Jalview Git

• 

  Gitlab User 26 Jul 2024 a92d9ee8c25e41770bf745b793262f9a7937893e

  Merge branch 'jims/JAL-4386_from_renia' into spike/JAL-4386_generate_multiple_leaves_for_ss_sources
   Conflicts:
          src/jalview/analysis/AlignmentUtils.java
          src/jalview/gui/CalculationChooser.java
          src/jalview/structure/StructureSelectionManager.java
• 

  Gitlab User 26 Jul 2024 a16e52efe8a069302d4aaa8230ed0dc2e592bcf4 m

  JAL-4386 i8n secondary structure score model

  • resources/lang/Messages.properties (version a16e52efe8a069302d4aaa8230ed0dc2e592bcf4) (diffs)
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  Gitlab User 25 Jul 2024 72d582b7cea3da49fb87b2fcaf154f78da8794c4 m

  JAL-4386 fix viewstyle autotests

  • src/jalview/viewmodel/styles/ViewStyle.java (version 72d582b7cea3da49fb87b2fcaf154f78da8794c4) (diffs)
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  Gitlab User 25 Jul 2024 f60b4a3ba645eec0525a400a525d3bc9dd247c4d m

  JAL-4441 new menu option to show or hide structure providers in secondary structure annotation rows

  • resources/lang/Messages.properties (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • schemas/jalview.xsd (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/api/ViewStyleI.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/gui/AlignFrame.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/gui/AlignViewport.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/gui/AnnotationLabels.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/gui/Preferences.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/jbgui/GAlignFrame.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/project/Jalview2XML.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/viewmodel/AlignmentViewport.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/viewmodel/styles/ViewStyle.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/AlcodonFrame.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/Annotation.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/AnnotationColourScheme.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/AnnotationElement.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/DoubleMatrix.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/DoubleVector.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/Feature.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/FeatureMatcher.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/FeatureMatcherSet.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/FilterBy.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/JalviewModel.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/JalviewUserColours.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/MapListType.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/MapOnAMatrixType.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/Mapping.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/MatrixType.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/NoValueColour.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/ObjectFactory.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/PcaDataType.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/Pdbentry.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/Property.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/Sequence.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/SequenceSet.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/SequenceType.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/ThresholdType.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/VAMSAS.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/WebServiceParameterSet.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
  • src/jalview/xml/binding/jalview/package-info.java (version f60b4a3ba645eec0525a400a525d3bc9dd247c4d) (diffs)
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  Gitlab User 25 Jul 2024 066b2ddcb06a5c4ff0a6f34999c19f9fc37801af m

  JAL-4386 TODOs re standardising and more efficient linking of PDB ID and provider to annotation row

  • .settings/org.eclipse.buildship.core.prefs (version 066b2ddcb06a5c4ff0a6f34999c19f9fc37801af) (diffs)
  • src/jalview/analysis/AlignmentUtils.java (version 066b2ddcb06a5c4ff0a6f34999c19f9fc37801af) (diffs)
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  Gitlab User 25 Jul 2024 f2439f8196e6cd04fd42683c2cb73d7486f886f4 m

  Merge branch 'develop' into feature/JAL-4386_calculate_tree_using_secondary_structure_annotation
   Conflicts:
          src/jalview/gui/AlignFrame.java
          src/jalview/gui/CalculationChooser.java
          src/jalview/viewmodel/AlignmentViewport.java
• 

  Gitlab User 25 Jul 2024 e8ca868ba1549b359ab12585147eb4c66cbe2a53 m

  JAL-4392 JAL-3987 store and restore consensus secondary structure row visualisation and shading settings

  • schemas/jalview.xsd (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/project/Jalview2XML.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/AlcodonFrame.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/Annotation.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/AnnotationColourScheme.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/AnnotationElement.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/DoubleMatrix.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/DoubleVector.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/Feature.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/FeatureMatcher.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/FeatureMatcherSet.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/FilterBy.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/JalviewModel.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/JalviewUserColours.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/MapListType.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/MapOnAMatrixType.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/Mapping.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/MatrixType.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/NoValueColour.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/ObjectFactory.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/PcaDataType.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/Pdbentry.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/Property.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/Sequence.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/SequenceSet.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/SequenceType.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/ThresholdType.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/VAMSAS.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/WebServiceParameterSet.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
  • src/jalview/xml/binding/jalview/package-info.java (version e8ca868ba1549b359ab12585147eb4c66cbe2a53) (diffs)
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  Renia Correya 25 Jul 2024 b97e6db2f6287e08feb3cad5532124e42975ec4a m

  JAL-4392 Fix compilation error in test

  • test/jalview/analysis/AlignmentUtilsTests.java (version b97e6db2f6287e08feb3cad5532124e42975ec4a) (diffs)
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  Renia Correya 25 Jul 2024 6f17b56f9b116a2843d61bb9d3363ddb3b616676 m

  JAL-4392 Secondary Structure Consensus save and load project

  • resources/lang/Messages.properties (version 6f17b56f9b116a2843d61bb9d3363ddb3b616676) (diffs)
  • src/jalview/api/ViewStyleI.java (version 6f17b56f9b116a2843d61bb9d3363ddb3b616676) (diffs)
  • src/jalview/datamodel/SequenceGroup.java (version 6f17b56f9b116a2843d61bb9d3363ddb3b616676) (diffs)
  • src/jalview/gui/AlignFrame.java (version 6f17b56f9b116a2843d61bb9d3363ddb3b616676) (diffs)
  • src/jalview/gui/PopupMenu.java (version 6f17b56f9b116a2843d61bb9d3363ddb3b616676) (diffs)
  • src/jalview/gui/SeqPanel.java (version 6f17b56f9b116a2843d61bb9d3363ddb3b616676) (diffs)
  • src/jalview/gui/SliderPanel.java (version 6f17b56f9b116a2843d61bb9d3363ddb3b616676) (diffs)
  • src/jalview/gui/TreeCanvas.java (version 6f17b56f9b116a2843d61bb9d3363ddb3b616676) (diffs)
  • src/jalview/jbgui/GAlignFrame.java (version 6f17b56f9b116a2843d61bb9d3363ddb3b616676) (diffs)
  • src/jalview/project/Jalview2XML.java (version 6f17b56f9b116a2843d61bb9d3363ddb3b616676) (diffs)
  • src/jalview/renderer/AnnotationRenderer.java (version 6f17b56f9b116a2843d61bb9d3363ddb3b616676) (diffs)
  • src/jalview/viewmodel/AlignmentViewport.java (version 6f17b56f9b116a2843d61bb9d3363ddb3b616676) (diffs)
  • src/jalview/viewmodel/styles/ViewStyle.java (version 6f17b56f9b116a2843d61bb9d3363ddb3b616676) (diffs)
  • src/jalview/xml/binding/jalview/JalviewModel.java (version 6f17b56f9b116a2843d61bb9d3363ddb3b616676) (diffs)
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  Renia Correya 25 Jul 2024 38291a0c2fb379a3680dd82dce86e5879869bc50 m

  JAL-4392 Print annotations Added colour by secondary structure conservation threshold to the output file

  • src/jalview/io/AnnotationFile.java (version 38291a0c2fb379a3680dd82dce86e5879869bc50) (diffs)
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  Renia Correya 24 Jul 2024 d46506c4ddd13830bf09a5f6fbad223e80d0eff2 m

  JAL-4392 Adding secondary structure provider Adding secondary structure provider in parenthesis for each secondary structure annotation.

  • src/jalview/gui/AnnotationLabels.java (version d46506c4ddd13830bf09a5f6fbad223e80d0eff2) (diffs)
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  Gitlab User 24 Jul 2024 e707f26dca29e3fac6566c1d813f3aa9baac44e2 m

  JAL-3063 added a brief description of how to update the jalview project POJO

  • doc/jalview-projects.md (version e707f26dca29e3fac6566c1d813f3aa9baac44e2) (diffs)
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  Renia Correya 17 Jul 2024 a3230b84fc1ef41e224e56aff496a65d9fbebd13 m

  JAL-4392 Updated the label "Show auto calculated annotations" to "Show autocalculated annotations" to match existing label

  • resources/lang/Messages.properties (version a3230b84fc1ef41e224e56aff496a65d9fbebd13) (diffs)
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  Renia Correya 12 Jul 2024 b3027d9c432a8242755a37c34267e80678f40b9a m

  JAL-4392 Implemented show/hide group consensus secondary structure
  Secondary structure provider options are made available in the pop up
  menu for sequence groups. User can set hide/show group consensus
  secondary structure for each group and providers separately.

  • resources/lang/Messages.properties (version b3027d9c432a8242755a37c34267e80678f40b9a) (diffs)
  • src/jalview/analysis/AlignmentAnnotationUtils.java (version b3027d9c432a8242755a37c34267e80678f40b9a) (diffs)
  • src/jalview/analysis/AlignmentUtils.java (version b3027d9c432a8242755a37c34267e80678f40b9a) (diffs)
  • src/jalview/datamodel/SequenceGroup.java (version b3027d9c432a8242755a37c34267e80678f40b9a) (diffs)
  • src/jalview/gui/AlignFrame.java (version b3027d9c432a8242755a37c34267e80678f40b9a) (diffs)
  • src/jalview/gui/PopupMenu.java (version b3027d9c432a8242755a37c34267e80678f40b9a) (diffs)
  • src/jalview/viewmodel/AlignmentViewport.java (version b3027d9c432a8242755a37c34267e80678f40b9a) (diffs)
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  Renia Correya 12 Jul 2024 445217db20f0636124211b25f00563500e446d20 m

  JAL-4411 Bug fix

  • src/jalview/structure/StructureSelectionManager.java (version 445217db20f0636124211b25f00563500e446d20) (diffs)