jalview

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JAL-3196 tidying repo

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    /gradle/jalview/jalview_getdown.install4j
JAL-3202 reduced scope of rendering flags

JAL-3202 reduced scope of rendering flags

JAL-3196 tidying for demo

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    /getdown/getdown-core-1.8.3-SNAPSHOT.jar
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    /getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar
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    /getdown/lib/getdown-launcher.jar
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    /gradle/jalview/jalview_getdown.install4j
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    /resources/images/jalview_logo_background_getdown-640x480.png
JAL-3202 discard zero percentages in extracted profile

Conflicts:

src/jalview/renderer/AnnotationRenderer.java

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    /src/jalview/analysis/AAFrequency.java
JAL-3202 discard zero percentages in extracted profile

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    /src/jalview/analysis/AAFrequency.java
JAL-3196 deleting old file

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    /gradle/jalview/OLD_build.gradle
JAL-3196 fixed getdown progress bar position

JAL-3196 Substantial addition of getdown automation in getdown, and new getdown-based launchers packaged by install4j

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    /getdown/files/resource/jalview_logo_background_getdown-640x480.png
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    /getdown/files/resource/jalview_logo_background_getdown-progress.png
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    /gradle/jalview/build.gradle
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    /gradle/jalview/jalview_getdown.install4j
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    /resources/images/jalview_logo_background_getdown-640x480.png
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    /resources/images/jalview_logo_background_getdown-progress.png
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    /resources/images/jetset_jalview_splash.bmp
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    /resources/images/jetset_jalview_splash.png
JAL-3201 JAL-2386 don't pre-select 'apply to all groups'

JAL-3201 group colour schemes distinct instances

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    /test/jalview/gui/AlignViewportTest.java
JAL-3196 new background image

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    /resources/images/jalview_logo_background_fade-640x480.png
JAL-3032 Jalview (as JS) parse query params to main arguments

JAL-3032 JalviewJS2 converts url query parameters to 'applet' args

JAL-3200 fast lookup of DSSP3 notation

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    /test/jalview/schemes/ResiduePropertiesTest.java
JAL-3196 some changes

JAL-3198 don't recalculate group conservation for Id Panel selection

JAL-3198 SequenceGroup 'bulk constructor' without duplicates check

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    /src/jalview/datamodel/SequenceGroup.java
JAL-3196 Initial addition of getdown

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    /getdown/files/getdown-launcher.jar
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    /getdown/files/getdown.txt
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    /getdown/getdown-core-1.8.3-SNAPSHOT.jar
JAL-3196 changed test Launcher to default to maxMem

JAL-3196 extra output file used for gradle incremental builds

JAL-3196 updates to install4j config

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    /resources/images/jalview_logo_background_fade-small.png
JAL-2915 don't recalculate Overview on scroll to position, ever!

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    /src/jalview/gui/AlignmentPanel.java
JAL-2738 don't set AF as feature score

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    /test/jalview/io/vcf/VCFLoaderTest.java
JAL-3141 improved message for asking whether to delete files (file modification time and size added to info to help user decide

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    /resources/lang/Messages_es.properties
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