Reviewing the alphafold + contact matrix patch for 2.11.2

Activity

CR-JAL-250 3

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    Participant Role Time Spent Comments Latest Comment
    Author 20m 3 patch needed for 2.11.2 - JAL-3518 - catch case when no r...
    Total   20m 3  
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    Objectives

    • basic hack to get (almost) equal height density plot
    • JAL-2348 custom renderer type
    • JAL-2349 interfaces and logic for adding contact matrices as an alignment’s annotation row
    • JAL-2349 dummy contact matrix annotation row
    • JAL-2348 row renderer interface
    • JAL-2348 row renderer factory interface
    • JAL-2348 contact map renderer refactored from hacked version of matrix row renderer
    • JAL-2348 JAL-2349 refactored contact map renderer and renderer factory implementation
    • JAL-2348 adjustable height for any non-label render type.
    • JAL-2348 JAL-2349 make contact maps non-editable so their display height can be adjusted
    • JAL-2349 add dummy contact for both applet and application
    • JAL-2349 contact renderer prototype (that doesn’t hang!)
    • JAL-2348 make debug message reporting renderer used to be optional
    • JAL-2349 tidying
    • JAL-2349 contact map interface todo
    • JAL-2349 method to get contact intensity for given site
    • JAL-2349 method to get display colour to represent a range of contacts
    • JAL-2349 fixed rendering method and switched to using color from contact range to allow subsampling
    • JAL-2349 JAL-2382 example contact prediction in RR format from raptorX (with alignment and 3D models as well)
    • JAL-2349 JAL-2382 contact matrix datamodel object
    • JAL-2349 JAL-2382 Contact prediction/CASP-RR importer
    • JAL-2349 better names for getColourForRange parameters
    • JAL-2349 javadoc dummy contact matrix
    • JAL-2349 rename ContactMatrixTest to SeqDistanceContactMatrix
    • JAL-2349 bean for getting max/min/avg for contact range
    • JAL-2349 bean holds mean and max for a range
    • JAL-2349 Abstract logic for colouring and computing over a range of contacts on a ContactListI from the data provider for the contact list.
    • JAL-2349 ContactMatrixI provided max/min getters
    • JAL-2349 colour shade computation refactored to annotation row renderer
    • JAL-2349 test for ContactMatrixI/ContactListI/ContactListProviderI chain
    • Merge branch 'develop' into spike/matrix_annot
    • Merge branch 'develop' into features/JAL-2349_matrixvis JAL-2349 update for refactor of hidden columns out of column selection
    • JAL-2349 min and max passed by renderer
    • JAL-2349 scaling matrix column to annotation height
    • JAL-3855 convenience method to check a URL will return a 200
    • Merge branch 'develop' into features/JAL-2349_matrixvis
    • JAL-3855 check for existence of an alpha fold model when pinging the PDBe
    • Merge branch 'features/JAL-2349_matrixvis' into merge/develop_JAL-2340_matrixvis
      Conflicts:
      src/jalview/datamodel/Alignment.java
      src/jalview/datamodel/AlignmentI.java
    • Merge branch 'develop' into features/JAL-2349_matrixvis
    • JAL-3855 check if an alpha fold ID and retrieve using that source
    • Merge branch 'merge/develop_JAL-2340_matrixvis' into features/JAL-2349_matrixvis
    • JAL-3855 ALPHAFOLD database source based on the PDB retriever
    • Merge branch 'features/JAL-2349_matrixvis' into features/JAL-2349_matrixvis_2112
    • JAL-3855 suppress NPE when trying to retrieve SIFTS mappings for Alphafold PDB IDs
    • JAL-2349 remove test code
    • JAL-3674 Jmol seems to sometimes return a null for some commands, handle it at source
    • JAL-2349 patch NPE exception during gradle test..
    • Merge branch 'feature/JAL-3855_ebi_alphafold_import' into features/JAL-2349_matrixvis_2112
    • JAL-2349 allow contact map to be associated with a reference sequence
    • JAL-2349 - deobfuscate the renderer and fix it .. work in progress

    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/testdata/.../models/0README Added
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    /examples/.../models/195600.model_summary Added
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    /examples/.../models/195600_model_1.pdb Added
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    /examples/.../models/195600_model_2.pdb Added
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    /examples/.../models/195600_model_3.pdb Added
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    /examples/.../models/195600_model_4.pdb Added
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    /examples/.../models/195600_model_5.pdb Added
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    /examples/testdata/raptorxeg/0README_total Added
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    /examples/testdata/raptorxeg/195600.a2m Added
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    /examples/.../raptorxeg/195600.contactmap.txt Added
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    /examples/testdata/raptorxeg/195600.fasta Added
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    /examples/testdata/raptorxeg/195600.gcnn Added
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    /examples/testdata/raptorxeg/195600.png Added
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    /src/jalview/api/AlignViewportI.java Changed
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    /src/.../appletgui/#OverviewPanel.java# Added
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    /src/.../appletgui/AnnotationPanel.java Changed
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    /src/jalview/datamodel/Alignment.java Changed
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    /src/.../datamodel/AlignmentAnnotation.java Changed
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    /src/jalview/datamodel/AlignmentI.java Changed
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    /src/jalview/datamodel/ContactListI.java Added
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    /src/.../datamodel/ContactListImpl.java Added
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    /src/.../datamodel/ContactListProviderI.java Added
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    /src/jalview/datamodel/ContactMatrix.java Added
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    /src/jalview/datamodel/ContactMatrixI.java Added
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    /src/.../datamodel/ContactMatrixTest.java Deleted
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    /src/jalview/datamodel/ContactRange.java Added
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    /src/jalview/datamodel/Profile.java~ Added
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    /src/jalview/datamodel/ProfileI.java~ Added
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    /src/jalview/datamodel/Profiles.java~ Added
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    /src/jalview/datamodel/ProfilesI.java~ Added
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    /src/jalview/datamodel/ResidueCount.java~ Added
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    /src/.../datamodel/SearchResultMatchI.java~ Added
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    /src/.../datamodel/SearchResultsI.java~ Added
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    /src/.../datamodel/SeqDistanceContactMatrix.java Added
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    /src/jalview/ext/jmol/JmolParser.java~ Added
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    /src/.../alphafold/AlphafoldRestClient.java Added
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    /src/jalview/.../pdb/PDBFTSRestClient.java Changed
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    /src/jalview/gui/#OverviewPanel.java# Added
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    /src/jalview/gui/AnnotationPanel.java Changed
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    /src/jalview/gui/AppJmol.java Changed
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    /src/jalview/gui/SeqCanvas.java.broken Added
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    /src/jalview/gui/StructureChooser.java~ Added
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    /src/jalview/gui/StructureViewerBase.java Changed 1
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    /src/jalview/gui/TreeCanvas.java~ Added
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    /src/jalview/io/AppletFormatAdapter.java Changed
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    /src/jalview/io/FileLoader.java Changed
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    /src/.../io/PContactPredictionFile.java Added
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    /src/.../api/AnnotationRendererFactoryI.java Added
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    /src/.../api/AnnotationRowRendererI.java Added
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    /src/.../renderer/AnnotationRenderer.java Changed
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    /src/.../renderer/AnnotationRendererFactory.java Added
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    /src/.../renderer/ContactMapRenderer.java Added
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    /src/.../structure/StructureSelectionManager.java Changed 1
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    /src/.../structure/StructureSelectionManager.java~ Added
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    /src/.../models/AAStructureBindingModel.java Changed 1
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    /src/jalview/util/HttpUtils.java Changed
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    /src/jalview/util/SparseCount.java~ Added
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    /src/.../viewmodel/AlignmentViewport.java Changed
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    /src/.../alphafold/PAEContactMatrix.java Added
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    /src/jalview/ws/dbsources/EBIAlfaFold.java Added
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    /src/jalview/ws/dbsources/Pdb.java~ Added
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    /src/jalview/ws/SequenceFetcher.java Changed
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    /test/.../datamodel/ContactMatrixTest.java Added
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    /test/.../datamodel/ContactRangeTest.java Added
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    /test/jalview/gui/SeqPanelTest.java Changed
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    /test/.../seqfetcher/DbRefFetcherTest.java Changed
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