hansonr [Sat, 29 Dec 2018 03:07:08 +0000 (21:07 -0600)]
JEditorPane <div>....<br><div>
hansonr [Sat, 29 Dec 2018 03:07:08 +0000 (21:07 -0600)]
support added for JEditorPane, JTextPane, JTextArea, JTextField
- default selection support for JTextArea and JTextField
- DefaultStyledDocument support for JTextPane
- includes font/color/bold/italic/sub/sup
hansonr [Tue, 25 Dec 2018 00:10:28 +0000 (18:10 -0600)]
#188, #195
- disabled submenus still opening (enable node should be li, not "a" tag
- popup requires double click (interference with JToolBar closing)
hansonr [Tue, 25 Dec 2018 00:05:25 +0000 (18:05 -0600)]
better Jmol help link
hansonr [Mon, 24 Dec 2018 22:52:53 +0000 (16:52 -0600)]
fixes #195 popup requires two clicks
(interference with JTooptip window closing)
hansonr [Sat, 22 Dec 2018 18:49:52 +0000 (12:49 -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
hansonr [Sat, 22 Dec 2018 18:49:32 +0000 (12:49 -0600)]
#179, #185 status bar flicker gone (?), Colour by Annotation working
gmungoc [Fri, 21 Dec 2018 11:48:28 +0000 (11:48 +0000)]
JAL-1767 minimise local variable scope
gmungoc [Fri, 21 Dec 2018 11:06:37 +0000 (11:06 +0000)]
JAL-3032 prefer Jalview.isJS() to j2sNative
hansonr [Fri, 21 Dec 2018 02:51:40 +0000 (20:51 -0600)]
menubar, menus, tables
- Menubar adjusted to height of menu item text
- popip menu hover highlight moved from <a> to <li> tag,
makes for full-width highlight
- popup menu hover to highlight bypasses <span> children by
using mouseover instead of mouseenter
- popup menu vertical and horizontal spacing tweaks
maybe still issues with menu exit/hiding
- tables now correctly respond to changed data[] model
- much streamlined processing on changes for better performance
- still could do more, but it seems pretty smooth
- not able to reproduce any issues with color picker
Make sure to do a clean build. There were files in JavaScript that did
not get updated in my recent pull of Mungo's work.
Jim Procter [Thu, 20 Dec 2018 13:36:33 +0000 (13:36 +0000)]
JAL-1767 port save/load PCA panel to JAXB - JAL-3063
hansonr [Thu, 20 Dec 2018 12:10:52 +0000 (06:10 -0600)]
JalviewFileChooser back to original; synth. ref fixed in j2sClazz.js
Jim Procter [Thu, 20 Dec 2018 11:46:25 +0000 (11:46 +0000)]
JAL-3171 JAL-3063 merge updates from JAL-1767
hansonr [Thu, 20 Dec 2018 11:41:12 +0000 (05:41 -0600)]
preliminary hack fix for synthetic reference issue
RecentlyOpened
inner/ /subclasses
JalviewFileChooser
\ /
JFileChooser
Component
So Component can be retrieved two ways through JFileChooser. (1) as the
original JalviewFileChooser object
(2) as the superclass of RecentlyOpened.
I will look into it. For now it is sufficient to simply move
RecentlyOpened to be at least a static class. I just made it another
top-level class.
hansonr [Thu, 20 Dec 2018 10:16:43 +0000 (04:16 -0600)]
fixes menu persistence issues
- closes all menus on any click
- adds persistence for clicking a submenu item
hansonr [Thu, 20 Dec 2018 08:59:04 +0000 (02:59 -0600)]
seq panel issue with shift-left-mouse drag fix
TODO: menus no longer close on their own
hansonr [Thu, 20 Dec 2018 07:26:10 +0000 (01:26 -0600)]
label work; adds preliminary _j2sclasslist.txt
- use get class list link on test page to save list
- run buildcore.xml, which creates j2s/core/core_jalview.z.js (3.8 Mb)
- open jalview_bin_JalviewJS_core.html (if it is not in site/ copy it
from site-resources -- the transpiler should do this, but not unless you
change the code)
On my machine, Chrome loads and displays the reference JAXB file in
under five seconds.
The mechanism of dynamic loading of core files (not just preloading,
like this) might not be implemented yet in SwingJS.
TODO: menus are not automatically closing on the 300-ms timer anymore. Something I did when reconfiguring CSS for menu items. Will check.
Jim Procter [Wed, 19 Dec 2018 16:53:33 +0000 (16:53 +0000)]
Merge branch 'features/JAL-1767pcaInProject' into bug/JAL-3171_maintain_datasets_across_views
gmungoc [Wed, 19 Dec 2018 15:11:05 +0000 (15:11 +0000)]
JAL-2621 Overview uses hand cursor in drag box, crosshair outside box
gmungoc [Wed, 19 Dec 2018 14:34:28 +0000 (14:34 +0000)]
JAL-3178 include non-positional features in their group on export
gmungoc [Wed, 19 Dec 2018 11:38:30 +0000 (11:38 +0000)]
JAL-2791 JAL-2808 correct Javadoc for api method
gmungoc [Wed, 19 Dec 2018 09:16:41 +0000 (09:16 +0000)]
JAL-3032 ignore /site also on non-JS branches
Jim Procter [Tue, 18 Dec 2018 19:20:32 +0000 (19:20 +0000)]
JAL-2846 ahem - proper release note for this fix from KJVDH !
Jim Procter [Tue, 18 Dec 2018 19:13:05 +0000 (19:13 +0000)]
JAL-3178 known defect in release notes
gmungoc [Tue, 18 Dec 2018 18:06:41 +0000 (18:06 +0000)]
JAL-3048 fix NPE in file chooser callbacks map
gmungoc [Tue, 18 Dec 2018 17:58:39 +0000 (17:58 +0000)]
Merge branch 'JAL-3048dialogRunner2' into Jalview-BH/JAL-3026-JAL-3063-JAXB
gmungoc [Tue, 18 Dec 2018 17:58:12 +0000 (17:58 +0000)]
JAL-3032 revert table repaint customisations
gmungoc [Tue, 18 Dec 2018 17:11:33 +0000 (17:11 +0000)]
JAL-3048 DialogRunnerI reduced to minimal implementation
hansonr [Tue, 18 Dec 2018 14:32:23 +0000 (08:32 -0600)]
removing special needs for JavaScript table repainting
gmungoc [Tue, 18 Dec 2018 12:31:57 +0000 (12:31 +0000)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' into
JAL-3048dialogRunner2
Conflicts:
test/jalview/util/dialogrunner/DialogRunnerTest.java
hansonr [Tue, 18 Dec 2018 05:16:22 +0000 (23:16 -0600)]
opening/closing windows closes all menus
hansonr [Tue, 18 Dec 2018 04:37:13 +0000 (22:37 -0600)]
table work
- fixed use of save/restore of ui nodes in tables
- default background white
- inadvertent resetting of table background via JPopupMenu
hansonr [Tue, 18 Dec 2018 00:02:58 +0000 (18:02 -0600)]
extraneous "Score >" on left of page removed
hansonr [Tue, 18 Dec 2018 00:02:58 +0000 (18:02 -0600)]
extraneous "Score >" on left of page removed
hansonr [Mon, 17 Dec 2018 22:44:18 +0000 (16:44 -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 [Mon, 17 Dec 2018 22:43:57 +0000 (16:43 -0600)]
fixes JTabbedPane missing labels; color chooser e.g.
Jim Procter [Mon, 17 Dec 2018 17:53:49 +0000 (17:53 +0000)]
JAL-3111 JAL-2846 release notes
Jim Procter [Mon, 17 Dec 2018 17:52:26 +0000 (17:52 +0000)]
Merge branch 'bug/JAL-2846' into develop
Jim Procter [Mon, 17 Dec 2018 17:39:40 +0000 (17:39 +0000)]
JAL-3111 tweaked release notes and documented JAL-2864
Jim Procter [Mon, 17 Dec 2018 17:30:44 +0000 (17:30 +0000)]
Merge branch 'bug/JAL-2864nullOverviewCanvas' into develop
gmungoc [Mon, 17 Dec 2018 17:28:28 +0000 (17:28 +0000)]
JAL-3048 updated test class (not on classpath!) for code changes
gmungoc [Mon, 17 Dec 2018 17:25:49 +0000 (17:25 +0000)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' into
JAL-3048dialogRunner2
Conflicts:
src/jalview/io/JalviewFileChooser.java
Jim Procter [Mon, 17 Dec 2018 17:19:48 +0000 (17:19 +0000)]
JAL-2865 release notes
Jim Procter [Mon, 17 Dec 2018 17:04:56 +0000 (17:04 +0000)]
Merge branch 'bug/JAL-2750' into develop
gmungoc [Mon, 17 Dec 2018 16:45:11 +0000 (16:45 +0000)]
Merge branch 'feature/JAL-3169cancelOverwrite' into trialMerge
Conflicts:
src/jalview/io/JalviewFileChooser.java
gmungoc [Mon, 17 Dec 2018 16:23:13 +0000 (16:23 +0000)]
JAL-3068 tidy status bar messaging
Jim Procter [Mon, 17 Dec 2018 16:00:33 +0000 (16:00 +0000)]
Merge branch 'task/JAL-3174_fixed_filename_tests' into develop
Jim Procter [Mon, 17 Dec 2018 15:59:32 +0000 (15:59 +0000)]
JAL-3174 backout un-needed stacktrace for exception raised during testing (since we expect it)
Ben Soares [Mon, 17 Dec 2018 15:16:57 +0000 (15:16 +0000)]
JAL-3174 Merging in some test filename-case fixes
Jim Procter [Mon, 17 Dec 2018 14:31:06 +0000 (14:31 +0000)]
Merge branch 'bug/JAL-2541cutRelocateFeatures' into develop
Jim Procter [Mon, 17 Dec 2018 14:30:11 +0000 (14:30 +0000)]
JAL-2541 JAL-2822 release notes
Jim Procter [Mon, 17 Dec 2018 14:29:50 +0000 (14:29 +0000)]
JAL-3111 bump release 2.11 release to January 2019
gmungoc [Mon, 17 Dec 2018 14:20:27 +0000 (14:20 +0000)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' into
JAL-3048dialogRunner2
Conflicts:
src/jalview/io/JalviewFileChooser.java
Jim Procter [Mon, 17 Dec 2018 11:54:21 +0000 (11:54 +0000)]
Merge branch 'develop' into bug/JAL-2541cutRelocateFeatures
hansonr [Sun, 16 Dec 2018 19:47:31 +0000 (13:47 -0600)]
Java2Script/SwingJS 3.2.4.05
- fixes FeatureIcon painting
Jim Procter [Fri, 14 Dec 2018 17:50:30 +0000 (17:50 +0000)]
JAL-3171 dataset reference tests now in Functional group
Jim Procter [Fri, 14 Dec 2018 17:44:25 +0000 (17:44 +0000)]
JAL-3171 record mapping between unmarshalled sequence’s dataset sequence ID and materialised dataset to allow belt-and-braces discovery of existing dataset - test now passes
Jim Procter [Fri, 14 Dec 2018 16:34:01 +0000 (16:34 +0000)]
JAL-3171 raise warning when a dataset reference exists *and* a different dataset exists for the sequenceSetID
Jim Procter [Fri, 14 Dec 2018 16:13:26 +0000 (16:13 +0000)]
JAL-3171 more complex project test - where sequences were copied from one alignment view into a new alignment and more views created.
Jim Procter [Fri, 14 Dec 2018 15:09:22 +0000 (15:09 +0000)]
JAL-3171 resolve dataset for imported projects via the alignment’s SequenceSetId
Jim Procter [Fri, 14 Dec 2018 12:28:24 +0000 (12:28 +0000)]
JAL-3171 failing test for legacy projects and fixing multiple dataset references
Jim Procter [Fri, 14 Dec 2018 11:59:45 +0000 (11:59 +0000)]
JAL-3171 register existing dataset for new view
Jim Procter [Fri, 14 Dec 2018 11:59:11 +0000 (11:59 +0000)]
JAL-3171 failing test checking preservation of dataset
hansonr [Thu, 13 Dec 2018 23:03:46 +0000 (17:03 -0600)]
SwingJS 3.2.4.05 should fix JFileChooser synthetic ref issue
adds better detection of HTTP_FILE_NOT_FOUND error if using jsmol.php
relay (which seems to always add \r\n and gives status 200, even if the
actual response was 404
gmungoc [Tue, 11 Dec 2018 08:34:41 +0000 (08:34 +0000)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' into JAL-3048dialogRunner2
gmungoc [Mon, 10 Dec 2018 15:29:08 +0000 (15:29 +0000)]
JAL-3048 wip externalise trigger from RunResponse
gmungoc [Mon, 10 Dec 2018 13:55:12 +0000 (13:55 +0000)]
Merge branch 'feature/JAL-3169cancelOverwrite' into
JAL-3048dialogRunner2
Conflicts:
src/jalview/io/JalviewFileChooser.java
gmungoc [Mon, 10 Dec 2018 12:09:43 +0000 (12:09 +0000)]
JAL-1421 added type to List and Vector
gmungoc [Mon, 10 Dec 2018 11:25:44 +0000 (11:25 +0000)]
JAL-3169 leave file browser open on Cancel in overwrite check
gmungoc [Mon, 10 Dec 2018 10:20:15 +0000 (10:20 +0000)]
JAL-3048 DialogRunner changes (wip)
gmungoc [Mon, 10 Dec 2018 10:19:42 +0000 (10:19 +0000)]
JAL-1544 corrected 'adjunst' to 'adjust'
hansonr [Mon, 10 Dec 2018 07:49:03 +0000 (01:49 -0600)]
Faster JTable processing; fixes Annotation painting issues (?)
gmungoc [Thu, 6 Dec 2018 15:02:15 +0000 (15:02 +0000)]
JAL-3048 response() renamed addResponse(); checkstyle warning fixes
gmungoc [Thu, 6 Dec 2018 14:54:30 +0000 (14:54 +0000)]
JAL-3048 explicit instead of default 'No' response handler
gmungoc [Thu, 6 Dec 2018 13:26:46 +0000 (13:26 +0000)]
Merge branch 'develop' into Jalview-BH/JAL-3026-JAL-3063-JAXB
gmungoc [Thu, 6 Dec 2018 10:06:25 +0000 (10:06 +0000)]
JAL-1854 fix Checkstyle import violations
gmungoc [Thu, 6 Dec 2018 10:05:57 +0000 (10:05 +0000)]
JAL-1854 Checkstyle updated to 8.12
gmungoc [Tue, 4 Dec 2018 13:22:55 +0000 (13:22 +0000)]
JAL-3032 set radio buttons transparent
hansonr [Tue, 4 Dec 2018 08:31:45 +0000 (02:31 -0600)]
SwingJS upgrade -- tables smoother, faster; more to do?
Still a problem with FeatureTypeSettings not responding to color chooser
OK properly. (Color is not setting.)
hansonr [Tue, 4 Dec 2018 01:18:28 +0000 (19:18 -0600)]
x,y switch in FeatureIcon
// g.fillRect(0, e1, width - e1, height); // BH 2018
g.fillRect(e1, 0, width - e1, height);
hansonr [Mon, 3 Dec 2018 17:11:31 +0000 (11:11 -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, 3 Dec 2018 15:03:53 +0000 (15:03 +0000)]
JAL-3063 Castor removed from codebase
gmungoc [Mon, 3 Dec 2018 14:19:18 +0000 (14:19 +0000)]
Merge branch 'feature/JAL-3063JAXB' into feature/JAL-3063jaxbNoCastor
gmungoc [Mon, 3 Dec 2018 11:30:09 +0000 (11:30 +0000)]
JAL-3168 include feature type in colour chooser dialog title
gmungoc [Mon, 3 Dec 2018 10:41:37 +0000 (10:41 +0000)]
JAL-3167 end cell editing on cancel in colour chooser
gmungoc [Mon, 3 Dec 2018 10:37:35 +0000 (10:37 +0000)]
JAL-3058 provide cancel callback method for colour chooser
hansonr [Sat, 1 Dec 2018 11:44:39 +0000 (05:44 -0600)]
adding jaxbtest.jvx and directing JalviewJS2.java to open it.
gmungoc [Fri, 30 Nov 2018 10:26:22 +0000 (10:26 +0000)]
JAL-2420 don't offer Reveal All over alignment panel
gmungoc [Fri, 30 Nov 2018 10:15:11 +0000 (10:15 +0000)]
JAL-3166 catch NPE if all sequences are hidden
gmungoc [Thu, 29 Nov 2018 15:05:56 +0000 (15:05 +0000)]
JAL-3140 updated IntervalStore jar
gmungoc [Thu, 29 Nov 2018 10:04:24 +0000 (10:04 +0000)]
JAL-3140 named tagged version of intervalstore.jar
gmungoc [Thu, 29 Nov 2018 09:42:43 +0000 (09:42 +0000)]
JAL-3140 NCList now via IntervalStore library
gmungoc [Wed, 28 Nov 2018 15:22:28 +0000 (15:22 +0000)]
JAL-3164 redraw complement overview on hide columns
gmungoc [Wed, 28 Nov 2018 12:01:17 +0000 (12:01 +0000)]
JAL-3158 additional calls to reset 'selection changed' flag after update
gmungoc [Tue, 27 Nov 2018 16:21:06 +0000 (16:21 +0000)]
JAL-3163 only log missing message keys once each
gmungoc [Mon, 26 Nov 2018 16:24:32 +0000 (16:24 +0000)]
JAL-3162 only allow start <= end while modifying
hansonr [Mon, 26 Nov 2018 12:29:29 +0000 (06:29 -0600)]
jsSlider null issue (was missing "this.")
hansonr [Mon, 26 Nov 2018 12:19:52 +0000 (06:19 -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 [Mon, 26 Nov 2018 12:19:19 +0000 (06:19 -0600)]
missing submenu fix
gmungoc [Mon, 26 Nov 2018 10:44:56 +0000 (10:44 +0000)]
JAL-3032 make JS properties conditional on Jalview.isJS()