jalview

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Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet

JAL-3070 set calcId and autocalculated flags for annotation returned by the service

JAL-3210 Two fixed tests (previously not compiling)

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    /test/jalview/ws/SequenceFetcherTest.java
JAL-3210 Two fixed tests (previously not compiling)

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    /test/jalview/ws/SequenceFetcherTest.java
Revert "JAL-3210 Moving j2s components around"

This reverts commit ea88f37133ba49aca6cd7bf0cc4242c0594cebf1.

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    /site-resources/examples/PF00111_seed.stk
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    /site-resources/examples/rna_ss_test.stk
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JAL-3210 Moving j2s components around

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    /site-resources/examples/PF00111_seed.stk
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    /site-resources/examples/jaxbtest.jvx
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    /site-resources/examples/rna_ss_test.stk
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JAL-3210 Moving j2s components around

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    /site-resources/examples/PF00111_seed.stk
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    /site-resources/examples/jaxbtest.jvx
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    /site-resources/examples/rna_ss_test.stk
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Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet

JAL-3444 missed commit of removal of object creation test.

Merge branch 'tasks/JAL-3070_wsinterfaces' into alpha/JAL-3066_Jalview_212_slivka-integration

JAL-3383 javadoc

JAL-3070 registerWorker start its thread automatically, so don’t also call startWorker !

JAL-3454 tidy comments

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    /src/jalview/io/AppletFormatAdapter.java
JAL-3070 use object identity equivalence for lists of workers and Cache.log.debug messages

JAL-3444 translucent overview

- oops, that broke Java!

JAL-3444 translucent overview

- was missing 2nd isJS block

- JS was setting pixel background to white instead of defaultColour

prior to transparent color painting

JAL-3456 re-use of existing jar files

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JAL-3456 Some task improvements for use in Eclipse as IDE

JAL-3456 Some task improvements for use in Eclipse as IDE

JAL-3066 Read parameters directly from args list allowing for multiple values.

Update slivka-client library: multiple form field values.

JAL-3066 Fix log files retrieval.

JAL-3456 fixed some backticks in README.md

JAL-3210 JAL-3456 Mothballing work done on using goomph for jalviewjs build

JAL-3210 JAL-3456 Mothballing work done on using goomph for jalviewjs build

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    /TODO/org.eclipse.jdt.launching.prefs
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

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    /src/jalview/project/Jalview2XML.java
JAL-3210 replacing j11lib/Jmol-14.29.17-no_netscape.jar with unsigned version. Temporary fix

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    /j11lib/Jmol-14.29.17-no_netscape.jar
JAL-3210 removed netscape.javascript objects from Jmol-14.29.17.jar to avoid blocking Java 11 clash with jdk.jsobject Java 11 module

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    /j11lib/Jmol-14.29.17-no_netscape.jar
JAL-3210 removed eclipse project, classpath and core settings files from branch. Now generate these (once only) with 'gradle eclipse'.

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    /.settings/org.eclipse.jdt.core.prefs
JAL-3436 debug comments out in JSPopupMenuUI.js

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    /swingjs/ver/3.2.4/SwingJS-site.zip