kjvdheide [Sat, 10 Feb 2018 20:35:53 +0000 (21:35 +0100)]
JAL-2797 added constructor including embedded/standalone boolean
kjvdheide [Sat, 10 Feb 2018 17:36:23 +0000 (18:36 +0100)]
JAL-2797 the big switch, all GUI method calls now go via the AptxFrame
interface
kjvdheide [Sat, 10 Feb 2018 17:34:50 +0000 (18:34 +0100)]
JAL-2797 standalone and embedded implementations of AptxFrame
kjvdheide [Sat, 10 Feb 2018 17:33:55 +0000 (18:33 +0100)]
JAL-2797 added adapter for the dummy frame listener
kjvdheide [Sat, 10 Feb 2018 17:33:12 +0000 (18:33 +0100)]
JAL-2797 added the frame and listener interfaces
kjvdheide [Tue, 30 Jan 2018 15:16:16 +0000 (15:16 +0000)]
JAL-2797 first attempt
kjvdheide [Thu, 25 Jan 2018 19:24:40 +0000 (19:24 +0000)]
JAL-2844 removed resetting line drawing to keep line on screen
kjvdheide [Fri, 19 Jan 2018 17:45:24 +0000 (17:45 +0000)]
JAL-2844 partitioning code made slightly clearer
kjvdheide [Fri, 19 Jan 2018 17:40:41 +0000 (17:40 +0000)]
Revert "JAL-2852 added framework for saving as EPS file"
This reverts commit
3087ea10ac51cf1a8b2eb8d8abe010513ce9998f.
kjvdheide [Thu, 4 Jan 2018 02:47:58 +0000 (02:47 +0000)]
JAL-2871 added inputstream constructor to Configuration
kjvdheide [Fri, 15 Dec 2017 20:01:36 +0000 (20:01 +0000)]
JAL-1953 JAL-2852 added public "paintFile" method
kjvdheide [Fri, 15 Dec 2017 16:55:12 +0000 (16:55 +0000)]
JAL-1953 equals and hashCode now takes node ID in account
kjvdheide [Tue, 12 Dec 2017 11:17:32 +0000 (11:17 +0000)]
JAL-2844 moved line drawing code
kjvdheide [Mon, 11 Dec 2017 20:31:42 +0000 (20:31 +0000)]
JAL-1953 method made public for interfacing
kjvdheide [Fri, 8 Dec 2017 17:13:49 +0000 (17:13 +0000)]
JAL-2844 work started on moving the graphical partitioning code to Aptx
kjvdheide [Fri, 8 Dec 2017 17:12:44 +0000 (17:12 +0000)]
JAL-2872 Undid inference disabling (done in Jalview instead)
kjvdheide [Tue, 5 Dec 2017 14:26:47 +0000 (14:26 +0000)]
JAL-2805 JAL-281 JAL-2847 set tree file made public as well (heh)
kjvdheide [Tue, 5 Dec 2017 11:29:22 +0000 (11:29 +0000)]
JAL-2805 JAL-2847 JAL-281 getTreeFile made public
kjvdheide [Wed, 29 Nov 2017 03:03:10 +0000 (03:03 +0000)]
JAL-2844 colouring subtree method made public
kjvdheide [Wed, 29 Nov 2017 02:06:44 +0000 (02:06 +0000)]
JAL-2797 added simple check for parent desktop to closing event
kjvdheide [Mon, 27 Nov 2017 16:47:05 +0000 (16:47 +0000)]
JAL-2853 fix small bug where the font of a not yet existing panel is set
kjvdheide [Mon, 27 Nov 2017 16:19:11 +0000 (16:19 +0000)]
JAL-2852 added framework for saving as EPS file
kjvdheide [Sun, 26 Nov 2017 23:06:29 +0000 (23:06 +0000)]
JAL-2847 needed methods made public
kjvdheide [Mon, 20 Nov 2017 15:25:47 +0000 (15:25 +0000)]
Merge remote-tracking branch 'forestergit/master' into JalviewIntegration
kjvdheide [Mon, 20 Nov 2017 12:37:04 +0000 (12:37 +0000)]
JAL-2805 added getFilename for Configuration
kjvdheide [Mon, 20 Nov 2017 12:36:29 +0000 (12:36 +0000)]
JAL-281 added new createApplication with Phylogeny[] and Configuration
kjvdheide [Thu, 16 Nov 2017 12:12:48 +0000 (12:12 +0000)]
JAL-2805 made needed color set methods public
cmzmasek [Wed, 15 Nov 2017 22:55:09 +0000 (14:55 -0800)]
in progress
cmzmasek [Wed, 15 Nov 2017 20:16:42 +0000 (12:16 -0800)]
added -rs option
cmzmasek [Wed, 15 Nov 2017 20:14:49 +0000 (12:14 -0800)]
added -rs option
kjvdheide [Mon, 13 Nov 2017 14:58:19 +0000 (14:58 +0000)]
JAL-2797 small start on creating either JFrame or JInternalFrame
kjvdheide [Mon, 13 Nov 2017 14:49:15 +0000 (14:49 +0000)]
JAL-1953 undid commenting out of message panels, should be more elegant
kjvdheide [Mon, 13 Nov 2017 14:47:57 +0000 (14:47 +0000)]
JAL-2796 first (ugly) start on changing Forester's MSA view to show seqs
kjvdheide [Mon, 13 Nov 2017 14:46:42 +0000 (14:46 +0000)]
JAL-2805 bunch of needed methods/constants made public
kjvdheide [Mon, 13 Nov 2017 14:43:59 +0000 (14:43 +0000)]
JAL-2805 Archaeopteryx main returns its created MainFrame instance
kjvdheide [Wed, 8 Nov 2017 17:48:49 +0000 (17:48 +0000)]
Made getters and setters for found nodes public (needed for Jalview)
kjvdheide [Mon, 30 Oct 2017 13:55:51 +0000 (13:55 +0000)]
removed unneeded import
kjvdheide [Sat, 28 Oct 2017 20:50:28 +0000 (21:50 +0100)]
Changed more concrete DistanceMatrix references to reference interface
kjvdheide [Sat, 28 Oct 2017 20:50:03 +0000 (21:50 +0100)]
Added getValues and write to DistanceMatrix interface for broader use
kjvdheide [Sat, 28 Oct 2017 20:26:02 +0000 (21:26 +0100)]
Redid changing concrete references to matrixes to interface references
kjvdheide [Fri, 27 Oct 2017 15:43:24 +0000 (16:43 +0100)]
Merge branch 'JalviewIntegration' of file:////Users/kjvanderheide/Documents/Archae/forester into JalviewIntegration
kjvdheide [Thu, 26 Oct 2017 09:21:17 +0000 (10:21 +0100)]
Merge branch 'master' of https://github.com/cmzmasek/forester.git into JalviewIntegration
kjvdheide [Thu, 26 Oct 2017 09:08:48 +0000 (10:08 +0100)]
capitalisation
cmzmasek [Wed, 25 Oct 2017 22:22:00 +0000 (15:22 -0700)]
removed diamond operator
kjvdheide [Thu, 12 Oct 2017 17:15:20 +0000 (18:15 +0100)]
Inference tab disabled and node frames now appear center of Aptx
kjvdheide [Thu, 12 Oct 2017 15:38:52 +0000 (16:38 +0100)]
disabled Archaeopteryx quit message
kjvdheide [Wed, 11 Oct 2017 20:12:19 +0000 (21:12 +0100)]
More generic uses of DistanceMatrix instead of concrete implementations
kjvdheide [Wed, 11 Oct 2017 20:03:44 +0000 (21:03 +0100)]
Use DistanceMatrix interface instead of the concrete implementation
kjvdheide [Wed, 11 Oct 2017 18:50:12 +0000 (19:50 +0100)]
made PhyloInferenceDialog constructor refer to null instead of mainframe
kjvdheide [Wed, 11 Oct 2017 14:48:56 +0000 (15:48 +0100)]
changed Mainframe from JFrame to JInternalFrame
cmzmasek [Wed, 20 Sep 2017 18:21:09 +0000 (11:21 -0700)]
in progress...
cmzmasek [Wed, 20 Sep 2017 18:20:34 +0000 (11:20 -0700)]
in progress...
cmzmasek [Tue, 19 Sep 2017 23:46:25 +0000 (16:46 -0700)]
in progress...
cmzmasek [Tue, 19 Sep 2017 17:34:51 +0000 (10:34 -0700)]
in progress...
cmzmasek [Fri, 15 Sep 2017 22:11:39 +0000 (15:11 -0700)]
cladinator v1.04
cmzmasek [Fri, 15 Sep 2017 22:10:52 +0000 (15:10 -0700)]
cladinator v1.04
cmzmasek [Fri, 15 Sep 2017 18:46:39 +0000 (11:46 -0700)]
in progress...
cmzmasek [Wed, 13 Sep 2017 19:08:38 +0000 (12:08 -0700)]
in progress...
cmzmasek [Wed, 13 Sep 2017 19:07:44 +0000 (12:07 -0700)]
in progress...
cmzmasek [Mon, 11 Sep 2017 23:03:21 +0000 (16:03 -0700)]
in progress
cmzmasek [Mon, 11 Sep 2017 23:02:28 +0000 (16:02 -0700)]
in progress...
cmzmasek [Wed, 6 Sep 2017 18:45:50 +0000 (11:45 -0700)]
added mapping
cmzmasek [Wed, 6 Sep 2017 18:45:15 +0000 (11:45 -0700)]
added mapping
cmzmasek [Wed, 6 Sep 2017 18:30:56 +0000 (11:30 -0700)]
in progress...
cmzmasek [Sun, 3 Sep 2017 02:17:46 +0000 (19:17 -0700)]
in progress...
cmzmasek [Sun, 3 Sep 2017 02:14:56 +0000 (19:14 -0700)]
old version...
cmzmasek [Sun, 3 Sep 2017 02:13:54 +0000 (19:13 -0700)]
in progress...
cmzmasek [Wed, 30 Aug 2017 23:39:29 +0000 (16:39 -0700)]
in progress...
cmzmasek [Wed, 30 Aug 2017 17:49:33 +0000 (10:49 -0700)]
in progress...
cmzmasek [Wed, 30 Aug 2017 17:48:53 +0000 (10:48 -0700)]
in progress...
cmzmasek [Wed, 23 Aug 2017 18:54:10 +0000 (11:54 -0700)]
in progress...
cmzmasek [Wed, 23 Aug 2017 18:52:34 +0000 (11:52 -0700)]
in progress...
cmzmasek [Wed, 23 Aug 2017 01:33:26 +0000 (18:33 -0700)]
in progress...
cmzmasek [Tue, 22 Aug 2017 19:08:12 +0000 (12:08 -0700)]
in progress....
cmzmasek [Mon, 21 Aug 2017 18:56:31 +0000 (11:56 -0700)]
in progress...
cmzmasek [Fri, 18 Aug 2017 21:49:00 +0000 (14:49 -0700)]
in progress...
cmzmasek [Thu, 17 Aug 2017 21:58:52 +0000 (14:58 -0700)]
in progress...
cmzmasek [Thu, 17 Aug 2017 16:41:48 +0000 (09:41 -0700)]
in progress...
cmzmasek [Thu, 17 Aug 2017 16:40:45 +0000 (09:40 -0700)]
in progress...
cmzmasek [Wed, 16 Aug 2017 19:22:09 +0000 (12:22 -0700)]
in progress...
cmzmasek [Tue, 15 Aug 2017 21:59:15 +0000 (14:59 -0700)]
in progress...
cmzmasek [Tue, 15 Aug 2017 21:58:11 +0000 (14:58 -0700)]
in progress...
cmzmasek [Fri, 11 Aug 2017 18:15:51 +0000 (11:15 -0700)]
confidence output added
cmzmasek [Fri, 11 Aug 2017 00:59:07 +0000 (17:59 -0700)]
tests...
cmzmasek [Fri, 11 Aug 2017 00:58:28 +0000 (17:58 -0700)]
tests...
cmzmasek [Fri, 11 Aug 2017 00:57:42 +0000 (17:57 -0700)]
in progress...
cmzmasek [Fri, 21 Jul 2017 22:54:29 +0000 (15:54 -0700)]
first prototype
cmzmasek [Fri, 21 Jul 2017 22:30:57 +0000 (15:30 -0700)]
first prototype
cmzmasek [Fri, 21 Jul 2017 19:54:34 +0000 (12:54 -0700)]
In progress...
cmzmasek [Tue, 18 Jul 2017 22:06:19 +0000 (15:06 -0700)]
updated
cmzmasek [Thu, 13 Jul 2017 20:21:30 +0000 (13:21 -0700)]
updated
cmzmasek [Wed, 12 Jul 2017 17:15:28 +0000 (10:15 -0700)]
in progress...
cmzmasek [Mon, 12 Jun 2017 22:45:38 +0000 (15:45 -0700)]
analyze pplacer output...
cmzmasek [Mon, 12 Jun 2017 22:44:50 +0000 (15:44 -0700)]
in progress..
cmzmasek [Fri, 9 Jun 2017 21:58:48 +0000 (14:58 -0700)]
pplacer
cmzmasek [Fri, 9 Jun 2017 20:39:20 +0000 (13:39 -0700)]
in progress...
cmzmasek [Fri, 9 Jun 2017 20:27:07 +0000 (13:27 -0700)]
in progress
cmzmasek [Fri, 9 Jun 2017 20:12:00 +0000 (13:12 -0700)]
in progress...
cmzmasek [Fri, 9 Jun 2017 20:11:15 +0000 (13:11 -0700)]
in progress...
cmzmasek [Thu, 18 May 2017 18:51:06 +0000 (11:51 -0700)]
in progress...
git://source.jalview.org / jalview.git / log