jalview

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JAL-2574 renamed findFeatures as findOverlappingFeatures to minimise confusion

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    /src/jalview/commands/EditCommand.java
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    /test/jalview/datamodel/SequenceTest.java
Merge branch 'develop' into bug/JAL-2541cutWithFeatures

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    /src/jalview/appletgui/SeqCanvas.java
Merge branch 'bug/JAL-2600resizeflicker' into develop

JAL-2600 Tidies

JAL-2600 updates following review

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    /src/jalview/appletgui/ScalePanel.java
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    /src/jalview/appletgui/SeqCanvas.java
JAL-2541 clean unit test of cut/undo (ungapped sequence)

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    /src/jalview/commands/EditCommand.java
JAL-2541 more useful assert message

Merge branch 'features/JAL-2446NCList' into bug/JAL-2541cutWithFeatures (Undo fails outstanding to resolve)

Conflicts:

src/jalview/datamodel/Sequence.java

src/jalview/datamodel/SequenceI.java

test/jalview/datamodel/SequenceTest.java

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    /src/jalview/datamodel/Sequence.java
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    /test/jalview/datamodel/SequenceTest.java
Merge branch 'develop' into features/JAL-2446NCList

Conflicts:

src/jalview/appletgui/SeqPanel.java

src/jalview/renderer/seqfeatures/FeatureRenderer.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/datamodel/Alignment.java
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/Jalview2XML.java
JAL-2600 Tidies

JAL-2600 Abandoned fastpaint for resize; now full repaint, single call

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    /src/jalview/gui/AnnotationPanel.java
JAL-2602 check for null or empty description when copying consensus

JAL-1858 highlights on wrapped panel - work in progress

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    /src/jalview/gui/SeqCanvas.java
JAL-147 scroll wrapped panel by one width's worth at a time

JAL-2600 Add in IdCanvas and checks for 0 size images

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    /src/jalview/gui/AnnotationPanel.java
JAL-2600 vertical fast paint too

JAL-2600 fast painting on resize

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    /src/jalview/gui/AnnotationPanel.java
JAL-2600 reinstate original behaviour

JAL-1858 ensure full redraw on 'remove all selections'

JAL-2589 unit test updated

JAL-2547 fix case of gap followed by enclosing contact feature position

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    /src/jalview/datamodel/Sequence.java
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    /test/jalview/datamodel/SequenceTest.java
JAL-1858 null img when doing full repaint of wrapped alignment

JAL-1858 don't fastpaint highlights if wrapped format

JAL-1858 refactored method to redraw previous/new highlighted positions

JAL-1858 handle hidden columns when computing region to redraw

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    /src/jalview/datamodel/SearchResults.java
JAL-1858 'fastPaint' of minimal region for highlights; todo: hidden columns

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    /src/jalview/gui/SeqCanvas.java
JAL-2481 JAL-2593 JAL-2526 further optimisation of feature/index finding

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    /src/jalview/datamodel/Sequence.java
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    /src/jalview/datamodel/SequenceI.java
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    /test/jalview/datamodel/SequenceTest.java
JAL-2480 simpler and safer test to avoid adding duplicates

JAL-2480 tidy generic initialisations, SequenceFeatures.varargToTypes

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    /test/jalview/datamodel/SequenceTest.java
JAL-2541 save/Undo only 'diffs' for features with Cut command

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    /src/jalview/commands/EditCommand.java