CR-JAL-102 JAL-2480: Encapsulate performant access to sequence features

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JAL-2480: Encapsulate performant access to sequence features

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Number of files included: 31

jalview 0
- Folder src/jalview 0
  - Folder analysis 0
    - File AlignmentUtils.java 0 Remove
  - Folder datamodel 0
    - Folder features 0
      - File ContiguousI.java 0 Remove
      - File FeatureLocationI.java 0 Remove
      - File FeatureStore.java 1 Remove
      - File NCList.java 0 Remove
      - File NCList.java 0 Remove
      - File NCNode.java 0 Remove
      - File Range.java 0 Remove
      - File RangeComparator.java 0 Remove
      - File SequenceFeatures.java 0 Remove
      - File SequenceFeaturesI.java 0 Remove
    - File ContiguousI.java 0 Remove
    - File Range.java 0 Remove
    - File Sequence.java 16 Remove
    - File SequenceFeature.java 0 Remove
    - File SequenceI.java 2 Remove
  - Folder ext 0
    - Folder ensembl 0
      - File EnsemblSeqProxy.java 0 Remove
    - Folder rbvi/chimera 0
      - File AtomSpecModel.java 0 Remove
  - Folder gui 0
    - File AnnotationExporter.java 0 Remove
    - File FeatureSettings.java 0 Remove
    - File SequenceFetcher.java 0 Remove
  - Folder renderer/seqfeatures 0
    - File FeatureRenderer.java 3 Remove
  - Folder util 0
    - File IntRangeComparator.java 0 Remove
    - File RangeComparator.java 0 Remove
- Folder test/jalview/datamodel 0
  - Folder features 0
    - File FeatureStoreTest.java 0 Remove
    - File NCListTest.java 0 Remove
    - File NCNodeTest.java 0 Remove
    - File RangeComparatorTest.java 0 Remove
    - File SequenceFeaturesTest.java 0 Remove
  - File SequenceTest.java 0 Remove
  - File SequenceTest.java 0 Remove

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

Linked Issue:
JAL-2480

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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).

Branches in review

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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.

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/src/jalview/.../features/ContiguousI.java Deleted

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/src/jalview/datamodel/features/Range.java Deleted

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CR-JAL-102

JAL-2480: Encapsulate performant access to sequence features

CR-JAL-102 22

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JAL-2480: Encapsulate performant access to sequence features

CR-JAL-102 22

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