kjvdheide [Thu, 9 Nov 2017 16:12:00 +0000 (16:12 +0000)]
JAL-2794 PaintRefresher support, Aptx node selection now shown on align
kjvdheide [Thu, 9 Nov 2017 16:09:23 +0000 (16:09 +0000)]
JAL-2794 interface comment
kjvdheide [Thu, 9 Nov 2017 16:08:46 +0000 (16:08 +0000)]
JAL-2794 Made HashMap with Nodes as keys and sequences as values as well
kjvdheide [Wed, 8 Nov 2017 17:59:24 +0000 (17:59 +0000)]
JAL-2794 Aptx instances get their parent alignment, start on binding
Binding from Alignment to Aptx is now functional (including shift and/or
ctrl presses for multiple sequences), other way around is WIP
kjvdheide [Wed, 8 Nov 2017 17:53:17 +0000 (17:53 +0000)]
JAL-2794 Cleaning up tree conversion, sequences are now in the tree
kjvdheide [Wed, 8 Nov 2017 17:50:02 +0000 (17:50 +0000)]
JAL-2794 getters and setters for finding nodes in forester made public
kjvdheide [Wed, 8 Nov 2017 17:46:52 +0000 (17:46 +0000)]
JAL-2795 created static class for forester conversions
kjvdheide [Wed, 8 Nov 2017 17:45:36 +0000 (17:45 +0000)]
JAL-2794 Interface name change (oops)
kjvdheide [Wed, 8 Nov 2017 17:44:54 +0000 (17:44 +0000)]
JAL-2794 made JalviewTreeViewerBinding an interface
kjvdheide [Wed, 8 Nov 2017 17:43:44 +0000 (17:43 +0000)]
JAL-2794 Added getter for AlignmentViewport to TreeBuilder
kjvdheide [Mon, 6 Nov 2017 18:11:50 +0000 (18:11 +0000)]
JAL-2794 simplified/clarified associating leaves to sequences
kjvdheide [Fri, 3 Nov 2017 09:25:23 +0000 (09:25 +0000)]
JAL-2794 created tree viewer binding class
kjvdheide [Fri, 3 Nov 2017 09:23:35 +0000 (09:23 +0000)]
JAL-2795 bunch of cleanup and comments
kjvdheide [Thu, 2 Nov 2017 17:58:05 +0000 (17:58 +0000)]
JAL-2795 added back test loop for Aptx tree naming & initTreePanel
kjvdheide [Thu, 2 Nov 2017 17:06:48 +0000 (17:06 +0000)]
JAL-2795 Reverted code changes needed to cluster from Forester
kjvdheide [Thu, 2 Nov 2017 16:58:50 +0000 (16:58 +0000)]
JAL-2795 Forester now NJ-clusters the DistanceMatrix from Jalview
kjvdheide [Thu, 2 Nov 2017 12:11:33 +0000 (12:11 +0000)]
JAL-2795 moved matrix conversion to the ForesterMatrix class
kjvdheide [Wed, 1 Nov 2017 16:13:18 +0000 (16:13 +0000)]
JAL-2795 Sequence[] references now as SequenceI[] & deleted double class
kjvdheide [Wed, 1 Nov 2017 15:54:14 +0000 (15:54 +0000)]
JAL-2795 removed sequences[] class variable, more comments
kjvdheide [Mon, 30 Oct 2017 18:29:11 +0000 (18:29 +0000)]
JAL-2795 neater error message
kjvdheide [Mon, 30 Oct 2017 18:09:38 +0000 (18:09 +0000)]
JAL-2795 added error catching for invalid identifier
kjvdheide [Mon, 30 Oct 2017 17:15:07 +0000 (17:15 +0000)]
JAL-2795 changed getting index of identifier to Stream (moved to Java 8)
Searching through with Stream prevents having to duplicate the array
with Arrays.toList
kjvdheide [Mon, 30 Oct 2017 16:29:31 +0000 (16:29 +0000)]
JAL-2795 rebuilt MatrixConverter to be purely static
kjvdheide [Mon, 30 Oct 2017 15:45:14 +0000 (15:45 +0000)]
JAL-2795 finalized method arguments; commited forester matrix changes
kjvdheide [Mon, 30 Oct 2017 15:38:35 +0000 (15:38 +0000)]
JAL-2795 removed unneeded for loop (woops) and initialized identifiers[]
kjvdheide [Mon, 30 Oct 2017 15:33:41 +0000 (15:33 +0000)]
JAL-2795 implemented getting/setting identifiers
kjvdheide [Mon, 30 Oct 2017 13:48:16 +0000 (13:48 +0000)]
JAL-2795 added comments links from ForesterMatrix to MatrixI
kjvdheide [Mon, 30 Oct 2017 13:23:57 +0000 (13:23 +0000)]
JAL-2795 removed now unneeded values variable in ForesterMatrix
kjvdheide [Mon, 30 Oct 2017 13:22:17 +0000 (13:22 +0000)]
JAL-2795 add get for all matrix values to MatrixI (and concrete classes)
kjvdheide [Mon, 30 Oct 2017 11:50:05 +0000 (11:50 +0000)]
JAL-2795 foresterMatrix now stores distance values itself
kjvdheide [Sun, 29 Oct 2017 16:51:31 +0000 (16:51 +0000)]
JAL-2795 more matrix implementations
kjvdheide [Sat, 28 Oct 2017 19:58:37 +0000 (20:58 +0100)]
JAL-2795 moved ForesterMatrix to ext.forester
kjvdheide [Fri, 27 Oct 2017 15:47:28 +0000 (16:47 +0100)]
JAL-2795 Added get and set values to the converted matrix
kjvdheide [Fri, 27 Oct 2017 15:42:09 +0000 (16:42 +0100)]
JAL-2795 start of Jalview's Matrix conversion
kjvdheide [Fri, 27 Oct 2017 15:33:26 +0000 (16:33 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into kjvdh/features/PhylogenyViewer
gmungoc [Fri, 27 Oct 2017 13:15:20 +0000 (14:15 +0100)]
JAL-2526 updated javadoc
kjvdheide [Thu, 26 Oct 2017 22:22:42 +0000 (23:22 +0100)]
Start of matrix converter
kjvdheide [Thu, 26 Oct 2017 20:57:16 +0000 (21:57 +0100)]
Added proper title to aptx trees
kjvdheide [Thu, 26 Oct 2017 20:57:01 +0000 (21:57 +0100)]
test name change
kjvdheide [Thu, 26 Oct 2017 20:37:40 +0000 (21:37 +0100)]
Made FreeUpMemoryTest compatible with modified CalculationChooser
kjvdheide [Thu, 26 Oct 2017 20:36:34 +0000 (21:36 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git
into kjvdh/features/PhylogenyViewer
Conflicts:
src/jalview/gui/TreePanel.java
Jim Procter [Thu, 26 Oct 2017 16:45:43 +0000 (17:45 +0100)]
JAL-2698 update version and cut release branch
Jim Procter [Thu, 26 Oct 2017 16:31:40 +0000 (17:31 +0100)]
JAL-2546 release notes
Jim Procter [Thu, 26 Oct 2017 16:18:57 +0000 (17:18 +0100)]
JAL-2488 patch causes of NPE during testStoreAndRecoverExpandedviews Jalview2xml tests.
kjvdheide [Thu, 26 Oct 2017 15:58:22 +0000 (16:58 +0100)]
Added getters for scoremodel & scoreparams in TreeBuilder
Jim Procter [Thu, 26 Oct 2017 15:26:06 +0000 (16:26 +0100)]
Merge branch 'feature/JAL-2488finalize' into develop
kjvdheide [Thu, 26 Oct 2017 15:20:25 +0000 (16:20 +0100)]
TreeBuilder now stores the used ScoreModel and ScoreParams
Jim Procter [Thu, 26 Oct 2017 15:20:14 +0000 (16:20 +0100)]
JAL-2036 2.10.3 release notes
kjvdheide [Thu, 26 Oct 2017 15:12:17 +0000 (16:12 +0100)]
small name fixes in TreeBuilder
kjvdheide [Thu, 26 Oct 2017 15:12:04 +0000 (16:12 +0100)]
Added TreeBuilder as parameter to the converter constructor
kjvdheide [Thu, 26 Oct 2017 15:10:25 +0000 (16:10 +0100)]
Name changed of aptx treebuilder to treeconverter
kjvdheide [Thu, 26 Oct 2017 14:49:56 +0000 (15:49 +0100)]
added getSeqData to TreeBuilder
Jim Procter [Thu, 26 Oct 2017 14:47:32 +0000 (15:47 +0100)]
JAL-2793 cancelling font changed dialog didn't call ap.fontChanged() to reset layout
kjvdheide [Thu, 26 Oct 2017 14:46:08 +0000 (15:46 +0100)]
Added full names to the tree algorithm enum
kjvdheide [Thu, 26 Oct 2017 14:17:58 +0000 (15:17 +0100)]
added abbreviations
kjvdheide [Thu, 26 Oct 2017 14:10:58 +0000 (15:10 +0100)]
added enum for the different tree algorithms
kjvdheide [Thu, 26 Oct 2017 13:59:22 +0000 (14:59 +0100)]
Couple more thread names
kjvdheide [Thu, 26 Oct 2017 13:53:04 +0000 (14:53 +0100)]
named most Jalview threads
Jim Procter [Thu, 26 Oct 2017 13:41:34 +0000 (14:41 +0100)]
JAL-2548 release notes
Jim Procter [Thu, 26 Oct 2017 10:51:35 +0000 (11:51 +0100)]
Merge branch 'bug/JAL-2776toggleGroupColour' into develop
Jim Procter [Thu, 26 Oct 2017 10:50:03 +0000 (11:50 +0100)]
JAL-2684 JAL-2685 release notes
Jim Procter [Thu, 26 Oct 2017 10:40:25 +0000 (11:40 +0100)]
JAL-2685 tidy up html doc
Jim Procter [Thu, 26 Oct 2017 10:14:38 +0000 (11:14 +0100)]
Merge branch 'features/JAL-2685pairwiseSeqLimits' into develop
Jim Procter [Thu, 26 Oct 2017 09:57:13 +0000 (10:57 +0100)]
JAL-2392 test asserts for progressbar creation on the Swing GUI thread.
kjvdheide [Thu, 26 Oct 2017 09:10:23 +0000 (10:10 +0100)]
removed accidental added enters, commented out broken memory test line
kjvdheide [Wed, 25 Oct 2017 18:27:36 +0000 (19:27 +0100)]
finished up tests for trees made from jalview data
kjvdheide [Wed, 25 Oct 2017 18:26:34 +0000 (19:26 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into kjvdh/features/PhylogenyViewer
kjvdheide [Wed, 25 Oct 2017 18:15:53 +0000 (19:15 +0100)]
Implemented distance tests
kjvdheide [Wed, 25 Oct 2017 17:30:02 +0000 (18:30 +0100)]
Implemented tree title test for tree made from Jalview
kjvdheide [Wed, 25 Oct 2017 17:26:09 +0000 (18:26 +0100)]
Added tree title test
kjvdheide [Wed, 25 Oct 2017 17:03:14 +0000 (18:03 +0100)]
Removed redundant annotations
Jim Procter [Wed, 25 Oct 2017 16:24:27 +0000 (17:24 +0100)]
JAL-2617 release notes
Jim Procter [Wed, 25 Oct 2017 16:23:03 +0000 (17:23 +0100)]
Merge branch 'bug/JAL-2617mappedStopCodon' into develop
Jim Procter [Wed, 25 Oct 2017 15:45:05 +0000 (16:45 +0100)]
JAL-2636 release notes
Jim Procter [Wed, 25 Oct 2017 15:37:57 +0000 (16:37 +0100)]
JAL-2667 release notes
Jim Procter [Wed, 25 Oct 2017 15:33:01 +0000 (16:33 +0100)]
Merge branch 'bug/JAL-2667mouseWheelWrapped' into develop
Jim Procter [Wed, 25 Oct 2017 15:08:20 +0000 (16:08 +0100)]
JAL-2727 release notes
kjvdheide [Wed, 25 Oct 2017 15:08:16 +0000 (16:08 +0100)]
Added branch name tests
Jim Procter [Wed, 25 Oct 2017 15:06:31 +0000 (16:06 +0100)]
JAL-2727 add not to Test failed message recommending re-running manually as per Mungo’s recommendation in comments
Jim Procter [Wed, 25 Oct 2017 14:53:29 +0000 (15:53 +0100)]
Merge branch 'bug/JAL-2727closeAllFreeMemory' into develop
kjvdheide [Wed, 25 Oct 2017 14:51:38 +0000 (15:51 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into kjvdh/features/PhylogenyViewer
kjvdheide [Wed, 25 Oct 2017 14:50:40 +0000 (15:50 +0100)]
Added abstract class for tree viewer testing, rearranged existing tests
Jim Procter [Wed, 25 Oct 2017 14:38:06 +0000 (15:38 +0100)]
JAL-2732 JAL-1900 JAL-1625 release notes
Jim Procter [Wed, 25 Oct 2017 14:37:16 +0000 (15:37 +0100)]
Merge branch 'bugs/JAL-2779_osx_dialogsequencingbroke' into develop
Jim Procter [Wed, 25 Oct 2017 14:36:42 +0000 (15:36 +0100)]
JAL-2779 remove empty block and if statement
Jim Procter [Wed, 25 Oct 2017 14:25:26 +0000 (15:25 +0100)]
JAL-2790 JAL-2392 release notes
Jim Procter [Wed, 25 Oct 2017 14:17:55 +0000 (15:17 +0100)]
Merge branch 'bug/JAL-2392_deadlockonpdbdisplay' into develop
Jim Procter [Wed, 25 Oct 2017 14:14:17 +0000 (15:14 +0100)]
JAL-2790 provide a cancel button for JABAWS and AACon jobs
Jim Procter [Wed, 25 Oct 2017 13:58:11 +0000 (14:58 +0100)]
JAL-2392 auto boxing rather than explicit Long as key
Jim Procter [Tue, 24 Oct 2017 16:55:12 +0000 (17:55 +0100)]
JAL-2495 release notes
gmungoc [Fri, 28 Apr 2017 14:55:32 +0000 (15:55 +0100)]
JAL-2495 highlight all mapped sequences from structure pick
Jim Procter [Tue, 24 Oct 2017 16:50:01 +0000 (17:50 +0100)]
JAL-2643 JAL-2524 release notes
Jim Procter [Tue, 24 Oct 2017 16:44:27 +0000 (17:44 +0100)]
JAL-2524 release notes
Jim Procter [Tue, 24 Oct 2017 16:42:16 +0000 (17:42 +0100)]
JAL-2733 JAL-2658 release notes
Jim Procter [Tue, 24 Oct 2017 16:33:08 +0000 (17:33 +0100)]
JAL-1980 release notes (retrodoc for 2.10.0)
Jim Procter [Tue, 24 Oct 2017 16:24:52 +0000 (17:24 +0100)]
JAL-2687 JAL-2608 release notes
Jim Procter [Tue, 24 Oct 2017 16:09:42 +0000 (17:09 +0100)]
Merge branch 'features/JAL-2608closeOverview' into develop
Jim Procter [Tue, 24 Oct 2017 15:58:27 +0000 (16:58 +0100)]
JAL-2542 release notes
kjvdheide [Tue, 24 Oct 2017 14:40:48 +0000 (15:40 +0100)]
Tests for Aptx tree created from a Phylogeny object added
gmungoc [Tue, 24 Oct 2017 10:28:56 +0000 (11:28 +0100)]
JAL-2788 corrected merge error in propertyChange
git://source.jalview.org / jalview.git / log