gmungoc [Wed, 27 Feb 2019 15:36:23 +0000 (15:36 +0000)]
JAL-2527 default Overview 'hide hidden' i.e. WYSIWYG
gmungoc [Wed, 27 Feb 2019 15:36:23 +0000 (15:36 +0000)]
JAL-2527 default Overview 'hide hidden' i.e. WYSIWYG
gmungoc [Wed, 27 Feb 2019 15:33:49 +0000 (15:33 +0000)]
JAL-3202 reduced scope of rendering flags
gmungoc [Wed, 27 Feb 2019 12:31:04 +0000 (12:31 +0000)]
JAL-3202 discard zero percentages in extracted profile
Conflicts:
src/jalview/renderer/AnnotationRenderer.java
gmungoc [Tue, 26 Feb 2019 11:39:34 +0000 (11:39 +0000)]
JAL-3201 JAL-2386 don't pre-select 'apply to all groups'
gmungoc [Tue, 26 Feb 2019 10:41:05 +0000 (10:41 +0000)]
JAL-3201 group colour schemes distinct instances
gmungoc [Mon, 25 Feb 2019 15:54:48 +0000 (15:54 +0000)]
JAL-3032 Jalview (as JS) parse query params to main arguments
gmungoc [Mon, 25 Feb 2019 15:24:57 +0000 (15:24 +0000)]
JAL-3032 JalviewJS2 converts url query parameters to 'applet' args
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 [Tue, 12 Feb 2019 10:37:54 +0000 (10:37 +0000)]
JAL-3032 default Autosearch to off for JalviewJS
gmungoc [Thu, 7 Feb 2019 11:41:02 +0000 (11:41 +0000)]
JAL-3140 updated to latest intervalstore.jar
hansonr [Tue, 5 Feb 2019 16:20:14 +0000 (10:20 -0600)]
latest transpiler and runtime
gmungoc [Tue, 5 Feb 2019 14:31:07 +0000 (14:31 +0000)]
JAL-3032 check enough sequences selected on construction
gmungoc [Tue, 5 Feb 2019 13:51:22 +0000 (13:51 +0000)]
Test (passes!) for dialog message truncation
gmungoc [Tue, 5 Feb 2019 13:36:49 +0000 (13:36 +0000)]
JAL-3048 JS-compatible confirm dialog on delete all
hansonr [Mon, 4 Feb 2019 17:17:11 +0000 (11:17 -0600)]
JSON parsing from a StringInputStream
hansonr [Mon, 4 Feb 2019 15:14:59 +0000 (09:14 -0600)]
SequenceFetcher JvCacheableInputBox isJS test
hansonr [Mon, 4 Feb 2019 14:52:01 +0000 (08:52 -0600)]
*new transpiler* and runtime.
hansonr [Mon, 4 Feb 2019 14:51:36 +0000 (08:51 -0600)]
refactoring for DBMODList
hansonr [Mon, 4 Feb 2019 14:50:46 +0000 (08:50 -0600)]
MIG -- explicitly sets Java9 switch to true for SwingJS
hansonr [Mon, 4 Feb 2019 14:49:55 +0000 (08:49 -0600)]
explicitly sets MIG platform defaults to WINDOWS_XP
hansonr [Mon, 4 Feb 2019 14:49:12 +0000 (08:49 -0600)]
adds protype size to JTextArea hack for nonexistent SwingJS editable
combo box
hansonr [Mon, 4 Feb 2019 14:48:05 +0000 (08:48 -0600)]
fixing array processing order
- does point out an issue with hiddenColumns joining adjacent hides
sometimes but not other times.
hansonr [Mon, 4 Feb 2019 14:46:42 +0000 (08:46 -0600)]
re-transpiled MIGLayout; JS-adapted AnnotationColumnChooser
hansonr [Mon, 4 Feb 2019 14:45:20 +0000 (08:45 -0600)]
Test suite try/catch reverted
hansonr [Mon, 4 Feb 2019 14:43:41 +0000 (08:43 -0600)]
unused - could be trashed.
hansonr [Mon, 4 Feb 2019 14:39:55 +0000 (08:39 -0600)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026-JAL-3063-JAXB
gmungoc [Mon, 4 Feb 2019 13:46:14 +0000 (13:46 +0000)]
Merge branch 'feature/JAL-3143ensemblJSON' into Jalview-BH/JAL-3026-JAL-3063-JAXB
gmungoc [Mon, 4 Feb 2019 12:18:29 +0000 (12:18 +0000)]
JAL-3143 update unit test for ID -> id change
hansonr [Fri, 1 Feb 2019 13:45:25 +0000 (07:45 -0600)]
fix for org.json.JSONObject writing (both in Java and JavaScript)
hansonr [Fri, 1 Feb 2019 13:44:50 +0000 (07:44 -0600)]
removes unnecessary org.xml.sax; these are in SwingJS
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
hansonr [Thu, 31 Jan 2019 06:29:21 +0000 (00:29 -0600)]
Split pane removing title bar for JInternalFrames
hansonr [Thu, 31 Jan 2019 00:11:41 +0000 (18:11 -0600)]
fixes org.json.JSONObject for fully qualified method signatures
hansonr [Thu, 31 Jan 2019 00:11:06 +0000 (18:11 -0600)]
removes org.json from srcjar
gmungoc [Wed, 30 Jan 2019 16:05:51 +0000 (16:05 +0000)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of
https://source.jalview.org/git/jalview.git into
Jalview-BH/JAL-3026-JAL-3063-JAXB
Conflicts:
src/jalview/gui/SequenceFetcher.java
gmungoc [Wed, 30 Jan 2019 15:40:53 +0000 (15:40 +0000)]
JAL-3144 don't change comma to semi-colon if not requested!
hansonr [Wed, 30 Jan 2019 15:26:02 +0000 (09:26 -0600)]
woops.
hansonr [Wed, 30 Jan 2019 14:57:38 +0000 (08:57 -0600)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026-JAL-3063-JAXB
hansonr [Wed, 30 Jan 2019 14:57:21 +0000 (08:57 -0600)]
Fix for textarea not updating value ("value", not "innerHTML")
hansonr [Wed, 30 Jan 2019 14:56:52 +0000 (08:56 -0600)]
fixes unidentified Java problem
when pasted text has white space trailing or preceding, error was
indicated that "" could not be loaded.
gmungoc [Wed, 30 Jan 2019 10:55:05 +0000 (10:55 +0000)]
JAL-3056 no export as BioJS in JalviewJS
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
hansonr [Tue, 29 Jan 2019 21:11:05 +0000 (15:11 -0600)]
classpath to include test always
hansonr [Tue, 29 Jan 2019 21:10:46 +0000 (15:10 -0600)]
JSON writing fix, JColorChooser (mnemonic change) fix
hansonr [Tue, 29 Jan 2019 18:52:22 +0000 (12:52 -0600)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026-JAL-3063-JAXB
hansonr [Tue, 29 Jan 2019 18:52:02 +0000 (12:52 -0600)]
test package fix for List<DBRefEntry> DBrefs (untested)
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 11:33:12 +0000 (11:33 +0000)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026-JAL-3063-JAXB
gmungoc [Tue, 29 Jan 2019 11:32:18 +0000 (11:32 +0000)]
Merge branch 'feature/JAL-3143ensemblJSON' into trialMerge
Conflicts:
src/jalview/ext/ensembl/EnsemblFeatures.java
gmungoc [Tue, 29 Jan 2019 11:17:48 +0000 (11:17 +0000)]
JAL-3143 format alleles array for feature description
hansonr [Tue, 29 Jan 2019 07:39:55 +0000 (01:39 -0600)]
Fetch Sequences...PDB - all tabs working
Could still be a problem with panels being moved to and from being
content panes.
hansonr [Tue, 29 Jan 2019 03:20:51 +0000 (21:20 -0600)]
experiment using a register buffer instead of creating thousands of
int[]. Turns out, it's no diffent in Chrome.
hansonr [Tue, 29 Jan 2019 03:04:35 +0000 (21:04 -0600)]
timing notes; SwingJS for StringBuilder/Buffer
hansonr [Tue, 29 Jan 2019 03:03:15 +0000 (21:03 -0600)]
iterators
hansonr [Tue, 29 Jan 2019 03:00:52 +0000 (21:00 -0600)]
time check, iterators
hansonr [Tue, 29 Jan 2019 03:00:31 +0000 (21:00 -0600)]
JSON moved to swingjs/json
hansonr [Tue, 29 Jan 2019 02:02:24 +0000 (20:02 -0600)]
JSON code moved to swingjs.json.JSON
hansonr [Tue, 29 Jan 2019 02:01:45 +0000 (20:01 -0600)]
more iterators out; some time checks
gmungoc [Mon, 28 Jan 2019 14:59:27 +0000 (14:59 +0000)]
JAL-3032 revert change to tooltip StringBuilder length
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
hansonr [Sat, 26 Jan 2019 16:58:31 +0000 (10:58 -0600)]
final timing checks for optimization
hansonr [Sat, 26 Jan 2019 16:58:04 +0000 (10:58 -0600)]
Platform.timecheck calls removed or commented out.
hansonr [Sat, 26 Jan 2019 05:51:50 +0000 (23:51 -0600)]
removing cyclic call
hansonr [Sat, 26 Jan 2019 05:13:29 +0000 (23:13 -0600)]
Jalview.isJS() --> Platform.isJS(), DBRefEntry[] --> List<DBRefEntry>
hansonr [Sat, 26 Jan 2019 04:06:47 +0000 (22:06 -0600)]
timestamp just before major refactoring in relation to preliminary
contructor/iterator optimization
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).
hansonr [Fri, 25 Jan 2019 09:25:18 +0000 (03:25 -0600)]
SwingJS update (maybe nothing?)
hansonr [Fri, 25 Jan 2019 09:24:52 +0000 (03:24 -0600)]
timing code
hansonr [Fri, 25 Jan 2019 09:24:37 +0000 (03:24 -0600)]
JSON refactoring
hansonr [Fri, 25 Jan 2019 09:23:54 +0000 (03:23 -0600)]
JavaScript browser-based JSON parsing
hansonr [Fri, 25 Jan 2019 09:23:21 +0000 (03:23 -0600)]
Timing code
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
hansonr [Thu, 24 Jan 2019 13:13:30 +0000 (07:13 -0600)]
adds File..Load Project file for JS
hansonr [Thu, 24 Jan 2019 12:24:10 +0000 (06:24 -0600)]
fixes DnD
Ben Soares [Thu, 24 Jan 2019 09:37:05 +0000 (09:37 +0000)]
JAL-3141 Reformatted code in eclipse
hansonr [Wed, 23 Jan 2019 21:27:02 +0000 (15:27 -0600)]
added _j2sclasslist.txt for buildcore.xml and
jalview_bin_JalviewJS_core.html
hansonr [Wed, 23 Jan 2019 21:19:59 +0000 (15:19 -0600)]
Menus close properly, toolips restored
minor bug in SeqPanel I introduced some time ago.
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.
hansonr [Wed, 23 Jan 2019 16:32:10 +0000 (10:32 -0600)]
menu, slider work
gmungoc [Wed, 23 Jan 2019 09:15:52 +0000 (09:15 +0000)]
JAL-3063 correct handling of absent choice element in DBRef Mapping
hansonr [Tue, 22 Jan 2019 14:18:17 +0000 (08:18 -0600)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026-JAL-3063-JAXB