jalview

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JAL-3560 Java 11 fix on JAL-3563 moving j11lib set up to top

JAL-3563 Bamboo testing

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    /test/jalview/gui/SeqCanvasTest.java
bamboo tests

    • -36
    • +7
    /test/jalview/gui/SeqCanvasTest.java
JAL-3563 Bamboo test with detail

JAL-3563 Bamboo test for range 3 instead of 13

    • -4
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    /test/jalview/gui/SeqCanvasTest.java
resetting Discoverer

JAL-3563 more tests for Bamboo

JAL-3563 tests in SeqCanvasTest

mostly just minor differences in font metrics

    • -6
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    /test/jalview/gui/SeqCanvasTest.java
JAL-3563 for merging to JAL-3253-applet

More Jalview.isSynchronized(), Jalview.execRunnable(), and

Jalview.execThread()

    • -9
    • +7
    /src/jalview/bin/JalviewAppLoader.java
JAL-3563 for merging to JAL-3253-applet

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    /test/jalview/bin/CommandLineOperations.java
JAL-3563 fix for SeqCanvasText

not recognizing test server's UI nuance

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    /test/jalview/gui/SeqCanvasTest.java
JAL-3563 adds Jalview.setSynchronous() testing

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    /test/jalview/bin/CommandLineOperations.java
JAL-3563 adds Jalview.setSynchronous()

- avoids NullPointerExceptions in CommandLineOperations and

Jalview2xmlTests

- allows headless processes to avoid spawning threads and using

SwingUtilities.invokeLater.

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    /src/jalview/project/Jalview2XML.java
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    /test/jalview/bin/CommandLineOperations.java
JAL-3560 Platform fixes.

Platform fix, missing check for jsutil == null

JAL-3560 SwingJS FeatureSettings table not clearing when all unchecked

    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
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()

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.

    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.9/net.sf.j2s.core-j11.jar
    • binary
    /swingjs/ver/3.2.9/net.sf.j2s.core.jar
JAL-3560 additional _j2sclasslist.txt fix

automated code fix

noting unnecessary use of new String("").

    • -2
    • +1
    /src/jalview/io/ModellerDescription.java
JAL-3560 adds swingjs/api/JSUtilI.js interface to _j2sclasslist.txt

JAL-3560 SwingJS upgrade

- JViewport, JTableUI fixing Graphics.setClip problem

- new JSUtilI interface

    • -0
    • +10
    /swingjs/ver/3.2.9-j11/DEV_NOTES.txt
    • binary
    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
    • -0
    • +412
    /swingjs/ver/3.2.9-j11/_j2sclasslist.txt
    • binary
    /swingjs/ver/3.2.9-j11/net.sf.j2s.core.jar
    • -0
    • +1
    /swingjs/ver/3.2.9-j11/timestamp
    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
JAL-3560 rewritten Platform with JSUtilI interface

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    /src/jalview/util/Platform.java
    • -0
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    /src/swingjs/api/JSUtilI.java
    • -0
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    /src/swingjs/api/js/HTML5Applet.java
comment only

debug comments removed

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.

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

    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
JAL-3560 moving JS-specific code to Platform, fix Platform.streamToFile

JAL-3560 better build xml names

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    • +125
    /build-2-core.xml
jmol.app.zip and SwingJS-site.zip; java2script 3.2.9-v1b

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    /swingjs/net.sf.j2s.core-j11.jar
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    /swingjs/ver/3.2.7/DEV_NOTES.txt
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    /swingjs/ver/3.2.7/SwingJS-site.zip
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    /swingjs/ver/3.2.7/_j2sclasslist.txt
    • binary
    /swingjs/ver/3.2.7/net.sf.j2s.core.jar
    • -0
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    /swingjs/ver/3.2.7/timestamp
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    /swingjs/ver/3.2.8/DEV_NOTES.txt
    • binary
    /swingjs/ver/3.2.8/SwingJS-site.zip
    • -0
    • +412
    /swingjs/ver/3.2.8/_j2sclasslist.txt
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