jalview

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Merge branch 'pathc_JAL-1354' into Release_2_8_1_Branch

JAL-1448 reinstate non-locale sensitive code for reading/writing last read date from RSS and Jalview preferences

JAL-1354 use real var-args method signature to avoid ambiguity

JAL-1354 quoted format strings are not substituted

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    • binary
    /forester/java/archaeopteryx_applets.jar
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Merge branch 'JAL-1447' into develop

Merge branch 'JAL-1447' into Release_2_8_1_Branch

JAL-1447 patch to correctly recognise FASTA files containing '*'

test and data for JAL-1447

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    /test/jalview/io/test_fasta_stars.fa
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    /test/jalview/io/test_fasta_stars2.fa
JAL-1447 - more flexible testing for file format Identity detection

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    • binary
    /forester/java/archaeopteryx_applets.jar
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Merge branch 'JAL-1445' into develop Carried over source formatting from 2.8.0b1 release

Conflicts:

src/jalview/analysis/StructureFrequency.java

src/jalview/ext/varna/VarnaCommands.java

src/jalview/gui/AppVarna.java

src/jalview/gui/PopupMenu.java

src/jalview/io/AppletFormatAdapter.java

src/jalview/io/StockholmFile.java

src/jalview/jbgui/GAlignFrame.java

src/jalview/jbgui/GDesktop.java

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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/datamodel/Annotation.java
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    /src/jalview/ext/varna/VarnaCommands.java
  1. … 23 more files in changeset.
Merge branch 'JAL-1445' into Release_2_8_1_Branch

clear out 2.8.0b1 what's new and add JAL-1445 to list of new features

JAL-1445 basic help docs for feature

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    /help/html/features/featuresettings.html
JAL-1445 JAL-1354 english strings for select by feature

JAL-1445 (shift+) double click on feature type in desktop feature settings to select columns (not) containing features

JAL-1446 use popup event trigger instead of right-click event

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JAL-1445 added menu items to select containing/non-containing features in FeatureSettings popup menu

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    /src/jalview/gui/FeatureSettings.java
JAL-1445 ported routine for selecting containing/non-containing columns from groovy example

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    /src/jalview/api/AlignViewControllerI.java
JAL-1445 expose columnSelection setter.

JAL-535 interface for GUI state update methods that the AlignViewController can call

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    /src/jalview/api/AlignViewControllerGuiI.java
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    /src/jalview/appletgui/AlignFrame.java