jalview.git
5 years agoJAL-3032 default Autosearch to off for JalviewJS
gmungoc [Tue, 12 Feb 2019 10:37:54 +0000 (10:37 +0000)]
JAL-3032 default Autosearch to off for JalviewJS

5 years agolatest transpiler and runtime
hansonr [Tue, 5 Feb 2019 16:20:14 +0000 (10:20 -0600)]
latest transpiler and runtime

5 years agoJAL-3032 check enough sequences selected on construction
gmungoc [Tue, 5 Feb 2019 14:31:07 +0000 (14:31 +0000)]
JAL-3032  check enough sequences selected on construction

5 years agoTest (passes!) for dialog message truncation
gmungoc [Tue, 5 Feb 2019 13:51:22 +0000 (13:51 +0000)]
Test (passes!) for dialog message truncation

5 years agoJAL-3048 JS-compatible confirm dialog on delete all
gmungoc [Tue, 5 Feb 2019 13:36:49 +0000 (13:36 +0000)]
JAL-3048 JS-compatible confirm dialog on delete all

5 years agoJSON parsing from a StringInputStream
hansonr [Mon, 4 Feb 2019 17:17:11 +0000 (11:17 -0600)]
JSON parsing from a StringInputStream

5 years agoSequenceFetcher JvCacheableInputBox isJS test
hansonr [Mon, 4 Feb 2019 15:14:59 +0000 (09:14 -0600)]
SequenceFetcher JvCacheableInputBox isJS test

5 years ago*new transpiler* and runtime.
hansonr [Mon, 4 Feb 2019 14:52:01 +0000 (08:52 -0600)]
*new transpiler* and runtime.

5 years agorefactoring for DBMODList
hansonr [Mon, 4 Feb 2019 14:51:36 +0000 (08:51 -0600)]
refactoring for DBMODList

5 years agoMIG -- explicitly sets Java9 switch to true for SwingJS
hansonr [Mon, 4 Feb 2019 14:50:46 +0000 (08:50 -0600)]
MIG -- explicitly sets Java9 switch to true for SwingJS

5 years agoexplicitly sets MIG platform defaults to WINDOWS_XP
hansonr [Mon, 4 Feb 2019 14:49:55 +0000 (08:49 -0600)]
explicitly sets MIG platform defaults to WINDOWS_XP

5 years agoadds protype size to JTextArea hack for nonexistent SwingJS editable
hansonr [Mon, 4 Feb 2019 14:49:12 +0000 (08:49 -0600)]
adds protype size to JTextArea hack for nonexistent SwingJS editable
combo box

5 years agofixing array processing order
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.

5 years agore-transpiled MIGLayout; JS-adapted AnnotationColumnChooser
hansonr [Mon, 4 Feb 2019 14:46:42 +0000 (08:46 -0600)]
re-transpiled MIGLayout; JS-adapted AnnotationColumnChooser

5 years agoTest suite try/catch reverted
hansonr [Mon, 4 Feb 2019 14:45:20 +0000 (08:45 -0600)]
Test suite try/catch reverted

5 years agounused - could be trashed.
hansonr [Mon, 4 Feb 2019 14:43:41 +0000 (08:43 -0600)]
unused - could be trashed.

5 years agoMerge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git...
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

5 years agoMerge branch 'feature/JAL-3143ensemblJSON' 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

5 years agoJAL-3143 update unit test for ID -> id change feature/JAL-3143ensemblJSON
gmungoc [Mon, 4 Feb 2019 12:18:29 +0000 (12:18 +0000)]
JAL-3143 update unit test for ID -> id change

5 years agofix for org.json.JSONObject writing (both in Java and JavaScript)
hansonr [Fri, 1 Feb 2019 13:45:25 +0000 (07:45 -0600)]
fix for org.json.JSONObject writing (both in Java and JavaScript)

5 years agoremoves unnecessary org.xml.sax; these are in SwingJS
hansonr [Fri, 1 Feb 2019 13:44:50 +0000 (07:44 -0600)]
removes unnecessary org.xml.sax; these are in SwingJS

5 years agoSplit pane removing title bar for JInternalFrames
hansonr [Thu, 31 Jan 2019 06:29:21 +0000 (00:29 -0600)]
Split pane removing title bar for JInternalFrames

5 years agofixes org.json.JSONObject for fully qualified method signatures
hansonr [Thu, 31 Jan 2019 00:11:41 +0000 (18:11 -0600)]
fixes org.json.JSONObject for fully qualified method signatures

5 years agoremoves org.json from srcjar
hansonr [Thu, 31 Jan 2019 00:11:06 +0000 (18:11 -0600)]
removes org.json from srcjar

5 years agoMerge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of
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

5 years agoJAL-3144 don't change comma to semi-colon if not requested!
gmungoc [Wed, 30 Jan 2019 15:40:53 +0000 (15:40 +0000)]
JAL-3144 don't change comma to semi-colon if not requested!

5 years agowoops.
hansonr [Wed, 30 Jan 2019 15:26:02 +0000 (09:26 -0600)]
woops.

5 years agoMerge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git...
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

5 years agoFix for textarea not updating value ("value", not "innerHTML")
hansonr [Wed, 30 Jan 2019 14:57:21 +0000 (08:57 -0600)]
Fix for textarea not updating value ("value", not "innerHTML")

5 years agofixes unidentified Java problem
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.

5 years agoJAL-3056 no export as BioJS in JalviewJS
gmungoc [Wed, 30 Jan 2019 10:55:05 +0000 (10:55 +0000)]
JAL-3056 no export as BioJS in JalviewJS

5 years agoclasspath to include test always
hansonr [Tue, 29 Jan 2019 21:11:05 +0000 (15:11 -0600)]
classpath to include test always

5 years agoJSON writing fix, JColorChooser (mnemonic change) fix
hansonr [Tue, 29 Jan 2019 21:10:46 +0000 (15:10 -0600)]
JSON writing fix, JColorChooser (mnemonic change) fix

5 years agoMerge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git...
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

5 years agotest package fix for List<DBRefEntry> DBrefs (untested)
hansonr [Tue, 29 Jan 2019 18:52:02 +0000 (12:52 -0600)]
test package fix for List<DBRefEntry> DBrefs (untested)

5 years agoMerge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git...
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

5 years agoMerge branch 'feature/JAL-3143ensemblJSON' into trialMerge
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

5 years agoJAL-3143 format alleles array for feature description
gmungoc [Tue, 29 Jan 2019 11:17:48 +0000 (11:17 +0000)]
JAL-3143 format alleles array for feature description

5 years agoFetch Sequences...PDB - all tabs working
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.

5 years agoexperiment using a register buffer instead of creating thousands of
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.

5 years agotiming notes; SwingJS for StringBuilder/Buffer
hansonr [Tue, 29 Jan 2019 03:04:35 +0000 (21:04 -0600)]
timing notes; SwingJS for StringBuilder/Buffer

5 years agoiterators
hansonr [Tue, 29 Jan 2019 03:03:15 +0000 (21:03 -0600)]
iterators

5 years agotime check, iterators
hansonr [Tue, 29 Jan 2019 03:00:52 +0000 (21:00 -0600)]
time check, iterators

5 years agoJSON moved to swingjs/json
hansonr [Tue, 29 Jan 2019 03:00:31 +0000 (21:00 -0600)]
JSON moved to swingjs/json

5 years agoJSON code moved to swingjs.json.JSON
hansonr [Tue, 29 Jan 2019 02:02:24 +0000 (20:02 -0600)]
JSON code moved to swingjs.json.JSON

5 years agomore iterators out; some time checks
hansonr [Tue, 29 Jan 2019 02:01:45 +0000 (20:01 -0600)]
more iterators out; some time checks

5 years agoJAL-3032 revert change to tooltip StringBuilder length
gmungoc [Mon, 28 Jan 2019 14:59:27 +0000 (14:59 +0000)]
JAL-3032 revert change to tooltip StringBuilder length

5 years agofinal timing checks for optimization
hansonr [Sat, 26 Jan 2019 16:58:31 +0000 (10:58 -0600)]
final timing checks for optimization

5 years agoPlatform.timecheck calls removed or commented out.
hansonr [Sat, 26 Jan 2019 16:58:04 +0000 (10:58 -0600)]
Platform.timecheck calls removed or commented out.

5 years agoremoving cyclic call
hansonr [Sat, 26 Jan 2019 05:51:50 +0000 (23:51 -0600)]
removing cyclic call

5 years agoJalview.isJS() --> Platform.isJS(), DBRefEntry[] --> List<DBRefEntry>
hansonr [Sat, 26 Jan 2019 05:13:29 +0000 (23:13 -0600)]
Jalview.isJS() --> Platform.isJS(), DBRefEntry[] --> List<DBRefEntry>

5 years agotimestamp just before major refactoring in relation to preliminary
hansonr [Sat, 26 Jan 2019 04:06:47 +0000 (22:06 -0600)]
timestamp just before major refactoring in relation to preliminary
contructor/iterator optimization

5 years agoSwingJS update (maybe nothing?)
hansonr [Fri, 25 Jan 2019 09:25:18 +0000 (03:25 -0600)]
SwingJS update (maybe nothing?)

5 years agotiming code
hansonr [Fri, 25 Jan 2019 09:24:52 +0000 (03:24 -0600)]
timing code

5 years agoJSON refactoring
hansonr [Fri, 25 Jan 2019 09:24:37 +0000 (03:24 -0600)]
JSON refactoring

5 years agoJavaScript browser-based JSON parsing
hansonr [Fri, 25 Jan 2019 09:23:54 +0000 (03:23 -0600)]
JavaScript browser-based JSON parsing

5 years agoTiming code
hansonr [Fri, 25 Jan 2019 09:23:21 +0000 (03:23 -0600)]
Timing code

5 years agoadds File..Load Project file for JS
hansonr [Thu, 24 Jan 2019 13:13:30 +0000 (07:13 -0600)]
adds File..Load Project file for JS

5 years agofixes DnD
hansonr [Thu, 24 Jan 2019 12:24:10 +0000 (06:24 -0600)]
fixes DnD

5 years agoadded _j2sclasslist.txt for buildcore.xml and
hansonr [Wed, 23 Jan 2019 21:27:02 +0000 (15:27 -0600)]
added _j2sclasslist.txt for buildcore.xml and
jalview_bin_JalviewJS_core.html

5 years agoMenus close properly, toolips restored
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.

5 years agomenu, slider work
hansonr [Wed, 23 Jan 2019 16:32:10 +0000 (10:32 -0600)]
menu, slider work

5 years agoMerge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git...
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

5 years agoFloat.isInfinite, popup menus, slider, spinner redux
hansonr [Tue, 22 Jan 2019 14:17:58 +0000 (08:17 -0600)]
Float.isInfinite, popup menus, slider, spinner redux

5 years agoTests for methods of Float
gmungoc [Tue, 22 Jan 2019 10:53:47 +0000 (10:53 +0000)]
Tests for methods of Float

5 years agorecompiled libs; JSONException fixed, JSlider, JSpinner
hansonr [Tue, 22 Jan 2019 05:41:01 +0000 (23:41 -0600)]
recompiled libs; JSONException fixed, JSlider, JSpinner

5 years agoadded Platform settings separating mouse use of win/mac difference
hansonr [Mon, 21 Jan 2019 18:46:50 +0000 (12:46 -0600)]
added Platform settings separating mouse use of win/mac difference

5 years agoadded Platform settings separating mouse use of win/mac difference
hansonr [Mon, 21 Jan 2019 18:23:59 +0000 (12:23 -0600)]
added Platform settings separating mouse use of win/mac difference

5 years agoisAMac() -> isAMacAndNotJS(), isWindows() -> isWindowsAndNotJS()
hansonr [Mon, 21 Jan 2019 17:39:57 +0000 (11:39 -0600)]
isAMac() -> isAMacAndNotJS(), isWindows() -> isWindowsAndNotJS()

Added Platform.isWin[Right|Middle]Button()

5 years agoisAMac() -> isAMacAndNotJS(), isWindows() -> isWindowsAndNotJS()
hansonr [Mon, 21 Jan 2019 17:38:23 +0000 (11:38 -0600)]
isAMac() -> isAMacAndNotJS(), isWindows() -> isWindowsAndNotJS()

Added Platform.isWin[Right|Middle]Button()

5 years agominor Platform.isAMac() clean up
hansonr [Mon, 21 Jan 2019 16:57:25 +0000 (10:57 -0600)]
minor Platform.isAMac() clean up

removes secondary references "MAC"
changes unnecessary instance creation new Platform().isAMac()

5 years agoremoving indirect references to Platform.isAMac()
hansonr [Mon, 21 Jan 2019 16:46:54 +0000 (10:46 -0600)]
removing indirect references to Platform.isAMac()

5 years agocomments only
hansonr [Mon, 21 Jan 2019 16:42:13 +0000 (10:42 -0600)]
comments only

5 years agofixes popup issue involving invocation from mousePressed event.
hansonr [Mon, 21 Jan 2019 06:08:38 +0000 (00:08 -0600)]
fixes popup issue involving invocation from mousePressed event.

5 years agomenu update; popup not functioning, though?? Working fine in test suite.
hansonr [Mon, 21 Jan 2019 04:52:03 +0000 (22:52 -0600)]
menu update; popup not functioning, though?? Working fine in test suite.
Will test.

5 years agomenu update; popup not functioning, though?? Working fine in test suite.
hansonr [Mon, 21 Jan 2019 04:52:03 +0000 (22:52 -0600)]
menu update; popup not functioning, though?? Working fine in test suite.
Will test.

5 years agomenu bug preventing closing - recompiled
hansonr [Sat, 19 Jan 2019 13:08:20 +0000 (07:08 -0600)]
menu bug preventing closing - recompiled

5 years agoJAL-3143 'id' not 'ID' attribute drives generation of variant link
gmungoc [Fri, 18 Jan 2019 09:59:45 +0000 (09:59 +0000)]
JAL-3143 'id' not 'ID' attribute drives generation of variant link

5 years agomenu bug preventing closing
hansonr [Fri, 18 Jan 2019 09:19:35 +0000 (03:19 -0600)]
menu bug preventing closing

I see the problem with label icons offset. Something I did when I was
doing mnemonics, I think....

5 years agocanvas line/font/pixel fixes; menu accelerators;
hansonr [Fri, 18 Jan 2019 08:57:57 +0000 (02:57 -0600)]
canvas line/font/pixel fixes; menu accelerators;

5 years agoMerge branch 'develop' into Jalview-BH/JAL-3026-JAL-3063-JAXB
gmungoc [Thu, 17 Jan 2019 15:29:29 +0000 (15:29 +0000)]
Merge branch 'develop' into Jalview-BH/JAL-3026-JAL-3063-JAXB

Conflicts:
.gitignore
resources/lang/Messages.properties
resources/lang/Messages_es.properties
src/jalview/commands/EditCommand.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/ScalePanel.java

5 years agoremoval of AlignmentFrame lines
hansonr [Tue, 15 Jan 2019 19:18:38 +0000 (13:18 -0600)]
removal of AlignmentFrame lines

5 years agosubimage height error
hansonr [Tue, 15 Jan 2019 19:17:16 +0000 (13:17 -0600)]
subimage height error

5 years agoJAL-3186 remove Variable Colour from popup menu
gmungoc [Mon, 14 Jan 2019 16:13:10 +0000 (16:13 +0000)]
JAL-3186 remove Variable Colour from popup menu

5 years agoJAL-3186 remove duplicate message keys
gmungoc [Mon, 14 Jan 2019 16:00:59 +0000 (16:00 +0000)]
JAL-3186 remove duplicate message keys

5 years agoJAL-2069 wider dialog so all fields show!
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

5 years agoJAL-3186 reorder popup menu slightly
gmungoc [Mon, 14 Jan 2019 15:04:04 +0000 (15:04 +0000)]
JAL-3186 reorder popup menu slightly

5 years agoJAL-2069 clear any error colour when setting threshold from slider
gmungoc [Mon, 14 Jan 2019 14:25:11 +0000 (14:25 +0000)]
JAL-2069 clear any error colour when setting threshold from slider

5 years agoJAL-3125 tidy up
gmungoc [Wed, 26 Sep 2018 14:08:11 +0000 (15:08 +0100)]
JAL-3125 tidy up

5 years agoJAL-3125 avoid slider 'rounding' threshold field value
gmungoc [Wed, 26 Sep 2018 11:05:01 +0000 (12:05 +0100)]
JAL-3125 avoid slider 'rounding' threshold field value

5 years agoMnemonics implemented fully for menus; will appear on standard buttons
hansonr [Mon, 14 Jan 2019 07:21:42 +0000 (01:21 -0600)]
Mnemonics implemented fully for menus; will appear on standard buttons
and the RootPane menubar, but they will not be active, as they are
actually not mnemonics. They are a form of implicit ALT-X accelerators
(which use InputMap). Accelerators are next to implement. Should be
relatively easy.  Not planning to implement mouse-down-and-hold for
mnemonic cycles (multiple mnemonics with the same letter).

5 years agoMerge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git...
hansonr [Fri, 11 Jan 2019 04:49:59 +0000 (22:49 -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

5 years agoSwingJS upgrade
hansonr [Fri, 11 Jan 2019 04:49:40 +0000 (22:49 -0600)]
SwingJS upgrade

5 years ago(commented out but potentially useful) methods to tap Java release
hansonr [Fri, 11 Jan 2019 04:49:20 +0000 (22:49 -0600)]
(commented out but potentially useful) methods to tap Java release
logging options -- used for tracing events

5 years agoJS optimization for too aggressive dynamic operation when entering PDB
hansonr [Fri, 11 Jan 2019 04:48:06 +0000 (22:48 -0600)]
JS optimization for too aggressive dynamic operation when entering PDB
IDs  (proposal only)

5 years agoadding (unnecessary, but informative super() call in Desktop
hansonr [Fri, 11 Jan 2019 04:46:25 +0000 (22:46 -0600)]
adding (unnecessary, but informative super() call in Desktop

5 years agoJAL-3032 stub JS tabbed pane removed as not used
gmungoc [Wed, 9 Jan 2019 15:54:50 +0000 (15:54 +0000)]
JAL-3032 stub JS tabbed pane removed as not used

5 years agoJAL-3032 tweak inner/outer class references
gmungoc [Wed, 9 Jan 2019 15:52:56 +0000 (15:52 +0000)]
JAL-3032 tweak inner/outer class references

5 years agoJAL-3032 refine 'empty status message' test (JS issue 179)
gmungoc [Wed, 9 Jan 2019 15:51:57 +0000 (15:51 +0000)]
JAL-3032 refine 'empty status message' test (JS issue 179)

5 years ago#179 status bar; #85 table repaint; #197?; #193 frame nonresizable;
hansonr [Wed, 9 Jan 2019 05:45:53 +0000 (23:45 -0600)]
#179 status bar; #85 table repaint; #197?; #193 frame nonresizable;

#191 JSON (String.toLowerCase$java_util_Locale missing)