hansonr [Mon, 21 Jan 2019 17:39:57 +0000 (11:39 -0600)]
isAMac() -> isAMacAndNotJS(), isWindows() -> isWindowsAndNotJS()
Added Platform.isWin[Right|Middle]Button()
hansonr [Mon, 21 Jan 2019 17:38:23 +0000 (11:38 -0600)]
isAMac() -> isAMacAndNotJS(), isWindows() -> isWindowsAndNotJS()
Added Platform.isWin[Right|Middle]Button()
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()
hansonr [Mon, 21 Jan 2019 16:46:54 +0000 (10:46 -0600)]
removing indirect references to Platform.isAMac()
hansonr [Mon, 21 Jan 2019 16:42:13 +0000 (10:42 -0600)]
comments only
Ben Soares [Mon, 21 Jan 2019 13:51:48 +0000 (13:51 +0000)]
JAL-3141 Fixed tests for new placement of suffix after extension
hansonr [Mon, 21 Jan 2019 06:08:38 +0000 (00:08 -0600)]
fixes popup issue involving invocation from mousePressed event.
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.
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.
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
hansonr [Sat, 19 Jan 2019 13:08:20 +0000 (07:08 -0600)]
menu bug preventing closing - recompiled
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
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....
hansonr [Fri, 18 Jan 2019 08:57:57 +0000 (02:57 -0600)]
canvas line/font/pixel fixes; menu accelerators;
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
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
hansonr [Tue, 15 Jan 2019 19:18:38 +0000 (13:18 -0600)]
removal of AlignmentFrame lines
hansonr [Tue, 15 Jan 2019 19:17:16 +0000 (13:17 -0600)]
subimage height error
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 15:04:04 +0000 (15:04 +0000)]
JAL-3186 reorder popup menu slightly
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
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).
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
hansonr [Fri, 11 Jan 2019 04:49:40 +0000 (22:49 -0600)]
SwingJS upgrade
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
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)
hansonr [Fri, 11 Jan 2019 04:46:25 +0000 (22:46 -0600)]
adding (unnecessary, but informative super() call in Desktop
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
gmungoc [Wed, 9 Jan 2019 15:54:50 +0000 (15:54 +0000)]
JAL-3032 stub JS tabbed pane removed as not used
gmungoc [Wed, 9 Jan 2019 15:52:56 +0000 (15:52 +0000)]
JAL-3032 tweak inner/outer class references
gmungoc [Wed, 9 Jan 2019 15:51:57 +0000 (15:51 +0000)]
JAL-3032 refine 'empty status message' test (JS issue 179)
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!
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)
hansonr [Wed, 9 Jan 2019 05:38:31 +0000 (23:38 -0600)]
simplification of FeatureSettings inner classes
No need here for additional private inner variables that cover outer
class's versions of the same thing. No need for a pointer to the outer
class, as "me" is already the "this" of the other class.
Added necessary JTable.repaint() to fix the problem that "stopping"
editing was relying upon the invalidation to be maintained throughout
the modal dialog, but JavaScript cannot keep the thread from doing its
repaints. So in JavaScript, while the modal dialog is loading, the
validate sequence from stopping editing fires. Thus, when the editing
dialog closes, it is already validated for the previous value, and we
need to explicitly repaint the table to see the update.
hansonr [Wed, 9 Jan 2019 05:33:45 +0000 (23:33 -0600)]
comment added in relation to status bar
Ben Soares [Wed, 9 Jan 2019 00:26:07 +0000 (00:26 +0000)]
JAL-3141 Made one more suggested change from code review
Ben Soares [Tue, 8 Jan 2019 23:22:10 +0000 (23:22 +0000)]
JAL-3141 Made some more suggested changes from code review
Ben Soares [Tue, 8 Jan 2019 23:13:08 +0000 (23:13 +0000)]
JAL-3141 Made some suggested changes from code review
gmungoc [Tue, 8 Jan 2019 11:41:22 +0000 (11:41 +0000)]
JAL-3180 Disabled 'By Annotation' group colour menu item
hansonr [Tue, 8 Jan 2019 07:26:16 +0000 (01:26 -0600)]
preliminary KeyListener, CaretListener
not quite working yet
gmungoc [Fri, 4 Jan 2019 16:29:28 +0000 (16:29 +0000)]
JAL-3180 fix By Annotation selection state in colour menu
gmungoc [Fri, 4 Jan 2019 10:32:21 +0000 (10:32 +0000)]
JAL-3181 refactor: extracted buildLinkMenu() for testability
gmungoc [Fri, 4 Jan 2019 08:19:36 +0000 (08:19 +0000)]
JAL-3181 simplified code and test
gmungoc [Thu, 3 Jan 2019 17:11:02 +0000 (17:11 +0000)]
JAL-3181 order link menu items
gmungoc [Thu, 3 Jan 2019 10:28:43 +0000 (10:28 +0000)]
JAL-1889 additional test for clover-added fields
gmungoc [Thu, 3 Jan 2019 09:16:15 +0000 (09:16 +0000)]
JAL-1889 ignore 'synthetic' fields added for jacoco
hansonr [Sat, 29 Dec 2018 04:40:54 +0000 (22:40 -0600)]
JEditorPane <div>....<br><div>
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