Jim Procter [Mon, 4 Mar 2019 16:26:02 +0000 (16:26 +0000)]
Merge branch 'develop' into documentation/JAL-3111_release_211
Jim Procter [Mon, 4 Mar 2019 16:15:40 +0000 (16:15 +0000)]
release notes for JAL-1767 JAL-2647 JAL-3198 JAL-3200 JAL-3018 JAL-3139 JAL-2587 JAL-2527 JAL-3140 JAL-3063 JAL-3171 JAL-3164 JAL-3158 JAL-3161 JAL-3154
gmungoc [Mon, 4 Mar 2019 12:30:09 +0000 (12:30 +0000)]
Merge branch 'bug/JAL-3099alignmentVisibleWidth' into merge/JAL-3099
Conflicts:
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/IdCanvas.java
test/jalview/datamodel/AlignmentTest.java
gmungoc [Mon, 4 Mar 2019 11:47:14 +0000 (11:47 +0000)]
Merge remote-tracking branch 'origin/tasks/JAL-3035_remove_dasobert_dependency' into merge/JAL-3035
gmungoc [Mon, 4 Mar 2019 10:54:27 +0000 (10:54 +0000)]
Merge branch 'bug/JAL-3120restoreFeatureColour' into merge/JAL-3120
Conflicts:
src/jalview/gui/Jalview2XML.java
test/jalview/io/Jalview2xmlTests.java
gmungoc [Fri, 1 Mar 2019 15:35:54 +0000 (15:35 +0000)]
Merge branch 'bug/JAL-2791exportFilteredFeature' into merge/JAL-2791
gmungoc [Fri, 1 Mar 2019 15:12:06 +0000 (15:12 +0000)]
Merge branch 'feature/JAL-3093wrappedModeTooltips' into merge/JAL-3093_JAL-3132
gmungoc [Fri, 1 Mar 2019 15:11:31 +0000 (15:11 +0000)]
JAL-3093 unit test adapts to actual number of annotation rows
gmungoc [Fri, 1 Mar 2019 14:30:03 +0000 (14:30 +0000)]
Merge branch 'feature/JAL-3093wrappedModeTooltips' into
merge/JAL-3093_JAL-3132
Conflicts:
src/jalview/gui/SeqPanel.java
test/jalview/gui/SeqPanelTest.java
gmungoc [Fri, 1 Mar 2019 12:26:45 +0000 (12:26 +0000)]
Merge branch 'feature/JAL-1244stretchStatusMsg' into merge/JAL-1244
Conflicts:
src/jalview/commands/EditCommand.java
gmungoc [Fri, 1 Mar 2019 12:12:04 +0000 (12:12 +0000)]
Merge branch 'bug/JAL-3139colocatedFeatures' into develop
gmungoc [Fri, 1 Mar 2019 11:23:39 +0000 (11:23 +0000)]
JAL-3154 disable reorder columns before adding to viewport
gmungoc [Fri, 1 Mar 2019 11:17:11 +0000 (11:17 +0000)]
Merge branch 'bug/JAL-3154tableColumnDrag' into develop
gmungoc [Fri, 1 Mar 2019 11:00:39 +0000 (11:00 +0000)]
Merge branch 'bug/JAL-3161annotationTooltipRange' into develop
gmungoc [Fri, 1 Mar 2019 10:57:17 +0000 (10:57 +0000)]
Merge branch 'bug/JAL-3158selectionBroadcasts' into merge/JAL-3158
gmungoc [Fri, 1 Mar 2019 10:07:54 +0000 (10:07 +0000)]
Merge branch 'bug/JAL-3164complementOverview' into merge/JAL-3164
gmungoc [Fri, 1 Mar 2019 10:00:28 +0000 (10:00 +0000)]
Merge branch 'merge/JAL-3140' into develop
gmungoc [Fri, 1 Mar 2019 09:59:24 +0000 (09:59 +0000)]
JAL-3140 update for change to SequenceI api
gmungoc [Fri, 1 Mar 2019 09:41:58 +0000 (09:41 +0000)]
Merge branch 'feature/intervalStoreJ' into merge/JAL-3140
gmungoc [Fri, 1 Mar 2019 09:23:11 +0000 (09:23 +0000)]
JAL-3140 reduced coupling to intervalstore.jar
gmungoc [Thu, 28 Feb 2019 16:41:55 +0000 (16:41 +0000)]
JAL-3140 confine intervalstore imports to jalview.datamodel.features
gmungoc [Thu, 28 Feb 2019 15:59:02 +0000 (15:59 +0000)]
Merge branch 'bug/JAL-2420revealAllMenu' into develop
gmungoc [Thu, 28 Feb 2019 15:58:47 +0000 (15:58 +0000)]
Merge branch 'bug/JAL-3166npeAllRowsHidden' into develop
gmungoc [Thu, 28 Feb 2019 15:51:18 +0000 (15:51 +0000)]
Merge branch 'feature/JAL-3169cancelOverwrite' into develop
Conflicts:
src/jalview/io/JalviewFileChooser.java
Jim Procter [Thu, 28 Feb 2019 15:31:19 +0000 (15:31 +0000)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
gmungoc [Thu, 28 Feb 2019 15:15:21 +0000 (15:15 +0000)]
Merge branch 'feature/JAL-3143ensemblJSON' into merge/JAL-3143
gmungoc [Thu, 28 Feb 2019 14:15:43 +0000 (14:15 +0000)]
Merge remote-tracking branch 'origin/feature/JAL-3141_backupfiles_for211' into merge/JAL3141
Jim Procter [Thu, 28 Feb 2019 13:46:48 +0000 (13:46 +0000)]
Merge branch 'feature/JAL-3141_backupfiles_for211' into develop
gmungoc [Wed, 27 Feb 2019 15:36:23 +0000 (15:36 +0000)]
JAL-2527 default Overview 'hide hidden' i.e. WYSIWYG
gmungoc [Tue, 26 Feb 2019 10:41:05 +0000 (10:41 +0000)]
JAL-3201 group colour schemes distinct instances
gmungoc [Mon, 25 Feb 2019 13:46:27 +0000 (13:46 +0000)]
JAL-3200 fast lookup of DSSP3 notation
gmungoc [Sun, 24 Feb 2019 08:58:51 +0000 (08:58 +0000)]
JAL-3198 don't recalculate group conservation for Id Panel selection
gmungoc [Sun, 24 Feb 2019 08:10:17 +0000 (08:10 +0000)]
JAL-3198 SequenceGroup 'bulk constructor' without duplicates check
gmungoc [Fri, 22 Feb 2019 11:27:59 +0000 (11:27 +0000)]
JAL-2915 don't recalculate Overview on scroll to position, ever!
gmungoc [Fri, 22 Feb 2019 10:04:02 +0000 (10:04 +0000)]
JAL-2738 don't set AF as feature score
Ben Soares [Fri, 22 Feb 2019 09:19:53 +0000 (09:19 +0000)]
JAL-3141 improved message for asking whether to delete files (file modification time and size added to info to help user decide
Ben Soares [Thu, 21 Feb 2019 17:59:25 +0000 (17:59 +0000)]
JAL-3141 Sensible refactoring for confirming deleting 'newer' old backup files
Ben Soares [Sun, 17 Feb 2019 18:19:42 +0000 (18:19 +0000)]
JAL-3141 User warning when deleting old backup files that are newer than the previous backup file
Ben Soares [Fri, 15 Feb 2019 19:38:34 +0000 (19:38 +0000)]
JAL-3141 re-order deletion of old files and check lastModified times with their replacements
Ben Soares [Thu, 14 Feb 2019 15:52:03 +0000 (15:52 +0000)]
JAL-3141 Added warning/confirmation when suffixReverse is changed without changing suffixTemplate or suffixDigits (Bad Things might happen to previous backup files)
Ben Soares [Thu, 14 Feb 2019 14:20:13 +0000 (14:20 +0000)]
JAL-3141 Moved 'Previously saved scheme' combo box preference out to 'Cancel changes' button. Tidied up the Summary box display.
gmungoc [Thu, 7 Feb 2019 11:41:02 +0000 (11:41 +0000)]
JAL-3140 updated to latest intervalstore.jar
gmungoc [Mon, 4 Feb 2019 12:18:29 +0000 (12:18 +0000)]
JAL-3143 update unit test for ID -> id change
Ben Soares [Fri, 1 Feb 2019 09:42:13 +0000 (09:42 +0000)]
JAL-3141 Slight efficiency gain in detecting backupfiles in the File Chooser
Ben Soares [Wed, 30 Jan 2019 10:10:42 +0000 (10:10 +0000)]
JAL-3141 Enabled the 'Include backpup files' checkbox for loading alignments from local file
Ben Soares [Tue, 29 Jan 2019 14:15:51 +0000 (14:15 +0000)]
JAL-3141 Found a good fix for updating the FileChooser list of files when 'Include backup files' checkbox is checked/unchecked.
Ben Soares [Tue, 29 Jan 2019 11:41:52 +0000 (11:41 +0000)]
JAL-3141 Found a (not ideal) fix for updating the FileChooser list of files when 'Include backup files' checkbox is checked/unchecked.
gmungoc [Tue, 29 Jan 2019 11:17:48 +0000 (11:17 +0000)]
JAL-3143 format alleles array for feature description
Ben Soares [Mon, 28 Jan 2019 10:53:32 +0000 (10:53 +0000)]
JAL-3141 improvement on BackupFilenameParts filename matching
Ben Soares [Mon, 28 Jan 2019 10:06:11 +0000 (10:06 +0000)]
JAL-3141 fixed test
Ben Soares [Fri, 25 Jan 2019 17:32:37 +0000 (17:32 +0000)]
JAL-3141. This adds quite a lot of code to allow an 'Include backup files' checkbox in the 'Load Project' JalviewFileChooser. However I cannot for the life of me get the file list in the FileChooser to refresh /reliably/ on a mac at least anyway (it does about 1 time in 9git status).
Ben Soares [Thu, 24 Jan 2019 16:54:21 +0000 (16:54 +0000)]
JAL-3141 Added a '.fa' to filename examples
Ben Soares [Thu, 24 Jan 2019 16:47:43 +0000 (16:47 +0000)]
JAL-3141 Change of label (change of '_' character to ' ')
Ben Soares [Thu, 24 Jan 2019 16:33:11 +0000 (16:33 +0000)]
JAL-3141 Change of label
Ben Soares [Thu, 24 Jan 2019 16:25:26 +0000 (16:25 +0000)]
JAL-3141 Removed border around example filenames in Backups Preferences pane
Ben Soares [Thu, 24 Jan 2019 15:56:58 +0000 (15:56 +0000)]
JAL-3141 New layout and wording of Backups Preferences pane after consultation with SD. Seriously rationalised 'backupfiles...SetEnable' to allow for more complex widget enabling/disabling depending on other widget values. Fixed a buglet or two when there's an unusual selection of options (when suffix has no '%n' or is completely empty).
Ben Soares [Thu, 24 Jan 2019 15:29:54 +0000 (15:29 +0000)]
JAL-3141 Eclipse re-formatting of file
gmungoc [Thu, 24 Jan 2019 14:30:31 +0000 (14:30 +0000)]
JAL-3018 Ensembl version updated to 9.0
Ben Soares [Thu, 24 Jan 2019 09:37:05 +0000 (09:37 +0000)]
JAL-3141 Reformatted code in eclipse
Ben Soares [Wed, 23 Jan 2019 20:33:20 +0000 (20:33 +0000)]
JAL-3141 Added Presets options in the Backups Preferences pane, with several presets available and sensible 'Default' option chosen first time.
gmungoc [Wed, 23 Jan 2019 09:15:52 +0000 (09:15 +0000)]
JAL-3063 correct handling of absent choice element in DBRef Mapping
Ben Soares [Tue, 22 Jan 2019 13:15:08 +0000 (13:15 +0000)]
JAL-3141 Fixed what happens when suffix template has no '%n' index
Ben Soares [Tue, 22 Jan 2019 13:14:06 +0000 (13:14 +0000)]
JAL-3141 New message translations
Ben Soares [Mon, 21 Jan 2019 22:56:41 +0000 (22:56 +0000)]
JAL-3141 Rejigged the Preferences tab and changed some text
Ben Soares [Mon, 21 Jan 2019 13:51:48 +0000 (13:51 +0000)]
JAL-3141 Fixed tests for new placement of suffix after extension
Ben Soares [Sun, 20 Jan 2019 15:50:31 +0000 (15:50 +0000)]
JAL-3141 removing diagnostic output
Ben Soares [Sun, 20 Jan 2019 01:10:59 +0000 (01:10 +0000)]
JAL-3141 Fixed example filenames in Preferences pane (no extension in BackupFiles now), and new default template.
Ben Soares [Sun, 20 Jan 2019 00:08:14 +0000 (00:08 +0000)]
JAL-3141 Changed suffix position to after the extension (removed extension detection altogether), and changed initial defaults.
Ben Soares [Sun, 20 Jan 2019 00:03:26 +0000 (00:03 +0000)]
JAL-3141 Re-added some changes in Jalview2XML missed in the merge
Jim Procter [Fri, 18 Jan 2019 14:18:57 +0000 (14:18 +0000)]
Merge branch 'feature/JAL-3063jaxbNoCastor' into feature/JAL-3141_Create_a_backup_when_saving_projects_and_other_files
JAL-3063 switched from castor to JAXB - backupFile bits added to jalview.project.Jalview2XML
Jim Procter [Fri, 18 Jan 2019 14:06:09 +0000 (14:06 +0000)]
Merge branch 'develop' into feature/JAL-3063jaxbNoCastor
gmungoc [Fri, 18 Jan 2019 09:59:45 +0000 (09:59 +0000)]
JAL-3143 'id' not 'ID' attribute drives generation of variant link
Jim Procter [Thu, 17 Jan 2019 12:29:06 +0000 (12:29 +0000)]
JAL-3116 clear out whitespace when materialising Sequence object from Uniprot XML
Ben Soares [Wed, 16 Jan 2019 14:27:12 +0000 (14:27 +0000)]
JAL-3141 Remove no longer used exampleLabel
Jim Procter [Wed, 16 Jan 2019 11:50:22 +0000 (11:50 +0000)]
Merge branch 'feature/JAL-3063jaxbNoCastor' into develop
JAL-3063 todo: add castor-1.1-cycle.jar back to libraries inorder to ensure VAMSAS functionality remains
Jim Procter [Wed, 16 Jan 2019 11:38:15 +0000 (11:38 +0000)]
Merge branch 'features/pca_jaxb_datasetrefs_JAL-3171_JAL-3063_JAL-1767' into develop
Jim Procter [Tue, 15 Jan 2019 13:12:10 +0000 (13:12 +0000)]
JAL-1767 test that changing view association for PCA panel can be restored
Jim Procter [Tue, 15 Jan 2019 13:10:42 +0000 (13:10 +0000)]
JAL-1767 refactor associated view logic to public method and synchronise PCAPanel.av/ap with RotateableCanvac.ap/av
Jim Procter [Tue, 15 Jan 2019 11:19:39 +0000 (11:19 +0000)]
JAL-1767 patch buggy PCA view association test
Ben Soares [Mon, 14 Jan 2019 23:53:16 +0000 (23:53 +0000)]
JAL-3141 Forgot this file, sorry!
Ben Soares [Mon, 14 Jan 2019 23:47:38 +0000 (23:47 +0000)]
JAL-3141 Added a 'Save Project as...' File menu item, always asks for filename. Altered 'Save Project' File menu item to automatically save if both 1) projectFile is set (e.g. loaded or previously saved), 2) Backups is enabled
Ben Soares [Mon, 14 Jan 2019 23:40:48 +0000 (23:40 +0000)]
JAL-3141 Made more constants
gmungoc [Mon, 14 Jan 2019 16:13:10 +0000 (16:13 +0000)]
JAL-3186 remove Variable Colour from popup menu
gmungoc [Mon, 14 Jan 2019 16:00:59 +0000 (16:00 +0000)]
JAL-3186 remove duplicate message keys
gmungoc [Fri, 16 Nov 2018 08:04:54 +0000 (08:04 +0000)]
JAL-2069 wider dialog so all fields show!
Conflicts:
src/jalview/gui/FeatureTypeSettings.java
gmungoc [Mon, 14 Jan 2019 14:25:11 +0000 (14:25 +0000)]
JAL-2069 clear any error colour when setting threshold from slider
gmungoc [Wed, 26 Sep 2018 14:08:11 +0000 (15:08 +0100)]
JAL-3125 tidy up
gmungoc [Wed, 26 Sep 2018 11:05:01 +0000 (12:05 +0100)]
JAL-3125 avoid slider 'rounding' threshold field value
Ben Soares [Wed, 9 Jan 2019 18:29:05 +0000 (18:29 +0000)]
JAL-3141 removed redundant method to tests
Jim Procter [Wed, 9 Jan 2019 17:29:21 +0000 (17:29 +0000)]
JAL-1767 failing test to check if the PCA view association is correctly saved and restored
Jim Procter [Wed, 9 Jan 2019 16:24:44 +0000 (16:24 +0000)]
Merge branch 'feature/JAL-3063JAXB' into features/pca_jaxb_datasetrefs_JAL-3171_JAL-3063_JAL-1767
Jim Procter [Wed, 9 Jan 2019 16:24:20 +0000 (16:24 +0000)]
Merge branch 'feature/JAL-3063JAXB' into feature/JAL-3063jaxbNoCastor
Jim Procter [Wed, 9 Jan 2019 16:23:37 +0000 (16:23 +0000)]
JAL-3063 remove stale JAXB binding POJO
Jim Procter [Wed, 9 Jan 2019 16:22:03 +0000 (16:22 +0000)]
Merge branch 'feature/JAL-3063JAXB' into features/pca_jaxb_datasetrefs_JAL-3171_JAL-3063_JAL-1767
Jim Procter [Wed, 9 Jan 2019 16:19:57 +0000 (16:19 +0000)]
Merge branch 'feature/JAL-3063JAXB' into feature/JAL-3063jaxbNoCastor
Jim Procter [Wed, 9 Jan 2019 16:16:45 +0000 (16:16 +0000)]
JAL-3063 - ant task for regenerating JAXB schema - could be optimised further
Ben Soares [Wed, 9 Jan 2019 08:45:11 +0000 (08:45 +0000)]
JAL-3141 language word ending corrections
Ben Soares [Wed, 9 Jan 2019 08:26:07 +0000 (08:26 +0000)]
JAL-3141 Added i18n for the example filenames in Preferences
Ben Soares [Wed, 9 Jan 2019 07:58:32 +0000 (07:58 +0000)]
JAL-3141 forgot to add this file after extracting the class!
Ben Soares [Wed, 9 Jan 2019 00:26:07 +0000 (00:26 +0000)]
JAL-3141 Made one more suggested change from code review
git://source.jalview.org / jalview.git / log