gmungoc [Thu, 26 Sep 2019 13:52:52 +0000 (14:52 +0100)]
JAL-3383 code tidying
gmungoc [Thu, 26 Sep 2019 13:05:05 +0000 (14:05 +0100)]
JAL-3397 revert loop to forwards order
gmungoc [Thu, 26 Sep 2019 08:52:47 +0000 (09:52 +0100)]
JAL-3397 skip instanceof check for JS's benefit
hansonr [Wed, 25 Sep 2019 07:37:09 +0000 (03:37 -0400)]
JAL-3437 JAL-3253-applet
SwingJS-site update for JVP files scanning using both
PARSE_TOP_LEVEL_ONLY and PARSE_ALL, despite requesting only top level.
clears "JSJAXBUnmarshaller could not associate a field..." message.
hansonr [Tue, 24 Sep 2019 14:23:58 +0000 (10:23 -0400)]
JAL-3253-applet JAL-3439 Preferences issues 1/2
minor tab ui changes in SwingJS
JScrollPane peer issue update in SwingJS
still an issue with Preferences Link tab table row height being set to 6
instead of 16 (suspect font size coming in as 0 for some reason -- will
investigate)
SUGGESTED sizing, positioning changes for Visual tab and overall size.
Issues involve Visual tab checkbox overflow, panel overflow, and Link
"double-click" header overflow
at least in Windows Java and JavaScript.
gmungoc [Tue, 24 Sep 2019 12:40:57 +0000 (13:40 +0100)]
JAL-3140 update intervalstore jar to v1-1 tagged version
hansonr [Tue, 24 Sep 2019 11:43:16 +0000 (07:43 -0400)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet
hansonr [Tue, 24 Sep 2019 11:43:01 +0000 (07:43 -0400)]
JAL-3253-applet JAL-4440 overview 1 pixel off in hidden row view
gmungoc [Tue, 24 Sep 2019 10:24:18 +0000 (11:24 +0100)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet
gmungoc [Tue, 24 Sep 2019 10:24:02 +0000 (11:24 +0100)]
JAL-3383 tidy up NCList and alternatives
hansonr [Tue, 24 Sep 2019 10:21:08 +0000 (06:21 -0400)]
JAL-3253-applet SwingJS fix for CardLayout (menus) broken by
ObjectStreamField overlay
hansonr [Mon, 23 Sep 2019 13:16:49 +0000 (09:16 -0400)]
JAL-3437 JVP reading broken in JS
updated SwingJS-site.zip
transpiler update just involves enhanced j2s.compiler.mode=debug option
hansonr [Mon, 23 Sep 2019 12:26:22 +0000 (08:26 -0400)]
JAL-3436 file...reload not working.
File.isDirectory() returns true in SwingJS.
hansonr [Mon, 23 Sep 2019 12:20:26 +0000 (08:20 -0400)]
JAL-3435 AlignFrame not setting JInternalFrameListener in JS
hansonr [Sun, 22 Sep 2019 16:35:42 +0000 (12:35 -0400)]
JAL-3253-applet JAL-3397
fixing CrossRef equals broken by reversion of changes relating to
equalsInterval.
adds equalsWithParent
hansonr [Sun, 22 Sep 2019 16:00:35 +0000 (12:00 -0400)]
JAL-3253-applet JAL-3397
hansonr [Sun, 22 Sep 2019 15:43:44 +0000 (11:43 -0400)]
JAL-3253-applet JAL-3397
- adds IntervalStore0Test
- adds nonc.IntervalStoreImpl
- adds nonc.IntervalStore0Impl
- sets FeatureStore options to these Impl classes in order to override
sameInterval for SequenceFeature and allow drop in of nonc.IntervalStore
without editing.
hansonr [Sun, 22 Sep 2019 15:03:22 +0000 (11:03 -0400)]
JAL-3253-applet JAL-3397
updates intervalstore.nonc to not use interval.equals() unnecessarily.
hansonr [Sun, 22 Sep 2019 11:31:43 +0000 (07:31 -0400)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet
hansonr [Sun, 22 Sep 2019 11:31:18 +0000 (07:31 -0400)]
test update
gmungoc [Thu, 19 Sep 2019 14:25:37 +0000 (15:25 +0100)]
JAL-3383 minor code tidying and commenting
gmungoc [Thu, 19 Sep 2019 12:59:07 +0000 (13:59 +0100)]
JAL-3210 updated IntervalStoreJ classes in srcjar
Jim Procter [Tue, 10 Sep 2019 15:11:00 +0000 (16:11 +0100)]
JAL-3397 updated intervalstore-site from intervalstore-1.1 source
Jim Procter [Tue, 10 Sep 2019 10:55:30 +0000 (11:55 +0100)]
JAL-3397 update eclipse-js classpath for intervalstore v1.1
gmungoc [Sun, 8 Sep 2019 19:00:14 +0000 (20:00 +0100)]
JAL-3397 timing comparisons for (add then query) IntervalStore
gmungoc [Sat, 7 Sep 2019 14:44:52 +0000 (15:44 +0100)]
JAL-3397 impl.IntervalStore and nonc.IntervalStore unified api
gmungoc [Thu, 5 Sep 2019 09:56:44 +0000 (10:56 +0100)]
JAL-3401 reset 'no repaint' flag after New View / copyAlignPanel
hansonr [Wed, 4 Sep 2019 18:49:36 +0000 (13:49 -0500)]
JAL-3397 final update
hansonr [Wed, 4 Sep 2019 06:27:00 +0000 (01:27 -0500)]
JAL-3429 JAL-3253-applet
OverviewRenderer not implementing hidden column mode using BitSet.
hansonr [Wed, 28 Aug 2019 16:48:01 +0000 (11:48 -0500)]
JAL-3253-applet JAL-3397 switch back to original (MC) IS+NCList after
testing complete.
hansonr [Wed, 28 Aug 2019 16:44:19 +0000 (11:44 -0500)]
JAL-3253-applet JAL-3423
CacheableInputBox direct update mode for testing removes need for wait.
JalviewJS complete PASS on Windows
(other than the usual three Xref fails)
hansonr [Wed, 28 Aug 2019 16:42:46 +0000 (11:42 -0500)]
JAL-3253-applet JAL-3423
AlignFrameTest fixes for timing and lack of ResidueShading conservation
data.
hansonr [Wed, 28 Aug 2019 15:01:03 +0000 (10:01 -0500)]
JAL-3253 JAL-3397 adds (original MC) intervalstore code to implement
modified api interfaces
hansonr [Wed, 28 Aug 2019 14:55:31 +0000 (09:55 -0500)]
JAL-3253-applet JAL-3423 TestNG/Win
hansonr [Wed, 28 Aug 2019 14:54:07 +0000 (09:54 -0500)]
fixes errant debug "return;" in j2sApplet key listener
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
git://source.jalview.org / jalview.git / log