kjvdheide [Mon, 13 Nov 2017 19:22:02 +0000 (19:22 +0000)]
JAL-2805 name change
kjvdheide [Mon, 13 Nov 2017 19:19:10 +0000 (19:19 +0000)]
JAL-2805 deleted old Aptx class for loading just Newick files
kjvdheide [Mon, 13 Nov 2017 19:16:43 +0000 (19:16 +0000)]
JAL-2805 more interface work
kjvdheide [Mon, 13 Nov 2017 19:03:58 +0000 (19:03 +0000)]
JAL-2794 removed unused interface
kjvdheide [Mon, 13 Nov 2017 19:02:16 +0000 (19:02 +0000)]
JAL-2805 undid accidental double (buggy) binding, more interface support
kjvdheide [Mon, 13 Nov 2017 15:43:56 +0000 (15:43 +0000)]
JAL-2805 warning messages added if Forester detects file loading issues
kjvdheide [Mon, 13 Nov 2017 14:22:27 +0000 (14:22 +0000)]
JAL-2805 First try at loading tree through Forester by calling Aptx main
Added file filters for Forester supported tree formats to the file
chooser window and Forester tree parser in the ActionPerformed of
loading an associated tree, also see Forester commits for more details
kjvdheide [Fri, 10 Nov 2017 15:31:40 +0000 (15:31 +0000)]
JAL-2794 reorganized node select code, added subtree selection support
kjvdheide [Fri, 10 Nov 2017 14:17:18 +0000 (14:17 +0000)]
JAL-2794 comments comments comments
kjvdheide [Fri, 10 Nov 2017 13:42:50 +0000 (13:42 +0000)]
JAL-2794 most method parameters/class variables made final
kjvdheide [Fri, 10 Nov 2017 13:38:33 +0000 (13:38 +0000)]
JAL-2794 comments, selected node now doesn't have to be external per se
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
git://source.jalview.org / jalview.git / log