Jalview Git

• 

  James Procter <j.procter@dundee.ac.uk> 24 Feb 2023 82ccd1295e4b80f2b22950f2db2ee8dffe6f5969

  JAL-629 JAL-4124 JAL-3855 test to check we can import PAE matrices in a variety of formats - additional test case

  • examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4_2023.json (version 82ccd1295e4b80f2b22950f2db2ee8dffe6f5969) (diffs)
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  James Procter <j.procter@dundee.ac.uk> 24 Feb 2023 7f98aeaa190d77fd40dcf80d55faedcace024d6f

  JAL-629 JAL-4124 JAL-3855 test to check we can import PAE matrices in a variety of formats - and fix up a casting issue (again?)

  • src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java (version 7f98aeaa190d77fd40dcf80d55faedcace024d6f) (diffs)
  • src/jalview/ws/dbsources/EBIAlfaFold.java (version 7f98aeaa190d77fd40dcf80d55faedcace024d6f) (diffs)
  • test/jalview/ws/dbsources/EBIAlphaFoldTest.java (version 7f98aeaa190d77fd40dcf80d55faedcace024d6f) (diffs)
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  James Procter <j.procter@dundee.ac.uk> 24 Feb 2023 8b5145f0837eeaeb1f029de179a3715a174dfa09

  Merge branch 'features/JAL-3858_PAEsInProjects' into develop
• 

  James Procter <j.procter@dundee.ac.uk> 24 Feb 2023 a939b4c646235d460df3b7b9377ef8d8569caaff

  Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects
   Conflicts:
          src/jalview/bin/Jalview.java
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  Ben Soares <b.soares@dundee.ac.uk> 24 Feb 2023 044e544652fa3a8205bdaae8303a03913fe812e8

  JAL-629 better test fixes. --props=... instead of --debug

  • test/jalview/bin/CommandLineOperations.java (version 044e544652fa3a8205bdaae8303a03913fe812e8) (diffs)
  • test/jalview/bin/HiDPISettingTest2.java (version 044e544652fa3a8205bdaae8303a03913fe812e8) (diffs)
  • test/jalview/util/Log4jTest.java (version 044e544652fa3a8205bdaae8303a03913fe812e8) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 24 Feb 2023 7057bdc72cbd324a4316f445118b509db4880499

  JAL-629 Made ArgValuesMap helper class, simplifies readability/writing of the code and will allow arg position lookups

  • src/jalview/bin/ArgParser.java (version 7057bdc72cbd324a4316f445118b509db4880499) (diffs)
  • src/jalview/bin/Commands.java (version 7057bdc72cbd324a4316f445118b509db4880499) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 23 Feb 2023 32a2c42a535d809dfcb48db1e8cc91bb03193f8e

  JAL-629 test fixing

  • test/jalview/bin/CommandLineOperations.java (version 32a2c42a535d809dfcb48db1e8cc91bb03193f8e) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 23 Feb 2023 bcc114c5106c3cee78db99955fee2392edece7df

  JAL-629 Add debug messages for more failing tests

  • test/jalview/bin/CommandLineOperations.java (version bcc114c5106c3cee78db99955fee2392edece7df) (diffs)
  • test/jalview/bin/HiDPISettingTest2.java (version bcc114c5106c3cee78db99955fee2392edece7df) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 23 Feb 2023 2a1686e13e5641fb7f353931e2160e76b1f548e4

  JAL-629 fixed a Log4j test by adding --debug arg

  • test/jalview/util/Log4jTest.java (version 2a1686e13e5641fb7f353931e2160e76b1f548e4) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 23 Feb 2023 3de8bf931e7b9e2a71a8959a7dd1260d33dc9034

  JAL-629 bootstrap args and properties. Remember index of args for 'previous structure' defaulting of other args

  • src/jalview/bin/ArgParser.java (version 3de8bf931e7b9e2a71a8959a7dd1260d33dc9034) (diffs)
  • src/jalview/bin/Cache.java (version 3de8bf931e7b9e2a71a8959a7dd1260d33dc9034) (diffs)
  • src/jalview/bin/Commands.java (version 3de8bf931e7b9e2a71a8959a7dd1260d33dc9034) (diffs)
  • src/jalview/bin/Console.java (version 3de8bf931e7b9e2a71a8959a7dd1260d33dc9034) (diffs)
  • src/jalview/bin/Jalview.java (version 3de8bf931e7b9e2a71a8959a7dd1260d33dc9034) (diffs)
  • src/jalview/log/JLogger.java (version 3de8bf931e7b9e2a71a8959a7dd1260d33dc9034) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 23 Feb 2023 17e4f20de9bae8c98c25ac61f61fba99d2da7b56

  JAL-629 nf-core sample alignment files and a2m versions

  • examples/test_fab41.result/sample.a2m (version 17e4f20de9bae8c98c25ac61f61fba99d2da7b56) (diffs)
  • examples/test_fab41.result/sample.a3m (version 17e4f20de9bae8c98c25ac61f61fba99d2da7b56) (diffs)
  • examples/test_fab41.result/test_fab41.a2m (version 17e4f20de9bae8c98c25ac61f61fba99d2da7b56) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 23 Feb 2023 8479d86d490c841168c9eed1ac80960ce4191c78

  JAL-629 fix a PAEMatrix casting error

  • src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java (version 8479d86d490c841168c9eed1ac80960ce4191c78) (diffs)
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  James Procter <j.procter@dundee.ac.uk> 23 Feb 2023 8135460a52c0551e4a40777d077843fd4e19c049

  JAL-3858 new MatrixType JAX-RI POJO

  • src/jalview/xml/binding/jalview/MatrixType.java (version 8135460a52c0551e4a40777d077843fd4e19c049) (diffs)
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  James Procter <j.procter@dundee.ac.uk> 23 Feb 2023 cfea32f10dfe5cde2b5223d8a6c1c26280ac0185

  JAL-4133 update validChar width when font is changed so characters are suppressed for small widths

  • src/jalview/gui/AlignmentPanel.java (version cfea32f10dfe5cde2b5223d8a6c1c26280ac0185) (diffs)
  • src/jalview/project/Jalview2XML.java (version cfea32f10dfe5cde2b5223d8a6c1c26280ac0185) (diffs)
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  James Procter <j.procter@dundee.ac.uk> 22 Feb 2023 ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530

  JAL-4133 store/restore alignment view’s charWidth and charHeight in Jalview project

  • schemas/jalview.xsd (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/gui/AlignViewport.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/project/Jalview2XML.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/embl/EntrySetType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/embl/EntryType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/embl/ObjectFactory.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/embl/ROOT.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/embl/XrefType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/AlcodonFrame.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/Annotation.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/AnnotationColourScheme.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/AnnotationElement.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/DoubleMatrix.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/DoubleVector.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/Feature.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/FeatureMatcher.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/FeatureMatcherSet.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/FilterBy.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/JalviewModel.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/JalviewUserColours.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/MapListType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/Mapping.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/NoValueColour.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/ObjectFactory.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/PcaDataType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/Pdbentry.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/Sequence.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/SequenceSet.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/SequenceType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/ThresholdType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/VAMSAS.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/WebServiceParameterSet.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/jalview/package-info.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/CitationType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/CofactorType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/CommentType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/ConsortiumType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/DbReferenceType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/Entry.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/EventType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/EvidenceType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/EvidencedStringType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/FeatureType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/GeneLocationType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/GeneNameType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/GeneType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/ImportedFromType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/InteractantType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/IsoformType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/KeywordType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/LocationType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/MoleculeType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/NameListType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/ObjectFactory.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/OrganismNameType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/OrganismType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/PersonType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/PositionType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/PropertyType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/ProteinExistenceType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/ProteinType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/ReactionType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/ReferenceType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/SequenceType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/SourceDataType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/SourceType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/StatusType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/SubcellularLocationType.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/Uniprot.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
  • src/jalview/xml/binding/uniprot/package-info.java (version ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 22 Feb 2023 335e6b12c126bcb6825cd3f66422677db7cd91c7

  JAL-3858 persist PAE matrix (only so far) as serialised floats in element on dataset sequence annotation. Rudimentary tests.

  • schemas/jalview.xsd (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • schemas/vamsas.xsd (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/datamodel/ContactMapHolder.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/datamodel/ContactMatrix.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/datamodel/ContactMatrixI.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/datamodel/SeqDistanceContactMatrix.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/io/PContactPredictionFile.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/project/Jalview2XML.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/embl/EntrySetType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/embl/EntryType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/embl/ObjectFactory.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/embl/ROOT.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/embl/XrefType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/AlcodonFrame.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/Annotation.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/AnnotationColourScheme.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/AnnotationElement.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/DoubleMatrix.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/DoubleVector.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/Feature.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/FeatureMatcher.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/FeatureMatcherSet.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/FilterBy.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/JalviewModel.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/JalviewUserColours.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/MapListType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/Mapping.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/NoValueColour.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/ObjectFactory.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/PcaDataType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/Pdbentry.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/Sequence.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/SequenceSet.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/SequenceType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/ThresholdType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/VAMSAS.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/WebServiceParameterSet.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/jalview/package-info.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/CitationType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/CofactorType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/CommentType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/ConsortiumType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/DbReferenceType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/Entry.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/EventType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/EvidenceType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/EvidencedStringType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/FeatureType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/GeneLocationType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/GeneNameType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/GeneType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/ImportedFromType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/InteractantType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/IsoformType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/KeywordType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/LocationType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/MoleculeType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/NameListType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/ObjectFactory.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/OrganismNameType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/OrganismType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/PersonType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/PositionType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/PropertyType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/ProteinExistenceType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/ProteinType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/ReactionType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/ReferenceType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/SequenceType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/SourceDataType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/SourceType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/StatusType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/SubcellularLocationType.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/Uniprot.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • src/jalview/xml/binding/uniprot/package-info.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
  • test/jalview/project/Jalview2xmlTests.java (version 335e6b12c126bcb6825cd3f66422677db7cd91c7) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 22 Feb 2023 9d9ad2a9237a50e305349a63eb01bb5548d028d0

  JAL-1551 source formatting

  • test/jalview/project/Jalview2xmlTests.java (version 9d9ad2a9237a50e305349a63eb01bb5548d028d0) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 22 Feb 2023 97725e865411eec548a4b400ed9277b591f3fb6e

  JAL-3858 simple test for PAE matrix recovery

  • test/jalview/project/Jalview2xmlTests.java (version 97725e865411eec548a4b400ed9277b591f3fb6e) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 22 Feb 2023 df3da405342b96c6630e280a2ac407864ac3a62f

  JAL-3858 construct a PAE direct from float array

  • src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java (version df3da405342b96c6630e280a2ac407864ac3a62f) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 22 Feb 2023 e8f870fb9e3ccb05b9c1c2163e01919d346ce9de

  Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629
• 

  Ben Soares <b.soares@dundee.ac.uk> 22 Feb 2023 969fe2931a113706ddd06888213c8f71f546d325

  JAL-4064 JAL-4054 Corrected the tgz top-level dir from './Contents' to 'Contents' for mac JRE bundles for install4j (not strictly used, but might be in the future).

  • utils/download_jres.sh (version 969fe2931a113706ddd06888213c8f71f546d325) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 22 Feb 2023 b8f69c187f02cf7213b92b4882afe36c7c16a733

  JAL-629 make sure we show GUI when not driven programmatically

  • src/jalview/gui/StructureChooser.java (version b8f69c187f02cf7213b92b4882afe36c7c16a733) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 22 Feb 2023 f346bddd94c1dc16ef893a1b6f1e61610603afb7

  JAL-4095 slightly better threshold setting and todos for improvement

  • src/jalview/gui/AnnotationPanel.java (version f346bddd94c1dc16ef893a1b6f1e61610603afb7) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 22 Feb 2023 5830c6b18969d8eb7801b9df28ea9fb2c4dd5152

  JAL-4095 magic fill behaviour is PAE specific

  • src/jalview/gui/AnnotationPanel.java (version 5830c6b18969d8eb7801b9df28ea9fb2c4dd5152) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 22 Feb 2023 a7bc89415a6749ff89eb97f75fbc950a433a4935

  Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629
• 

  James Procter <j.procter@dundee.ac.uk> 22 Feb 2023 d300c87891d25a5542f47e1bc3cbb9a0b547bb24

  JAL-3858 JAL-2381 allow different linear shading schemes for selected/non-selected regions of contact matrix heat map

  • src/jalview/renderer/AnnotationRendererFactory.java (version d300c87891d25a5542f47e1bc3cbb9a0b547bb24) (diffs)
  • src/jalview/renderer/ContactMapRenderer.java (version d300c87891d25a5542f47e1bc3cbb9a0b547bb24) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 22 Feb 2023 c2dd443026847395d0c9dc824c6c90457de9a675

  JAL-4027 JAL-3858 rename CUSTOM_RENDERER to CONTACT_MATRIX annotation.graph type, with actual matrix type stored in calcId

  • src/jalview/datamodel/AlignmentAnnotation.java (version c2dd443026847395d0c9dc824c6c90457de9a675) (diffs)
  • src/jalview/datamodel/ColumnSelection.java (version c2dd443026847395d0c9dc824c6c90457de9a675) (diffs)
  • src/jalview/datamodel/ContactMapHolder.java (version c2dd443026847395d0c9dc824c6c90457de9a675) (diffs)
  • src/jalview/datamodel/ContactMatrix.java (version c2dd443026847395d0c9dc824c6c90457de9a675) (diffs)
  • src/jalview/datamodel/ContactMatrixI.java (version c2dd443026847395d0c9dc824c6c90457de9a675) (diffs)
  • src/jalview/datamodel/SeqDistanceContactMatrix.java (version c2dd443026847395d0c9dc824c6c90457de9a675) (diffs)
  • src/jalview/gui/AnnotationPanel.java (version c2dd443026847395d0c9dc824c6c90457de9a675) (diffs)
  • src/jalview/io/PContactPredictionFile.java (version c2dd443026847395d0c9dc824c6c90457de9a675) (diffs)
  • src/jalview/renderer/AnnotationRendererFactory.java (version c2dd443026847395d0c9dc824c6c90457de9a675) (diffs)
  • src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java (version c2dd443026847395d0c9dc824c6c90457de9a675) (diffs)
  • test/jalview/ws/seqfetcher/DbRefFetcherTest.java (version c2dd443026847395d0c9dc824c6c90457de9a675) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 21 Feb 2023 cd46ad8d4118e305b3cdf92ca8dc51cc9c354be7

  JAL-4088 Updated j8libs/*.jar in THIRDPARTYLIBS

  • THIRDPARTYLIBS (version cd46ad8d4118e305b3cdf92ca8dc51cc9c354be7) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 20 Feb 2023 f5b4426851a1950286204b97e488f205d1573c10

  JAL-3416 Turn off (partial) flatlaf scaling for HiDPI in Linux and Java 8 - Some GUI parts unusable

  • src/jalview/bin/Jalview.java (version f5b4426851a1950286204b97e488f205d1573c10) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 20 Feb 2023 b26bea3c3421ce3e233dc18d3077b231f972c5f8

  JAL-4064 JAL-4054 Correct names of mac arch installer DMG files

  • utils/install4j/install4j10_template.install4j (version b26bea3c3421ce3e233dc18d3077b231f972c5f8) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 20 Feb 2023 50caa2bce4379ecdb02a2c0eccc44078487f2f0b

  Merge branch 'develop' into improvement/JAL-4111_suffixed_DEVELOP_channels
• 

  Ben Soares <b.soares@dundee.ac.uk> 20 Feb 2023 e6e897ddf845d4e79ff5e6c7afddf66766c7d31d

  JAL-4128 Catch RasterFormatException caused whilst resizing Overview window, recalculate OverviewDimensions od instead. Prevent negative OverviewDimensions being set to avoid problem with vertically fully shrunk overview window 'losing' the alignement canvas.

  • src/jalview/gui/OverviewCanvas.java (version e6e897ddf845d4e79ff5e6c7afddf66766c7d31d) (diffs)
  • src/jalview/viewmodel/OverviewDimensions.java (version e6e897ddf845d4e79ff5e6c7afddf66766c7d31d) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 20 Feb 2023 a327fd39320e482fad4b57f256f3e3c8ebcf015b

  Merge branch 'develop' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
• 

  James Procter <j.procter@dundee.ac.uk> 16 Feb 2023 0de37d1a047209510bab82225109ae2a47931f79

  Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects
   Conflicts:
          src/jalview/bin/Jalview.java
• 

  James Procter <j.procter@dundee.ac.uk> 16 Feb 2023 d6eab72955158d1e070b45dfd93e55c64a47ff86

  JAL-1713 don’t close an automatically created overview window for projects from Jalview versions older than 2.11.3

  • src/jalview/project/Jalview2XML.java (version d6eab72955158d1e070b45dfd93e55c64a47ff86) (diffs)
  • test/jalview/project/Jalview2xmlTests.java (version d6eab72955158d1e070b45dfd93e55c64a47ff86) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 15 Feb 2023 284b555bcff969e2b92d32241ede65e4c7e538bb

  Merge branch 'develop' into feature/JAL-1713_overviewInProject
• 

  James Procter <j.procter@dundee.ac.uk> 15 Feb 2023 164a8192345f622c2f9c62d3b0c6e593b5f08af4

  Passing test for JAL-4127 failing on the JAL-1713 branch

  • test/jalview/project/Jalview2xmlTests.java (version 164a8192345f622c2f9c62d3b0c6e593b5f08af4) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 15 Feb 2023 17863d983fe946ec642e3d6d86cabd2e01be3b19

  JAL-4090 move 2.11.3 series release notes to 2.11.3.0 release and premptively list issues already or nearly addressed in this version

  • help/markdown/releases/release-2_11_3.md (version 17863d983fe946ec642e3d6d86cabd2e01be3b19) (diffs)
  • help/markdown/releases/release-2_11_3_0.md (version 17863d983fe946ec642e3d6d86cabd2e01be3b19) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 13 Feb 2023 75509b3431c75337de94bb92c74d0cc35701ee52

  Merge branch 'develop' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
• 

  Ben Soares <b.soares@dundee.ac.uk> 13 Feb 2023 23886ff208184dbdb811ea445cfd6dbad7087fab

  JAL-4125 Spanish translations

  • resources/lang/Messages_es.properties (version 23886ff208184dbdb811ea445cfd6dbad7087fab) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 13 Feb 2023 5a166386ec498f9887de88dc3221fa48f9287d4c

  Merge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
• 

  Ben Soares <b.soares@dundee.ac.uk> 13 Feb 2023 9b943e6d79fd92f78a61916a6f6eb047ba0a9755

  JAL-4125 Move confirmation of closing external viewer windows into the quit handler, and allow all to close or not in closeViewer whilst quitting.

  • resources/lang/Messages.properties (version 9b943e6d79fd92f78a61916a6f6eb047ba0a9755) (diffs)
  • src/jalview/api/structures/JalviewStructureDisplayI.java (version 9b943e6d79fd92f78a61916a6f6eb047ba0a9755) (diffs)
  • src/jalview/gui/Desktop.java (version 9b943e6d79fd92f78a61916a6f6eb047ba0a9755) (diffs)
  • src/jalview/gui/QuitHandler.java (version 9b943e6d79fd92f78a61916a6f6eb047ba0a9755) (diffs)
  • src/jalview/gui/StructureViewerBase.java (version 9b943e6d79fd92f78a61916a6f6eb047ba0a9755) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 13 Feb 2023 b303b657375dee5ac79e2f52ef96803652a2fbd1

  Merge branch 'develop' into feature/JAL-1713_overviewInProject
• 

  James Procter <j.procter@dundee.ac.uk> 10 Feb 2023 421c0cd3daea00db58f42af499c8415608fb0aaa

  JAL-3077 broken conflict resolve resulted in failing test (nb - still not resolved the issue of (promoted) dbrefs!)

  • test/jalview/ws/dbsources/UniprotTest.java (version 421c0cd3daea00db58f42af499c8415608fb0aaa) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 10 Feb 2023 e7623d0a250b5d4908c45d50f52a78be4e339ce7

  Fix for JAL-4126 - don’t automatically create a threshold line when no threshold line is needed when reconstructing the annotation colour scheme from a project file

  • src/jalview/project/Jalview2XML.java (version e7623d0a250b5d4908c45d50f52a78be4e339ce7) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 10 Feb 2023 a473afe5d67b0368c7627c001c65fe9a6117dd16

  JAL-4126 comment out closeAll - so we can visually check the alignment frame as it is restored

  • test/jalview/project/Jalview2xmlTests.java (version a473afe5d67b0368c7627c001c65fe9a6117dd16) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 10 Feb 2023 dcb4c919fdf50dd481eb411c11a657611ab4f63b

  JAL-4126 failing test - colour scheme appears to be being created and configured, but the renderer is not actually using the colour scheme to shade the sequence when the project is restored.

  • test/jalview/project/Jalview2xmlTests.java (version dcb4c919fdf50dd481eb411c11a657611ab4f63b) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 09 Feb 2023 b865b46f6f34e82f5d10fccfe646f00b8ae2e7a1

  JAL-4125 Additions to JvOptionPane and QuitHandler with StructureViewerBase handling closed frame during quit differently. Still not working as dialog content does not appear until after quithandling thread has finished (it's blocking EDT).  Need to break the doDesktopQuit Callable up into sections, that add another bit to the end when necessary.

  • src/jalview/gui/Desktop.java (version b865b46f6f34e82f5d10fccfe646f00b8ae2e7a1) (diffs)
  • src/jalview/gui/JvOptionPane.java (version b865b46f6f34e82f5d10fccfe646f00b8ae2e7a1) (diffs)
  • src/jalview/gui/QuitHandler.java (version b865b46f6f34e82f5d10fccfe646f00b8ae2e7a1) (diffs)
  • src/jalview/gui/StructureViewerBase.java (version b865b46f6f34e82f5d10fccfe646f00b8ae2e7a1) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 03 Feb 2023 01f8ff469a507604ed961418f7c80f9b245e60ca

  JAL-629 Fasta sequence id reading whitespace fix. Flexioble pae json keys and structure. Headless fixes. Logging fixes (MessageManager -- test broken). ArgParser and Console helper methods. Commands added e.g. --colour=gecos:flower.

  • src/jalview/bin/ArgParser.java (version 01f8ff469a507604ed961418f7c80f9b245e60ca) (diffs)
  • src/jalview/bin/Commands.java (version 01f8ff469a507604ed961418f7c80f9b245e60ca) (diffs)
  • src/jalview/bin/Console.java (version 01f8ff469a507604ed961418f7c80f9b245e60ca) (diffs)
  • src/jalview/bin/Jalview.java (version 01f8ff469a507604ed961418f7c80f9b245e60ca) (diffs)
  • src/jalview/gui/AlignFrame.java (version 01f8ff469a507604ed961418f7c80f9b245e60ca) (diffs)
  • src/jalview/gui/StructureChooser.java (version 01f8ff469a507604ed961418f7c80f9b245e60ca) (diffs)
  • src/jalview/io/AlignFile.java (version 01f8ff469a507604ed961418f7c80f9b245e60ca) (diffs)
  • src/jalview/log/JLogger.java (version 01f8ff469a507604ed961418f7c80f9b245e60ca) (diffs)
  • src/jalview/util/MapUtils.java (version 01f8ff469a507604ed961418f7c80f9b245e60ca) (diffs)
  • src/jalview/util/MessageManager.java (version 01f8ff469a507604ed961418f7c80f9b245e60ca) (diffs)
  • src/jalview/util/StringUtils.java (version 01f8ff469a507604ed961418f7c80f9b245e60ca) (diffs)
  • src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java (version 01f8ff469a507604ed961418f7c80f9b245e60ca) (diffs)
  • src/jalview/ws/dbsources/EBIAlfaFold.java (version 01f8ff469a507604ed961418f7c80f9b245e60ca) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 03 Feb 2023 5d01a31888d046245981a4171850acd63a1f2862

  JAL-629 "updated" json-simple

  • examples/test_fab41.result/sample.a3m (version 5d01a31888d046245981a4171850acd63a1f2862) (diffs)
  • j11lib/json-simple-1.1.1.jar (version 5d01a31888d046245981a4171850acd63a1f2862) (diffs)
  • j11lib/json_simple-1.1.jar (version 5d01a31888d046245981a4171850acd63a1f2862) (diffs)
  • j8lib/json-simple-1.1.1.jar (version 5d01a31888d046245981a4171850acd63a1f2862) (diffs)
  • j8lib/json_simple-1.1.jar (version 5d01a31888d046245981a4171850acd63a1f2862) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 03 Feb 2023 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35

  JAL-1551 remove temp file in src

  • src/jalview/appletgui/#OverviewPanel.java# (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
  • src/jalview/datamodel/Profile.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
  • src/jalview/datamodel/ProfileI.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
  • src/jalview/datamodel/Profiles.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
  • src/jalview/datamodel/ProfilesI.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
  • src/jalview/datamodel/ResidueCount.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
  • src/jalview/datamodel/SearchResultMatchI.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
  • src/jalview/datamodel/SearchResultsI.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
  • src/jalview/ext/jmol/JmolParser.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
  • src/jalview/gui/#OverviewPanel.java# (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
  • src/jalview/gui/StructureChooser.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
  • src/jalview/gui/TreeCanvas.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
  • src/jalview/structure/StructureSelectionManager.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
  • src/jalview/util/SparseCount.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
  • src/jalview/ws/dbsources/Pdb.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 03 Feb 2023 4a59f639cf5769d9ec66142ebecfa4961c5d3b04

  Merge branch 'develop' into features/r2_11_2_alphafold/JAL-2349_JAL-3855
• 

  James Procter <j.procter@dundee.ac.uk> 31 Jan 2023 3659ecfe7bb17dd25a0a6b5c94a7d9dab4525136

  JAL-1713 update from Jalview 2.11.3 develop Merge branch 'develop' into feature/JAL-1713_overviewInProject regenerated jaxb classes to resolve conflicts
• 

  Ben Soares <b.soares@dundee.ac.uk> 30 Jan 2023 140b350c1bb78f0d6b46f9fcbfc523a05c32beba

  JAL-1988 Make sensible choices if only the opening file has been opened, and alter the message if an alignment has been fetched but not changed

  • resources/lang/Messages.properties (version 140b350c1bb78f0d6b46f9fcbfc523a05c32beba) (diffs)
  • resources/lang/Messages_es.properties (version 140b350c1bb78f0d6b46f9fcbfc523a05c32beba) (diffs)
  • src/jalview/bin/Jalview.java (version 140b350c1bb78f0d6b46f9fcbfc523a05c32beba) (diffs)
  • src/jalview/gui/QuitHandler.java (version 140b350c1bb78f0d6b46f9fcbfc523a05c32beba) (diffs)
  • src/jalview/io/DataSourceType.java (version 140b350c1bb78f0d6b46f9fcbfc523a05c32beba) (diffs)
  • src/jalview/io/FileLoader.java (version 140b350c1bb78f0d6b46f9fcbfc523a05c32beba) (diffs)
  • src/jalview/viewmodel/AlignmentViewport.java (version 140b350c1bb78f0d6b46f9fcbfc523a05c32beba) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 26 Jan 2023 dbdd2bd3493e0aef8aa3c0fe054c6bceedc31316

  JAL-4118 remove unnecessary sleep from QuitHandlerTest

  • test/jalview/gui/QuitHandlerTest.java (version dbdd2bd3493e0aef8aa3c0fe054c6bceedc31316) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 26 Jan 2023 cd443f0faad6561791b4ae9a617bed680036959a

  JAL-4118 fix a small buglet in BackupFiles exhibited in tests on build server. Possible problem with filename with dirs in passed to BackupFiles.

  • src/jalview/io/BackupFiles.java (version cd443f0faad6561791b4ae9a617bed680036959a) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 26 Jan 2023 f205bfec471719e5735229689cab62e9b675ee2a

  JAL-1988 Add a sleep to file save test to give time for file to save

  • test/jalview/gui/QuitHandlerTest.java (version f205bfec471719e5735229689cab62e9b675ee2a) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 26 Jan 2023 453fa24ab502aaca4ffccf3590f97c897b9580b3

  JAL-629 example files from nf-core

  • examples/test_fab41.result/cite.bibtex (version 453fa24ab502aaca4ffccf3590f97c897b9580b3) (diffs)
  • examples/test_fab41.result/config.json (version 453fa24ab502aaca4ffccf3590f97c897b9580b3) (diffs)
  • examples/test_fab41.result/test_fab41.a3m (version 453fa24ab502aaca4ffccf3590f97c897b9580b3) (diffs)
  • examples/test_fab41.result/test_fab41_PAE.png (version 453fa24ab502aaca4ffccf3590f97c897b9580b3) (diffs)
  • examples/test_fab41.result/test_fab41_coverage.png (version 453fa24ab502aaca4ffccf3590f97c897b9580b3) (diffs)
  • examples/test_fab41.result/test_fab41_plddt.png (version 453fa24ab502aaca4ffccf3590f97c897b9580b3) (diffs)
  • examples/test_fab41.result/test_fab41_predicted_aligned_error_v1.json (version 453fa24ab502aaca4ffccf3590f97c897b9580b3) (diffs)
  • examples/test_fab41.result/test_fab41_template_domain_names.json (version 453fa24ab502aaca4ffccf3590f97c897b9580b3) (diffs)
  • examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb (version 453fa24ab502aaca4ffccf3590f97c897b9580b3) (diffs)
  • examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json (version 453fa24ab502aaca4ffccf3590f97c897b9580b3) (diffs)
  • examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb (version 453fa24ab502aaca4ffccf3590f97c897b9580b3) (diffs)
  • examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4_scores.json (version 453fa24ab502aaca4ffccf3590f97c897b9580b3) (diffs)
  • examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb (version 453fa24ab502aaca4ffccf3590f97c897b9580b3) (diffs)
  • examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2_scores.json (version 453fa24ab502aaca4ffccf3590f97c897b9580b3) (diffs)
  • examples/test_fab41.result/test_fab41_unrelaxed_rank_4_model_5.pdb (version 453fa24ab502aaca4ffccf3590f97c897b9580b3) (diffs)
  • examples/test_fab41.result/test_fab41_unrelaxed_rank_4_model_5_scores.json (version 453fa24ab502aaca4ffccf3590f97c897b9580b3) (diffs)
  • examples/test_fab41.result/test_fab41_unrelaxed_rank_5_model_1.pdb (version 453fa24ab502aaca4ffccf3590f97c897b9580b3) (diffs)
  • examples/test_fab41.result/test_fab41_unrelaxed_rank_5_model_1_scores.json (version 453fa24ab502aaca4ffccf3590f97c897b9580b3) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 26 Jan 2023 7e9057db7b5e80ed727411fdd0bf83c8008f0822

  JAL-629 helper eclipse CLI run

  • utils/eclipse/jalview (version 7e9057db7b5e80ed727411fdd0bf83c8008f0822) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 26 Jan 2023 08646d1f0486e645adeaf4ea9a6c0f6b599f980c

  JAL-629 adjust arg type for tempfac-shading -- was grabbing next argument

  • src/jalview/bin/ArgParser.java (version 08646d1f0486e645adeaf4ea9a6c0f6b599f980c) (diffs)
  • src/jalview/bin/Commands.java (version 08646d1f0486e645adeaf4ea9a6c0f6b599f980c) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 25 Jan 2023 15a605b8a12026b453e252477b416b2c82b6344a

  JAL-4116 relegate the failed to promote warning to Console.debug so most users won’t even see it (or be slowed down by it).

  • src/jalview/util/DBRefUtils.java (version 15a605b8a12026b453e252477b416b2c82b6344a) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 25 Jan 2023 09be4c7dd6a31d9a39e5317cc8dc9eb21e8e6ebf

  Merge branch 'new_feature/JAL-4019_ambiguous_base_colourscheme' into develop
• 

  James Procter <j.procter@dundee.ac.uk> 24 Jan 2023 f09ab2df2e8be8cdcf2e21d3e962470815743ff4

  JAL-4090 Release 2.11.3.0 release notes and version bump

  • RELEASE (version f09ab2df2e8be8cdcf2e21d3e962470815743ff4) (diffs)
  • help/markdown/releases/release-2_11_3_0.md (version f09ab2df2e8be8cdcf2e21d3e962470815743ff4) (diffs)
  • help/markdown/whatsnew/whatsnew-2_11_3_0.md (version f09ab2df2e8be8cdcf2e21d3e962470815743ff4) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 24 Jan 2023 6ff51fcc01238abb8f337aca7b6984fdc0b8368a

  Merge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064' into develop
• 

  James Procter <j.procter@dundee.ac.uk> 24 Jan 2023 3cea1ee2c1c9a2ad0a3b2c76bac165b1b6a3ff2a

  JAL-629 hacked in --tempfac-shading - hardcoded to use existing colours in per-sequence annotation

  • src/jalview/bin/Commands.java (version 3cea1ee2c1c9a2ad0a3b2c76bac165b1b6a3ff2a) (diffs)
  • src/jalview/gui/AnnotationColourChooser.java (version 3cea1ee2c1c9a2ad0a3b2c76bac165b1b6a3ff2a) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 24 Jan 2023 d1acebdf5841982b3825f95d7c9ea09a48f586ad

  JAL-629 suggest not breaking out of the structure processing loop if just one structure has a bunk sequence association..

  • src/jalview/bin/Commands.java (version d1acebdf5841982b3825f95d7c9ea09a48f586ad) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 24 Jan 2023 9c05fc8a07869007db06cc7efc54f2ac41e4575c

  JAL-629 need to delay call to AlignFile.parse() if StructureFile needs to configure itself at construction time

  • src/jalview/ext/jmol/JmolParser.java (version 9c05fc8a07869007db06cc7efc54f2ac41e4575c) (diffs)
  • src/jalview/io/AppletFormatAdapter.java (version 9c05fc8a07869007db06cc7efc54f2ac41e4575c) (diffs)
  • src/jalview/io/StructureFile.java (version 9c05fc8a07869007db06cc7efc54f2ac41e4575c) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 24 Jan 2023 09eebd8c6997a33049084e307078717cc1a693a6

  JAL-629 don’t carry on Jalview.main if we’ve already processed command line args another way

  • src/jalview/bin/Commands.java (version 09eebd8c6997a33049084e307078717cc1a693a6) (diffs)
  • src/jalview/bin/Jalview.java (version 09eebd8c6997a33049084e307078717cc1a693a6) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 24 Jan 2023 97708f316b561ec5f9f03d402945b522085b0d5b

  JAL-629 don’t trash user’s system property file when adjusting settings to process CL args

  • src/jalview/bin/Cache.java (version 97708f316b561ec5f9f03d402945b522085b0d5b) (diffs)
  • src/jalview/bin/Commands.java (version 97708f316b561ec5f9f03d402945b522085b0d5b) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 24 Jan 2023 6860179ce5f69173f230c05bd5fe6e85c73886a3

  JAL-629 don’t complain for Unary args

  • src/jalview/bin/ArgParser.java (version 6860179ce5f69173f230c05bd5fe6e85c73886a3) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 24 Jan 2023 c84d2601499c7d332cfd208f589686af8e3b1a20

  JAL-629 labelled breaks are frowned upon by everyone

  • src/jalview/bin/ArgParser.java (version c84d2601499c7d332cfd208f589686af8e3b1a20) (diffs)
  • src/jalview/bin/Commands.java (version c84d2601499c7d332cfd208f589686af8e3b1a20) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 24 Jan 2023 82fd9c4f22f03dd93e1b2f5f2024eb4d93cc4c6e

  Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL-3855' into features/r2_11_2_alphafold/JAL-629
• 

  James Procter <j.procter@dundee.ac.uk> 24 Jan 2023 a8c998b5e5debd0dc8a17daa8005a1cc3ca07078

  Merge branch 'develop' (JAL-4102 2.11.2.6 patch release) into features/r2_11_2_alphafold/JAL-2349_JAL-3855
• 

  Ben Soares <b.soares@dundee.ac.uk> 23 Jan 2023 1128674a17df402a2219d278ab332c291cb93443

  JAL-629 Attempts to add PAE to structure. --headless working. Make HTML output single threaded in headless mode. Delete an editor temp file.

  • src/jalview/bin/ArgParser.java (version 1128674a17df402a2219d278ab332c291cb93443) (diffs)
  • src/jalview/bin/Commands.java (version 1128674a17df402a2219d278ab332c291cb93443) (diffs)
  • src/jalview/bin/Jalview.java (version 1128674a17df402a2219d278ab332c291cb93443) (diffs)
  • src/jalview/gui/LineartOptions.java (version 1128674a17df402a2219d278ab332c291cb93443) (diffs)
  • src/jalview/io/HTMLOutput.java (version 1128674a17df402a2219d278ab332c291cb93443) (diffs)
  • src/jalview/structure/StructureSelectionManager.java (version 1128674a17df402a2219d278ab332c291cb93443) (diffs)
  • src/jalview/structure/StructureSelectionManager.java~ (version 1128674a17df402a2219d278ab332c291cb93443) (diffs)
  • src/jalview/ws/dbsources/EBIAlfaFold.java (version 1128674a17df402a2219d278ab332c291cb93443) (diffs)
• 

  James Procter <j.procter@dundee.ac.uk> 23 Jan 2023 d5bd34eb49f43735e240058f8875ab0bfcae4441

  JAL-4104 JAL-4102 update help docs with script to add jalview command line tool to osx path

  • help/help/html/features/commandline.html (version d5bd34eb49f43735e240058f8875ab0bfcae4441) (diffs)
• 

  Jim Procter <j.procter@dundee.ac.uk> 23 Jan 2023 c3eb495269d836f7a8a2addf402425acbcc53c7b

  JAL-4102 whatsNew for 2.11.2.6

  • help/markdown/whatsnew/whatsnew-2_11_2_6.md (version c3eb495269d836f7a8a2addf402425acbcc53c7b) (diffs)
• 

  Jim Procter <j.procter@dundee.ac.uk> 20 Jan 2023 bd30c068414c3dcd87312befe7249202108b78e1

  Merge branch 'patch/JAL-4114_updated_3dbeacons_api' into develop
• 

  Jim Procter <j.procter@dundee.ac.uk> 20 Jan 2023 456e7b01bf201167e0063d0e8b56d4717322d6c0

  JAL-4114 model_page_url not required in v2.0 response

  • src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java (version 456e7b01bf201167e0063d0e8b56d4717322d6c0) (diffs)
• 

  Jim Procter <j.procter@dundee.ac.uk> 20 Jan 2023 3d3cc73c14a48c9af73bf0a33a4897b37a66856b

  JAL-4102 update date and release notes for 2.11.2.6

  • help/markdown/releases/release-2_11_2_6.md (version 3d3cc73c14a48c9af73bf0a33a4897b37a66856b) (diffs)
• 

  Jim Procter <j.procter@dundee.ac.uk> 20 Jan 2023 49702354dac6b1b590030070690c0737d31e3766

  Merge branch 'patch/JAL-4114_updated_3dbeacons_api' into develop
• 

  Jim Procter <j.procter@dundee.ac.uk> 20 Jan 2023 da11f432f67f80f1848d75f862495e5e9dd9076b

  Merge branch 'patch/Release_2_11_2_6_Branch' into develop
• 

  Jim Procter <j.procter@dundee.ac.uk> 20 Jan 2023 5faac1104c41690e38e259fae5bb700236021360

  JAL-2353 primary ref candidates that should be promoted should preserve original version string

  • src/jalview/util/DBRefUtils.java (version 5faac1104c41690e38e259fae5bb700236021360) (diffs)
  • src/jalview/ws/dbsources/Uniprot.java (version 5faac1104c41690e38e259fae5bb700236021360) (diffs)
  • test/jalview/ws/dbsources/UniprotTest.java (version 5faac1104c41690e38e259fae5bb700236021360) (diffs)
• 

  Jim Procter <j.procter@dundee.ac.uk> 20 Jan 2023 fdb8d739d02975e003eaa044bc299c843e474a0c

  JAL-4114 missing mock server response

  • test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt5_resp.txt (version fdb8d739d02975e003eaa044bc299c843e474a0c) (diffs)
• 

  Jim Procter <j.procter@dundee.ac.uk> 20 Jan 2023 1a80985facca80167fb54ca70d9778b1c3bcf9f1

  JAL-4114 only rank model qualities that are computed with the same method, and uprank models with pLDDT over other types of models in the same model type category

  • src/jalview/gui/structurechooser/TDBResultAnalyser.java (version 1a80985facca80167fb54ca70d9778b1c3bcf9f1) (diffs)
• 

  Jim Procter <j.procter@dundee.ac.uk> 20 Jan 2023 a3f8f05c73d08184254a8751c99824cfd126c4be

  JAL-4114 alphafold now marked as AB-INITIO so adjust ranking in categories

  • src/jalview/gui/structurechooser/TDBResultAnalyser.java (version a3f8f05c73d08184254a8751c99824cfd126c4be) (diffs)
• 

  Jim Procter <j.procter@dundee.ac.uk> 20 Jan 2023 4314e53ec6134b03f48578bf3e78d1bd7eaec6a9

  JAL-4114 additional warnings when PDBe doesn’t return as many responses as queries made to it when adding in additional metadata

  • src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java (version 4314e53ec6134b03f48578bf3e78d1bd7eaec6a9) (diffs)
• 

  Jim Procter <j.procter@dundee.ac.uk> 20 Jan 2023 66270dda280788c15956c7a0485f0b9adf03c62a

  JAL-4114 patch REST client for changed JSON schema in 3D beacons v2 API

  • src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java (version 66270dda280788c15956c7a0485f0b9adf03c62a) (diffs)
• 

  Jim Procter <j.procter@dundee.ac.uk> 20 Jan 2023 1bf6c31ad57e146c40fb46ac471caa0cb3b9b975

  JAL-4114 formatting

  • src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java (version 1bf6c31ad57e146c40fb46ac471caa0cb3b9b975) (diffs)
• 

  Jim Procter <j.procter@dundee.ac.uk> 20 Jan 2023 c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a

  JAL-4114 updated mock tests and responses for v2.0 api

  • test/jalview/fts/service/pdb/PDBFTSRestClientTest.java (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
  • test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
  • test/jalview/fts/threedbeacons/p01308_pdbfts_query.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
  • test/jalview/fts/threedbeacons/p01308_pdbfts_query_pt1.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
  • test/jalview/fts/threedbeacons/p01308_pdbfts_query_pt1_resp.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
  • test/jalview/fts/threedbeacons/p01308_pdbfts_query_pt2.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
  • test/jalview/fts/threedbeacons/p01308_pdbfts_query_pt2_resp.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
  • test/jalview/fts/threedbeacons/p01308_pdbfts_resp.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
  • test/jalview/fts/threedbeacons/p01308_tdb_fts_query_resp.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
  • test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt1.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
  • test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt1_resp.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
  • test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt2.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
  • test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt2_resp.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
  • test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt3.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
  • test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt3_resp.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
  • test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt4.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
  • test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt4_resp.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
  • test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt5.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
  • test/jalview/fts/threedbeacons/p0dtd1_tdb_fts_query_resp.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
  • test/jalview/fts/threedbeacons/p27787_tdb_fts_query_resp.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
  • test/jalview/fts/threedbeacons/p38398_tdb_fts_query_resp.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
  • test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 18 Jan 2023 33a6a7aaa26c01c06bc2db56a549137de5812a49

  JAL-629 make sequence id key 'seqid'

  • src/jalview/bin/Commands.java (version 33a6a7aaa26c01c06bc2db56a549137de5812a49) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 17 Jan 2023 a0fed91447e5411f87869be995666b88b59302ea

  JAL-3416 No longer needed

  • src/jalview/gui/AquaInternalFrameManager.java (version a0fed91447e5411f87869be995666b88b59302ea) (diffs)
  • src/jalview/gui/Desktop.java (version a0fed91447e5411f87869be995666b88b59302ea) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 17 Jan 2023 6f5ac0e759db06db212ea8025f1db8c2b0092d89

  Merge branch 'develop' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
• 

  Ben Soares <b.soares@dundee.ac.uk> 16 Jan 2023 9b3bed72df9fa38b8f8007b87a019356d55a030b

  JAL-3416 More tweaking of FlatLaf. Problem with macOS themed FlatLaf solved with new DesktopManager

  • j11lib/VAqua5-patch.jar (version 9b3bed72df9fa38b8f8007b87a019356d55a030b) (diffs)
  • j11lib/quaqua-filechooser-only-8.0.jar (version 9b3bed72df9fa38b8f8007b87a019356d55a030b) (diffs)
  • j8lib/VAqua5-patch.jar (version 9b3bed72df9fa38b8f8007b87a019356d55a030b) (diffs)
  • j8lib/quaqua-filechooser-only-8.0.jar (version 9b3bed72df9fa38b8f8007b87a019356d55a030b) (diffs)
  • src/jalview/bin/Jalview.java (version 9b3bed72df9fa38b8f8007b87a019356d55a030b) (diffs)
  • src/jalview/gui/Desktop.java (version 9b3bed72df9fa38b8f8007b87a019356d55a030b) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 11 Jan 2023 a800086bf169fc6495fef3effa56338f5cff4804

  JAL-1988 JAL-3772 Mark the _default_ STARTUP_FILE as 'all saved' after initial opening

  • src/jalview/bin/Jalview.java (version a800086bf169fc6495fef3effa56338f5cff4804) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 11 Jan 2023 90d223fe952193d290b7b53d499c40007b5b7786

  JAL-629 added Alphafold cif, pdb and PAE json files to examples/AlphaFold

  • examples/AlphaFold/AF-Q5VSL9-F1-model_v4.cif (version 90d223fe952193d290b7b53d499c40007b5b7786) (diffs)
  • examples/AlphaFold/AF-Q5VSL9-F1-model_v4.pdb (version 90d223fe952193d290b7b53d499c40007b5b7786) (diffs)
  • examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4.json (version 90d223fe952193d290b7b53d499c40007b5b7786) (diffs)
  • examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4B.json (version 90d223fe952193d290b7b53d499c40007b5b7786) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 11 Jan 2023 34ce5193c8766085422c32544246d92f12d0c975

  JAL-629 refactoring TFType.  Remove i18n identification of annotation.

  • src/jalview/bin/Commands.java (version 34ce5193c8766085422c32544246d92f12d0c975) (diffs)
  • src/jalview/datamodel/AlignmentAnnotation.java (version 34ce5193c8766085422c32544246d92f12d0c975) (diffs)
  • src/jalview/datamodel/annotations/AlphaFoldAnnotationRowBuilder.java (version 34ce5193c8766085422c32544246d92f12d0c975) (diffs)
  • src/jalview/datamodel/annotations/AnnotationRowBuilder.java (version 34ce5193c8766085422c32544246d92f12d0c975) (diffs)
  • src/jalview/ext/jmol/JmolParser.java (version 34ce5193c8766085422c32544246d92f12d0c975) (diffs)
  • src/jalview/io/AlignFile.java (version 34ce5193c8766085422c32544246d92f12d0c975) (diffs)
  • src/jalview/io/AppletFormatAdapter.java (version 34ce5193c8766085422c32544246d92f12d0c975) (diffs)
  • src/jalview/io/FileLoader.java (version 34ce5193c8766085422c32544246d92f12d0c975) (diffs)
  • src/jalview/io/FormatAdapter.java (version 34ce5193c8766085422c32544246d92f12d0c975) (diffs)
  • src/jalview/io/StructureFile.java (version 34ce5193c8766085422c32544246d92f12d0c975) (diffs)
  • src/jalview/structure/StructureImportSettings.java (version 34ce5193c8766085422c32544246d92f12d0c975) (diffs)
  • src/jalview/ws/dbsources/EBIAlfaFold.java (version 34ce5193c8766085422c32544246d92f12d0c975) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 06 Jan 2023 614526a57b61c771de369d422407eb993454bd72

  JAL-3416 More explicit setting of FlatLaf macOS theme

  • src/jalview/bin/Jalview.java (version 614526a57b61c771de369d422407eb993454bd72) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 06 Jan 2023 6da716e5be79482b04d4582004c3317de53999ac

  JAL-3416 Upgraded FlatLaf to 3.0 and added macOS theme for macOS

  • j11lib/flatlaf-2.3.jar (version 6da716e5be79482b04d4582004c3317de53999ac) (diffs)
  • j11lib/flatlaf-3.0.jar (version 6da716e5be79482b04d4582004c3317de53999ac) (diffs)
  • j11lib/flatlaf-extras-2.3.jar (version 6da716e5be79482b04d4582004c3317de53999ac) (diffs)
  • j11lib/flatlaf-extras-3.0.jar (version 6da716e5be79482b04d4582004c3317de53999ac) (diffs)
  • j8lib/flatlaf-2.3.jar (version 6da716e5be79482b04d4582004c3317de53999ac) (diffs)
  • j8lib/flatlaf-3.0.jar (version 6da716e5be79482b04d4582004c3317de53999ac) (diffs)
  • j8lib/flatlaf-extras-2.3.jar (version 6da716e5be79482b04d4582004c3317de53999ac) (diffs)
  • j8lib/flatlaf-extras-3.0.jar (version 6da716e5be79482b04d4582004c3317de53999ac) (diffs)
  • src/jalview/bin/Jalview.java (version 6da716e5be79482b04d4582004c3317de53999ac) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 06 Jan 2023 77c09ec649cf7f3e9152d93431ff30121885af57

  JAL-3416 remove a missed panel titlebar icon in TreePanel

  • src/jalview/gui/TreePanel.java (version 77c09ec649cf7f3e9152d93431ff30121885af57) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 06 Jan 2023 24b2b95d1aa552dbf4a0c98aa6d18bdaf1e22e4d

  JAL-3416 Fix file permissions on bundled macOS JREs

  • utils/install4j/install4j10_template.install4j (version 24b2b95d1aa552dbf4a0c98aa6d18bdaf1e22e4d) (diffs)