JAL-2674 Transferred updated unit tests from first 2674 branch

Activity

CR-JAL-149 0

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    Participant Role Time Spent Comments Latest Comment
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    Reviewer - 0% reviewed 21m    
    Total   21m 0  
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    Objectives

    • JAL-2674 Transferred updated unit tests from first 2674 branch
    • JAL-2674 fix up interface of locateVisibleBoundsOfSequence
    • JAL-2674 Reset tests
    • JAL-2674 Rewrote propagateInsertions
    • JAL-2674 unit test for gapBitSet
    • JAL-2674 Made gui ScalePanel reveal menus consistent with applet
    • JAL-2674 add bounds to findHiddenRegionPositions
    • Merge remote-tracking branch 'origin/bug/JAL-2739' into feature/JAL-2674take2
    • JAL-2647 Added iterators and associated tests and benchmarks
    • JAL-2674 HiddenColumns interface tidies
    • Merge remote-tracking branch 'origin/bug/JAL-2740' into feature/JAL-2674take2
    • Merge remote-tracking branch 'origin/bug/JAL-2740' into feature/JAL-2674take2
    • JAL-2674 Changes to pasting
    • JAL-2674 Unit test for new copy constructor.
    • JAL-2674 more List<int[]> -> HiddenColumns copy changes
    • JAL-2674 Changed CigarArray constructor to use HiddenColumns iterator
    • Merge remote-tracking branch 'origin/bug/JAL-2742' into feature/JAL-2674take2
      Conflicts:
      src/jalview/datamodel/CigarArray.java
    • JAL-2674 uncomment test
    • Merge remote-tracking branch 'origin/bug/JAL-2742' into feature/JAL-2674take2
    • JAL-2674 tidied up CigarArray
    • JAL-2674 Removing most calls to getHiddenColumnsCopy
    • JAL-2647 more iterators
    • JAL-2674 reverted attempt at visible regions iterator
    • JAL=2674 Removed getHiddenColumnsCopy
    • JAL-2674 finish with iterators for now
    • JAL-2674 Tidies
    • JAL-2674 iterator for visible blocks with absolute positions
    • JAL-2674 2nd attempt to refactor seqcanvas drawing to iterator
    • JAL-2674 working refactor of drawPanel iteration
    • JAL-2674 testing
    • JAL-2647 unit test
    • JAL-2674 tidy
    • JAL-2674 Simplify locateVisibleBoundsOfSequence
      Take advantage of sequence cursor changes where possible
    • JAL-2674 more adjustments to locateVisibleBoundsOfSequence
    • JAL-2674 Adjustments to hideColumns
    • JAL-2674 Rationalising iterators and retesting
    • JAL-2674 Removed a stray Vector
    • JAL-2647 stashing
    • JAL-2674 Last moves to iterators
    • JAL-2674 iterator updates
    • JAL-2759 Rearranged iterators
    • JAL-2759 working first pass cursor
    • JAL-2759 hiddenColumns null check
    • JAL-2759 fix getHiddenOffset iterating backwards
    • Merge branch 'develop' into feature/JAL-2759
      Conflicts:
      src/jalview/gui/SeqCanvas.java
      src/jalview/renderer/ScaleRenderer.java
      test/jalview/datamodel/SequenceTest.java
    • JAL-2759 make bounds correct for left scrolling with hidden cols
    • JAL-2759 Converted getHiddenBoundaryLeft/Right to use cursor
    • JAL-2759 convert findColumnPosition to use cursor
    • JAL-2759 HiddenColumnsCursor tests
    • JAL-2759 Convert reveal to use cursor

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    Issues Raised From Comments

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    /benchmarking/.../jalview/HiddenColsIteratorsBenchmark.java Added
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    /benchmarking/.../jalview/HiddenColumnsBenchmark.java Changed
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    /benchmarking/README Changed
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    /src/jalview/analysis/Dna.java Changed
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    /src/jalview/appletgui/AlignFrame.java Changed
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    /src/.../appletgui/AnnotationColumnChooser.java Changed
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    /src/.../appletgui/AnnotationLabels.java Changed
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    /src/.../appletgui/AnnotationPanel.java Changed
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    /src/jalview/appletgui/IdCanvas.java Changed
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    /src/jalview/appletgui/ScalePanel.java Changed
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    /src/jalview/appletgui/SeqCanvas.java Changed
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    /src/jalview/appletgui/SeqPanel.java Changed
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    /src/jalview/bin/JalviewLite.java Changed
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    /src/.../datamodel/BoundedHiddenColsIterator.java Deleted
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    /src/.../datamodel/BoundedStartRegionIterator.java Deleted
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    /src/jalview/datamodel/CigarArray.java Changed
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    /src/.../datamodel/HiddenColsIterator.java Deleted
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    /src/.../datamodel/HiddenColumnsCursor.java Added
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    /src/.../datamodel/HiddenCursorPosition.java Added
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    /src/jalview/datamodel/RangeIterator.java Added
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    /src/.../datamodel/ReverseRegionsIterator.java Deleted
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    /src/jalview/datamodel/Sequence.java Changed
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    /src/jalview/datamodel/SequenceI.java Changed
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    /src/.../datamodel/StartRegionIterator.java Added
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    /src/.../datamodel/VisibleColsCollection.java Changed
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    /src/.../datamodel/VisibleColsIterator.java Deleted
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    /src/.../datamodel/VisibleContigsIterator.java Added
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    /src/jalview/gui/AlignViewport.java Changed
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    /src/jalview/gui/AlignmentPanel.java Changed
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    /src/.../gui/AnnotationColumnChooser.java Changed
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    /src/jalview/gui/AnnotationLabels.java Changed
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    /src/jalview/gui/AnnotationPanel.java Changed
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    /src/jalview/gui/IdCanvas.java Changed
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    /src/jalview/gui/Jalview2XML.java Changed
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    /src/jalview/gui/PopupMenu.java Changed
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    /src/jalview/gui/ScalePanel.java Changed
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    /src/jalview/gui/SeqCanvas.java Changed
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    /src/jalview/gui/SeqPanel.java Changed
    /src/jalview/gui/VamsasApplication.java Changed
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    /src/jalview/io/AnnotationFile.java Changed
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    /src/jalview/io/FormatAdapter.java Changed
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    /src/.../renderer/AnnotationRenderer.java Changed
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    /src/jalview/renderer/ScaleRenderer.java Changed
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    /src/jalview/util/MappingUtils.java Changed
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    /src/.../viewmodel/AlignmentViewport.java Changed
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    /src/.../viewmodel/OverviewDimensionsHideHidden.java Changed
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    /src/.../viewmodel/OverviewDimensionsShowHidden.java Changed
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    /src/jalview/viewmodel/ViewportRanges.java Changed
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    /src/jalview/ws/jws1/JPredThread.java Changed
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    /test/jalview/analysis/DnaTest.java Changed
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    /test/.../datamodel/AlignmentAnnotationTests.java Changed
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    /test/jalview/datamodel/AlignmentTest.java Changed
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    /test/.../datamodel/BoundedStartRegionIteratorTest.java Deleted
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    /test/.../datamodel/CigarArrayTest.java Changed
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    /test/.../datamodel/ColumnSelectionTest.java Changed
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    /test/.../datamodel/HiddenColumnsCursorTest.java Added
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    /test/.../datamodel/HiddenColumnsTest.java Changed
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    /test/.../datamodel/RangeElementsIteratorTest.java Added
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    /test/jalview/datamodel/SequenceTest.java Changed
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    /test/.../datamodel/StartRegionIteratorTest.java Added
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    /test/.../datamodel/VisibleColsIteratorTest.java Deleted
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    /test/.../datamodel/VisibleContigsIteratorTest.java Added
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    /test/jalview/gui/AlignFrameTest.java Changed
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    /test/.../gui/AnnotationColumnChooserTest.java Changed
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    /test/jalview/io/JSONFileTest.java Changed
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    /test/jalview/util/MappingUtilsTest.java Changed
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