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JAL-3446 unused imports removed

  1. … 36 more files in changeset.
Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

resolved conflicts and adapted to some upstream changes. no detailed functional testing as yet (see next commit :) )

Conflicts:

resources/lang/Messages.properties

resources/lang/Messages_es.properties

src/jalview/api/AlignViewportI.java

src/jalview/bin/Jalview.java

src/jalview/datamodel/Sequence.java

src/jalview/datamodel/SequenceI.java

src/jalview/gui/AlignFrame.java

src/jalview/gui/JvSwingUtils.java

src/jalview/gui/OverviewPanel.java

src/jalview/gui/PopupMenu.java

src/jalview/gui/SplitFrame.java

src/jalview/gui/WsJobParameters.java

src/jalview/io/AlignmentFileReaderI.java

src/jalview/io/FileLoader.java

src/jalview/io/StockholmFile.java

src/jalview/jbgui/GAlignFrame.java

src/jalview/jbgui/GPreferences.java

src/jalview/renderer/AnnotationRenderer.java

src/jalview/viewmodel/AlignmentViewport.java

src/jalview/ws/jws2/Jws2Discoverer.java

test/jalview/analysis/AAFrequencyTest.java

test/jalview/gui/AlignFrameTest.java

test/jalview/gui/AlignViewportTest.java

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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.

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JAL-3210 Just about working transpilation. Some work needed for new Java 11 classes

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unused old SwingJS dependencies

    • -0
    • +1541
    ./JSONArray.java
    • -0
    • +45
    ./JSONException.java
    • -0
    • +2411
    ./JSONObject.java
    • -0
    • +293
    ./JSONPointer.java
    • -0
    • +45
    ./JSONPointerException.java
    • -0
    • +43
    ./JSONPropertyIgnore.java
    • -0
    • +47
    ./JSONPropertyName.java
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removing temp files for build of libjs

    • -23
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    ./simple/parser/ContainerFactory.java
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    ./simple/parser/ContentHandler.java
    • -90
    • +0
    ./simple/parser/ParseException.java
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JAL-3026 fixes MigLayout, JSON parser

MiG layout was referencing java.beans only for serialization

JSONParser was using a bitwise syntax for char not supported in

transpiler

SwingJS jalview.javascript.web proxy for WebResources not set up

properly

- JSONParser is working

- PDB REST service call is working

- MiGLayout is loading, but is not laying out properly.

    • -510
    • +588
    ./simple/parser/JSONParser.java
    • -144
    • +214
    ./simple/parser/Yylex.java
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org.json.simple

    • -0
    • +147
    ./simple/ItemList.java
    • -0
    • +381
    ./simple/JSONArray.java
    • -0
    • +12
    ./simple/JSONAware.java
    • -0
    • +132
    ./simple/JSONObject.java
    • -0
    • +15
    ./simple/JSONStreamAware.java
    • -0
    • +316
    ./simple/JSONValue.java
    • -0
    • +23
    ./simple/parser/ContainerFactory.java
    • -0
    • +110
    ./simple/parser/ContentHandler.java
    • -0
    • +533
    ./simple/parser/JSONParser.java
    • -0
    • +90
    ./simple/parser/ParseException.java
    • -0
    • +688
    ./simple/parser/Yylex.java
    • -0
    • +58
    ./simple/parser/Yytoken.java
  1. … 1 more file in changeset.