jalview

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JAL-3609 system properties to force a scale, or automatically choose based on OS, Screen DPI and Screen height in pixels

    • binary
    /getdown/lib/getdown-launcher-local.jar
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    • +80
    /src/jalview/bin/HiDPISetting.java
Merge branch 'develop' into feature/JAL-3551Pymol

Conflicts:

src/jalview/ext/jmol/JalviewJmolBinding.java

src/jalview/ext/jmol/JmolCommands.java

src/jalview/gui/AppJmol.java

src/jalview/gui/AppJmolBinding.java

src/jalview/gui/ChimeraViewFrame.java

src/jalview/gui/StructureViewerBase.java

src/jalview/jbgui/GPreferences.java

src/jalview/jbgui/GStructureViewer.java

src/jalview/project/Jalview2XML.java

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    • +15
    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
    • -7
    • +8
    /src/jalview/appletgui/AlignFrame.java
    • -1
    • +1
    /src/jalview/appletgui/AppletJmol.java
    • -12
    • +46
    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    • +173
    /src/jalview/ext/jmol/JmolCommands.java
    • -383
    • +484
    /src/jalview/gui/AlignFrame.java
    • -25
    • +13
    /src/jalview/gui/AppJmolBinding.java
    • -10
    • +4
    /src/jalview/gui/ChimeraViewFrame.java
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    • +89
    /src/jalview/gui/Preferences.java
  1. … 5 more files in changeset.
JAL-3624 use temp file for SIFT download in JS, correct unmarshalling

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    /src/jalview/ws/sifts/SiftsClient.java
JAL-3624 use temp file for SIFT download in JS, correct unmarshalling

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    • +48
    /src/jalview/ws/sifts/SiftsClient.java
JAL-3609 Added a -DforceHiDPISetting=true option mainly for testing, and updated getdown HiDPISetting

    • binary
    /getdown/lib/getdown-launcher-local.jar
    • -15
    • +29
    /src/jalview/bin/HiDPISetting.java
JAL-3609 Added a -DforceHiDPISetting=true option mainly for testing, and updated getdown HiDPISetting

    • binary
    /getdown/lib/getdown-launcher-local.jar
    • -15
    • +29
    /src/jalview/bin/HiDPISetting.java
JAL-3463 avoid Thread.sleep() as not supported in SwingJS

    • -31
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    /src/jalview/ws/DBRefFetcher.java
JAL-3463 avoid Thread.sleep() as not supported in SwingJS

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    /src/jalview/ws/DBRefFetcher.java
JAL-3621 update to intervalstore v1.1

    • binary
    /j11lib/intervalstore-v1.1.jar
    • binary
    /j8lib/intervalstore-v1.1.jar
JAL-3621 update to intervalstore v1.1

    • binary
    /j11lib/intervalstore-v1.1.jar
    • binary
    /j8lib/intervalstore-v1.1.jar
JAL-3621 update to intervalstore v1.1

    • binary
    /j11lib/intervalstore-v1.1.jar
    • binary
    /j8lib/intervalstore-v1.1.jar
Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

resolved conflicts and adapted to some upstream changes. no detailed functional testing as yet (see next commit :) )

Conflicts:

resources/lang/Messages.properties

resources/lang/Messages_es.properties

src/jalview/api/AlignViewportI.java

src/jalview/bin/Jalview.java

src/jalview/datamodel/Sequence.java

src/jalview/datamodel/SequenceI.java

src/jalview/gui/AlignFrame.java

src/jalview/gui/JvSwingUtils.java

src/jalview/gui/OverviewPanel.java

src/jalview/gui/PopupMenu.java

src/jalview/gui/SplitFrame.java

src/jalview/gui/WsJobParameters.java

src/jalview/io/AlignmentFileReaderI.java

src/jalview/io/FileLoader.java

src/jalview/io/StockholmFile.java

src/jalview/jbgui/GAlignFrame.java

src/jalview/jbgui/GPreferences.java

src/jalview/renderer/AnnotationRenderer.java

src/jalview/viewmodel/AlignmentViewport.java

src/jalview/ws/jws2/Jws2Discoverer.java

test/jalview/analysis/AAFrequencyTest.java

test/jalview/gui/AlignFrameTest.java

test/jalview/gui/AlignViewportTest.java

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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    /src/jalview/analysis/AAFrequency.java
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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/api/AlignViewportI.java
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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/appletgui/AlignViewport.java
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    • +1
    /src/jalview/appletgui/OverviewPanel.java
    • -4
    • +1
    /src/jalview/appletgui/TitledPanel.java
    • -20
    • +76
    /src/jalview/datamodel/Alignment.java
  1. … 60 more files in changeset.
JAL-3529 test updated for revised signature of getDBRefs()

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    • +15
    /test/jalview/io/StockholmFileTest.java
Merge branch 'Jalview-JS/develop' into develop

Conflicts:

build.gradle

src/jalview/gui/PopupMenu.java

src/jalview/io/SequenceAnnotationReport.java

src/jalview/io/StockholmFile.java

src/jalview/util/DBRefUtils.java

src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java

    • -1
    • +1
    /src/jalview/appletgui/APopupMenu.java
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    • +6
    /src/jalview/ext/ensembl/EnsemblInfo.java
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    • +22
    /src/jalview/ext/ensembl/EnsemblMap.java
    • -31
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    /src/jalview/gui/IdPanel.java
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    /src/jalview/gui/PopupMenu.java
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    • +195
    /src/jalview/gui/SeqPanel.java
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    • +54
    /src/jalview/io/StockholmFile.java
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    • +529
    /src/jalview/util/DBRefUtils.java
  1. … 5 more files in changeset.

changeset discussion

  1. Jim Procter: relevant issue is JAL-3626
JAL-3613 remove debug code committed in error

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    /src/jalview/util/BrowserLauncher.java
JAL-3613 remove debug code committed in error

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    /src/jalview/util/BrowserLauncher.java
JAL-3613 remove debug code committed in error

    • -5
    • +1
    /src/jalview/util/BrowserLauncher.java
JAL-3609 HiDPI scale setting done via system prop in getdown or halview.bin.Launcher

    • binary
    /getdown/lib/getdown-launcher-local.jar
    • -0
    • +48
    /src/jalview/bin/HiDPISetting.java
JAL-3609 HiDPI scale setting done via system prop in getdown or halview.bin.Launcher

    • binary
    /getdown/lib/getdown-launcher-local.jar
    • -0
    • +48
    /src/jalview/bin/HiDPISetting.java
JAL-2422 JAL-3551 unit tests updated for code changes

    • -13
    • +12
    /test/jalview/ext/jmol/JmolCommandsTest.java
JAL-3619 default silently to Jmol if viewerType absent (Jalview < 2.9)

JAL-3551 pull up Close Viewer dialog to base class

    • -2
    • +2
    /resources/lang/Messages_es.properties
    • -20
    • +20
    /src/jalview/appletgui/AppletJmol.java
    • -10
    • +0
    /src/jalview/ext/jmol/JalviewJmolBinding.java
    • -45
    • +2
    /src/jalview/gui/ChimeraViewFrame.java
    • -3
    • +4
    /src/jalview/gui/PymolBindingModel.java
    • -0
    • +46
    /src/jalview/gui/StructureViewerBase.java
Merge branch 'feature/JAL-3551Pymol' into feature/JAL-2422ChimeraX

JAL-3551 raise label on ('highlight') structure residue (wip)

    • -0
    • +41
    /src/jalview/gui/PymolBindingModel.java
JAL-3541 Fixed report path for build artifacts

JAL-3541 Fixed report path for build artifacts

JAL-3541 Added mem setting and jvmArgs for cloverReporting

JAL-3541 Added mem setting and jvmArgs for cloverReporting

JAL-3541 Individual tests now instrumented and reported. Added cloverConsoleReport.

JAL-3541 Individual tests now instrumented and reported. Added cloverConsoleReport.