BobHanson [Tue, 7 Apr 2020 22:17:59 +0000 (17:17 -0500)]
JAL 3591 simple coding error in appletgui/SeqPanel
BobHanson [Sat, 4 Apr 2020 16:21:05 +0000 (11:21 -0500)]
JAL-3253 JAL-3032 upgrade to SwingJS-3.2.9.v1e complete 2/2
- random tests failing can be ignored (just thread timing issues)
(AlignmentPanelTest and SeqCanvasTest). Problem is clearly from
concurrent thread interference not likely to affect standard
operation.
- branch can be deleted after merging.
BobHanson [Sat, 4 Apr 2020 16:18:58 +0000 (11:18 -0500)]
JAL-3253 JAL-3032 upgrade to SwingJS-3.2.9.v1e complete
- random tests failing can be ignored (just thread timing issues)
(AlignmentPanelTest and SeqCanvasTest). Problem is clearly from
concurrent thread interference not likely to affect standard
operation.
- branch can be deleted after merging.
BobHanson [Sat, 4 Apr 2020 15:42:22 +0000 (10:42 -0500)]
JAL-3253 JAL-3260 SwingJS-3.2.9.v1e and tests
BobHanson [Tue, 24 Mar 2020 17:03:30 +0000 (12:03 -0500)]
Bamboo test #13
BobHanson [Tue, 24 Mar 2020 17:02:45 +0000 (12:02 -0500)]
unneeded debug message
BobHanson [Mon, 23 Mar 2020 23:20:12 +0000 (18:20 -0500)]
Bamboo test #13 AlignViewport resize and jscrollbar set
removing synchronize I just added.
BobHanson [Mon, 23 Mar 2020 22:35:49 +0000 (17:35 -0500)]
Bamboo stalled?
BobHanson [Mon, 23 Mar 2020 22:20:48 +0000 (17:20 -0500)]
Bamboo test#12.1 adding flushEvents()
BobHanson [Mon, 23 Mar 2020 22:12:54 +0000 (17:12 -0500)]
Bamboo test#12 adding flushEvents()
BobHanson [Mon, 23 Mar 2020 21:15:12 +0000 (16:15 -0500)]
Bamboo test#12 reporting stack trace for ViewportRanges by EventQueue
BobHanson [Mon, 23 Mar 2020 20:53:07 +0000 (15:53 -0500)]
Bamboo test #11 - adding single threaded and thread names
BobHanson [Mon, 23 Mar 2020 20:25:22 +0000 (15:25 -0500)]
Build #8 test showing thread activity on ViewportRanges.endSeq.
BobHanson [Mon, 23 Mar 2020 20:17:11 +0000 (15:17 -0500)]
Bamboo reproducibility test #2 -- only README.txt changed.
In test #1 (build #7) a new test failure occurred in
and SeqCanvasTest showed the very strange message:
SC1 15 [ViewportRange startRes=0 endRes=66 startSeq=0 endSeq=13]
indicating that between the first and the last of these few lines:
av.getRanges().setStartEndSeq(0, 3);
int h = av.getRanges().getVisibleAlignmentHeight();
String s = "";
s += " SC1 " + av.getRanges().getVisibleAlignmentHeight() + " "
+ av.getRanges();
av's range gets set to 13 instead of 3.
BobHanson [Mon, 23 Mar 2020 19:55:32 +0000 (14:55 -0500)]
Bamboo reproducibility test -- only README.txt changed.
BobHanson [Mon, 23 Mar 2020 16:12:09 +0000 (11:12 -0500)]
JAL-3253 JAL-3260 SeqCanvasTest.java should be working
but it makes no sense that just adding System.out messages would make it
do so. ?????
BobHanson [Mon, 23 Mar 2020 15:49:50 +0000 (10:49 -0500)]
Bamboo test #5 - intentional SeqCanvasTest fail for debugging
BobHanson [Mon, 23 Mar 2020 15:11:30 +0000 (10:11 -0500)]
Bamboo test #4 (possibly) - intentional SeqCanvasTest fail for debugging
BobHanson [Mon, 23 Mar 2020 14:47:03 +0000 (09:47 -0500)]
testing in Bamboo; no problem locally
BobHanson [Mon, 23 Mar 2020 14:46:14 +0000 (09:46 -0500)]
bamboo test
BobHanson [Mon, 23 Mar 2020 14:36:14 +0000 (09:36 -0500)]
bamboo test
BobHanson [Mon, 23 Mar 2020 14:34:20 +0000 (09:34 -0500)]
bamboo testing only
BobHanson [Mon, 23 Mar 2020 14:15:14 +0000 (09:15 -0500)]
JAL-3253 SwingJS-32.9.v1e
- Platform upgrade
- SwingJS upgrade
- java2script upgrade
- test fixes for thread concurrency
BobHanson [Mon, 23 Mar 2020 14:00:00 +0000 (09:00 -0500)]
JAL-3253 temporary branch SwingJS upgrade with testNG fixes Java 8
BobHanson [Mon, 2 Dec 2019 16:22:06 +0000 (10:22 -0600)]
JAL-3487 help/splash <html> wrap issue + associated tooltip breaking
BobHanson [Mon, 2 Dec 2019 16:17:51 +0000 (10:17 -0600)]
jmol-app.zip update for java2script 3.2.5.v1
BobHanson [Mon, 2 Dec 2019 16:16:57 +0000 (10:16 -0600)]
JAL-3487 splash/help fix
BobHanson [Wed, 27 Nov 2019 05:46:46 +0000 (23:46 -0600)]
SwingJS transpiler to 3.2.5.v1 (fixed java.util.stream)
- required transpiler fixes and redesign of final variables for stream
objects
- required redesign of $init$ and $static$ to exactly reproduce the full
class loading sequence of (1) method definition with default static
values, (2) superclass-sequenced initialization of static fields (3)
superclass-sequenced initialization of static fields, (4)
superclass-sequenced constructor initialization, in that order, able to
handle any complex situation
-includes fixes for JLabelUI HTML label wrapping issues
BobHanson [Tue, 5 Nov 2019 18:33:23 +0000 (12:33 -0600)]
new transpiler - important!
fixes null pointer exception report for bad package declaration in a
Java file.
BobHanson [Wed, 30 Oct 2019 19:44:46 +0000 (14:44 -0500)]
JAL-3210 new transpiler fixes problem that it could have a null-pointer
exception for comparison to history, where, apparently,
IProject.getProject().getLocation() is null.
BobHanson [Tue, 29 Oct 2019 16:36:24 +0000 (11:36 -0500)]
JAL-3210 .j2s fix to exclude /utils directory
BobHanson [Tue, 29 Oct 2019 16:35:35 +0000 (11:35 -0500)]
JAL-3210 transpiler resource recursion fix for package foo in path
.../foo/.../foo
gmungoc [Thu, 24 Oct 2019 14:42:42 +0000 (15:42 +0100)]
JAL-3453 removed unused Desktop.instanceOnly
hansonr [Wed, 23 Oct 2019 16:58:09 +0000 (11:58 -0500)]
JAL-3463 SwingJS-site.zip update for Thread.sleep()
- throws InterruptedException if called in JavaScript
Mungo Carstairs [Tue, 22 Oct 2019 15:44:03 +0000 (16:44 +0100)]
JAL-3423 more System.lineSeparator() in place of \n
Mungo Carstairs [Tue, 22 Oct 2019 15:35:14 +0000 (16:35 +0100)]
JAL-3423 test coverage
Mungo Carstairs [Tue, 22 Oct 2019 15:30:18 +0000 (16:30 +0100)]
JAL-3253 rename method, add Javadoc
Mungo Carstairs [Tue, 22 Oct 2019 14:50:52 +0000 (15:50 +0100)]
JAL-3423 use System.lineSeparator() in code and tests
Mungo Carstairs [Tue, 22 Oct 2019 13:21:10 +0000 (14:21 +0100)]
JAL-32423 tidying
hansonr [Mon, 21 Oct 2019 12:41:33 +0000 (07:41 -0500)]
JAL-3463 Thread.sleep()
setting sleep() to throw InterruptedException()
hansonr [Mon, 21 Oct 2019 02:53:46 +0000 (21:53 -0500)]
JAL-3463 alert for Thread.sleep; JAL-3378 java.util.logging.Logger
implemented.
gmungoc [Thu, 17 Oct 2019 15:48:06 +0000 (16:48 +0100)]
JAL-3436 null large object reference, tidy method visibility
gmungoc [Thu, 17 Oct 2019 15:10:43 +0000 (16:10 +0100)]
JAL-3436 save filePath from fileObject, tidy updateRecentlyOpened
gmungoc [Thu, 17 Oct 2019 13:02:21 +0000 (14:02 +0100)]
JAL-3436 move/rename/private fields refactoring only
gmungoc [Thu, 17 Oct 2019 12:55:30 +0000 (13:55 +0100)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet
hansonr [Thu, 17 Oct 2019 12:37:03 +0000 (07:37 -0500)]
JAL-3436 broken reader - SwingJS issue (wrong JAL number in last commit)
- java.util.logging.Logger not fully implemented.
- this fix just removes Logger calls from javax.xml classes.
- see JAL-3461 for full fix TODO
gmungoc [Thu, 17 Oct 2019 12:33:44 +0000 (07:33 -0500)]
JAL-3261 broken reader - SwingJS issue
- java.util.logging.Logger not fully implemented.
- this fix just removes Logger calls from javax.xml classes.
- see JAL-3461 for full fix TODO
gmungoc [Thu, 17 Oct 2019 09:35:09 +0000 (10:35 +0100)]
Merge branch 'Jalview-jJS/JAL-3253-applet-JAL-3436' into Jalview-JS/JAL-3253-applet
gmungoc [Thu, 17 Oct 2019 08:59:32 +0000 (09:59 +0100)]
JAL-3368 removed parsing web colours (now on a separate branch)
hansonr [Tue, 15 Oct 2019 09:06:42 +0000 (05:06 -0400)]
JAL-3437 Desktop File...Load Project fails in JalviewJS
- just needed to use the File object rather than the file name in the
call to Jalview2XML.loadJalviewAlign
hansonr [Mon, 14 Oct 2019 14:24:00 +0000 (10:24 -0400)]
adding SwingJS notes for JAR file source in srcjar/
hansonr [Sun, 13 Oct 2019 04:17:13 +0000 (06:17 +0200)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet
hansonr [Sun, 13 Oct 2019 04:17:01 +0000 (06:17 +0200)]
JAL-3459 org.json code removed
- moved to unused/
- supplied by SwingJS-site.zip
- only differences are in a few JavaScript-specific issues
- this move has NO EFFECT on the JavaScript, as SwingJS-site.zip is
unzipped last, overwriting whatever this code would have placed in
site/swingjs/j2s anyway.
gmungoc [Fri, 11 Oct 2019 14:32:44 +0000 (15:32 +0100)]
JAL-3261 no save in setColourPropertyNoSave !
gmungoc [Fri, 11 Oct 2019 14:26:35 +0000 (15:26 +0100)]
JAL-3261 tidy up get/set properties in Cache, Javadoc, tests
gmungoc [Fri, 11 Oct 2019 10:52:03 +0000 (11:52 +0100)]
JAL-3458 redraw alignment and Overview on Cancel in Feature Settings
hansonr [Fri, 11 Oct 2019 09:19:33 +0000 (11:19 +0200)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet
gmungoc [Thu, 10 Oct 2019 14:15:34 +0000 (15:15 +0100)]
JAL-3444 missed commit of removal of object creation test.
gmungoc [Thu, 10 Oct 2019 14:15:34 +0000 (15:15 +0100)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet
gmungoc [Thu, 10 Oct 2019 14:15:26 +0000 (15:15 +0100)]
JAL-3383 javadoc
gmungoc [Thu, 10 Oct 2019 14:14:31 +0000 (15:14 +0100)]
JAL-3454 tidy comments
hansonr [Thu, 10 Oct 2019 13:39:23 +0000 (15:39 +0200)]
JAL-3444 translucent overview
- oops, that broke Java!
hansonr [Thu, 10 Oct 2019 12:41:27 +0000 (14:41 +0200)]
JAL-3444 translucent overview
- was missing 2nd isJS block
- JS was setting pixel background to white instead of defaultColour
prior to transparent color painting
hansonr [Tue, 8 Oct 2019 17:21:24 +0000 (19:21 +0200)]
JAL-3436 fix for reload not reloading files
-- fix for Jalview projects reload where reload was using just the file
name.
-- will test further to ensure this is only in relation to JVP files
hansonr [Tue, 8 Oct 2019 15:36:55 +0000 (17:36 +0200)]
JAL-3436 debug comments out in JSPopupMenuUI.js
hansonr [Tue, 8 Oct 2019 13:25:29 +0000 (15:25 +0200)]
JAL-3453
test to see if the build testing passes this test.
Slight modifications from Mungo's last commit to account for recent
changes in public/private fields, but that is all.
Passing tests on Bob's Windows machine.
hansonr [Mon, 7 Oct 2019 05:57:11 +0000 (07:57 +0200)]
JAL-3453 Some tests require different Desktop constructor
even better, simpler idea:
static boolean instanceOnly
public static Desktop getInstanceOnly()
{
instanceOnly = true;
return getInstance();
}
hansonr [Mon, 7 Oct 2019 05:50:08 +0000 (07:50 +0200)]
JAL-3453 Some tests require different Desktop constructor
better idea:
Desktop.getInstanceOnly()
- creates an instance with no dialog prompting and no frame display,
similar to headless mode, but not fully bypassing the code that
Jalview.headless bypasses.
hansonr [Sun, 6 Oct 2019 19:09:18 +0000 (21:09 +0200)]
JAL-3453 better JavaDoc
hansonr [Sun, 6 Oct 2019 19:03:21 +0000 (21:03 +0200)]
JAL-2114 just noting where the exo-location error presents itself.
hansonr [Sun, 6 Oct 2019 18:59:56 +0000 (20:59 +0200)]
JAL-3454 file loading string-only (testNG) fails for PDB file
hansonr [Sun, 6 Oct 2019 18:56:57 +0000 (20:56 +0200)]
JAL-3453 Some tests require different Desktop constructor
hansonr [Sun, 6 Oct 2019 10:44:23 +0000 (12:44 +0200)]
JAL-3451 setting dimensions for AlignFrame if embedded
hansonr [Sun, 6 Oct 2019 10:43:46 +0000 (12:43 +0200)]
JAL-3451 updated SwingJS-site.zip
hansonr [Sun, 6 Oct 2019 10:42:02 +0000 (12:42 +0200)]
updated _j2sclasslist.txt and _j2sclasslist_jmol.txt
hansonr [Sun, 6 Oct 2019 10:41:22 +0000 (12:41 +0200)]
JAL-3451 JalviewJS embedded mode not resizing
- adds Platform.getDimIfEmbedded(frame, defaultWidth, defaultHeight)
- implemented for AlignFrame, TreePanel, and PCAPanel
hansonr [Sun, 6 Oct 2019 06:53:23 +0000 (08:53 +0200)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet
hansonr [Sun, 6 Oct 2019 06:53:02 +0000 (08:53 +0200)]
Desktop JavaDoc comments for Mungo from gitter discussion
hansonr [Sun, 6 Oct 2019 06:51:50 +0000 (08:51 +0200)]
JAL-3451 older embedding test html removed
Current test is site/jalview_embedded_example1.html
gmungoc [Fri, 4 Oct 2019 14:18:36 +0000 (15:18 +0100)]
JAL-3253 miscellaneous tidying up before merge to JS-develop
gmungoc [Fri, 4 Oct 2019 09:52:42 +0000 (10:52 +0100)]
JAL-3253 extract methods for getConservation/PIDSlider
gmungoc [Fri, 4 Oct 2019 09:31:17 +0000 (10:31 +0100)]
JAL-3345 small simplification
gmungoc [Thu, 3 Oct 2019 14:57:11 +0000 (15:57 +0100)]
JAL-3383 tidy method signature and Javadoc
gmungoc [Thu, 3 Oct 2019 13:36:10 +0000 (14:36 +0100)]
JAL-3253 one global singleton instance of EnsemblInfo suffices
gmungoc [Thu, 3 Oct 2019 12:39:53 +0000 (13:39 +0100)]
JAL-3383 code and unit test tweaks
gmungoc [Thu, 3 Oct 2019 12:39:28 +0000 (13:39 +0100)]
JAL-3444 transparent colour for alignment in JS
gmungoc [Thu, 3 Oct 2019 11:41:09 +0000 (12:41 +0100)]
JAL-3383 removed FeatureStore.getFeatures() as 'breaks encapsulation'
gmungoc [Thu, 3 Oct 2019 10:30:28 +0000 (11:30 +0100)]
JAL-3383 unit tests and bug fix for SequenceFeatures.hasFeatures(type)
gmungoc [Thu, 3 Oct 2019 10:16:12 +0000 (11:16 +0100)]
JAL-3383 tests and fixes for overloaded SequenceFeatures.findFeatures
gmungoc [Thu, 3 Oct 2019 08:31:23 +0000 (09:31 +0100)]
JAL-3442 removing reinstated code
gmungoc [Wed, 2 Oct 2019 07:54:40 +0000 (08:54 +0100)]
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet
gmungoc [Wed, 2 Oct 2019 07:54:29 +0000 (08:54 +0100)]
JAL-3253 JAL-3442 just comment tidying
hansonr [Tue, 1 Oct 2019 21:36:04 +0000 (23:36 +0200)]
JAL-3444 SwingJS-site.zip fix and renderer.seqfeatures fixes
- BufferedImage implements Image.flush() to clear pixel cache;
- JSGraphics2D check for opacity 1 before clearing HTML5 canvas
AlphaComposite
- FeatureColourFinder applies
ifJS() {
g.setColor(Color.white);
g.fillRect(0, 0, 1, 1);
}
so as to clear the HTML5 canvas image before applying any other color.
Also applies
if (Platform.isJS())
{
offscreenImage.flush();
}
just before offscreenImage.getRGB(0,0) to force the image to recreate
its cached pixel from the HTML5 canvas, which is drawn to directly.
hansonr [Tue, 1 Oct 2019 09:57:25 +0000 (11:57 +0200)]
mistakenly uploaded test version
hansonr [Tue, 1 Oct 2019 09:53:36 +0000 (11:53 +0200)]
JAL-3437 issue with
System.getProperty("javax.xml.datatype.DatatypeFactory")
1/2 ?
hansonr [Mon, 30 Sep 2019 00:39:40 +0000 (20:39 -0400)]
moving 10-poxgenomes.bbb and newer IdentifyFile.java to "unused";
revering IdentifyFile.
hansonr [Mon, 30 Sep 2019 00:32:04 +0000 (20:32 -0400)]
reverting FileFormat; moving BSMLFile and related FileFormat to unused
for now.
hansonr [Sun, 29 Sep 2019 04:15:54 +0000 (00:15 -0400)]
JAL-3445 preliminary BSML reader
- was missing org.w3c.xml.Node implementation of getTextContent() in
swingjs.xml.JSXMLNode.java
- now working in JavaScript
hansonr [Sat, 28 Sep 2019 12:55:20 +0000 (08:55 -0400)]
JAL-3445 preliminary BSML reader
- only dna type
- only GENE class features
- only primary strand reading, not complement
- test file put into examples/testdata
- uses javax.xml.parsers.DocumentBuilder
- seems to work in Java; needs TestNG test
- not tested in JavaScript
- for discussion only
gmungoc [Fri, 27 Sep 2019 11:27:35 +0000 (12:27 +0100)]
JAL-3383 get color as int options removed (to separate branch 3443)
git://source.jalview.org / jalview.git / log