jalview

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JAL-3141 Sensible refactoring for confirming deleting 'newer' old backup files

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    /resources/lang/Messages_es.properties
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    /src/jalview/io/BackupFiles.java
JAL-3187 handle no mapping / complement features without NPE

Merge branch 'feature/JAL-3143ensemblJSON' into feature/JAL-3187linkedFeatures

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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
JAL-3187 read peptide variant from CSQ:HGVSp if present (VCF/VEP data)

Merge branch 'feature/JAL-3187linkedFeatures' into merge/JAL-3187_JAL-3010

Conflicts:

src/jalview/gui/FeatureSettings.java

src/jalview/renderer/seqfeatures/FeatureRenderer.java

JAL-3187 hacks to get peptide variant in to Jmol hover tooltip

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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/datamodel/MappedFeatures.java
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    /src/jalview/ext/jmol/JalviewJmolBinding.java
JAL-3187 reset ViewStyle on Cancel in FeatureSettings

JAL-3141 User warning when deleting old backup files that are newer than the previous backup file

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    /resources/lang/Messages_es.properties
JAL-3141 re-order deletion of old files and check lastModified times with their replacements

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    /resources/lang/Messages_es.properties
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    /src/jalview/io/BackupFiles.java
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    /src/jalview/jbgui/GPreferences.java
Merge branch 'features/JAL-3010ontologyFeatureSettings' into merge/JAL-3187_JAL-3010

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    /src/jalview/gui/FeatureSettings.java
JAL-3010 getColumnClass() never return null

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    /src/jalview/gui/FeatureSettings.java
JAL-3010 getColumnClass() never return null

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    /src/jalview/gui/FeatureSettings.java
JAL-3141 Added warning/confirmation when suffixReverse is changed without changing suffixTemplate or suffixDigits (Bad Things might happen to previous backup files)

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    /resources/lang/Messages_es.properties
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    /src/jalview/jbgui/GPreferences.java
JAL-3141 Moved 'Previously saved scheme' combo box preference out to 'Cancel changes' button. Tidied up the Summary box display.

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    /resources/lang/Messages_es.properties
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    /src/jalview/jbgui/GPreferences.java
JAL-3187 'on top' optional for complementary features

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    /src/jalview/gui/FeatureSettings.java
JAL-3187 'on top' optional for complementary features

Conflicts:

src/jalview/gui/FeatureSettings.java

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    /src/jalview/gui/FeatureSettings.java
JAL-3196 Changes install4jHomeDir depending on Mac or Linux *needs improvingadd build.gradle

Merge branch 'features/JAL-3010ontologyFeatureSettings' into merge/JAL-3187_JAL-3010

Conflicts:

resources/lang/Messages.properties

resources/lang/Messages_es.properties

src/jalview/gui/FeatureSettings.java

src/jalview/gui/FeatureTypeSettings.java

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    /resources/lang/Messages_es.properties
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    /src/jalview/gui/FeatureSettings.java
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    /src/jalview/gui/FeatureTypeSettings.java
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    /test/jalview/gui/AlignFrameTest.java
JAL-3032 default Autosearch to off for JalviewJS

JAL-3195 revised SequenceIdMatcher (tests todo)

JAL-3196 install4j media builder in gradle

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    /gradle/jalview/jalview.install4j
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    /resources/images/jetset_jalview_splash.gif
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    /src/jalview/bin/Launcher.java
JAL-3194 new launcher, use like: java -cp classes:lib/* jalview.bin.Launcher -maxMem

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    /src/jalview/bin/Launcher.java
JAL-3179 pre-install4j config

JAL-3140 updated to latest intervalstore.jar

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    /lib/intervalstore-v0.3.jar
JAL-2738 use GeneLocus extends DBRefEntry to hold chromosomal mappings

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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/datamodel/DBRefEntry.java
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    /src/jalview/datamodel/GeneLocus.java
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    /src/jalview/datamodel/Sequence.java
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    /src/jalview/ext/ensembl/EnsemblGene.java
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    /src/jalview/ext/ensembl/EnsemblLookup.java
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    /src/jalview/ext/ensembl/EnsemblMap.java
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    /src/jalview/project/Jalview2XML.java
latest transpiler and runtime

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    /swingjs/ver/3.2.4/SwingJS-site.zip
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    /swingjs/ver/3.2.4/net.sf.j2s.core.jar
JAL-3032 check enough sequences selected on construction

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    /src/jalview/gui/CalculationChooser.java
Test (passes!) for dialog message truncation

JAL-3048 JS-compatible confirm dialog on delete all

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    /src/jalview/gui/AlignFrame.java
JSON parsing from a StringInputStream

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