jalview

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JAL-2674 Added missing null check

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    /src/jalview/datamodel/HiddenColumns.java
JAL-2674 iterator updates

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    /src/jalview/datamodel/HiddenColumns.java
JAL-2674 Last moves to iterators

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    /src/jalview/datamodel/HiddenColumns.java
JAL-2647 stashing

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    /src/jalview/datamodel/HiddenColumns.java
JAL-2674 Removed a stray Vector

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    /src/jalview/datamodel/HiddenColumns.java
JAL-2674 Rationalising iterators and retesting

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    /src/jalview/datamodel/HiddenColumns.java
JAL-2674 Adjustments to hideColumns

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    /src/jalview/datamodel/HiddenColumns.java
JAL-2674 more adjustments to locateVisibleBoundsOfSequence

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    /src/jalview/datamodel/HiddenColumns.java
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    /src/jalview/renderer/ScaleRenderer.java
JAL-2674 Simplify locateVisibleBoundsOfSequence

Take advantage of sequence cursor changes where possible

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    /src/jalview/datamodel/HiddenColumns.java
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    /src/jalview/renderer/ScaleRenderer.java
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    /src/jalview/datamodel/HiddenColumns.java
JAL-2647 unit test

JAL-2674 testing

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    /src/jalview/datamodel/HiddenColumns.java
JAL-2674 working refactor of drawPanel iteration

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    /src/jalview/appletgui/SeqCanvas.java
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    /src/jalview/datamodel/HiddenColumns.java
JAL-2674 2nd attempt to refactor seqcanvas drawing to iterator

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    /src/jalview/datamodel/HiddenColumns.java
JAL-2674 iterator for visible blocks with absolute positions

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    /src/jalview/datamodel/HiddenColumns.java
JAL-2674 Tidies

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    /src/jalview/datamodel/HiddenColumns.java
JAL-2674 finish with iterators for now

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    /src/jalview/datamodel/HiddenColumns.java
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    /src/jalview/gui/VamsasApplication.java
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    /test/jalview/analysis/DnaTest.java
JAL=2674 Removed getHiddenColumnsCopy

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    /src/jalview/appletgui/ScalePanel.java
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    /src/jalview/datamodel/CigarArray.java
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    /src/jalview/datamodel/HiddenColumns.java
JAL-2674 reverted attempt at visible regions iterator

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    /src/jalview/appletgui/SeqCanvas.java
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    /src/jalview/datamodel/HiddenColumns.java
JAL-2647 more iterators

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    /src/jalview/appletgui/SeqCanvas.java
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    /src/jalview/datamodel/HiddenColumns.java
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    /src/jalview/gui/VamsasApplication.java
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    /test/jalview/analysis/DnaTest.java
JAL-2674 Removing most calls to getHiddenColumnsCopy

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    /src/jalview/datamodel/HiddenColumns.java
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    /test/jalview/gui/AlignFrameTest.java
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    /test/jalview/util/MappingUtilsTest.java
JAL-2674 tidied up CigarArray

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    /src/jalview/datamodel/CigarArray.java
Merge remote-tracking branch 'origin/bug/JAL-2742' into feature/JAL-2674take2

JAL-2742 uncomment test

JAL-2674 uncomment test

Merge remote-tracking branch 'origin/bug/JAL-2742' into feature/JAL-2674take2

Conflicts:

src/jalview/datamodel/CigarArray.java

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    /src/jalview/datamodel/CigarArray.java
JAL-2742 fixed

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    /src/jalview/datamodel/CigarArray.java
JAL-2742 CigarArray constructor unit test

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    /test/jalview/datamodel/CigarArrayTest.java
JAL-2674 Changed CigarArray constructor to use HiddenColumns iterator

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    /src/jalview/datamodel/CigarArray.java
JAL-2674 more List<int[]> -> HiddenColumns copy changes

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    /src/jalview/gui/AnnotationLabels.java