Jim Procter [Sun, 7 Jun 2015 18:01:45 +0000 (19:01 +0100)]
JAL-653 basic GFF3 alignment import wrapper class
Jim Procter [Sat, 6 Jun 2015 17:00:53 +0000 (18:00 +0100)]
JAL-653 make sure dummy sequences created during GFF parsing are actually resolved and annotated
Jim Procter [Sat, 6 Jun 2015 16:59:39 +0000 (17:59 +0100)]
JAL-653 first stab at parsing GFF3 pragmas to support ##fasta
Jim Procter [Sat, 6 Jun 2015 16:58:18 +0000 (17:58 +0100)]
JAL-653 gff version number field
Jim Procter [Sat, 6 Jun 2015 16:57:53 +0000 (17:57 +0100)]
JAL-653 test and testdata for importing GFF3 file with ##fasta pragma
Jim Procter [Sat, 6 Jun 2015 16:56:22 +0000 (17:56 +0100)]
JAL-653 missing imports after rebase
Jim Procter [Sat, 6 Jun 2015 16:54:34 +0000 (17:54 +0100)]
JAL-653 test for SequenceDummy methods
Jim Procter [Sat, 6 Jun 2015 16:46:27 +0000 (17:46 +0100)]
JAL-653 allow a dummy sequence to take on attributes from a fully instantiated sequence via Sequence copy constructor
Jim Procter [Fri, 5 Jun 2015 15:28:56 +0000 (16:28 +0100)]
Merge branch 'develop' into features/JAL-653_gffalignments
Jim Procter [Fri, 5 Jun 2015 15:27:36 +0000 (16:27 +0100)]
JAL-653 abstract sequence model to support file backed alignment/data views
gmungoc [Fri, 5 Jun 2015 15:26:15 +0000 (16:26 +0100)]
JAL-1752 structure highlight scoped to only its mapped sequences
gmungoc [Fri, 5 Jun 2015 14:51:07 +0000 (15:51 +0100)]
JAL-1588 error dialog if Chimera project opened on a m/c w/o Chimera
gmungoc [Fri, 5 Jun 2015 14:15:01 +0000 (15:15 +0100)]
JAL-1622 fix bug computing superposition + associated refactorings
gmungoc [Fri, 5 Jun 2015 14:09:25 +0000 (15:09 +0100)]
JAL-1746 return empty string rather than null in getStateInfo
gmungoc [Fri, 5 Jun 2015 13:59:21 +0000 (14:59 +0100)]
JAL-1622 Chimera command timeout increased to 5 secs (+minor changes)
gmungoc [Fri, 5 Jun 2015 13:52:10 +0000 (14:52 +0100)]
JAL-1622 duplicate assignment removed (no functional change)
gmungoc [Fri, 5 Jun 2015 13:49:22 +0000 (14:49 +0100)]
JAL-1753 JAL-1596 asynchronous command to Chimera (with progress update)
gmungoc [Fri, 5 Jun 2015 13:43:00 +0000 (14:43 +0100)]
JAL-1622 code tidy only, no functional change
gmungoc [Fri, 5 Jun 2015 12:54:18 +0000 (13:54 +0100)]
JAL-1749 correcting snafu in last commit
Jim Procter [Thu, 19 Feb 2015 15:23:47 +0000 (15:23 +0000)]
JAL-653 refactor sequence interface to separate concrete sequence data methods from sequence metadata methods & containers
Jim Procter [Thu, 19 Feb 2015 15:22:36 +0000 (15:22 +0000)]
JAL-845 jim @mungo: should this be in a package local to jalview.analysis.Dna ?
Jim Procter [Thu, 19 Feb 2015 15:21:30 +0000 (15:21 +0000)]
JAL-1551 formatting
Jim Procter [Thu, 19 Feb 2015 15:20:51 +0000 (15:20 +0000)]
JAL-653 set the warningMessage for the file source to allow the GUI to report problems if necessary.
Jim Procter [Thu, 19 Feb 2015 15:20:14 +0000 (15:20 +0000)]
JAL-653 GFF attributes parsing mechanism, with first attempt at processing exonerate's 'similarity' features as cDNA/protein mappings
Jim Procter [Thu, 19 Feb 2015 15:12:04 +0000 (15:12 +0000)]
JAL-653 trim initial tab in sequence feature ATTRIBUTES
Jim Procter [Thu, 19 Feb 2015 15:11:12 +0000 (15:11 +0000)]
JAL-653 allow dummy sequences to be created if a sequence ID is not found in the dataset
Jim Procter [Thu, 19 Feb 2015 15:07:55 +0000 (15:07 +0000)]
JAL-1551 formatting
Jim Procter [Thu, 19 Feb 2015 15:01:35 +0000 (15:01 +0000)]
JAL-653 convenience method to resolve strand attribute for feature
Jim Procter [Thu, 19 Feb 2015 15:00:03 +0000 (15:00 +0000)]
JAL-1115 JAL-653 partial introduction of List interface for sequence matcher
Jim Procter [Thu, 19 Feb 2015 14:57:01 +0000 (14:57 +0000)]
JAL-653 JAL-966 TODO and avoid NPE when desktop instance unavailable
Jim Procter [Thu, 19 Feb 2015 14:55:44 +0000 (14:55 +0000)]
JAL-653 codon frames go on the dataset
Jim Procter [Thu, 19 Feb 2015 14:55:10 +0000 (14:55 +0000)]
JAL-653 refactored exonerate full output to separate text file, leaving gffv2 fragment for first testcase
Jim Procter [Wed, 18 Feb 2015 12:18:46 +0000 (12:18 +0000)]
JAL-653 JAL-845 test to check exonerate cDNA-Protein mappings import as GFF3
Jim Procter [Wed, 18 Feb 2015 11:14:26 +0000 (11:14 +0000)]
JAL-1482 JAL-653 refactor feature file import code to alignview controller
Jim Procter [Wed, 18 Feb 2015 11:08:00 +0000 (11:08 +0000)]
JAL-1482 refactor setTableData to more sensible name for feature settings api
Jim Procter [Tue, 17 Feb 2015 18:40:35 +0000 (18:40 +0000)]
JAL-1551 formatting
gmungoc [Thu, 4 Jun 2015 15:29:40 +0000 (16:29 +0100)]
Clear status bar message when initialisation complete
gmungoc [Thu, 4 Jun 2015 15:09:30 +0000 (16:09 +0100)]
JAL-1750 small tidy of AlignSeq.printMapping (+Junit)
gmungoc [Thu, 4 Jun 2015 14:40:27 +0000 (15:40 +0100)]
JAL-1544 spelling in javadoc only
gmungoc [Thu, 4 Jun 2015 14:39:29 +0000 (15:39 +0100)]
JAL-1622 code tidy (+Junit) of collateForPdb()
gmungoc [Thu, 4 Jun 2015 14:07:41 +0000 (15:07 +0100)]
JAL-1747 close all windows on Quit (+small bug fix)
gmungoc [Thu, 4 Jun 2015 13:43:53 +0000 (14:43 +0100)]
toString method added to aid viewing in the debugger
gmungoc [Thu, 4 Jun 2015 13:43:12 +0000 (14:43 +0100)]
JAL-1270 testToString added
gmungoc [Thu, 4 Jun 2015 13:37:13 +0000 (14:37 +0100)]
JAL-1750 View Mapping scoped to that viewer's mappings only
gmungoc [Thu, 4 Jun 2015 13:08:04 +0000 (14:08 +0100)]
JAL-1743 new Chimera menu option to 'fit to window'
gmungoc [Thu, 4 Jun 2015 13:01:27 +0000 (14:01 +0100)]
JAL-1743 View Chain sub-menu now being populated
gmungoc [Thu, 4 Jun 2015 12:53:21 +0000 (13:53 +0100)]
JAL-1753 statusPanel added (for ProgressBar); 'Fit to Window' menu
option added
gmungoc [Thu, 4 Jun 2015 12:40:55 +0000 (13:40 +0100)]
JAL-1753 ChimeraViewFrame hosts its own ProgressBar
gmungoc [Thu, 4 Jun 2015 11:05:55 +0000 (12:05 +0100)]
JAL-1742 don't offer to align another chain to the same structure
gmungoc [Thu, 4 Jun 2015 10:51:47 +0000 (11:51 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 4 Jun 2015 10:51:28 +0000 (11:51 +0100)]
JAL-1757 match only first altloc CA in PDB structure for superposition
tcofoegbu [Thu, 4 Jun 2015 10:45:31 +0000 (11:45 +0100)]
JAL-1641 added some JSON libraries to appletlib
tcofoegbu [Thu, 4 Jun 2015 10:20:42 +0000 (11:20 +0100)]
clean up
tcofoegbu [Thu, 4 Jun 2015 10:12:03 +0000 (11:12 +0100)]
JAL-1756 fix failed test as a result of runing the BioJS updater from a new thread
gmungoc [Thu, 4 Jun 2015 10:07:28 +0000 (11:07 +0100)]
JAL-1421 generic collections in MCView package (+unit tests)
tcofoegbu [Thu, 4 Jun 2015 09:52:06 +0000 (10:52 +0100)]
Merge branch 'features/JAL-1641_JSON-extension' into develop
tcofoegbu [Thu, 4 Jun 2015 09:42:08 +0000 (10:42 +0100)]
JAL-1756 bug-fix
tcofoegbu [Thu, 4 Jun 2015 09:04:47 +0000 (10:04 +0100)]
JAL-1641 updated json schema to make it more generic in order to accomodate more dynamic parameters
tcofoegbu [Tue, 2 Jun 2015 16:59:23 +0000 (17:59 +0100)]
fixed bug in build.xml
tcofoegbu [Tue, 2 Jun 2015 15:51:56 +0000 (16:51 +0100)]
Merge branch 'features/JAL-1641_JSON-extension' into develop
tcofoegbu [Tue, 2 Jun 2015 15:51:30 +0000 (16:51 +0100)]
JAL-1641 updated build.xml
tcofoegbu [Tue, 2 Jun 2015 14:54:44 +0000 (15:54 +0100)]
JAL-1641 updated examples/applets.html
tcofoegbu [Tue, 2 Jun 2015 14:12:45 +0000 (15:12 +0100)]
Merge branch 'features/JAL-1641_JSON-extension' into develop
tcofoegbu [Tue, 2 Jun 2015 14:11:50 +0000 (15:11 +0100)]
JAL-1641 applet build fix
tcofoegbu [Mon, 1 Jun 2015 15:59:19 +0000 (16:59 +0100)]
Merge branch 'features/JAL-1641_JSON-extension' into develop
tcofoegbu [Mon, 1 Jun 2015 15:58:38 +0000 (16:58 +0100)]
JAL-1641 remove all refs/imports from gui package
tcofoegbu [Mon, 1 Jun 2015 14:23:16 +0000 (15:23 +0100)]
Merge branch 'bug/JAL-1703_hint_select_by_annot' into develop
tcofoegbu [Mon, 1 Jun 2015 14:19:06 +0000 (15:19 +0100)]
JAL-1703 added tooltip hints to components of the Select by Annotation UI
tcofoegbu [Mon, 1 Jun 2015 10:15:34 +0000 (11:15 +0100)]
Merge branch 'bug/JAL-1734_misleading-progress-bar' into develop
tcofoegbu [Mon, 1 Jun 2015 10:15:04 +0000 (11:15 +0100)]
JAL-1734 updated progress bar messages
tcofoegbu [Fri, 29 May 2015 15:41:21 +0000 (16:41 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Fri, 29 May 2015 15:41:10 +0000 (16:41 +0100)]
JAL-1748 house keeping
gmungoc [Fri, 29 May 2015 13:56:48 +0000 (14:56 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Fri, 29 May 2015 13:56:36 +0000 (14:56 +0100)]
JAL-1753 declare field with interface type; check for null dereference
Jim Procter [Fri, 29 May 2015 13:23:34 +0000 (14:23 +0100)]
Merge branch 'JAL-1755_npe_groupconsensus' into develop
Jim Procter [Fri, 29 May 2015 13:22:38 +0000 (14:22 +0100)]
JAL-1755 fix for NPE when setting up temporary variables
gmungoc [Fri, 29 May 2015 13:07:56 +0000 (14:07 +0100)]
JAL-1753 Junit for new class
gmungoc [Fri, 29 May 2015 11:06:20 +0000 (12:06 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Fri, 29 May 2015 11:01:09 +0000 (12:01 +0100)]
JAL-1753 duplicated code refactored to new class ProgressBar
tcofoegbu [Fri, 29 May 2015 10:22:37 +0000 (11:22 +0100)]
Merge branch 'bug/JAL-1748_extend-pdb-query-opt' into develop
tcofoegbu [Fri, 29 May 2015 10:21:04 +0000 (11:21 +0100)]
JAL-1748 and employ preprocessing routine when return action event is triggered
tcofoegbu [Fri, 29 May 2015 08:53:50 +0000 (09:53 +0100)]
validate PDB selections on mouse release event
tcofoegbu [Thu, 28 May 2015 15:47:25 +0000 (16:47 +0100)]
JAL-1700 made PDB service error mechanism more user friendly
tcofoegbu [Thu, 28 May 2015 10:46:35 +0000 (11:46 +0100)]
Merge branch 'bug/JAL-1751_make-table-uneditable' into develop
tcofoegbu [Thu, 28 May 2015 10:45:50 +0000 (11:45 +0100)]
JAL-1751 provided method to overide isCellEditable for the PDB response table model
tcofoegbu [Thu, 28 May 2015 10:05:00 +0000 (11:05 +0100)]
Merge branch 'bug/JAL-1749_reinstate-rna-viewing' into develop
tcofoegbu [Thu, 28 May 2015 10:03:04 +0000 (11:03 +0100)]
JAL-1749 reinstated the ability to view RNA structures
tcofoegbu [Thu, 28 May 2015 08:20:33 +0000 (09:20 +0100)]
JAL-1740 minor house keeping
tcofoegbu [Wed, 27 May 2015 17:01:16 +0000 (18:01 +0100)]
Removed redundant classes and dependencies pulled in from last merge of features/JAL-1740_Decoup-BioJS branch
tcofoegbu [Wed, 27 May 2015 16:55:38 +0000 (17:55 +0100)]
Merge branch 'features/JAL-1740_Decoup-BioJS' into develop
tcofoegbu [Wed, 27 May 2015 16:49:47 +0000 (17:49 +0100)]
JAL-1740 updated synch codes to use a git repo rather than FTP
tcofoegbu [Tue, 26 May 2015 11:44:16 +0000 (12:44 +0100)]
JAL-1627 bug fix to remove wierd space in Sequence Features/Sequence Group tooltip on windows
tcofoegbu [Mon, 25 May 2015 15:04:22 +0000 (16:04 +0100)]
build fix
tcofoegbu [Fri, 22 May 2015 16:03:32 +0000 (17:03 +0100)]
Merge branch 'features/JAL-1745_PDB-redownload' into develop
tcofoegbu [Fri, 22 May 2015 16:02:55 +0000 (17:02 +0100)]
JAL-1745, JAL-1717 improvement to ensure cached PDB entries are unique within a sequence. Also only truly downloaded files should be shown in the cache view
tcofoegbu [Fri, 22 May 2015 11:09:58 +0000 (12:09 +0100)]
Merge branch 'features/JAL-1745_PDB-redownload' into develop
tcofoegbu [Fri, 22 May 2015 11:09:09 +0000 (12:09 +0100)]
JAL-1745 improvement to retreive already downloaded pdb structure file from cache
tcofoegbu [Thu, 21 May 2015 10:37:29 +0000 (11:37 +0100)]
JAL-1740 implemented auto-update of BioJsMSA, introduced FTP client for downloading remote BioJs Templates
gmungoc [Wed, 20 May 2015 13:41:54 +0000 (14:41 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Wed, 20 May 2015 13:41:38 +0000 (14:41 +0100)]
JAL-1741 nucleotide-aware colour schemes applied to structures
git://source.jalview.org / jalview.git / log