1. Jalview Code Reviews

CR-JAL-72

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Goal and implementation review for hmmer3 model import and visualisation

Activity

CR-JAL-72 13

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    Details

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    Participant Role Time Spent Comments Latest Comment
    Thomas van Aalten
    		Author 44m    
    Jim Procter
    		Reviewer - 0% reviewed 1h 12m 13 this looks particularly weird - what's going on ?
    Total   1h 56m 13  
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    Objectives

    • Add HiddenMarkovModel class
    • Update HiddenMarkovModel class
    • add HMMFile class to read and write HMM files
    • add tests for HMMFile class
    • restructure file exporter
    • create method to test HMM model as string
    • fully integrate HMMER3 file format into Jalview
    • add HMMER colour scheme
    • test HMMER colour scheme
    • transferred the storage position of the HMM to annotations
    • add information content calculations
    • complete Information Content annotation
    • test HMM annotaTION

    Branches in review

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    Issues Raised From Comments

    Key Summary State Assignee
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    General Comments

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    /examples/uniref50_hmm Added
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    /resources/lang/Messages.properties Changed
    /src/jalview/analysis/AAFrequency.java Changed 1
    /src/jalview/analysis/SeqsetUtils.java Changed
    /src/jalview/api/AlignViewportI.java Changed
    /src/jalview/appletgui/AlignFrame.java Changed
    /src/jalview/appletgui/AlignViewport.java Changed
    /src/jalview/bin/Cache.java Changed
    /src/jalview/bin/Jalview.java Changed
    /src/jalview/datamodel/Alignment.java Changed
    /src/.../datamodel/AlignmentAnnotation.java Changed
    /src/jalview/datamodel/AlignmentI.java Changed
    /src/jalview/datamodel/AlignmentOrder.java Changed
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    /src/.../datamodel/AnnotatedCollectionI.java Changed
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    /src/.../datamodel/EValueStatistic.java Deleted
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    /src/jalview/datamodel/HMMNode.java Added
    /src/.../datamodel/HiddenMarkovModel.java Added 7
    /src/jalview/datamodel/ResidueCount.java Changed
    /src/jalview/datamodel/Sequence.java Changed
    /src/.../datamodel/SequenceCollectionI.java Changed
    /src/jalview/datamodel/SequenceGroup.java Changed
    /src/jalview/datamodel/SequenceI.java Changed
    /src/jalview/gui/AlignFrame.java Changed 2
    /src/jalview/gui/AlignViewport.java Changed
    /src/jalview/gui/AnnotationLabels.java Changed 1
    /src/jalview/gui/OptsAndParamsPage.java Changed
    /src/jalview/gui/PopupMenu.java Changed
    /src/jalview/gui/Preferences.java Changed
    /src/jalview/gui/WsJobParameters.java Changed
    /src/jalview/hmmer/HMMAlignThread.java Added
    /src/jalview/hmmer/HMMBuildThread.java Added
    /src/jalview/hmmer/HMMERCommands.java Added
    /src/jalview/hmmer/HMMERParamStore.java Added
    /src/jalview/hmmer/HMMERPreset.java Added
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    /src/jalview/hmmer/HMMSearchThread.java Added
    /src/jalview/hmmer/alignment_buffer.sto Deleted
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    /src/jalview/hmmer/alignment_input.sto Deleted
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    /src/jalview/hmmer/hmm_buffer.hmm Deleted
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    /src/jalview/io/AlignFile.java Changed
    /src/jalview/io/FileFormat.java Changed 1
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    /src/jalview/io/FileLoader.java Changed
    /src/jalview/io/HMMFile.java Added 1
    /src/jalview/io/IdentifyFile.java Changed
    /src/jalview/io/StockholmFile.java Changed
    /src/jalview/jbgui/GAlignFrame.java Changed
    /src/jalview/jbgui/GPreferences.java Changed
    /src/.../renderer/AnnotationRenderer.java Changed
    /src/jalview/renderer/ResidueShader.java Changed
    /src/jalview/renderer/ResidueShaderI.java Changed
    /src/.../schemes/HMMERAlignmentColourScheme.java Added
    /src/.../schemes/HMMERColourScheme.java Added
    /src/.../schemes/JalviewColourScheme.java Changed
    /src/.../schemes/ResidueProperties.java Changed
    /src/.../util/HMMProbabilityDistributionAnalyser.java Added
    /src/.../util/ProbabilityAnalyserKickstarter.java Added
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    /src/.../viewmodel/AlignmentViewport.java Changed
    /src/jalview/workers/AlignCalcManager.java Changed
    /src/.../workers/InformationThread.java Added
    /src/jalview/ws/jws2/MsaWSThread.java Changed
    /src/jalview/.../simple/DoubleParameter.java Added
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    /src/.../simple/LogarithmicParameter.java Added
    /src/jalview/.../simple/StringParameter.java Added
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    /src/jalview/.../params/ValueConstrainI.java Changed
    /test/.../analysis/AAFrequencyTest.java Changed
    /test/.../datamodel/HiddenMarkovModelTest.java Added
    /test/jalview/hmmer/HMMERTest.java Added
    /test/jalview/io/FileFormatsTest.java Changed
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    /test/jalview/io/FormatAdapterTest.java Changed
    /test/jalview/io/HMMFileTest.java Added
    /test/jalview/io/test_MADE1_hmm.txt Added
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    /test/jalview/io/test_PKinase_hmm.txt Added
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    /test/jalview/io/test_export_hmm.txt Added
    /test/jalview/io/test_fn3_hmm.txt Added
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    /test/.../schemes/HMMERColourSchemeTest.java Added
    /test/jalview/util/Binned.csv Added
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    /test/.../util/HMMProbabilityDistributionAnalyserTest.java Added