jalview

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JAL-3611 added quotation marks for appdir argument install4j uses to invoke getdown-launcher.jar

JAL-3611 added quotation marks for appdir argument install4j uses to invoke getdown-launcher.jar

JAL-3223 updated swingjs as of 2020-04-28

Merge branch 'develop' into feature/JAL-3551Pymol

Merge branch 'develop' into alpha/JAL-3362_Jalview_212_alpha update for 2.11.1 release

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    /resources/lang/Messages_es.properties
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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/gui/AnnotationLabels.java
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    /src/jalview/gui/AssociatePdbFileWithSeq.java
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    /src/jalview/gui/CalculationChooser.java
  1. … 28 more files in changeset.
Merge branch 'alpha/JAL-3066_Jalview_212_slivka-integration' into alpha/JAL-3362_Jalview_212_alpha

JAL-3608 JAL-3416 Added a 'gtk' option. Not currently used unless specified as -Dlaf=gtk

JAL-3225 save auto formatting settings in org.eclipse.jdt.ui.prefs. Not yet put into place, but these settings should be used

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    /utils/eclipse/org.eclipse.jdt.ui.prefs
JAL-3608 saved in Eclipse with auto formatting

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    /src/jalview/bin/Jalview.java
JAL-3608 non-JS cherry-pick

Cleaned up Look and Feel selection and enabled specific selections via "laf" property or .jalview_properties property "PREFERRED_LAF".

Default behaviour is the same as before for all platforms except Linux which will now always default to "Metal" (ignoring the property 'swing.defaultlaf=com.sun.java.swing.plaf.gtk.GTKLookAndFeel' that is set by the system in Ubuntu [and plausibly other OSes, though not Kubuntu]). If a laf property is set then this obviously gets used if possible.

Also added an optional gradle 'testLaf' property (e.g. gradle -PtestLaf=metal test) which will set the laf property during tests. Possibly handy to spot differences to test results between mac and build server (which will default to Metal).

Recognised values of "laf" are:

(specific LaFs) "metal", "gtk", "quaqua", "vaqua", "nimbus",

(best guess LaFs) "mac", "system", "crossplatform"

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    /src/jalview/bin/Jalview.java
JAL-3608 Added CrossPlatform LaF and made configurable with the 'laf' system property. Also set laf for tests

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    /src/jalview/bin/Jalview.java
Merge branch 'releases/Release_2_11_1_Branch'

Merge branch 'documentation/JAL-3407_2.11.1_release' into releases/Release_2_11_1_Branch

Merge branch 'documentation/JAL-3407_2.11.1_release' into develop

JAL-3407 add GPL license to Jalview source files

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    /src/jalview/analysis/GeneticCodeI.java
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    /src/jalview/analysis/GeneticCodes.java
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    /src/jalview/bin/JalviewTaskbar.java
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    /src/jalview/bin/MemorySetting.java
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    /src/jalview/datamodel/GeneLociI.java
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    /src/jalview/datamodel/GeneLocus.java
  1. … 29 more files in changeset.
JAL-3407 release notes - JAL-247 - for auto-set-ID, and revise wording for transferring virtual features in chimera

Merge branch 'documentation/JAL-3407_2.11.1_release' into releases/Release_2_11_1_Branch

Merge branch 'documentation/JAL-3407_2.11.1_release' into develop

JAL-3407 fix JAL-3574 - remove from known issues for 2.11.1.0

Merge branch 'documentation/JAL-3407_2.11.1_release' into releases/Release_2_11_1_Branch

Merge branch 'documentation/JAL-3407_2.11.1_release' into develop

JAL-3574 JAL-3407 release notes

Merge branch 'bug/JAL-3574filterByPOS' into documentation/JAL-3407_2.11.1_release

Merge branch 'develop' into releases/Release_2_11_1_Branch

Merge branch 'documentation/JAL-3407_2.11.1_release' into releases/Release_2_11_1_Branch

Merge branch 'documentation/JAL-3407_2.11.1_release' into develop

JAL-3407 add and document ComputePeptideVariants.groovy

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    /examples/groovy/ComputePeptideVariants.groovy
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    /help/help/html/features/importvcf.html
JAL-3577 changed default RELEASE dir in build.gradle to use absolute path to help buildship when importing project for first time

Merge branch 'develop' into releases/Release_2_11_1_Branch

Merge branch 'develop' of http://source.jalview.org/git/jalview into develop