hansonr [Tue, 15 Oct 2019 16:02:16 +0000 (11:02 -0500)]
JAL-3442 (Aug 28 commit) option to use/not use cache
hansonr [Tue, 15 Oct 2019 15:54:53 +0000 (10:54 -0500)]
Commit 113cc13-2019.09.28 with added transparency fix
hansonr [Wed, 28 Aug 2019 05:27:09 +0000 (00:27 -0500)]
JalviewJS2 optional headless, output
commented out unless desired for testing
hansonr [Wed, 28 Aug 2019 05:25:48 +0000 (00:25 -0500)]
JAL-3253-applet JAL-3423 Windows TestNG
FeatureColourFinderTest error only in batch mode
hansonr [Wed, 28 Aug 2019 05:12:34 +0000 (00:12 -0500)]
JAL-3253-applet JAL-3423 Windows TestNG
SeqPanelTest error only in batch mode
hansonr [Wed, 28 Aug 2019 04:52:24 +0000 (23:52 -0500)]
JAL-3253-applet JAL-3423 Windows TestNG
mac CTRL test is only for Macs.
hansonr [Wed, 28 Aug 2019 04:51:43 +0000 (23:51 -0500)]
JAL-3253-applet JAL-3423 Windows TestNG
Bug found in wrap tool tip (also in Jalview-Develop) due to some
messages having only one of <html> or </html> and some having neither
but still having <br> (potentially)
hansonr [Wed, 28 Aug 2019 04:49:52 +0000 (23:49 -0500)]
JAL-3253-applet JAL-3423 Windows TestNG
Bob bug found in IntervalStore-noNCList
hansonr [Wed, 28 Aug 2019 04:49:16 +0000 (23:49 -0500)]
note that identifier can be null, resulting in a null pointer exception
hansonr [Wed, 28 Aug 2019 04:48:24 +0000 (23:48 -0500)]
JAL-3253-applet JAL-3423 Windows TestNG
Bob Bug found in boolean testing of FeatureRendererModel
hansonr [Wed, 28 Aug 2019 04:46:52 +0000 (23:46 -0500)]
JAL-3253-applet JAL-3423 Windows TestNG
CommandLineOperations indicates absolute file path; adding output file
option to JavaScript
hansonr [Wed, 28 Aug 2019 04:41:23 +0000 (23:41 -0500)]
JAL-3253-applet JAL-3423 Windows TestNG
- PDBEntry file name needs to normalize \ and /.
hansonr [Wed, 28 Aug 2019 00:24:39 +0000 (19:24 -0500)]
TestNG find for JAL-3253-applet
hansonr [Tue, 27 Aug 2019 23:25:22 +0000 (18:25 -0500)]
JAL-3253-applet JAL-3424 headless fix for Windows
hansonr [Tue, 27 Aug 2019 22:18:24 +0000 (17:18 -0500)]
JAL-3253-applet JAL-3424 headless fix for Windows
hansonr [Tue, 27 Aug 2019 03:21:49 +0000 (22:21 -0500)]
hard-codes workingDir for TestNG for unknown necessity.
hansonr [Tue, 27 Aug 2019 03:13:27 +0000 (22:13 -0500)]
developer note pnly
*
* BH Note: It is critical that any call to
* AlignViewportI.setGlobalColourScheme is followed closely, if not
* immediately, by a call to AlignPanel.repaint(true, true) so that
the
* overview is updated. When that happens, the sequence overview color
caches
* are cleared.
*
hansonr [Tue, 27 Aug 2019 03:12:33 +0000 (22:12 -0500)]
JAL-3397 JAL-3253-applet
TEMPORARY disabling of NCList due to incompatibility with API in TestNG.
hansonr [Tue, 27 Aug 2019 03:11:02 +0000 (22:11 -0500)]
JAL-3253-applet no-NCList IntervalStore fixes
hansonr [Tue, 27 Aug 2019 03:05:31 +0000 (22:05 -0500)]
JAL-3423 testNG fixes for Windows
- \r\n, slightly differerent font metrics
hansonr [Mon, 26 Aug 2019 18:42:31 +0000 (13:42 -0500)]
JAL-3423 testNG fix for revised tooltip html format
hansonr [Mon, 26 Aug 2019 17:40:45 +0000 (12:40 -0500)]
Transpiler update fixes nuisance null-pointer error message when .j2s is
set to disabled.
hansonr [Mon, 26 Aug 2019 17:39:46 +0000 (12:39 -0500)]
JAL-3423 TestNG test bugs
PDBEntry needs to normalize file names under Windows, particularly for
TestNG tests.
hansonr [Mon, 26 Aug 2019 17:38:49 +0000 (12:38 -0500)]
JAL-3423 TestNG test bugs
Cache logger not initializing early enough for some TestNG tests.
hansonr [Mon, 26 Aug 2019 17:35:04 +0000 (12:35 -0500)]
JAL-3422 JAL-3253-applet
SwingJS-site.zip fix for FontChooser combobox missing all text and
dropdown.
Jim Procter [Wed, 21 Aug 2019 09:23:35 +0000 (10:23 +0100)]
Merge branch 'Jalview-JS/jim/JAL-3253-JAL-3418' into Jalview-JS/JAL-3253-applet
Jim Procter [Wed, 21 Aug 2019 09:15:38 +0000 (10:15 +0100)]
JAL-3235 -Dtestng-verbosity=10 to trace execution of TestNG tests
Jim Procter [Wed, 21 Aug 2019 09:15:01 +0000 (10:15 +0100)]
JAL-3253 fix scrollTo termination check.
Jim Procter [Tue, 20 Aug 2019 17:49:53 +0000 (18:49 +0100)]
JAL-3418 debug testng execution - verbosity=10
hansonr [Sat, 17 Aug 2019 14:26:33 +0000 (09:26 -0500)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet
hansonr [Fri, 16 Aug 2019 17:49:26 +0000 (12:49 -0500)]
JAL-3253-applet JAL-3397 delete fix
hansonr [Fri, 16 Aug 2019 17:49:26 +0000 (12:49 -0500)]
JAL-3253-applet JAL-3414 Display Settings dialog slow to open
SwingJS-site.zip
corrects code in JSDialog that called parent.addNotify() every time, not
just before it has been connected.
hansonr [Fri, 16 Aug 2019 12:43:39 +0000 (07:43 -0500)]
JAL-3253-applet JAL-3397 JAL-3383 fast IntervalStore for JavaScript
fully commented and cleaned code
hansonr [Fri, 16 Aug 2019 04:09:33 +0000 (23:09 -0500)]
JAL-3253-applet JAL-3397 JAL-3383 fast IntervalStore for JavaScript
needs testing in JavaScript
hansonr [Thu, 8 Aug 2019 02:17:21 +0000 (21:17 -0500)]
JAL-3401 JAL-3253-applet
fixes too-early multiple calls to AlignPanel.repaint() and, via repaint
manager to the desktop, also SeqCanvas.paintComponent. See
Jalview2XML.java
hansonr [Thu, 8 Aug 2019 00:34:13 +0000 (19:34 -0500)]
Platform.timeCheck - just resetting duration for
reset/set-mark..set-mark/get sequence.
hansonr [Thu, 8 Aug 2019 00:33:02 +0000 (19:33 -0500)]
JAL-3383 JAL-3253-applet shortcut binary search when position is out of
range.
hansonr [Tue, 6 Aug 2019 21:25:13 +0000 (16:25 -0500)]
JAL-3383 JAL-3397 JAL-3253-applet IntervalStore options
In SequenceFeatures:
INTERVAL_STORE_NCLIST (default for Java)
- no changes from previous
INTERVAL_STORE_NONCLIST (Java option)
- uses intervalstore.nonc.IntervalStore
- optional "lazy" just-in-time sorting
- passes the following TestNG tests:
IntervalStoreJ.test.intervalstore.nonc...
NoNCListBuilderTest.java
NoNCListIntervalIteratorTest.java
NoNCListIntervalStoreTest.java
NoNCListIntervalTest.java
NoNCListLoadTest.java
NoNCListRandomisedTest.java
NoNCListTimingTests.java
test.jalview.datamodel.features...
FeatureStoreNoNCTest.java
FeatureStoreJSTest.java
SequenceFeaturesTest.java
hansonr [Tue, 6 Aug 2019 21:18:36 +0000 (16:18 -0500)]
JAL-3253-applet comments/Overrides only
hansonr [Mon, 5 Aug 2019 14:31:27 +0000 (09:31 -0500)]
JAL-3383 JAL-3253-applet
-adds timing test reports.
hansonr [Mon, 5 Aug 2019 14:19:59 +0000 (09:19 -0500)]
JAL-3383 JAL-3253-applet
-adds equivalent of features.contains()
-timing within 0.5 sec for braf.jvp load of human variants.
hansonr [Sun, 4 Aug 2019 16:04:39 +0000 (11:04 -0500)]
JAL-3383 JAL-3253-applet
possibly a bit faster as a static reference to the Function.
hansonr [Sun, 4 Aug 2019 15:39:36 +0000 (10:39 -0500)]
JAL-3383 JAL-3253-applet
-- Dissociates IntervalStore and BinarySearch from FeatureStoreJS.
-- Adds test FeatureStoreJS
-- cursory timing test in TestNG suggest JS version is 2x faster in
*Java* (TestNG FeatureStoreTest 120 ms vs. FeatueStoreJSTest 66 ms) for
default test.
-- hypothesize that overhead of lambda functions is coming into play
here. Needs a more heavy-duty test.
hansonr [Sun, 4 Aug 2019 03:41:20 +0000 (22:41 -0500)]
JAL-3383 JAL-3253-applet
-- Adds FileStoreI interface
-- Makes FileStore.java abstract superclass for FileStoreImpl (for Java)
and FileStoreJS (for JavaScript)
-- Passing all FeatureStoreJSTest TestNG tests
-- Passing all SequenceFeatureTest TestNG tests
-- About 10% faster for Java on TestNG tests.
-- full rendering in < 250 ms for JavaScript -- this is approximately 15
times faster than before I started this experiment.
Platform: timer mark 13.396 0.209 overviewrender 16000 pixels row:14 redraw:false
Platform: timer mark 14.884 0.186 overviewrender 16000 pixels row:14 redraw:false
Platform: timer mark 15.989 0.185 overviewrender 16000 pixels row:14 redraw:false
Platform: timer mark 17.216 0.229 overviewrender 16000 pixels row:14 redraw:false
Platform: timer mark 18.148 0.239 overviewrender 16000 pixels row:14 redraw:false
Platform: timer mark 18.924 0.198 overviewrender 16000 pixels row:14 redraw:false
Platform: timer mark 21.827 0.233 overviewrender 16000 pixels row:14 redraw:false
hansonr [Sun, 4 Aug 2019 03:34:38 +0000 (22:34 -0500)]
JAL-3383 JAL-3253-applet
-- Adds FileStoreI interface
-- Makes FileStore.java abstract superclass for FileStoreImpl (for Java)
and FileStoreJS (for JavaScript)
-- Passing all FeatureStoreJSTest TestNG tests
-- Passing all SequenceFeatureTest TestNG tests
-- About 10% faster for Java on TestNG tests.
-- full rendering in < 250 ms for JavaScript -- this is approximately 15
times faster than before I started this experiment.
Platform: timer mark 13.396 0.209 overviewrender 16000 pixels row:14 redraw:false
Platform: timer mark 14.884 0.186 overviewrender 16000 pixels row:14 redraw:false
Platform: timer mark 15.989 0.185 overviewrender 16000 pixels row:14 redraw:false
Platform: timer mark 17.216 0.229 overviewrender 16000 pixels row:14 redraw:false
Platform: timer mark 18.148 0.239 overviewrender 16000 pixels row:14 redraw:false
Platform: timer mark 18.924 0.198 overviewrender 16000 pixels row:14 redraw:false
Platform: timer mark 21.827 0.233 overviewrender 16000 pixels row:14 redraw:false
hansonr [Sat, 3 Aug 2019 05:07:15 +0000 (00:07 -0500)]
JavaDoc comments; minor code clean-up
hansonr [Sat, 3 Aug 2019 04:57:55 +0000 (23:57 -0500)]
adds comments JAL-3383
hansonr [Sat, 3 Aug 2019 04:26:18 +0000 (23:26 -0500)]
JAL-3383 JAL-3253-applet additional efficiencies; FeatureStore
alternative to IntervalStore
- implemented for JavaScript only (see SequenceFeatures):
boolean useIntervalStore = /**
* @j2sNative false &&
*/
true;
but can be tested in Java and JavaScript by changing either of those to
true/false.
- only requires storage for one sorted array in FeatureSorter:
private SequenceFeature[] orderedFeatureStarts;
and one additional linked-list field pointer in SequenceFeature:
SequenceFeature containedBy
- when running, the position is looked up in the begin-sorted feature
array, and then the containedBy links are simply traversed using:
SequenceFeature sf = findClosestFeature(orderedFeatureStarts, pos);
while (sf != null) {
if (sf.end >= pos)
{
result.add(sf);
}
sf = sf.containedBy;
}
- my preliminary timing tests suggest this is 2x faster than
IntervalStore in JavaScript.
hansonr [Thu, 1 Aug 2019 17:49:09 +0000 (12:49 -0500)]
JAL-3253-applet JAL-3383 Overview
additional int for Color (shader)
fixes problem with JavaScript timing for container resized
hansonr [Thu, 1 Aug 2019 17:14:06 +0000 (12:14 -0500)]
debug comment out
hansonr [Thu, 1 Aug 2019 10:07:19 +0000 (05:07 -0500)]
JAL-3253-applet JAL-3383 Overview speed up -- see Issue comments.
hansonr [Thu, 1 Aug 2019 09:35:29 +0000 (04:35 -0500)]
JAL-3383 minor coding aesthetics and debug messages out
hansonr [Thu, 1 Aug 2019 09:16:27 +0000 (04:16 -0500)]
removes debugging code
hansonr [Wed, 31 Jul 2019 23:57:43 +0000 (18:57 -0500)]
JAL-3383 JAL-3253-applet fixes issue with X+Y scroll of Overview
trashing vertical alignment. Uncertain why, but it is working OK in
Java, where there was only a transient, occasional vertical offset
issue.
hansonr [Wed, 31 Jul 2019 23:54:03 +0000 (18:54 -0500)]
JAL-3392 calculation workers notify Jalview
hansonr [Wed, 31 Jul 2019 23:50:23 +0000 (18:50 -0500)]
JAL-3253 adds simple stacktrace debugging
hansonr [Tue, 30 Jul 2019 19:39:06 +0000 (14:39 -0500)]
JAL-3253-applet SwingJS-site.zip
- improves String.toCharArray$()
- speeds processing by a factor of 3-10 just by using split("") followed
by streamlined array typing.
hansonr [Tue, 30 Jul 2019 19:24:22 +0000 (14:24 -0500)]
JAL-3383 unneeded change
hansonr [Tue, 30 Jul 2019 18:09:40 +0000 (13:09 -0500)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet
hansonr [Mon, 29 Jul 2019 21:05:34 +0000 (16:05 -0500)]
JAL-3253-applet JAL-3383
Significant improvement to Overview rendering. See JAL-3383 issue for
details.
hansonr [Mon, 29 Jul 2019 21:05:34 +0000 (16:05 -0500)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet
hansonr [Mon, 29 Jul 2019 20:34:41 +0000 (15:34 -0500)]
JAL-3383 JAL-3253-applet removes unnecessary updateOverviewImage()
hansonr [Mon, 29 Jul 2019 20:34:41 +0000 (15:34 -0500)]
JAL-3383 JAL-3253-applet Allows for possibility of a sequence caching
its colors for speed; not implemented
hansonr [Mon, 29 Jul 2019 20:33:47 +0000 (15:33 -0500)]
JAL-3383 JAL-3253-applet ScalePanel bug -- should not have to cause an
AlignmentPanel repaint as a result of an Overview range change.
hansonr [Mon, 29 Jul 2019 20:32:06 +0000 (15:32 -0500)]
JAL-3383 JAL-3253-applet FeatureColourFinder avoiding unnec. creation of
image graphics
hansonr [Mon, 29 Jul 2019 20:30:34 +0000 (15:30 -0500)]
JAL-3383 JAL-3253-applet bug in FontChooser calls for full redraw;
should be just a new box.
hansonr [Mon, 29 Jul 2019 20:29:36 +0000 (15:29 -0500)]
JAL-3383 JAL-3253-applet Java8 switches to clarify ViewportRanges
listeners
hansonr [Mon, 29 Jul 2019 20:24:46 +0000 (15:24 -0500)]
JAL-3369 JAL-3253-applet adds embedded dim checking for overview frame
hansonr [Mon, 29 Jul 2019 20:14:51 +0000 (15:14 -0500)]
JAL-3369 JAL-3253-applet adds JS app.showOverview()
hansonr [Mon, 29 Jul 2019 20:09:16 +0000 (15:09 -0500)]
JAL-3387 no-annotation too early
hansonr [Mon, 29 Jul 2019 08:34:57 +0000 (10:34 +0200)]
JAL-3380 allows JalviewJS to get embedded div attributes
hansonr [Mon, 29 Jul 2019 08:31:05 +0000 (10:31 +0200)]
JAL-3379 Javascript applet.app
hansonr [Mon, 29 Jul 2019 08:21:53 +0000 (10:21 +0200)]
JAL-3778 moving Java logging to Platform.
hansonr [Wed, 24 Jul 2019 06:42:25 +0000 (07:42 +0100)]
JAL-3253-applet adds NOMENUBAR, NOSTATUS, NOCALCULATION, SHOWOVERVIEW
adds "overview" name for overview panel.
hansonr [Wed, 24 Jul 2019 05:31:01 +0000 (06:31 +0100)]
JAL-3374 "noannotation" and menu sync
hansonr [Wed, 24 Jul 2019 04:25:57 +0000 (05:25 +0100)]
issue JAL-3373, JAL-3253-applet SwingJS update
sticky tooltip over menu items
hansonr [Fri, 19 Jul 2019 09:13:14 +0000 (10:13 +0100)]
new SwingJS-site.zip fixes menu persistence issues
hansonr [Fri, 19 Jul 2019 09:12:41 +0000 (10:12 +0100)]
JAL-3253 embedded example1
hansonr [Thu, 18 Jul 2019 07:47:10 +0000 (08:47 +0100)]
JAL-3269 ready for testing embedded interface
hansonr [Thu, 18 Jul 2019 06:22:15 +0000 (07:22 +0100)]
JAL-3370 sep ignored in getAlignmentOrderFrom(AlignFrameI alf, String
sep)
hansonr [Thu, 18 Jul 2019 06:15:38 +0000 (07:15 +0100)]
JAL-3269 JAL-3370 JalviewJS interface upgrade
hansonr [Tue, 16 Jul 2019 21:48:23 +0000 (22:48 +0100)]
minor fixes for JComboBox and also fixes issue with menu accelerator
(ESC in this case) not triggered when a non-key-active component has the
focus. (A result of focus traversal now working, with default focus
gained initially.) Upgrade of JTextPane and JEditorPane, but these are
not used in Jalview. Still issues there.
hansonr [Tue, 16 Jul 2019 21:46:06 +0000 (22:46 +0100)]
issue JAL-3368 and JAL-3253-applet
Color names not supported.
gmungoc [Mon, 15 Jul 2019 12:12:47 +0000 (13:12 +0100)]
JAL-3032 fine tuning appearance of button
gmungoc [Mon, 15 Jul 2019 10:49:13 +0000 (11:49 +0100)]
JAL-3345 small tidying
hansonr [Fri, 12 Jul 2019 07:02:25 +0000 (08:02 +0100)]
JAL-3366 JAL-3253-applet
adds RendererPanel default inner size.
hansonr [Wed, 10 Jul 2019 11:24:15 +0000 (12:24 +0100)]
2/2 JAL-3253-applet several fixes in SwingJS only:
JAL-3357 multiline HTML tooltips not wrapping
JAL-3358 tooltips in ComboBoxes
JAL-3359 custom ComboBoxes with detailed event callbacks
adds ToolTip for Search...Find; not perfect.
hansonr [Wed, 10 Jul 2019 08:59:06 +0000 (09:59 +0100)]
1/2 JAL-3253-applet several fixes in SwingJS only:
JAL-3357 multiline HTML tooltips not wrapping
JAL-3358 tooltips in ComboBoxes
JAL-3359 custom ComboBoxes with detailed event callbacks
hansonr [Wed, 10 Jul 2019 08:55:53 +0000 (09:55 +0100)]
JAL-3253-applet JAL-3360 HTML tooltips not trimming properly; need <div>
for sizing in JavaScript
hansonr [Wed, 10 Jul 2019 08:53:56 +0000 (09:53 +0100)]
JAL-3253-applet minor fix to reduce number of times cell renderer is
fired.
hansonr [Tue, 9 Jul 2019 15:19:43 +0000 (16:19 +0100)]
Jal-3357 ISSUE JAL-3253-applet tooltip for PHOSPHORYLATION missing
hansonr [Thu, 4 Jul 2019 16:15:35 +0000 (17:15 +0100)]
JAL-3354 key listener issue JS#213,215
hansonr [Wed, 3 Jul 2019 09:35:29 +0000 (10:35 +0100)]
fixing failure issue in build server
hansonr [Wed, 3 Jul 2019 09:34:44 +0000 (10:34 +0100)]
temp only
hansonr [Tue, 2 Jul 2019 18:34:22 +0000 (20:34 +0200)]
JAL-3346 JAL-3253-applet JS Code issue 131 Carried forward - no
mouseExited in ScalePanel on mouse drag out and right over SeqPanel
border
hansonr [Tue, 2 Jul 2019 18:27:13 +0000 (20:27 +0200)]
JAL-3345 JAL3253 Smoother ScalePanel-based scrolling
hansonr [Tue, 2 Jul 2019 13:31:52 +0000 (15:31 +0200)]
JAL-3253 updated _j2sclasslist.txt, SwingJS-site.zip
hansonr [Tue, 2 Jul 2019 13:29:54 +0000 (15:29 +0200)]
JAL-3253 srcjar_unused/ moved to unused/
hansonr [Tue, 2 Jul 2019 12:35:57 +0000 (14:35 +0200)]
SwingJS-site.zip update after Wuppertal.
hansonr [Tue, 2 Jul 2019 12:35:33 +0000 (14:35 +0200)]
JAL-3253 FeatureTypeSettings use of override paint(g) for "x" button
allows same characterists in Mac and Windows for button background and
border
git://source.jalview.org / jalview.git / log