jalview

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JAL-2137 prevent NPE when inFile is null. Not sure this is correct ?

JAL-2137 create 1:1 mapping between model and query sequence

JAL-2137 hack to locate a StructureSelectionManager from some context

JAL-2137 resolve safely for URI and local paths

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    /src/jalview/io/AnnotationFile.java
JAL-2137 resolve baseURI for prepending to alignments/PDBs for STRUCTMODEL statement (needs test!)

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    /src/jalview/io/AnnotationFile.java
Merge branch 'develop' into spike/JAL-2040_JAL-2137_phyre2

JAL-2135 bugfix for error preventing processing of secondary structure annotation for model produced by Phyre2

JAL-2074 Improvement to StructureChooser and FTS interfaces to remember the user preferences for summary table columns, window size & positions

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    /src/jalview/fts/api/GFTSPanelI.java
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    /src/jalview/fts/core/FTSRestResponse.java
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    /src/jalview/fts/core/GFTSPanel.java
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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/jbgui/GStructureChooser.java
JAL-2137 basic implementation of STRUCTMODEL annotation file statement

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    /src/jalview/io/AnnotationFile.java
JAL-2137 JAL-2040 test and data for importing models/template sequences

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    /examples/testdata/phyre2/c1o1nA_.9.fasta.jal
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    /examples/testdata/phyre2/c1o1nA_.9.pdb
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    /examples/testdata/phyre2/c1ut0A_.14.fasta.jal
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    /examples/testdata/phyre2/c1ut0A_.14.pdb
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    /examples/testdata/phyre2/c1x3kA_.11.fasta.jal
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    /examples/testdata/phyre2/c1x3kA_.11.pdb
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    /examples/testdata/phyre2/c1yhuW_.19.fasta.jal
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    /examples/testdata/phyre2/c1yhuW_.19.pdb
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    /examples/testdata/phyre2/c2olpB_.5.fasta.jal
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    /examples/testdata/phyre2/c2olpB_.5.pdb
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    /examples/testdata/phyre2/c2zs0A_.17.fasta.jal
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    /examples/testdata/phyre2/c2zs0A_.17.pdb
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    /examples/testdata/phyre2/c3pt8B_.3.fasta.jal
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    /examples/testdata/phyre2/c3pt8B_.3.pdb
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    /examples/testdata/phyre2/c4b4yA_.7.fasta.jal
  1. … 28 more files in changeset.
JAL-1919 updated PDBSequenceFetcherTest and JMol parser config settings to enable proper processing of mmCIF files

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    /src/jalview/io/AppletFormatAdapter.java
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    /test/jalview/ws/PDBSequenceFetcherTest.java
JAL-2137 STRUCTMODEL statement added, logic not yet implemented

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    /src/jalview/io/AnnotationFile.java
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

JAL-1479 added test case to elaborate getEntityByMostOptimalMatchedId method

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    /test/jalview/io/2nq2.pdb
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    /test/jalview/ws/sifts/SiftsClientTest.java
JAL-1270 avoid overwriting .jalview_properties with test service urls

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    /test/jalview/ws/gui/Jws2ParamView.java
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

JAL-1479 improved Sifts PID calculation for determining an Entity to process

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    /src/jalview/ws/sifts/SiftsClient.java
JAL-1369 fix bug reloading a project with group sequence reps

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    /src/jalview/gui/Jalview2XML.java
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    /test/jalview/io/Jalview2xmlTests.java
JAL-1479 minor refactor and housekeeping

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    /src/jalview/ws/sifts/SiftsClient.java
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    /test/jalview/ws/sifts/SiftsClientTest.java
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

JAL-1479 improved SiftsClient test coverage and implemented previously unimplemented test cases

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    /src/jalview/ws/sifts/MappingOutputPojo.java
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    /src/jalview/ws/sifts/SiftsClient.java
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    /test/jalview/io/1a70.pdb
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    /test/jalview/ws/sifts/SiftsClientTest.java
tidied loop with generic iteration / loop variable

JAL-2133 refactored duplicated code to AlignmentViewport

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    /src/jalview/appletgui/APopupMenu.java
JAL-1369 additional asserts in testStoreAndRecoverReferenceSeqSettings

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    /test/jalview/io/Jalview2xmlTests.java
JAL-1270 unit tests for HiddenSequences

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    /test/jalview/datamodel/HiddenSequencesTest.java
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

JAL-1960 updated unit test to include the test case where a sequences has no PDBId entry(s) but has Uniprot & PDB dbrefs

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    /src/jalview/gui/StructureChooser.java
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    /test/jalview/gui/StructureChooserTest.java
JAL-2130 now simply viewer.dispose() to close down Jmol threads

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
JAL-1996 added notes for an alternative way to view example pages source code

Merge branch 'develop' of https://source.jalview.org/git/jalview into develop