JAL-3187 basic first version for tooltips only (rendering yet to do)

Activity

CR-JAL-203 0

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    Objectives

    • JAL-3187 basic first version for tooltips only (rendering yet to do)
    • JAL-3187 (hacked up) show complement features on structure/Overview
    • JAL-3187 repaint a 'following' complementary view on change
    • JAL-3187 findFeaturesAtResidue answer in render order (tests TODO)
    • JAL-3187 unit tests updated and errors caught
    • JAL-3187 draw complement features on alignment / structure
    • JAL-3187 also repaint complement on change in FeatureTypeSettings
    • JAL-3187 clunky sort by renderorder in findComplementFeaturesAtResidue
    • Merge branch 'develop' into feature/JAL-3187linkedFeatures
    • JAL-3187 fix out by one feature on structure position
    • JAL-3187 don't compute variant features on peptide, show on demand
    • JAL-3187 set initial state of checkbox from viewport
    • JAL-3187 return a colour for linked features with transparency
    • JAL-3010 getColumnClass() never return null
    • JAL-3187 'on top' optional for complementary features
      Conflicts:
      src/jalview/gui/FeatureSettings.java
    • JAL-3187 reset ViewStyle on Cancel in FeatureSettings
    • JAL-3187 hacks to get peptide variant in to Jmol hover tooltip
    • JAL-3187 read peptide variant from CSQ:HGVSp if present (VCF/VEP data)
    • Merge branch 'feature/JAL-3143ensemblJSON' into feature/JAL-3187linkedFeatures
    • JAL-3187 handle no mapping / complement features without NPE
    • JAL-3187 commit to enable merge from develop
    • Merge branch 'develop' into trialMerge
      Conflicts:
      src/jalview/datamodel/features/SequenceFeatures.java
      src/jalview/gui/FeatureSettings.java
      src/jalview/gui/Jalview2XML.java
      src/jalview/gui/SeqPanel.java
      src/jalview/project/Jalview2XML.java
      src/jalview/renderer/seqfeatures/FeatureRenderer.java
      src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
      test/jalview/io/Jalview2xmlTests.java
    • JAL-3187 deletions (of Castor code) after merge from develop
    • Merge branch 'bug/JAL-3288splitFrameMenusJava11' into trialMerge
    • Merge branch 'develop' into feature/JAL-3187linkedFeatures
    • JAL-3187 change fields to local variables
    • JAL-3187 save and restore flags for show complement features
    • JAL-3187 CDS has same dataset sequence as transcript
    • Merge branch 'develop' into feature/JAL-3187linkedFeatures
    • Merge branch 'develop' into feature/JAL-3187linkedFeatures
    • JAL-3303 ignore deletions when computing peptide variants
    • JAL-3302 transfer visible 'linked' features to Chimera
    • JAL-3187 add sequence to feature details table (and refactor PopupMenu)
    • JAL-3187 update unit test - protein variants not now precomputed
    • JAL-3187 update alignAs code and unit tests for 'shared dataset' case
    • JAL-2792 JAL-3187 linked features (if shown) in Feature details submenu
    • JAL-3305 mirror popup menu column selections in split frame
    • JAL-3187 i18n show linked features checkboxes
    • JAL-3304 option to export linked features in Jalview format
    • JAL-3377 include seq-annotation spacing in getWrappedHeight()
    • JAL-3304 option to export linked features also for GFF format
    • JAL-3377 corrected wrapped widths height for IdCanvas
    • JAL-3187 javadoc
    • JAL-3377 Javadoc added for getWrappedHeight()
    • JAL-1544 fixed a html encoding of '<' (%lt; -> <) in commandline.html
    • JAL-1793 apply URL decoding when saving VCF attribute values (%3D -> =)
    • JAL-3377 add seq-annotations gap to cheight not to hgap
    • JAL-3289 bamboo properties for ‘BUILD’ getdown channel
    • JAL-3187 initial refactoring towards peptide variant in tooltip
    • JAL-3377 more reused of SeqCanvas.computeWrappedGeometry

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