jalview

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JAL-2776 repaint everything on toggle group colour

JAL-1854 keep fallthrough but with comment to suppress error

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
JAL-1854 remove fallthrough of switch case (Checkstyle error)

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
JAL-2737 JAL-1854 corrected package suppressions, updated import controls

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    /utils/checkstyle/checkstyle-suppress.xml
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    /utils/checkstyle/import-control.xml
Merge branch 'patch/JAL-547_pid_groovyscript' into develop

JAL-547 fix NPE when no selection available

JAL-547 only generate matrix for current selection if available. better comments.

JAL-547 PID script in release notes

Merge branch 'patch/JAL-547_pid_groovyscript' into develop

JAL-547 updated the PID script for 2.10.x series score model architecture

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    /examples/groovy/PIDmatrix.groovy
JAL-2782 remark about possible exception due to unsafe regex

JAL-2777 JAL-2773 release notes

Merge branch 'bugs/JAL-2777_whitespaceChain' into develop

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    /src/jalview/gui/FeatureSettings.java
JAL-2777 remove duplicate code outside conditional from rebase artefact

JAL-2777 release notes

Merge branch 'features/JAL-2773_dontalwaysrecolourstructureonrepaintofoverview' into develop

JAL-2773 renamed flags for clarity

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    /src/jalview/gui/FeatureColourChooser.java
JAL-2777 patch for whitespace chain

JAL-2777 test for the whitespace chain

JAL-2481 patch to fix findFeatureColour for end-of-sequence test

JAL-2481 test correct behaviour of findFeatureColour for final residue in sequence

JAL-2777 noticed exception raised on construction of feature settings because transparency slider 'setMax' triggers a repaint

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    /src/jalview/gui/FeatureSettings.java
JAL-2773 add new flag to paintAlignment(updateOverview,updateStructures) and first pass at limiting updates of structure to just those that are necessary.

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    /src/jalview/api/AlignmentViewPanel.java
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    /src/jalview/appletgui/APopupMenu.java
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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/appletgui/FontChooser.java
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    /src/jalview/appletgui/OverviewPanel.java
  1. … 39 more files in changeset.
JAL-2772 check array bounds for sequence access

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    /test/jalview/datamodel/SequenceTest.java
Merge branch 'bug/JAL-2742' into develop

JAL-2742 set HiddenColumns null for no hidden coluns test to match Jalview usage

JAL-2757 release notes

Merge branch 'bug/JAL-2757_uniprotftsbadquery' into develop

JAL-2757 fix PDB also; suppress stack trace and compiler warnings

JAL-2742 test updates following review