jalview

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JAL-2933 pass viewport in Finder constructor, find acts on viewport selection if any

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    /src/jalview/analysis/Finder.java
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    /test/jalview/analysis/FinderTest.java
JAL-2933 gui and applet Finder hold a FinderI per viewport

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    /src/jalview/analysis/Finder.java
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    /src/jalview/api/FinderI.java
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    /src/jalview/appletgui/Finder.java
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    /test/jalview/analysis/FinderTest.java
JAL-2839 refactored out getNextVisibleSequenceRegion

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    /src/jalview/analysis/Finder.java
JAL-2839 additional test case

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    /test/jalview/analysis/FinderTest.java
JAL-2839 refactored analysis.Finder and tests

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    /src/jalview/analysis/Finder.java
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    /src/jalview/appletgui/Finder.java
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    /test/jalview/analysis/AlignSeqTest.java
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    /test/jalview/analysis/FinderTest.java
JAL-2839 addResult ignores duplicates

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    /src/jalview/datamodel/SearchResults.java
JAL-2933 remember Find position per viewport

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    /src/jalview/appletgui/Finder.java
JAL-2839 don't search minimised panels from Finder

JAL-2839 Finder refactoring prior to fixing the defect

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    /src/jalview/analysis/Finder.java
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    /src/jalview/datamodel/SearchResults.java
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    /test/jalview/analysis/FinderTest.java
Merge remote-tracking branch 'origin/releases/Release_2_10_4_Branch' into merges/JAL-2906_update2_11_from_2_10_4

JAL-2885 tests updated for code changes

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    /test/jalview/ws/dbsources/PfamFullTest.java
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    /test/jalview/ws/dbsources/PfamSeedTest.java
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    /test/jalview/ws/dbsources/RfamFullTest.java
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    /test/jalview/ws/dbsources/RfamSeedTest.java
JAL-2930 use MouseWheelEvent.getPreciseWheelRotation, not getWheelRotation

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    /src/jalview/gui/RotatableCanvas.java
Merge branch 'releases/Release_2_10_4_Branch' into develop check carefully that JAL-2885 (configurable Ensembl/Genomes Endpoints) functionality is still present

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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/datamodel/Sequence.java
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    /src/jalview/datamodel/SequenceI.java
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    /src/jalview/ext/ensembl/EnsemblInfo.java
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    /src/jalview/ext/ensembl/EnsemblLookup.java
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AnnotationLabels.java
  1. … 7 more files in changeset.
Merge branch 'bugs/JAL-2922' into releases/Release_2_10_4_Branch

JAL-2922 [2] not [1] for Boolean column of table

Merge branch 'bugs/JAL-2922' into releases/Release_2_10_4_Branch

JAL-2922 i18n and bespoke handler for Invert Selection

Merge branch 'bug/JAL-2924nullTooltip' into releases/Release_2_10_4_Branch

JAL-2926 fix copy group consensus (and paste sequence with space in name)

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    /src/jalview/appletgui/AlignFrame.java
JAL-2925 handle empty annotation when copying group consensus

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    /src/jalview/datamodel/SequenceGroup.java
JAL-2913 use FIGURE_USERIDWIDTH for fixed id width property

JAL-2924 no tooltip over null annotation positions

Merge branch 'releases/Release_2_10_4_Branch_merged_JAL-2759' into releases/Release_2_10_4_Branch

JAL-2759 release notes for 2.10.4

Merge branch 'feature/JAL-2759' into merge/JAL-2759_2104

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    /src/jalview/datamodel/Alignment.java
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AnnotationLabels.java
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    /src/jalview/gui/ScalePanel.java
fix for JAL-2922 - update states all at once and then refresh

Merge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch

JAL-984 remove all references to idwidth.gif - in build.xml too :)

JAL-2885 release notes

Merge branch 'features/JAL-2885UniprotHttps' into releases/Release_2_10_4_Branch

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    /src/jalview/ext/ensembl/EnsemblLookup.java