jalview

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JAL-2609 tiny tidy

JAL-2609 corrections for print wrapped view

JAL-2609 unit test for annotations displayed case

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    /test/jalview/gui/SeqCanvasTest.java
JAL-2609 tweaks to, and tests for, calculateWrappedGeometry

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    /test/jalview/gui/SeqCanvasTest.java
Merge branch 'develop' into features/JAL-2609fastPaintWrapped

JAL-2609 tweaks including fully erasing scale above

JAL-2680 clear down all mappings before test

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    /test/jalview/gui/AlignViewportTest.java
Merge branch 'develop' into features/JAL-2609fastPaintWrapped

Conflicts:

src/jalview/gui/SeqCanvas.java

Merge branch 'develop' into features/JAL-2446NCList

Conflicts:

src/MCview/PDBChain.java

src/jalview/analysis/AlignmentSorter.java

src/jalview/analysis/AlignmentUtils.java

src/jalview/analysis/Dna.java

src/jalview/appletgui/AlignFrame.java

src/jalview/appletgui/FeatureRenderer.java

src/jalview/appletgui/Finder.java

src/jalview/appletgui/SeqPanel.java

src/jalview/commands/EditCommand.java

src/jalview/datamodel/AlignedCodonFrame.java

src/jalview/datamodel/Sequence.java

src/jalview/datamodel/SequenceFeature.java

src/jalview/datamodel/xdb/embl/EmblEntry.java

src/jalview/ext/ensembl/EnsemblGene.java

src/jalview/gui/AlignmentPanel.java

src/jalview/gui/AnnotationExporter.java

src/jalview/gui/CutAndPasteTransfer.java

src/jalview/gui/FeatureRenderer.java

src/jalview/gui/Finder.java

src/jalview/gui/PopupMenu.java

src/jalview/gui/SeqCanvas.java

src/jalview/gui/SeqPanel.java

src/jalview/io/FeaturesFile.java

src/jalview/io/JSONFile.java

src/jalview/io/gff/InterProScanHelper.java

src/jalview/io/vamsas/Datasetsequence.java

src/jalview/renderer/seqfeatures/FeatureRenderer.java

src/jalview/util/RangeComparator.java

src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java

src/jalview/ws/jws2/AADisorderClient.java

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    /src/jalview/analysis/AAFrequency.java
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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/analysis/Conservation.java
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    /src/jalview/analysis/CrossRef.java
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    /src/jalview/analysis/SeqsetUtils.java
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    /src/jalview/appletgui/APopupMenu.java
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    /src/jalview/appletgui/AlignFrame.java
  1. … 66 more files in changeset.
JAL-2675 bump version for branch to 2.10.2b1

JAL-1551 formatting

JAL-2675 release notes entry for 2.10.2b1, updated what’s new and link to latest notes in help.

JAL-2418 ahem - correct year for what's new

JAL-2418 JAL-2116 use single j2se 7+ argumant with java 9 add-modules - seems to work on java 8 (windows, osx, linux) without 'use latest version' popup and also on java 9

JAL-2418 JAL-2116 make sure java 8,7 vm args are also listed

Merge branch 'develop' into releases/Release_2_10_2_Branch

Merge branch 'documentation/JAL-2418_release2102' into develop

JAL-2418 formatting

JAL-2418 occupancy row in What’s New

Merge branch 'develop' into releases/Release_2_10_2_Branch

JAL-2418 add GPL to main sources

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    /src/jalview/analysis/TreeBuilder.java
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    /src/jalview/analysis/scoremodels/ScoreModels.java
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    /src/jalview/api/analysis/ScoreModelI.java
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    /src/jalview/gui/ColourMenuHelper.java
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    /src/jalview/gui/ComboBoxTooltipRenderer.java
  1. … 23 more files in changeset.
JAL-2418 source formatting

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    /src/MCview/AppletPDBCanvas.java
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    /src/MCview/AppletPDBViewer.java
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    /src/jalview/analysis/AAFrequency.java
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    /src/jalview/analysis/AlignSeq.java
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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/analysis/Conservation.java
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    /src/jalview/analysis/CrossRef.java
  1. … 450 more files in changeset.
Merge branch 'develop' into releases/Release_2_10_2_Branch

Merge branch 'documentation/JAL-2418_release2102' into develop

JAL-2418 mirror fonts option doc tweak

Merge branch 'documentation/JAL-2418_release2102' into develop

JAL-2418 whats new for 2.10.2

JAL-2418 reclassify some issues to features/bugs resolved

JAL-2418 typos in release notes

JAL-2418 check groovy script one-liners for restoring legacy score model behaviour