jalview

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JAL-3805 Remove Uninstall Old Jalview.app in Release_2_11_1_Branch

JAL-3805 Remove Uninstall Old Jalview.app in Release_2_11_1_Branch

JAL-3038 corrected code that reads editable JComboBox text input

Merge branch 'feature/JAL-3690_callback-based-web-services' into alpha/JAL-3066_Jalview_212_slivka-integration

JAL-3690 AlignCalcManager - add full support for oneshot workers

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    /src/jalview/workers/AlignCalcManager2.java
JAL-3690 AlignCalcManager - add full support for oneshot workers

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    /src/jalview/workers/AlignCalcManager2.java
JAL-3690 AACon ws menu entry fix.

JAL-3690 AACon ws menu entry fix.

JAL-3690 Allow unregistered workers to be run with CalcManager.

JAL-3690 Allow unregistered workers to be run with CalcManager.

JAL-3690 Fix typo in enum name in slivka client.

JAL-3690 Fix typo in enum name in slivka client.

    • binary
    /utils/jalviewjs/libjs/slivka-client-site.zip
Merge remote-tracking branch 'origin/merge/Jalview-JS/develop_feature/JAL-3690_callback-based-web-services' into feature/JAL-3690_callback-based-web-services

JAL-3690 Fixed slivka wsmenu categories.

JAL-3690 Fixed slivka wsmenu categories.

JAL-3796 update signature for uninstaller on OSX

JAL-3796 update to Install4j 8.0.10 and add config for code notarization

JAL-3789 Use j2s.config.altfileproperty in .j2s for alternative temporary build/jalviewjs/config/j2s settings file when running a headless build in gradle

JAL-3789 Use j2s.config.altfileproperty in .j2s for alternative temporary build/jalviewjs/config/j2s settings file when running a headless build in gradle

JAL-3789 New swingjs for Java2Script 3.2.10 with j2s.config.altfileproperty

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    /swingjs/ver/3.2.10-j11/DEV_NOTES.txt
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    /swingjs/ver/3.2.10-j11/SwingJS-site.zip
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    /swingjs/ver/3.2.10-j11/_j2sclasslist.txt
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    /swingjs/ver/3.2.10-j11/differences.txt
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    /swingjs/ver/3.2.10-j11/net.sf.j2s.core-j11.jar
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    /swingjs/ver/3.2.10-j11/timestamp
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    /swingjs/ver/3.2.10/DEV_NOTES.txt
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    /swingjs/ver/3.2.10/SwingJS-site.zip
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    /swingjs/ver/3.2.10/_j2sclasslist.txt
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    /swingjs/ver/3.2.10/differences.txt
  1. … 24 more files in changeset.
JAL-3789 New swingjs for Java2Script 3.2.10 with j2s.config.altfileproperty

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    /swingjs/differences.txt
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    /swingjs/ver/3.2.10-j11/DEV_NOTES.txt
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    /swingjs/ver/3.2.10-j11/SwingJS-site.zip
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    /swingjs/ver/3.2.10-j11/_j2sclasslist.txt
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    /swingjs/ver/3.2.10-j11/differences.txt
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    /swingjs/ver/3.2.10-j11/net.sf.j2s.core-j11.jar
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    /swingjs/ver/3.2.10-j11/timestamp
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    /swingjs/ver/3.2.10/DEV_NOTES.txt
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    /swingjs/ver/3.2.10/SwingJS-site.zip
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    /swingjs/ver/3.2.10/_j2sclasslist.txt
  1. … 32 more files in changeset.
JAL-3117 raise AlignFrame or SplitFrame when Overview clicked

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AlignmentPanel.java
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    /src/jalview/gui/ViewSelectionMenu.java
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    /src/jalview/jbgui/GAlignFrame.java
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    /test/jalview/gui/FreeUpMemoryTest.java
JAL-3419 improved look of tabs

JAL-3794 X and N are counted as DNA characters, but we also check how many Ns - if there were no real nucleotide characters we always return protein for poly-asparagine

JAL-3794 X and N are counted as DNA characters, but we also check how many Ns - if there were no real nucleotide characters we always return protein for poly-asparagine

JAL-3794 new test for recognition of protein or DNA with ambiguity characters, including the ‘all N’ case (that should be protein..).

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    /test/jalview/datamodel/SequenceTest.java
JAL-3794 new test for recognition of protein or DNA with ambiguity characters, including the ‘all N’ case (that should be protein..).

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    • +17
    /test/jalview/datamodel/SequenceTest.java
JAL-3416 Added FlatLightLaf, use with -Dlaf=flat property

    • binary
    /j11lib/flatlaf-0.46.jar
JAL-3788 synchronize concurrent findColour() and alignmentChanged()

JAL-3788 synchronize concurrent findColour() and alignmentChanged()