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JAL-3446 unused imports removed

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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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JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from the applet branch. AND IT WORKS (sometimes)

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    ./jibble/epsgraphics/EpsGraphics2D.java
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JAL-3210 Barebones gradle/buildship/eclipse. See README

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    ./jibble/epsgraphics/EpsGraphics2D.java
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JAL-3210 Merge branch 'develop' into trialMerge

Conflicts:

.classpath

.project

.settings/org.eclipse.jdt.core.prefs

.settings/org.eclipse.jdt.ui.prefs

build.xml

resources/lang/Messages_es.properties

src/MCview/AppletPDBCanvas.java

src/MCview/Atom.java

src/MCview/PDBCanvas.java

src/jalview/analysis/AAFrequency.java

src/jalview/appletgui/EmbmenuFrame.java

src/jalview/appletgui/OverviewPanel.java

src/jalview/appletgui/SeqPanel.java

src/jalview/bin/Cache.java

src/jalview/bin/Jalview.java

src/jalview/datamodel/DBRefEntry.java

src/jalview/datamodel/Sequence.java

src/jalview/ext/ensembl/EnsemblMap.java

src/jalview/ext/paradise/Annotate3D.java

src/jalview/fts/service/pdb/PDBFTSRestClient.java

src/jalview/gui/Desktop.java

src/jalview/gui/FeatureRenderer.java

src/jalview/gui/FeatureTypeSettings.java

src/jalview/gui/WebserviceInfo.java

src/jalview/io/BackupFiles.java

src/jalview/io/FileLoader.java

src/jalview/jbgui/GDesktop.java

src/jalview/jbgui/GPreferences.java

src/jalview/project/Jalview2XML.java

src/jalview/util/ImageMaker.java

src/jalview/util/Platform.java

src/jalview/ws/SequenceFetcher.java

    • -2
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    ./jibble/epsgraphics/EpsGraphics2D.java
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Merge branch 'develop' into trialMerge

Conflicts:

.classpath

.project

.settings/org.eclipse.jdt.core.prefs

.settings/org.eclipse.jdt.groovy.core.prefs

.settings/org.eclipse.jdt.ui.prefs

build.xml

src/MCview/AppletPDBCanvas.java

src/MCview/Atom.java

src/MCview/PDBCanvas.java

src/jalview/appletgui/EmbmenuFrame.java

src/jalview/appletgui/OverviewPanel.java

src/jalview/appletgui/SeqPanel.java

src/jalview/bin/Jalview.java

src/jalview/ext/paradise/Annotate3D.java

src/jalview/gui/AlignFrame.java

src/jalview/gui/Desktop.java

src/jalview/gui/FeatureRenderer.java

src/jalview/gui/FeatureTypeSettings.java

src/jalview/io/FileLoader.java

src/jalview/jbgui/GDesktop.java

src/jalview/util/ImageMaker.java

src/jalview/util/Platform.java

    • -2
    • +89
    ./jibble/epsgraphics/EpsGraphics2D.java
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JAL-3010 TEMPORARY patch for BioJava bug to save all synonyms

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    ./biojava/nbio/ontology/Synonym.java
unused old SwingJS dependencies

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    • +276
    ./jibble/epsgraphics/EpsDocument.java
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    • +31
    ./jibble/epsgraphics/EpsException.java
    • -0
    • +1492
    ./jibble/epsgraphics/EpsGraphics2D.java
    • -0
    • +169
    ./json/Cookie.java
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    • +86
    ./json/CookieList.java
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    ./json/HTTPTokener.java
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    ./json/JSONArray.java
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    • +45
    ./json/JSONException.java
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    • +542
    ./json/JSONML.java
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    • +2411
    ./json/JSONObject.java
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    • +293
    ./json/JSONPointer.java
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    • +45
    ./json/JSONPointerException.java
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    • +43
    ./json/JSONPropertyIgnore.java
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unused old SwingJS dependencies

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    ./apache/harmony/luni/util/Msg.java
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    ./apache/harmony/luni/util/MsgHelp.java
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    ./apache/tools/bzip2/BZip2Constants.java
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    ./apache/tools/bzip2/CBZip2InputStream.java
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    ./jibble/epsgraphics/EpsDocument.java
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    ./jibble/epsgraphics/EpsException.java
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    ./jibble/epsgraphics/EpsGraphics2D.java
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    ./stackoverflowusers/file/WindowsShortcut.java
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JAL-3130 Replaced deprecated Class.newInstance() with Class.getDeclaredConstructor().newInstance(). Some eclipse fixes have appeared too.

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    ./jibble/epsgraphics/EpsGraphics2D.java
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removes unnecessary org.xml.sax; these are in SwingJS

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    ./xml/sax/SAXNotRecognizedException.java
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    ./xml/sax/SAXNotSupportedException.java
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    ./xml/sax/SAXParseException.java
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Java2Script 3.2.2 upgrade

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    ./apache/harmony/luni/util/MsgHelp.java
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JAL-3048 all image export (alignment, tree, PCA, Jmol) now via ImageExporter and JalviewJS compatible

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removing temp files for build of libjs

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    ./json/simple/parser/ContainerFactory.java
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    ./json/simple/parser/ContentHandler.java
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    ./json/simple/parser/JSONParser.java
    • -90
    • +0
    ./json/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
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    ./json/simple/parser/JSONParser.java
    • -144
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    ./json/simple/parser/Yylex.java
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JAL-3026 adds org.json.simple to srcjars and jsonsimple-site.zip

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    • +0
    ./jibble/epsgraphics/EpsException.java
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    • +0
    ./jibble/epsgraphics/EpsGraphics2D.java
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org.json.simple

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    ./json/simple/ItemList.java
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    ./json/simple/JSONArray.java
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    • +12
    ./json/simple/JSONAware.java
    • -0
    • +132
    ./json/simple/JSONObject.java
    • -0
    • +15
    ./json/simple/JSONStreamAware.java
    • -0
    • +316
    ./json/simple/JSONValue.java
    • -0
    • +4
    ./json/simple/README.txt
    • -0
    • +23
    ./json/simple/parser/ContainerFactory.java
    • -0
    • +110
    ./json/simple/parser/ContentHandler.java
    • -0
    • +533
    ./json/simple/parser/JSONParser.java
    • -0
    • +90
    ./json/simple/parser/ParseException.java
    • -0
    • +688
    ./json/simple/parser/Yylex.java
    • -0
    • +58
    ./json/simple/parser/Yytoken.java
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update of javajs package; adds org.apache.harmony, org.xml.sax.helpers

File format identified as Fasta

    • -0
    • +311
    ./apache/harmony/luni/util/ExternalMessages.properties
    • -0
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    ./apache/harmony/luni/util/ExternalMessages.properties.js
    • -0
    • +228
    ./apache/harmony/luni/util/Msg.java
    • -0
    • +124
    ./apache/harmony/luni/util/MsgHelp.java
    • -0
    • +109
    ./apache/tools/bzip2/BZip2Constants.java
    • -0
    • +1063
    ./apache/tools/bzip2/CBZip2InputStream.java
    • -0
    • +21
    ./apache/tools/bzip2/CBZip2InputStreamFactory.java
    • -0
    • +141
    ./apache/tools/bzip2/CRC.java
    • -0
    • +193
    ./xml/sax/AttributeList.java
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    • +257
    ./xml/sax/Attributes.java
    • -0
    • +419
    ./xml/sax/ContentHandler.java
    • -0
    • +117
    ./xml/sax/DTDHandler.java
    • -0
    • +232
    ./xml/sax/DocumentHandler.java
    • -0
    • +119
    ./xml/sax/EntityResolver.java
    • -0
    • +139
    ./xml/sax/ErrorHandler.java
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Update spike branch to latest (HMMSearch file chooser arg)

    • -0
    • +215
    ./stackoverflowusers/file/WindowsShortcut.java
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The method that begins where the comment is - see context - transferFromDropTarget

The method that begins where the comment is - see context - transferFromDropTarget

nope - it might work with them though (since it didn't work for URL links!)

nope - it might work with them though (since it didn't work for URL links!)

which method ?

which method ?

Same behaviour I would expect, since file drags are covered by existing code in the drag handler, and this code doesn't seem to get called at all. FYI: JAL-510 covers doing sensible things when dr...

Same behaviour I would expect, since file drags are covered by existing code in the drag handler, and this code doesn't seem to get called at all.

FYI: JAL-510 covers doing sensible things when dragging a directory - we don't do anything right now as you noticed.

What happens if you drag a directory to Jalview Desktop? Mac: exception thrown by IdentifyFile / FileParse "FILE IS A DIRECTORY". Windows: ?

What happens if you drag a directory to Jalview Desktop?
Mac: exception thrown by IdentifyFile / FileParse "FILE IS A DIRECTORY".
Windows: ?

Has this been tested for Windows symbolic link files as well as for URLs?

Has this been tested for Windows symbolic link files as well as for URLs?

Would like some Javadoc to describe what this method does (and doesn't?) handle

Would like some Javadoc to describe what this method does (and doesn't?) handle