JAL-3899 Refactor sequence de/uniquification.

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CR-JAL-254 9

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    Participant Role Time Spent Comments Latest Comment
    Author 38m 3 SequencesInfo which is an individual object is doable, bu...
    Reviewer - 100% reviewed 28m 6 one class with a static factory method seems to be better...
    Total   1h 6m 9  
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    Objectives

    • JAL-3899 Refactor sequence de/uniquification.
    • JAL-3899 Update usages of uniquify and deuniquify.

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    Issues Raised From Comments

    Key Summary State Assignee
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    General Comments

    Jim Procter

    it's a reasonable first pass, though stylistically all you've done is transfo...

    it's a reasonable first pass, though stylistically all you've done is transformed a single concrete instance (Hashtable) to a more strongly typed verbose instance (Map<String,SequenceInfo>). Why not go further and have a SequencesInfo object that records metadata for one or more sequences ?

    There are also other requirements: SequenceInfo sets will need to be persisted for a web services job. You could expand JAL-3899 to incorporate this perhaps - JAL-1786 is the relevant epic for that.

    Mateusz Warowny

    SequencesInfo which is an individual object is doable, but I feel like it wou...

    SequencesInfo which is an individual object is doable, but I feel like it would be just a wrapper around a Map. What additional functionality would SequencesInfo have over a traditional Map?

    I'm not very familiar with serialization in java, I know there are libraries that can serialize beans to json or xml, but what are your expectations in this case?

    /src/jalview/analysis/SeqsetUtils.java Changed 7
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    /src/jalview/datamodel/SeqCigar.java Changed
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    /src/jalview/hmmer/HMMAlign.java Changed
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    /src/jalview/hmmer/HMMBuild.java Changed
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    /src/jalview/hmmer/HmmerCommand.java Changed
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    /src/jalview/hmmer/Search.java Changed
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    /src/jalview/io/packed/JalviewDataset.java Changed
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    /src/jalview/ws/jws1/JPredClient.java Changed
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    /src/jalview/ws/jws1/JPredThread.java Changed
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    /src/jalview/ws/jws2/JPredThread.java Changed
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    /src/jalview/ws/rest/RestJob.java Changed
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    /src/jalview/ws/AWsJob.java Changed
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    /test/.../analysis/SeqsetUtilsTest.java Changed
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