jalview

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JAL-3446 adds Jmol viewer embedding.

JAL-3446 adds Jmol viewer embedding.

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    /src/jalview/api/JalviewJSApp.java
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    /src/jalview/bin/JalviewJSApi.java
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    /src/jalview/datamodel/PDBEntry.java
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    /src/jalview/gui/AlignmentPanel.java
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    /src/jalview/gui/StructureChooser.java
Jmol 15.1.3 rebuilt

JAL-3379 JalviewJS-API specs - preliminary

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    /doc/JalviewJS-API.md
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    /src/jalview/api/JalviewJSApp.java
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    /src/jalview/bin/JalviewJSApi.java
JAL-3446 embedded file for proper name matching

web app name "Jalview"

div id="Jalview-desktop-div"

So whatever name you give the applet must match the div tags.

Previously, the div name was associated with a different name,

Info.j2sAppID, or something like that. This is much more sensible.

Just don't name it "jalview", because that is a package name!

JAL-3446 UrlDownloadClient and Test

- moving download to Platform

- trivializing JavaScript method

- expanding SwingJS to allow for nio methods

Note: SwingJS preserves byte[] in the File, Path, or FileOutputStream

objects as well as in J2S._javaFileCache. Because of that, one thing you

have to look out for is stale references. In this case, we have:

temp = new Path(...);

fos = new FileOutputStream(temp.toString);

now two independent pointers both refer to the tmp file.

rbc = new

ReadableByteChannel(url.openStream());

fos.getChannel().transferFrom(rbc);

Now the bytes are in fos's channel, but they are not associated yet with

"tmp".

Files.copy(tmp, outfile);

This wasn't working in JavaScript, because Path tmp was out of date, and

so no bytes were being copied.

Working now, but still far to complicated for the simple operation of

transferring bytes from an InputStream to a File in JavaScript.

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    /src/jalview/ws/utils/UrlDownloadClient.java
JAL-3446 Desktop JS needs getIdentifiersOrgData();

JAL-3446 forgot to escape Java in modified Platform.getAppID

JAL-3446 new Locale("") moved to Platform for review.

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    /src/jalview/util/MessageManager.java
JAL-3446 AlignmentSorter/Test more documentation; bit cleaner code

JAL-3446 AlignmentSorter/Test fixed for instance

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    /src/jalview/analysis/AlignmentSorter.java
JAL-3446 removes all JalviewJSApp dependency from jalview.bin.Jalview; cleans up logic in Jalview.doMain

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    /src/jalview/bin/Jalview.java
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    /src/jalview/jbgui/GStructureViewer.java
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop

Refactoring of Jalview, JalviewAppLoader, JalviewApp, various applet-related interfaces

- makes JalviewJSApp the JavaScript interface "app" class

- removes JS interface from Jalview

- removes JalviewAppLoader and associated duplication of classes

- adds JavaScript selection and "oninit" listeners (untested)

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    /src/jalview/api/JalviewJSApp.java
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    /src/jalview/appletgui/js/JSFunctionExec.java
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    /src/jalview/appletgui/js/JalviewLiteJsApi.java
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    /src/jalview/appletgui/js/JsCallBack.java
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    /src/jalview/appletgui/js/JsSelectionSender.java
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    /src/jalview/appletgui/js/MouseOverListener.java
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    /src/jalview/appletgui/js/MouseOverStructureListener.java
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    /src/jalview/bin/AppletParams.java
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    /src/jalview/bin/ArgsParser.java
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    /src/jalview/bin/Jalview.java
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    /src/jalview/bin/JalviewAppLoader.java
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    /src/jalview/bin/JalviewJSApi.java
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    /src/jalview/bin/JalviewLite.java
  1. … 15 more files in changeset.
SwingJS upgrade for JSUtil and JSUtilI

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    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
JAL-3446 new Jmol 15.1.3 jar

- into j8lib

- removes netscape package dependence

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    /j8lib/Jmol-15.1.3.jar
JAL-3225 Minor change to building.md for flexmark, and html output files from the process, handy to have in repo for developers

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    /doc/releaseprocess.html
JAL-3225 Minor change to building.md for flexmark, and html output files from the process, handy to have in repo for developers

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    /doc/releaseprocess.html
JAL-3225 Removed dependency on command line pandoc to convert .md files to .html. Now all files in doc/*.md will get converted to doc/*.html using flexmark within gradle process.

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    /utils/doc/github.css
JAL-3225 Removed dependency on command line pandoc to convert .md files to .html. Now all files in doc/*.md will get converted to doc/*.html using flexmark within gradle process.

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    /utils/doc/github.css
JAL-1191 reduce logging level for warnings

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    /src/jalview/ext/so/SequenceOntology.java
JAL-1191 reduce logging level for warnings

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    /src/jalview/ext/so/SequenceOntology.java
JAL-3446 post-merge unit test fixes, formatting

I see...

adds link for __j2sflags.htm to template.html

updated template.html

_jvjmol.txt

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    /utils/jalviewjs/classlists/_jvjmol.txt
JAL-3664 support for new Locale(""), meaning "not actually a ResourceBundle, just one file (MessageManager)

JAL-3664 support for user.home, user.dir, user

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    /src/jalview/urls/IdentifiersUrlProvider.java
    • binary
    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
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    /utils/jalviewjs/classlists/_j2sclasslist_jmol.txt
JAL-3446 adds SIFTs JAL-3625 SiftsClient

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    /src/jalview/ws/sifts/SiftsClient.java
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    /src/jalview/ws/sifts/SiftsSettings.java
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    /test/jalview/ws/sifts/SiftsClientTest.java