BobHanson [Sun, 22 Mar 2020 23:05:55 +0000 (18:05 -0500)]
JAL-3563 fix for SeqCanvasText
not recognizing test server's UI nuance
BobHanson [Sun, 22 Mar 2020 12:59:01 +0000 (07:59 -0500)]
JAL-3563 adds Jalview.setSynchronous() testing
BobHanson [Sun, 22 Mar 2020 11:33:16 +0000 (06:33 -0500)]
JAL-3563 adds Jalview.setSynchronous()
- avoids NullPointerExceptions in CommandLineOperations and
Jalview2xmlTests
- allows headless processes to avoid spawning threads and using
SwingUtilities.invokeLater.
BobHanson [Sat, 21 Mar 2020 23:39:59 +0000 (18:39 -0500)]
JAL-3560 Platform fixes.
BobHanson [Sat, 21 Mar 2020 19:04:29 +0000 (14:04 -0500)]
Platform fix, missing check for jsutil == null
BobHanson [Sat, 21 Mar 2020 18:44:49 +0000 (13:44 -0500)]
JAL-3560 SwingJS FeatureSettings table not clearing when all unchecked
BobHanson [Sat, 21 Mar 2020 14:28:01 +0000 (09:28 -0500)]
JAL-3560 tweak to force use of standard Java HashSet
adds Platform.getOrderedHashSet()
adds Platform.setJavaScriptMapObjectEnabled(boolean enabled)
sets the results from
SequenceFeatures.getFeatureGroups(...)
(for FeatureSettings)
and
SequenceFeatures.getFeatureTypesForGroups(...)
(for SeqCanvas and OverviewCanvas painting)
to be a standard Java HashSet, not using the JavaScript Map object.
Sets the
Platform.getJavaOrderedHashSet()
BobHanson [Sat, 21 Mar 2020 14:05:07 +0000 (09:05 -0500)]
JAL-3560 tweak to force use of standard Java HashSet
adds Platform.getOrderedHashSet()
adds Platform.setJavaScriptMapObjectEnabled(boolean enabled)
sets the results from SequenceFeatures.getFeatureTypesForGroups(...) to
be a standard Java HashSet, not using the JavaScript Map object.
BobHanson [Fri, 20 Mar 2020 05:42:16 +0000 (00:42 -0500)]
JAL-3560 additional _j2sclasslist.txt fix
BobHanson [Fri, 20 Mar 2020 05:38:37 +0000 (00:38 -0500)]
automated code fix
noting unnecessary use of new String("").
BobHanson [Fri, 20 Mar 2020 05:37:20 +0000 (00:37 -0500)]
JAL-3560 adds swingjs/api/JSUtilI.js interface to _j2sclasslist.txt
BobHanson [Fri, 20 Mar 2020 05:18:41 +0000 (00:18 -0500)]
JAL-3560 SwingJS upgrade
- JViewport, JTableUI fixing Graphics.setClip problem
- new JSUtilI interface
BobHanson [Fri, 20 Mar 2020 05:16:36 +0000 (00:16 -0500)]
JAL-3560 rewritten Platform with JSUtilI interface
BobHanson [Fri, 20 Mar 2020 05:13:48 +0000 (00:13 -0500)]
comment only
BobHanson [Fri, 20 Mar 2020 05:13:28 +0000 (00:13 -0500)]
debug comments removed
BobHanson [Fri, 20 Mar 2020 05:12:33 +0000 (00:12 -0500)]
JAL-3560 avoiding Graphics.setClip
Now that Graphics.setClip is supported, it is important to avoid it
whenever possible. It requires a full run back through the graphics
stack and return twice in order to clear the clip and reset it with all
other characteristics of the graphics state intact. This was
particularly notable in JViewport, creating very sluggish handling of
FeatureSettings, particularly in Firefox.
BobHanson [Thu, 19 Mar 2020 13:15:46 +0000 (08:15 -0500)]
SwingJS runtime update 3.2.9-v1b
- mostly fixes from recent SwingJS work involving
-- expanded FileSystem and temp file management
-- super-fast HashMap (faster than Java!), HashTable,
StringBuilder, StringBuffer, NumberFormat, DecimalFormat
-- improved ResourceBundle
-- full Locale information
-- additional BufferedImage/ColorModel/Raster support
- fixes temp files not cached (JSTempFile, for Jmol)
- fixes AbstractStringBuilder.replace() typo
- reverts recent HashSet acceleration due to Jalview
using String.hashCode() for display order of features
BobHanson [Thu, 19 Mar 2020 13:08:02 +0000 (08:08 -0500)]
JAL-3560 moving JS-specific code to Platform, fix Platform.streamToFile
BobHanson [Thu, 19 Mar 2020 13:06:43 +0000 (08:06 -0500)]
JAL-3560 better build xml names
BobHanson [Thu, 19 Mar 2020 01:44:42 +0000 (20:44 -0500)]
jmol.app.zip and SwingJS-site.zip; java2script 3.2.9-v1b
BobHanson [Wed, 18 Mar 2020 17:59:23 +0000 (12:59 -0500)]
Java 11/Gradle 2.5 upgrade
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)
gmungoc [Thu, 26 Sep 2019 15:36:29 +0000 (16:36 +0100)]
JAL-3383 removing colour caching (to a separate branch)
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
git://source.jalview.org / jalview.git / log