JAL-2480: Encapsulate performant access to sequence features

Activity

CR-JAL-102 22

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    Participant Role Time Spent Comments Latest Comment
    Author 22m 8 I would suggest separate from SequenceCursor management -...
    Reviewer - Complete 1h 10m 14 not quite. we need to record the type of gap (insertion, ...
    Total   1h 32m 22  
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    Objectives

    Scope of this issue is the datamodel and public API for read and write of features for a sequence. A performant data store is made possible by the use of NCList (JAL-2446) for nested features, and can be tailored to the requirements of Jalview (JAL-2444).

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    Issues Raised From Comments

    Key Summary State Assignee
    JAL-2767
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    General Comments

    There are no general comments on this review.
    /src/jalview/analysis/AlignmentUtils.java Changed
    /src/jalview/.../features/ContiguousI.java Deleted
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    /src/.../features/FeatureLocationI.java Changed
    /src/jalview/.../features/FeatureStore.java Changed 1
    /src/jalview/.../features/NCList.java Changed
    /src/jalview/.../features/NCList.java Changed
    /src/jalview/.../features/NCNode.java Changed
    /src/jalview/datamodel/features/Range.java Deleted
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    /src/jalview/.../features/RangeComparator.java Changed
    /src/.../features/SequenceFeatures.java Changed
    /src/.../features/SequenceFeaturesI.java Changed
    /src/jalview/datamodel/ContiguousI.java Added
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    /src/jalview/datamodel/Range.java Added
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    /src/jalview/datamodel/Sequence.java Changed 16
    /src/.../datamodel/SequenceFeature.java Changed
    /src/jalview/datamodel/SequenceI.java Changed 2
    /src/jalview/.../ensembl/EnsemblSeqProxy.java Changed
    /src/jalview/.../chimera/AtomSpecModel.java Changed
    /src/jalview/gui/AnnotationExporter.java Changed
    /src/jalview/gui/FeatureSettings.java Changed
    /src/jalview/gui/SequenceFetcher.java Changed
    /src/.../seqfeatures/FeatureRenderer.java Changed 3
    /src/jalview/util/IntRangeComparator.java Added
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    /src/jalview/util/RangeComparator.java Deleted
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    /test/.../features/FeatureStoreTest.java Changed
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    /test/jalview/.../features/NCListTest.java Changed
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    /test/jalview/.../features/NCNodeTest.java Changed
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    /test/.../features/RangeComparatorTest.java Changed
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    /test/.../features/SequenceFeaturesTest.java Changed
    /test/jalview/datamodel/SequenceTest.java Changed
    /test/jalview/datamodel/SequenceTest.java Changed

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