
Merge branch 'develop' into features/JAL-2360colourSchemeApplicability
gmungoc [Thu, 5 Jan 2017 16:31:55 +0000 (16:31 +0000)]
JAL-2374 unit test for (modified) Alignment.findGroup()
gmungoc [Thu, 5 Jan 2017 16:00:23 +0000 (16:00 +0000)]
JAL-2374 fix popup out by one and multiple groups bugs
gmungoc [Thu, 5 Jan 2017 12:24:37 +0000 (12:24 +0000)]
Merge branch 'develop' into features/JAL-2360colourSchemeApplicability
Conflicts:
src/jalview/gui/PopupMenu.java
gmungoc [Thu, 5 Jan 2017 11:35:21 +0000 (11:35 +0000)]
JAL-2373 set state of Above PID, By Conservation in Popup Menu
gmungoc [Thu, 29 Dec 2016 11:59:17 +0000 (11:59 +0000)]
JAL-2630 first pass groovy colour scheme (with slight refactoring)
gmungoc [Fri, 23 Dec 2016 13:48:01 +0000 (13:48 +0000)]
JAL-2360 removed UserDefinedColours.userColourSchemes
gmungoc [Fri, 23 Dec 2016 09:17:22 +0000 (09:17 +0000)]
JAL-2120 JAL-2360 remove obsolete PDBViewer
gmungoc [Thu, 22 Dec 2016 14:03:20 +0000 (14:03 +0000)]
JAL-2360 fix bug that prematurely created a SequenceGroup
gmungoc [Thu, 22 Dec 2016 13:12:33 +0000 (13:12 +0000)]
JAL-2360 structure viewers now using ColourMenuHelper, obsolete methods
and fields removed, more methods pulled up
gmungoc [Wed, 21 Dec 2016 16:52:12 +0000 (16:52 +0000)]
JAL-2360 set new/loaded colour scheme name correctly
gmungoc [Wed, 21 Dec 2016 16:00:29 +0000 (16:00 +0000)]
JAL-2360 simplified code to create a new colour scheme
gmungoc [Wed, 21 Dec 2016 15:19:38 +0000 (15:19 +0000)]
JAL-2360 added a table to show score colours
gmungoc [Wed, 21 Dec 2016 15:18:41 +0000 (15:18 +0000)]
JAL-2360 ColourMenuHelper now builds and selects items in colour menu
for align frame and popup menus
gmungoc [Wed, 21 Dec 2016 15:17:10 +0000 (15:17 +0000)]
JAL-2360 comment only
gmungoc [Wed, 21 Dec 2016 15:16:34 +0000 (15:16 +0000)]
JAL-2360 tidy up, simplify isApplicableTo test
gmungoc [Wed, 21 Dec 2016 15:15:33 +0000 (15:15 +0000)]
JAL-2360 no RNAHelices colouring for groups
gmungoc [Wed, 21 Dec 2016 14:51:43 +0000 (14:51 +0000)]
JAL-2361 Blosum is enabled for peptide
gmungoc [Wed, 21 Dec 2016 14:50:48 +0000 (14:50 +0000)]
JAL-1421 add types to Map
gmungoc [Wed, 21 Dec 2016 14:49:19 +0000 (14:49 +0000)]
JAL-2360 fix incorrect action on Cancel user defined colour for group
gmungoc [Wed, 21 Dec 2016 14:41:43 +0000 (14:41 +0000)]
JAL-2360 tidy spelling and file contents order only
gmungoc [Wed, 21 Dec 2016 14:39:19 +0000 (14:39 +0000)]
JAL-2360 Javadoc and test cases for findAnnotation
gmungoc [Tue, 20 Dec 2016 16:01:41 +0000 (16:01 +0000)]
JAL-2360 testRegisterColourScheme to demonstrate a 'plug-in' scheme
gmungoc [Tue, 20 Dec 2016 14:06:42 +0000 (14:06 +0000)]
JAL-2360 ColourSchemes holds configured schemes, AlignFrame colour menu
construction and actions done dynamically
gmungoc [Mon, 19 Dec 2016 11:21:47 +0000 (11:21 +0000)]
JAL-2360 amended toAppletParameter() for reproducible behaviour
gmungoc [Mon, 19 Dec 2016 10:44:31 +0000 (10:44 +0000)]
JAL-2361 select colour menu item by matching its name to colour scheme
name
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 [Fri, 16 Dec 2016 15:14:55 +0000 (15:14 +0000)]
JAL-2360 report line number when threshold cannot be parsed as a value
gmungoc [Fri, 16 Dec 2016 13:13:30 +0000 (13:13 +0000)]
JAL-2360 added UserColourScheme.toAppletParameter+test, hid
parseAppletParameter()
gmungoc [Fri, 16 Dec 2016 10:43:35 +0000 (10:43 +0000)]
JAL-2360 getColour() renamed to getColourScheme(), handling of "None"
corrected, tests added
gmungoc [Fri, 16 Dec 2016 09:45:09 +0000 (09:45 +0000)]
JAL-1705 JAL-98 use SortedMap as more accurate type than Map
gmungoc [Fri, 16 Dec 2016 09:37:11 +0000 (09:37 +0000)]
JAL-2360 refactoring for JalviewColourScheme enum,
ColourSchemeI.getSchemeName(), isApplicableTo()
gmungoc [Fri, 16 Dec 2016 08:55:13 +0000 (08:55 +0000)]
JAL-1354 use i18n text for expected value
gmungoc [Wed, 14 Dec 2016 15:36:52 +0000 (15:36 +0000)]
JAL-2360 test added
gmungoc [Wed, 14 Dec 2016 15:36:13 +0000 (15:36 +0000)]
JAL-2360 added check for null annotations array
gmungoc [Wed, 14 Dec 2016 15:33:08 +0000 (15:33 +0000)]
JAL-1544 JAL-2360 reformatted help page a bit nicer + spelling fix
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 [Tue, 13 Dec 2016 11:09:48 +0000 (11:09 +0000)]
JAL-2365 test for lightgray, darkgray not lightGray, darkGray
gmungoc [Tue, 13 Dec 2016 10:57:13 +0000 (10:57 +0000)]
JAL-2360 code formatting only and if-else changed to switch
gmungoc [Tue, 13 Dec 2016 10:46:04 +0000 (10:46 +0000)]
JAL-2361 adding items to applet colour menus, TCoffee colour to desktop
popup menu, extracted PopupMenu.buildColourMenu()
gmungoc [Mon, 12 Dec 2016 22:09:57 +0000 (22:09 +0000)]
JAL-2361 extract methods to (re-)build colour menu
gmungoc [Mon, 12 Dec 2016 22:01:47 +0000 (22:01 +0000)]
JAL-2360 simplify nucleotide flag, remove setter
gmungoc [Mon, 12 Dec 2016 21:59:20 +0000 (21:59 +0000)]
JAL-2361 use consistent colour names on menus
gmungoc [Mon, 12 Dec 2016 19:47:44 +0000 (19:47 +0000)]
JAL-1544 backgroud -> background
gmungoc [Mon, 12 Dec 2016 12:28:32 +0000 (12:28 +0000)]
JAL-2362 return correct lower-case colour; Javadoc; unit test
gmungoc [Mon, 12 Dec 2016 12:20:44 +0000 (12:20 +0000)]
JAL-2632 corrected lookup of residue colour
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
git://source.jalview.org / jalview.git / log