Jim Procter [Tue, 2 Dec 2014 10:22:40 +0000 (10:22 +0000)]
Merge branch 'JAL-1602_282_release' into Release_2_8_2_Branch
Jim Procter [Tue, 2 Dec 2014 10:22:21 +0000 (10:22 +0000)]
JAL-1602 add missing jars to install
Jim Procter [Mon, 1 Dec 2014 23:56:13 +0000 (23:56 +0000)]
Merge branch 'JAL-1602_282_release' into Release_2_8_2_Branch
Jim Procter [Mon, 1 Dec 2014 23:55:44 +0000 (23:55 +0000)]
JAL-1602 upgrade to InstallAnywhere 2014 J17 runtimes
Jim Procter [Mon, 1 Dec 2014 15:39:42 +0000 (15:39 +0000)]
Merge branch 'bug/JAL-1610refAnnotationsInViews' into Release_2_8_2_Branch
Jim Procter [Mon, 1 Dec 2014 15:38:26 +0000 (15:38 +0000)]
file for JAL-1268 jalview.io.Jalview2xmlTests.testTCoffeeScores
Jim Procter [Fri, 28 Nov 2014 16:01:37 +0000 (16:01 +0000)]
Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch
Jim Procter [Fri, 28 Nov 2014 16:01:03 +0000 (16:01 +0000)]
JAL-1517 first stab at release notes... lots of documentation to go!
gmungoc [Fri, 28 Nov 2014 15:48:48 +0000 (15:48 +0000)]
JAL-1610 check reference annotations against alignment, not sequence
Jim Procter [Fri, 28 Nov 2014 14:58:00 +0000 (14:58 +0000)]
JAL-1522 output installation type to stdout
Jim Procter [Fri, 28 Nov 2014 14:47:37 +0000 (14:47 +0000)]
JAL-1522 remove build/deployment details imported from user preferences file
Jim Procter [Fri, 28 Nov 2014 14:46:41 +0000 (14:46 +0000)]
JAL-1517 formatting
Jim Procter [Fri, 28 Nov 2014 14:46:04 +0000 (14:46 +0000)]
JAL-1611 revise log level to reduce verbosity
Jim Procter [Fri, 28 Nov 2014 14:20:23 +0000 (14:20 +0000)]
JAL-1583 javadoc and fix constructor signature
Jim Procter [Fri, 28 Nov 2014 14:07:39 +0000 (14:07 +0000)]
JAL-1342 document argument to specify preferred JABA server
Jim Procter [Fri, 28 Nov 2014 14:06:08 +0000 (14:06 +0000)]
JAL-1604 formatting
Jim Procter [Fri, 28 Nov 2014 14:05:42 +0000 (14:05 +0000)]
JAL-1604 revised wording and internationalised dialog
Jim Procter [Fri, 28 Nov 2014 14:04:16 +0000 (14:04 +0000)]
JAL-1583 back out original fix and simply check MSAWSThread.hasValidInput flag before displaying job window and starting the web service job thread.
Jim Procter [Fri, 28 Nov 2014 14:01:27 +0000 (14:01 +0000)]
JAL-1583 formatting
Jim Procter [Fri, 28 Nov 2014 14:01:15 +0000 (14:01 +0000)]
JAL-1583 new validInput flag set according to validity of all MSA jobs prepared for submission
Jim Procter [Fri, 28 Nov 2014 13:58:51 +0000 (13:58 +0000)]
JAL-1583 refactored addInternalFrame to allow webservice job frame to be added but not automatically made visible
Jim Procter [Fri, 28 Nov 2014 13:55:05 +0000 (13:55 +0000)]
JAL-1517 formatting/tidy
Jim Procter [Tue, 25 Nov 2014 11:24:43 +0000 (11:24 +0000)]
JAL-1517 svg==scalable :)
Jim Procter [Thu, 27 Nov 2014 16:02:21 +0000 (16:02 +0000)]
Merge branch 'patchJAL-674_offset' into Release_2_8_2_Branch
Jim Procter [Thu, 27 Nov 2014 15:59:39 +0000 (15:59 +0000)]
JAL-674 add sequence associated annotation rows to flanking alignment
Jim Procter [Thu, 27 Nov 2014 15:58:51 +0000 (15:58 +0000)]
JAL-1177 JAL-905 cannot recover sequences from dataset if dataset is currently being recovered
Jim Procter [Thu, 27 Nov 2014 14:56:35 +0000 (14:56 +0000)]
JAL-674 avoid writing \0 for chain code
Jim Procter [Thu, 27 Nov 2014 14:39:32 +0000 (14:39 +0000)]
Merge branch 'patchJAL-674_offset' into Release_2_8_2_Branch
Jim Procter [Thu, 27 Nov 2014 14:32:52 +0000 (14:32 +0000)]
JAL-674 patch to fix bug with showing reference annotation for legacy jalview example file v2.7
Jim Procter [Thu, 27 Nov 2014 14:32:08 +0000 (14:32 +0000)]
JAL-674 formatting
Jim Procter [Thu, 27 Nov 2014 14:31:20 +0000 (14:31 +0000)]
JAL-674 unused variable
Jim Procter [Thu, 27 Nov 2014 14:31:05 +0000 (14:31 +0000)]
JAL-674 bug in test
gmungoc [Thu, 27 Nov 2014 11:56:25 +0000 (11:56 +0000)]
JAL-1603 if Chimera selected in Preferences, warn if not installed/found
gmungoc [Thu, 27 Nov 2014 11:53:50 +0000 (11:53 +0000)]
Merge branch 'Release_2_8_2_Branch' of https://source.jalview.org/git/jalview.git into Release_2_8_2_Branch
Jim Procter [Thu, 27 Nov 2014 10:37:06 +0000 (10:37 +0000)]
JAL-674 test that PDB annotation created when importing a legacy jalview example file is mapped to the correct place as the manually created version (temperature factor in exampleFile_2_7.jar
Jim Procter [Thu, 27 Nov 2014 10:35:58 +0000 (10:35 +0000)]
JAL-674 patch NPE bug when test run in isolation
Jim Procter [Thu, 27 Nov 2014 10:35:23 +0000 (10:35 +0000)]
JAL-674 fix test properties path and add properties file
Jim Procter [Thu, 27 Nov 2014 10:31:31 +0000 (10:31 +0000)]
JAL-674 JAL-966 new method to retrieve all views
Jim Procter [Thu, 27 Nov 2014 10:29:55 +0000 (10:29 +0000)]
organise imports
Jim Procter [Thu, 27 Nov 2014 10:29:00 +0000 (10:29 +0000)]
JAL-966 promote getName to an api method
Charles Ofoegbu [Thu, 27 Nov 2014 10:15:59 +0000 (10:15 +0000)]
Merge branch 'bug/JAL-1604_Entire-alignment-submission' into Release_2_8_2_Branch
Charles Ofoegbu [Thu, 27 Nov 2014 10:13:39 +0000 (10:13 +0000)]
JAL-1604 Entire sequence submision for MSA job bugfix
Charles Ofoegbu [Thu, 27 Nov 2014 09:23:26 +0000 (09:23 +0000)]
Merge branch 'bug/JAL-1583_MSA_webservice_validation' into Release_2_8_2_Branch
Charles Ofoegbu [Thu, 27 Nov 2014 09:20:45 +0000 (09:20 +0000)]
modified regex for sequence validation
gmungoc [Thu, 27 Nov 2014 08:39:32 +0000 (08:39 +0000)]
Merge branch 'Release_2_8_2_Branch' of https://source.jalview.org/git/jalview.git into Release_2_8_2_Branch
Charles Ofoegbu [Wed, 26 Nov 2014 16:59:07 +0000 (16:59 +0000)]
Merge branch 'bug/JAL-207_pairwise-alignment-context-loss' into Release_2_8_2_Branch
Charles Ofoegbu [Wed, 26 Nov 2014 16:57:23 +0000 (16:57 +0000)]
JAL-207 pairwise alignment sequence contexts propergation bugfix
Charles Ofoegbu [Wed, 26 Nov 2014 16:06:04 +0000 (16:06 +0000)]
Merge branch 'bug/JAL-998_wrap-sequence-tooltip' into Release_2_8_2_Branch
Charles Ofoegbu [Wed, 26 Nov 2014 15:52:36 +0000 (15:52 +0000)]
JAL-998 fixed empty tooltip bug when only one sequence feature is present
Jim Procter [Wed, 26 Nov 2014 14:52:59 +0000 (14:52 +0000)]
Merge branch 'JAL-674_fixannotlabels' into Release_2_8_2_Branch
Jim Procter [Wed, 26 Nov 2014 14:48:28 +0000 (14:48 +0000)]
JAL-674 make RNAML-extracted secondary structure lines consistent with those from Jmol
Jim Procter [Wed, 26 Nov 2014 14:47:54 +0000 (14:47 +0000)]
JAL-1578 fix logic for showing score when no description present
Jim Procter [Wed, 26 Nov 2014 14:43:27 +0000 (14:43 +0000)]
JAL-674 JAL-1578 commented code for displaying annotation properties in tooltip
Jim Procter [Wed, 26 Nov 2014 14:41:50 +0000 (14:41 +0000)]
JAL-674 friendly name for PDB file included in secondary structure tooltip
Jim Procter [Wed, 26 Nov 2014 14:41:18 +0000 (14:41 +0000)]
JAL-674 employ the provided DNA/Protein matrix string when mapping from sequence to structure
Jim Procter [Wed, 26 Nov 2014 14:40:16 +0000 (14:40 +0000)]
JAL-674 disable addition of PDBRESNUM annotation line
Jim Procter [Wed, 26 Nov 2014 14:39:15 +0000 (14:39 +0000)]
JAL-674 nicer temperature factor labelling and include PDB ID
gmungoc [Wed, 26 Nov 2014 14:26:39 +0000 (14:26 +0000)]
JAL-1528 NullPointer check / more informative PDB fetch status bar
Jim Procter [Tue, 25 Nov 2014 21:45:56 +0000 (21:45 +0000)]
Merge branch 'bug/JAL-689' into Release_2_8_2_Branch
Jim Procter [Tue, 25 Nov 2014 21:43:42 +0000 (21:43 +0000)]
fix for JAL-689 ensure fastpainting flag set only when actually fastpainting
Jim Procter [Tue, 25 Nov 2014 21:42:32 +0000 (21:42 +0000)]
formatting
Jim Procter [Tue, 25 Nov 2014 21:41:55 +0000 (21:41 +0000)]
patch for JAL-1599 - annotation row constructed by initAutoAnnotation
Jim Procter [Tue, 25 Nov 2014 21:34:43 +0000 (21:34 +0000)]
Merge branch 'patch_JAL-689' into Release_2_8_2_Branch
Jim Procter [Tue, 25 Nov 2014 21:13:10 +0000 (21:13 +0000)]
back out duplicate jfree classpath entry
Charles Ofoegbu [Tue, 25 Nov 2014 17:46:14 +0000 (17:46 +0000)]
Merge branch 'features/JAL-1469_svg-output-for-figure-export' into Release_2_8_2_Branch
Charles Ofoegbu [Tue, 25 Nov 2014 17:43:48 +0000 (17:43 +0000)]
merge commit
Charles Ofoegbu [Tue, 25 Nov 2014 17:37:25 +0000 (17:37 +0000)]
JAL-1469 Added SVGOptions.java for lineart/text rendering rendering of svg
gmungoc [Tue, 25 Nov 2014 16:55:09 +0000 (16:55 +0000)]
JFAL-1594 fix Undo bug; enum EditCommand.Action; basic JUnit
Jim Procter [Mon, 24 Nov 2014 22:17:25 +0000 (22:17 +0000)]
Merge branch 'JAL-1569_wuss_vienna_broke' into Release_2_8_2_Branch
Jim Procter [Mon, 24 Nov 2014 16:07:45 +0000 (16:07 +0000)]
JAL-1593 refactor rna helix colours to static singleton for consistent shading
Jim Procter [Mon, 24 Nov 2014 16:06:31 +0000 (16:06 +0000)]
JAL-1264 update annotation panel dimensions before refresh
Jim Procter [Mon, 24 Nov 2014 16:02:58 +0000 (16:02 +0000)]
JAL-1595 update annotation sort on opening of the 'sort' menu..
Jim Procter [Mon, 24 Nov 2014 16:01:33 +0000 (16:01 +0000)]
JAL-1595 annotation score is total number of rna helices
Jim Procter [Sun, 23 Nov 2014 20:18:05 +0000 (20:18 +0000)]
JAL-1569 interactive editing of secondary structure char for RNA secondary structure
Jim Procter [Sun, 23 Nov 2014 17:22:05 +0000 (17:22 +0000)]
Merge branch 'JAL-1569_wuss_vienna_broke' into Release_2_8_2_Branch
Jim Procter [Sun, 23 Nov 2014 16:43:54 +0000 (16:43 +0000)]
employ test and secondary structure character for determining base pairing direction for rendering rna annotation
Jim Procter [Sun, 23 Nov 2014 16:42:55 +0000 (16:42 +0000)]
JAL-1569 formatting
Jim Procter [Sun, 23 Nov 2014 16:42:01 +0000 (16:42 +0000)]
JAL-1593 allow per-sequence shading of RNA helix (stored in each annotation element's value field for a paired base)
Jim Procter [Sun, 23 Nov 2014 16:37:33 +0000 (16:37 +0000)]
JAL-1569 test for open/close RNA parenthesis character
Jim Procter [Sun, 23 Nov 2014 16:35:56 +0000 (16:35 +0000)]
JAL-1569 formatting
Jim Procter [Sun, 23 Nov 2014 16:34:42 +0000 (16:34 +0000)]
JAL-1569 refactoring of stockholm test
Jim Procter [Sun, 23 Nov 2014 16:33:59 +0000 (16:33 +0000)]
JAL-1569 consistent handling of sequence and alignment associated annotation export in stockholm
Jim Procter [Sun, 23 Nov 2014 16:32:37 +0000 (16:32 +0000)]
JAL-1569 revise tests to count number and type of annotation in each file
Jim Procter [Sun, 23 Nov 2014 16:31:26 +0000 (16:31 +0000)]
JAL-1569 formatting
Jim Procter [Sun, 23 Nov 2014 16:29:58 +0000 (16:29 +0000)]
JAL-1569 preserve input ordering for stockholm files (Hashtable implementation changed possibly ?)
Jim Procter [Sun, 23 Nov 2014 16:22:25 +0000 (16:22 +0000)]
JAL-1569 remove stdout on parsing RNA
Jim Procter [Sun, 23 Nov 2014 16:21:34 +0000 (16:21 +0000)]
JAL-1152 avoid NPE on null alignment annotation vector
gmungoc [Fri, 21 Nov 2014 14:33:08 +0000 (14:33 +0000)]
JAL-1528 found and readded Colour by Chain ('rainbow color')
gmungoc [Fri, 21 Nov 2014 14:30:33 +0000 (14:30 +0000)]
Merge branch 'Release_2_8_2_Branch' of https://source.jalview.org/git/jalview.git into Release_2_8_2_Branch
Jim Procter [Fri, 21 Nov 2014 09:01:03 +0000 (09:01 +0000)]
JAL-674 add RNA sequence associated annotation to alignment as hidden annotation
Jim Procter [Fri, 21 Nov 2014 08:59:49 +0000 (08:59 +0000)]
JAL-1569 formatting
Jim Procter [Fri, 21 Nov 2014 08:56:52 +0000 (08:56 +0000)]
JAL-1140 sensible name for seuqences in RNAML files that have no ID
Jim Procter [Fri, 21 Nov 2014 08:55:38 +0000 (08:55 +0000)]
JAL-1489 change initial value to distinguish non-rna from valid and invalid RNA structure with one call to .isValidStructure()
Jim Procter [Fri, 21 Nov 2014 08:54:11 +0000 (08:54 +0000)]
JAL-1592 JAL-1489 avoid invalid RNA structure and distinguish alignment associated from sequence associated structure lines
Jim Procter [Thu, 20 Nov 2014 14:54:01 +0000 (14:54 +0000)]
JAL-1569 rna pair code in secondary structure character of annotation
Jim Procter [Thu, 20 Nov 2014 14:52:22 +0000 (14:52 +0000)]
JAL-674 JAL-1569 mark RNA helix number in the value field
Jim Procter [Thu, 20 Nov 2014 14:49:36 +0000 (14:49 +0000)]
JAL-1569 remove log output during RNA secondary structure processing
Charles Ofoegbu [Wed, 19 Nov 2014 16:53:36 +0000 (16:53 +0000)]
JAL-1583 MSA webservice validation
gmungoc [Wed, 19 Nov 2014 12:55:39 +0000 (12:55 +0000)]
JAL-1342 new command-line parameter -jabaws <URL>
Charles Ofoegbu [Wed, 19 Nov 2014 12:20:50 +0000 (12:20 +0000)]
merge commit
git://source.jalview.org / jalview.git / log