jalview

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JAL-3730 retry ping before failing; sysout logging changed to Cache.log

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    /src/jalview/ext/ensembl/EnsemblMap.java
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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
JAL-3018 updated reviewed REST version to 12.0

Merge branch 'task/JAL-3597memoryLeakTest' into develop

JAL-3597 Increased heap passmark to <= 45MB and report smallest of failed attempts heap size

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    /test/jalview/gui/FreeUpMemoryTest.java
Merge branch 'task/JAL-3608_property_set_laf_and_tests' into develop

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    /src/jalview/bin/Jalview.java
JAL-3477 Improved command line arguments description in memory.html

JAL-3477 Added -help text for jvmmempc and jvmmemmax. Fixed typo and slight rewording in help/memory.html

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    /help/help/html/features/clarguments.html
JAL-3477 added help documentation for executable jar command line arguments -jvmmempc and -jvmmemmax

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    /help/help/html/features/clarguments.html
Merge branch 'bug/JAL-2983negativeSliderMin' into develop

Conflicts:

src/jalview/gui/FeatureSettings.java

src/jalview/gui/FeatureTypeSettings.java

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    /src/jalview/gui/AnnotationColourChooser.java
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    /src/jalview/gui/AnnotationColumnChooser.java
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    /src/jalview/gui/FeatureTypeSettings.java
JAL-3371 JAL-2983 don't modify 'extent' of slider - this is managed by look and feel

Merge branch 'feature/JAL-3615gzipXfam' into develop

JAL-3615 JAL-2656 missing import after cherrypick

JAL-2656 recognise non-HTTP URI input streams as gzipped by detecting the gzip magic header

JAL-2656 recognise Gzipped file input streams by their content, not their filename

Conflicts:

src/jalview/io/FileParse.java

cherypicked from 2.11.1.1 release patch

JAL-3615 update tests for Rfam/Pfam specific gzip endpoints

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    /test/jalview/ws/dbsources/PfamFullTest.java
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    /test/jalview/ws/dbsources/PfamSeedTest.java
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    /test/jalview/ws/dbsources/RfamFullTest.java
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    /test/jalview/ws/dbsources/RfamSeedTest.java
JAL-3697 show total number of features not shown

JAL-3696 log the error message from the exception to the console

JAL-3695 htsjdk 2.12 -> 2.23 (library change only, no code change. needs gradle refresh in eclipse)

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    /j11lib/htsjdk-2.23.0.jar
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    /j8lib/htsjdk-2.23.0.jar
JAL-3597 slight tidying of code and Javadoc, passmark now heap <= 38MB

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    /test/jalview/gui/FreeUpMemoryTest.java
JAL-1421 last change tidied up properly

JAL-1421 types added to nameHash and nodeHash maps

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    /src/jalview/gui/TreeCanvas.java
JAL-3597 additional references nulled, bug in test corrected

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    /test/jalview/gui/FreeUpMemoryTest.java
JAL-3608 Changes from code review CR-JAL-236

JAL-1424 streamlined message checker, corrected applet lookup keys

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    /src/jalview/appletgui/APopupMenu.java
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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/appletgui/AppletJmol.java
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    /utils/MessageBundleChecker.java
JAL-1424 slight tidying of reporting

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    /utils/MessageBundleChecker.java
JAL-3311 JAL-3141 JAL-3144 tidying obsolete message bundle entries

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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    /src/jalview/fts/core/FTSRestClient.java
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    /src/jalview/gui/VamsasApplication.java
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    /src/jalview/io/VamsasAppDatastore.java
JAL-3518 Spanish text for 'write features'

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    /resources/lang/Messages_es.properties
JAL-3570 JAL-3187 spanish translations for tabbed feature settings

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    /resources/lang/Messages_es.properties
JAL-3570 updated external help links

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    /help/help/html/webServices/AACon.html
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    /help/help/html/webServices/msaclient.html
JAL-2656 JAL-3615 check response headers to test for gzipped url reply

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    /test/jalview/io/FileParseTest.java