Jalview Git

• 

  Gitlab User 26 Jul 2024 a16e52efe8a069302d4aaa8230ed0dc2e592bcf4

  JAL-4386 i8n secondary structure score model

  • resources/lang/Messages.properties (version a16e52efe8a069302d4aaa8230ed0dc2e592bcf4) (diffs)
• 

  Gitlab User 25 Jul 2024 72d582b7cea3da49fb87b2fcaf154f78da8794c4

  JAL-4386 fix viewstyle autotests

  • src/jalview/viewmodel/styles/ViewStyle.java (version 72d582b7cea3da49fb87b2fcaf154f78da8794c4) (diffs)
• 

  Gitlab User 25 Jul 2024 f60b4a3ba645eec0525a400a525d3bc9dd247c4d

  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)
• 

  Gitlab User 25 Jul 2024 066b2ddcb06a5c4ff0a6f34999c19f9fc37801af

  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)
• 

  Gitlab User 25 Jul 2024 f2439f8196e6cd04fd42683c2cb73d7486f886f4

  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

  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)
• 

  Renia Correya 25 Jul 2024 b97e6db2f6287e08feb3cad5532124e42975ec4a

  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

  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)
• 

  Renia Correya 25 Jul 2024 38291a0c2fb379a3680dd82dce86e5879869bc50

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

  • src/jalview/io/AnnotationFile.java (version 38291a0c2fb379a3680dd82dce86e5879869bc50) (diffs)
• 

  Renia Correya 24 Jul 2024 d46506c4ddd13830bf09a5f6fbad223e80d0eff2

  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)
• 

  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)
• 

  Renia Correya 17 Jul 2024 a3230b84fc1ef41e224e56aff496a65d9fbebd13

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

  • resources/lang/Messages.properties (version a3230b84fc1ef41e224e56aff496a65d9fbebd13) (diffs)
• 

  Renia Correya 12 Jul 2024 b3027d9c432a8242755a37c34267e80678f40b9a

  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)
• 

  Renia Correya 12 Jul 2024 445217db20f0636124211b25f00563500e446d20

  JAL-4411 Bug fix

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

  Gitlab User 03 Jul 2024 c99eae6fd25077f99ab20316f69fc9cb8d8189b7 m

  JAL-3631 rebuild getdown jars after merge to develop

  • getdown/lib/getdown-core.jar (version c99eae6fd25077f99ab20316f69fc9cb8d8189b7) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version c99eae6fd25077f99ab20316f69fc9cb8d8189b7) (diffs)
  • getdown/lib/getdown-launcher.jar (version c99eae6fd25077f99ab20316f69fc9cb8d8189b7) (diffs)
  • j11lib/getdown-core.jar (version c99eae6fd25077f99ab20316f69fc9cb8d8189b7) (diffs)
  • j8lib/getdown-core.jar (version c99eae6fd25077f99ab20316f69fc9cb8d8189b7) (diffs)
• 

  Gitlab User 03 Jul 2024 94221f0819ebe1a2d7de347da835c3c1fa990111 m

  Merge branch 'feature/JAL-3631_allow_jalview_to_work_from_user-space_directory' into develop
• 

  Ben Soares <b.soares@dundee.ac.uk> 01 Jul 2024 79a7d13627ff731e4fec9d0eb86191bc7c786e8c m

  JAL-3631 Slightly larger wizard

  • utils/install4j/install4j10_template.install4j (version 79a7d13627ff731e4fec9d0eb86191bc7c786e8c) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 01 Jul 2024 50ba227f13bb12d416af472b0271390395c39e9e m

  JAL-3631 Harden defence against looping getdown relaunches. Null checked in HttpUtils. Remove unnecessary code in getdown

  • getdown/lib/getdown-core.jar (version 50ba227f13bb12d416af472b0271390395c39e9e) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version 50ba227f13bb12d416af472b0271390395c39e9e) (diffs)
  • getdown/lib/getdown-launcher.jar (version 50ba227f13bb12d416af472b0271390395c39e9e) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java (version 50ba227f13bb12d416af472b0271390395c39e9e) (diffs)
  • getdown/src/getdown/core/src/main/java/jalview/util/HttpUtils.java (version 50ba227f13bb12d416af472b0271390395c39e9e) (diffs)
  • getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/GetdownApp.java (version 50ba227f13bb12d416af472b0271390395c39e9e) (diffs)
  • j11lib/getdown-core.jar (version 50ba227f13bb12d416af472b0271390395c39e9e) (diffs)
  • j8lib/getdown-core.jar (version 50ba227f13bb12d416af472b0271390395c39e9e) (diffs)
  • src/jalview/util/HttpUtils.java (version 50ba227f13bb12d416af472b0271390395c39e9e) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 29 Jun 2024 2987943975f888af6c6d7a14d0614aa407a04663 m

  JAL-3631 JVL file with appbase now relaunches getdown

  • getdown/lib/getdown-core.jar (version 2987943975f888af6c6d7a14d0614aa407a04663) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version 2987943975f888af6c6d7a14d0614aa407a04663) (diffs)
  • getdown/lib/getdown-launcher.jar (version 2987943975f888af6c6d7a14d0614aa407a04663) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java (version 2987943975f888af6c6d7a14d0614aa407a04663) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java (version 2987943975f888af6c6d7a14d0614aa407a04663) (diffs)
  • getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/Getdown.java (version 2987943975f888af6c6d7a14d0614aa407a04663) (diffs)
  • getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/GetdownApp.java (version 2987943975f888af6c6d7a14d0614aa407a04663) (diffs)
  • j11lib/getdown-core.jar (version 2987943975f888af6c6d7a14d0614aa407a04663) (diffs)
  • j8lib/getdown-core.jar (version 2987943975f888af6c6d7a14d0614aa407a04663) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 28 Jun 2024 396920381f5a83687e42628eca96cc8ae7d39010 m

  JAL-3631 Made an isAdmin flag to work in Windows Admin mode installation

  • utils/install4j/install4j10_template.install4j (version 396920381f5a83687e42628eca96cc8ae7d39010) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 28 Jun 2024 2174ff91f8e904011cbff62bcff60138a3a1cfdf m

  JAL-3830 Added some quotation marks to jalview.bat for folders with spaces

  • utils/getdown/bin/jalview.bat (version 2174ff91f8e904011cbff62bcff60138a3a1cfdf) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 28 Jun 2024 072ba76684a943ac43df7ce91c40e18fde0a91cf m

  JAL-3631 Remove the checkboxes from the Finish screen. Now moved to pre-install screen.

  • utils/install4j/install4j10_template.install4j (version 072ba76684a943ac43df7ce91c40e18fde0a91cf) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 28 Jun 2024 aefc27d707d32de1e13fbb873b14c34886a97977 m

  JAL-3631 Group USERSPACE and SYSTEMSPACE tasks (and other groups of tasks) together for neatness

  • utils/install4j/install4j10_template.install4j (version aefc27d707d32de1e13fbb873b14c34886a97977) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 28 Jun 2024 a5b64ff2533e26a8c342dc323f8f34c12e1db496 m

  JAL-3631 Change in user path for locally installed Jalview to avoid collision with old installation. Tidy a null check for Java Console output

  • getdown/lib/getdown-core.jar (version a5b64ff2533e26a8c342dc323f8f34c12e1db496) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version a5b64ff2533e26a8c342dc323f8f34c12e1db496) (diffs)
  • getdown/lib/getdown-launcher.jar (version a5b64ff2533e26a8c342dc323f8f34c12e1db496) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java (version a5b64ff2533e26a8c342dc323f8f34c12e1db496) (diffs)
  • j11lib/getdown-core.jar (version a5b64ff2533e26a8c342dc323f8f34c12e1db496) (diffs)
  • j8lib/getdown-core.jar (version a5b64ff2533e26a8c342dc323f8f34c12e1db496) (diffs)
  • src/jalview/bin/Cache.java (version a5b64ff2533e26a8c342dc323f8f34c12e1db496) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 28 Jun 2024 62a939a6cfcdcda6345343ba02e793ebb24c5818 m

  JAL-3631 Change to Windows user-space default location, now same as default installation location

  • getdown/lib/getdown-core.jar (version 62a939a6cfcdcda6345343ba02e793ebb24c5818) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version 62a939a6cfcdcda6345343ba02e793ebb24c5818) (diffs)
  • getdown/lib/getdown-launcher.jar (version 62a939a6cfcdcda6345343ba02e793ebb24c5818) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java (version 62a939a6cfcdcda6345343ba02e793ebb24c5818) (diffs)
  • j11lib/getdown-core.jar (version 62a939a6cfcdcda6345343ba02e793ebb24c5818) (diffs)
  • j8lib/getdown-core.jar (version 62a939a6cfcdcda6345343ba02e793ebb24c5818) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 28 Jun 2024 7a053adc38972f2c3aefa23b22fafe57f158140e m

  JAL-3631 Fixed a getdown Exception when launching Jalview in windows

  • getdown/lib/getdown-core.jar (version 7a053adc38972f2c3aefa23b22fafe57f158140e) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version 7a053adc38972f2c3aefa23b22fafe57f158140e) (diffs)
  • getdown/lib/getdown-launcher.jar (version 7a053adc38972f2c3aefa23b22fafe57f158140e) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java (version 7a053adc38972f2c3aefa23b22fafe57f158140e) (diffs)
  • j11lib/getdown-core.jar (version 7a053adc38972f2c3aefa23b22fafe57f158140e) (diffs)
  • j8lib/getdown-core.jar (version 7a053adc38972f2c3aefa23b22fafe57f158140e) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 28 Jun 2024 a04f8a0b0781506739d06451f5ef55e1c6889f47 m

  JAL-3631 Adjustments to the Windows installer

  • utils/install4j/install4j10_template.install4j (version a04f8a0b0781506739d06451f5ef55e1c6889f47) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 28 Jun 2024 5ff5778fd85eeab05bc23d10c9a9665dfe1c9a63 m

  JAL-3631 spelling correction

  • getdown/lib/getdown-core.jar (version 5ff5778fd85eeab05bc23d10c9a9665dfe1c9a63) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version 5ff5778fd85eeab05bc23d10c9a9665dfe1c9a63) (diffs)
  • getdown/lib/getdown-launcher.jar (version 5ff5778fd85eeab05bc23d10c9a9665dfe1c9a63) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java (version 5ff5778fd85eeab05bc23d10c9a9665dfe1c9a63) (diffs)
  • j11lib/getdown-core.jar (version 5ff5778fd85eeab05bc23d10c9a9665dfe1c9a63) (diffs)
  • j8lib/getdown-core.jar (version 5ff5778fd85eeab05bc23d10c9a9665dfe1c9a63) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 27 Jun 2024 e9899166c9af58f552caf24a06e54ab4c106e2f9 m

  JAL-3631 Installers with separate actions for user/administrator installation

  • utils/install4j/install4j10_template.install4j (version e9899166c9af58f552caf24a06e54ab4c106e2f9) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 27 Jun 2024 c71422b81d7741434287b8645bc42abc7a8c59d1 m

  JAL-3631 Add property to let log4j know we're not running in a servlet (or it issues a warning which breaks cli headless output)

  • src/jalview/bin/Jalview.java (version c71422b81d7741434287b8645bc42abc7a8c59d1) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 27 Jun 2024 19ed57b4dea47513cf3fb02bde8ef7857632898e m

  JAL-3631 Log4j logging to .jalview.log file when requested. Clean(ish) handover of log file from getdown to jalview.

  • getdown/lib/getdown-core.jar (version 19ed57b4dea47513cf3fb02bde8ef7857632898e) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version 19ed57b4dea47513cf3fb02bde8ef7857632898e) (diffs)
  • getdown/lib/getdown-launcher.jar (version 19ed57b4dea47513cf3fb02bde8ef7857632898e) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java (version 19ed57b4dea47513cf3fb02bde8ef7857632898e) (diffs)
  • getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/Getdown.java (version 19ed57b4dea47513cf3fb02bde8ef7857632898e) (diffs)
  • getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/GetdownApp.java (version 19ed57b4dea47513cf3fb02bde8ef7857632898e) (diffs)
  • j11lib/getdown-core.jar (version 19ed57b4dea47513cf3fb02bde8ef7857632898e) (diffs)
  • j8lib/getdown-core.jar (version 19ed57b4dea47513cf3fb02bde8ef7857632898e) (diffs)
  • src/jalview/bin/Console.java (version 19ed57b4dea47513cf3fb02bde8ef7857632898e) (diffs)
  • src/jalview/bin/Jalview.java (version 19ed57b4dea47513cf3fb02bde8ef7857632898e) (diffs)
  • src/jalview/log/JLogger.java (version 19ed57b4dea47513cf3fb02bde8ef7857632898e) (diffs)
  • src/jalview/log/JLoggerLog4j.java (version 19ed57b4dea47513cf3fb02bde8ef7857632898e) (diffs)
  • src/jalview/util/Log4j.java (version 19ed57b4dea47513cf3fb02bde8ef7857632898e) (diffs)
  • src/jalview/ws/jws2/Jws2Discoverer.java (version 19ed57b4dea47513cf3fb02bde8ef7857632898e) (diffs)
  • utils/dev_install.sh (version 19ed57b4dea47513cf3fb02bde8ef7857632898e) (diffs)
  • utils/install4j/install4j10_template.install4j (version 19ed57b4dea47513cf3fb02bde8ef7857632898e) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 25 Jun 2024 0c4f07ff146c45096e6a723c061a9760dc7bca49 m

  JAL-3631 JAL-3384 Install4j launch now redirects STDOUT/STDERR to ~/.jalview_develop.log and passes the file on to getdown and Jalview which will also now log to this file.  Single log file.

  • build.gradle (version 0c4f07ff146c45096e6a723c061a9760dc7bca49) (diffs)
  • getdown/lib/getdown-core.jar (version 0c4f07ff146c45096e6a723c061a9760dc7bca49) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version 0c4f07ff146c45096e6a723c061a9760dc7bca49) (diffs)
  • getdown/lib/getdown-launcher.jar (version 0c4f07ff146c45096e6a723c061a9760dc7bca49) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java (version 0c4f07ff146c45096e6a723c061a9760dc7bca49) (diffs)
  • getdown/src/getdown/core/src/main/java/jalview/util/ErrorLog.java (version 0c4f07ff146c45096e6a723c061a9760dc7bca49) (diffs)
  • getdown/src/getdown/core/src/main/java/jalview/util/LaunchUtils.java (version 0c4f07ff146c45096e6a723c061a9760dc7bca49) (diffs)
  • getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/Getdown.java (version 0c4f07ff146c45096e6a723c061a9760dc7bca49) (diffs)
  • getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/GetdownApp.java (version 0c4f07ff146c45096e6a723c061a9760dc7bca49) (diffs)
  • j11lib/getdown-core.jar (version 0c4f07ff146c45096e6a723c061a9760dc7bca49) (diffs)
  • j8lib/getdown-core.jar (version 0c4f07ff146c45096e6a723c061a9760dc7bca49) (diffs)
  • src/jalview/bin/Cache.java (version 0c4f07ff146c45096e6a723c061a9760dc7bca49) (diffs)
  • src/jalview/bin/Jalview.java (version 0c4f07ff146c45096e6a723c061a9760dc7bca49) (diffs)
  • src/jalview/util/ErrorLog.java (version 0c4f07ff146c45096e6a723c061a9760dc7bca49) (diffs)
  • src/jalview/util/LaunchUtils.java (version 0c4f07ff146c45096e6a723c061a9760dc7bca49) (diffs)
  • utils/install4j/install4j10_template.install4j (version 0c4f07ff146c45096e6a723c061a9760dc7bca49) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 25 Jun 2024 b2fe62bb0a703da119270c9fba9799ee3fcfb949 m

  JAL-3631 Use the icon file passed by install4j if a newer getdown-launcher is relaunched

  • getdown/lib/FJVL_VERSION (version b2fe62bb0a703da119270c9fba9799ee3fcfb949) (diffs)
  • getdown/lib/JVL_VERSION (version b2fe62bb0a703da119270c9fba9799ee3fcfb949) (diffs)
  • getdown/lib/getdown-core.jar (version b2fe62bb0a703da119270c9fba9799ee3fcfb949) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version b2fe62bb0a703da119270c9fba9799ee3fcfb949) (diffs)
  • getdown/lib/getdown-launcher.jar (version b2fe62bb0a703da119270c9fba9799ee3fcfb949) (diffs)
  • getdown/src/getdown/ant/pom.xml (version b2fe62bb0a703da119270c9fba9799ee3fcfb949) (diffs)
  • getdown/src/getdown/core/pom.xml (version b2fe62bb0a703da119270c9fba9799ee3fcfb949) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java (version b2fe62bb0a703da119270c9fba9799ee3fcfb949) (diffs)
  • getdown/src/getdown/launcher/pom.xml (version b2fe62bb0a703da119270c9fba9799ee3fcfb949) (diffs)
  • getdown/src/getdown/mvn_cmd (version b2fe62bb0a703da119270c9fba9799ee3fcfb949) (diffs)
  • getdown/src/getdown/pom.xml (version b2fe62bb0a703da119270c9fba9799ee3fcfb949) (diffs)
  • j11lib/getdown-core.jar (version b2fe62bb0a703da119270c9fba9799ee3fcfb949) (diffs)
  • j8lib/getdown-core.jar (version b2fe62bb0a703da119270c9fba9799ee3fcfb949) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 25 Jun 2024 725d33acf5eeca25549f438feba5c61c63b5ad31 m

  JAL-3631 Allow icon file name to be passed to launcher by install4j

  • build.gradle (version 725d33acf5eeca25549f438feba5c61c63b5ad31) (diffs)
  • utils/install4j/install4j10_template.install4j (version 725d33acf5eeca25549f438feba5c61c63b5ad31) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 25 Jun 2024 f1e4a084d18cf14bff0a3bfabfb04ee3ccbfe8e8 m

  JAL-3631 Forgot to add this file for 'Change parity of comparison for convention' commit

  • getdown/src/getdown/core/src/main/java/jalview/util/LaunchUtils.java (version f1e4a084d18cf14bff0a3bfabfb04ee3ccbfe8e8) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 25 Jun 2024 489361286985f3f28253142b9ed3e75afbf1f914 m

  JAL-3631 Tests for version comparisons and Jar version comparisons and Jar version checking

  • test/jalview/util/LaunchUtilsTest.java (version 489361286985f3f28253142b9ed3e75afbf1f914) (diffs)
  • test/jalview/util/fake-getdown-launchers/fake-getdown-launcher-1.8.3-1.4.3.jar (version 489361286985f3f28253142b9ed3e75afbf1f914) (diffs)
  • test/jalview/util/fake-getdown-launchers/fake-getdown-launcher-1.8.3-1.4.4.jar (version 489361286985f3f28253142b9ed3e75afbf1f914) (diffs)
  • test/jalview/util/fake-getdown-launchers/fake-getdown-launcher-1.8.3-1.5.0.jar (version 489361286985f3f28253142b9ed3e75afbf1f914) (diffs)
  • test/jalview/util/fake-getdown-launchers/fake-getdown-launcher-1.8.4-1.5.0.jar (version 489361286985f3f28253142b9ed3e75afbf1f914) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 25 Jun 2024 c3eae48d65c79ce6e3e96dd6792a650e1a9f32ed m

  JAL-3631 Change parity of comparison for convention

  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java (version c3eae48d65c79ce6e3e96dd6792a650e1a9f32ed) (diffs)
  • src/jalview/util/LaunchUtils.java (version c3eae48d65c79ce6e3e96dd6792a650e1a9f32ed) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 25 Jun 2024 b76879d727de4c4bf0e0593311b0d45501fe116b m

  JAL-3631 Report getCanonicalPath for installer appdir

  • src/jalview/bin/Cache.java (version b76879d727de4c4bf0e0593311b0d45501fe116b) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 25 Jun 2024 1cf32cdac3840df102b4f4b9261a310dc18e14bc m

  JAL-3631 Check Implementation-Version of getdown-launcher.jar in installation appdir and user's appdir, and only use the user one if it's newer.  Remove content digest check for getdown-launcher.jar comparison since version now being checked.

  • getdown/lib/FJVL_VERSION (version 1cf32cdac3840df102b4f4b9261a310dc18e14bc) (diffs)
  • getdown/lib/JVL_VERSION (version 1cf32cdac3840df102b4f4b9261a310dc18e14bc) (diffs)
  • getdown/lib/getdown-core.jar (version 1cf32cdac3840df102b4f4b9261a310dc18e14bc) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version 1cf32cdac3840df102b4f4b9261a310dc18e14bc) (diffs)
  • getdown/lib/getdown-launcher.jar (version 1cf32cdac3840df102b4f4b9261a310dc18e14bc) (diffs)
  • getdown/src/getdown/ant/pom.xml (version 1cf32cdac3840df102b4f4b9261a310dc18e14bc) (diffs)
  • getdown/src/getdown/core/pom.xml (version 1cf32cdac3840df102b4f4b9261a310dc18e14bc) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java (version 1cf32cdac3840df102b4f4b9261a310dc18e14bc) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java (version 1cf32cdac3840df102b4f4b9261a310dc18e14bc) (diffs)
  • getdown/src/getdown/core/src/main/java/jalview/util/LaunchUtils.java (version 1cf32cdac3840df102b4f4b9261a310dc18e14bc) (diffs)
  • getdown/src/getdown/launcher/pom.xml (version 1cf32cdac3840df102b4f4b9261a310dc18e14bc) (diffs)
  • getdown/src/getdown/mvn_cmd (version 1cf32cdac3840df102b4f4b9261a310dc18e14bc) (diffs)
  • getdown/src/getdown/pom.xml (version 1cf32cdac3840df102b4f4b9261a310dc18e14bc) (diffs)
  • j11lib/getdown-core.jar (version 1cf32cdac3840df102b4f4b9261a310dc18e14bc) (diffs)
  • j8lib/getdown-core.jar (version 1cf32cdac3840df102b4f4b9261a310dc18e14bc) (diffs)
  • src/jalview/util/LaunchUtils.java (version 1cf32cdac3840df102b4f4b9261a310dc18e14bc) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 21 Jun 2024 7ae9e3404464d0f0de85ea2ece2e85d44dfe3548 m

  JAL-3631 updated getdown jars

  • getdown/lib/getdown-core.jar (version 7ae9e3404464d0f0de85ea2ece2e85d44dfe3548) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version 7ae9e3404464d0f0de85ea2ece2e85d44dfe3548) (diffs)
  • getdown/lib/getdown-launcher.jar (version 7ae9e3404464d0f0de85ea2ece2e85d44dfe3548) (diffs)
  • j11lib/getdown-core.jar (version 7ae9e3404464d0f0de85ea2ece2e85d44dfe3548) (diffs)
  • j8lib/getdown-core.jar (version 7ae9e3404464d0f0de85ea2ece2e85d44dfe3548) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 21 Jun 2024 28a9807f9a59300158c71405c933a02b003c1d45 m

  Merge branch 'develop' into feature/JAL-3631_allow_jalview_to_work_from_user-space_directory
• 

  Ben Soares <b.soares@dundee.ac.uk> 21 Jun 2024 15b87d323c07694dadea3417bab50a6d8acdd6b8 m

  JAL-3631 Changed label for consistency

  • src/jalview/bin/Cache.java (version 15b87d323c07694dadea3417bab50a6d8acdd6b8) (diffs)
• 

  Gitlab User 21 Jun 2024 389ce756b388fe2896987278f6d425a93fc43f13 m

  Merge branch 'improvement/JAL-4409_implement_extra_schemes_in_getdown' into develop
• 

  Ben Soares <b.soares@dundee.ac.uk> 21 Jun 2024 763aa1ad25a2f352c5cffb3972b4d906bb847c6f m

  Merge branch 'improvement/JAL-4409_implement_extra_schemes_in_getdown' into feature/JAL-3631_allow_jalview_to_work_from_user-space_directory
• 

  Ben Soares <b.soares@dundee.ac.uk> 21 Jun 2024 c2893a5ec37de7d2b72ec954ab0eb10a6fc52d73 m

  JAL-4409 Add two empty args to getdown call from install4j for backward compatibility, and further arguments such as JVL file.  Improve handling of a JVL file with an appbase in it.

  • getdown/lib/getdown-core.jar (version c2893a5ec37de7d2b72ec954ab0eb10a6fc52d73) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version c2893a5ec37de7d2b72ec954ab0eb10a6fc52d73) (diffs)
  • getdown/lib/getdown-launcher.jar (version c2893a5ec37de7d2b72ec954ab0eb10a6fc52d73) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java (version c2893a5ec37de7d2b72ec954ab0eb10a6fc52d73) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java (version c2893a5ec37de7d2b72ec954ab0eb10a6fc52d73) (diffs)
  • getdown/src/getdown/core/src/main/java/jalview/util/LaunchUtils.java (version c2893a5ec37de7d2b72ec954ab0eb10a6fc52d73) (diffs)
  • j11lib/getdown-core.jar (version c2893a5ec37de7d2b72ec954ab0eb10a6fc52d73) (diffs)
  • j8lib/getdown-core.jar (version c2893a5ec37de7d2b72ec954ab0eb10a6fc52d73) (diffs)
  • src/jalview/util/LaunchUtils.java (version c2893a5ec37de7d2b72ec954ab0eb10a6fc52d73) (diffs)
  • utils/install4j/install4j10_template.install4j (version c2893a5ec37de7d2b72ec954ab0eb10a6fc52d73) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 21 Jun 2024 0a9d2d927d759106beb2b7622f7b58c245140abd m

  JAL-4409 Don't merge JVL configs when changing appbase

  • build.gradle (version 0a9d2d927d759106beb2b7622f7b58c245140abd) (diffs)
  • gradle.properties (version 0a9d2d927d759106beb2b7622f7b58c245140abd) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 20 Jun 2024 608366fa3737db782a97216223a22bae3d97239f m

  JAL-4409 Use fixed 'latest' artifact URL

  • build.gradle (version 608366fa3737db782a97216223a22bae3d97239f) (diffs)
  • gradle.properties (version 608366fa3737db782a97216223a22bae3d97239f) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 20 Jun 2024 cd2512d151bda956401619b00147ef63feacdce8 m

  JAL-4409 Changes in BUILD channel appbase to tie in with Getdown DEVELOP Launcher build plan

  • build.gradle (version cd2512d151bda956401619b00147ef63feacdce8) (diffs)
  • gradle.properties (version cd2512d151bda956401619b00147ef63feacdce8) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 20 Jun 2024 74caf4a97a80d94a284cb98f1a5283ab5026288d m

  JAL-3631 Now sending launcher.appdir from within getdown

  • gradle.properties (version 74caf4a97a80d94a284cb98f1a5283ab5026288d) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 19 Jun 2024 1848a8863b6e4020fca7a94677795f6ef521694c m

  JAL-3631 Rename/rationalise informational system property names. Re-order display of information on Java Console. Supply info from authoratitive sources (getdown-launcher.jar rather than gradle.properties).

  • build.gradle (version 1848a8863b6e4020fca7a94677795f6ef521694c) (diffs)
  • getdown/lib/getdown-core.jar (version 1848a8863b6e4020fca7a94677795f6ef521694c) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version 1848a8863b6e4020fca7a94677795f6ef521694c) (diffs)
  • getdown/lib/getdown-launcher.jar (version 1848a8863b6e4020fca7a94677795f6ef521694c) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java (version 1848a8863b6e4020fca7a94677795f6ef521694c) (diffs)
  • j11lib/getdown-core.jar (version 1848a8863b6e4020fca7a94677795f6ef521694c) (diffs)
  • j8lib/getdown-core.jar (version 1848a8863b6e4020fca7a94677795f6ef521694c) (diffs)
  • src/jalview/bin/Cache.java (version 1848a8863b6e4020fca7a94677795f6ef521694c) (diffs)
  • src/jalview/bin/Jalview.java (version 1848a8863b6e4020fca7a94677795f6ef521694c) (diffs)
  • src/jalview/bin/Launcher.java (version 1848a8863b6e4020fca7a94677795f6ef521694c) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 18 Jun 2024 4ff34511d5c6dca2db76db9a12ed7d158bc02d66 m

  JAL-3631 macos dev install script incorporated into dev_install.sh

  • utils/dev_macos_install.sh (version 4ff34511d5c6dca2db76db9a12ed7d158bc02d66) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 18 Jun 2024 d05883aa5914cd8926b89179251282d3c1410d02 m

  JAL-4358 slight improvement to detecting desktop creation to close getdown splash screen

  • getdown/lib/getdown-core.jar (version d05883aa5914cd8926b89179251282d3c1410d02) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version d05883aa5914cd8926b89179251282d3c1410d02) (diffs)
  • getdown/lib/getdown-launcher.jar (version d05883aa5914cd8926b89179251282d3c1410d02) (diffs)
  • getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/Getdown.java (version d05883aa5914cd8926b89179251282d3c1410d02) (diffs)
  • j11lib/getdown-core.jar (version d05883aa5914cd8926b89179251282d3c1410d02) (diffs)
  • j8lib/getdown-core.jar (version d05883aa5914cd8926b89179251282d3c1410d02) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 18 Jun 2024 8c888a7b06bcd577dde3028941eb5900ec69f817 m

  JAL-3631 gradle-build-and-re-install script, works with macOS or Linux

  • utils/dev_install.sh (version 8c888a7b06bcd577dde3028941eb5900ec69f817) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 18 Jun 2024 d2145b21b3be14def63b9623953eb7be88fe3fd1 m

  JAL-3631 Substantial additions to Getdown (through jalview.util.LaunchUtils) to re-launch getdown-launcher.jar when the user's version differs from the installed version.  install4j vmoptions file allows administrator to prevent any automatic updates.

  • getdown/lib/getdown-core.jar (version d2145b21b3be14def63b9623953eb7be88fe3fd1) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version d2145b21b3be14def63b9623953eb7be88fe3fd1) (diffs)
  • getdown/lib/getdown-launcher.jar (version d2145b21b3be14def63b9623953eb7be88fe3fd1) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java (version d2145b21b3be14def63b9623953eb7be88fe3fd1) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java (version d2145b21b3be14def63b9623953eb7be88fe3fd1) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/LaunchUtil.java (version d2145b21b3be14def63b9623953eb7be88fe3fd1) (diffs)
  • getdown/src/getdown/core/src/main/java/jalview/bin/Console.java (version d2145b21b3be14def63b9623953eb7be88fe3fd1) (diffs)
  • getdown/src/getdown/core/src/main/java/jalview/util/ErrorLog.java (version d2145b21b3be14def63b9623953eb7be88fe3fd1) (diffs)
  • getdown/src/getdown/core/src/main/java/jalview/util/LaunchUtils.java (version d2145b21b3be14def63b9623953eb7be88fe3fd1) (diffs)
  • getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/Getdown.java (version d2145b21b3be14def63b9623953eb7be88fe3fd1) (diffs)
  • getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/GetdownApp.java (version d2145b21b3be14def63b9623953eb7be88fe3fd1) (diffs)
  • getdown/src/getdown/mvn_cmd (version d2145b21b3be14def63b9623953eb7be88fe3fd1) (diffs)
  • j11lib/getdown-core.jar (version d2145b21b3be14def63b9623953eb7be88fe3fd1) (diffs)
  • j8lib/getdown-core.jar (version d2145b21b3be14def63b9623953eb7be88fe3fd1) (diffs)
  • src/jalview/bin/Launcher.java (version d2145b21b3be14def63b9623953eb7be88fe3fd1) (diffs)
  • src/jalview/util/ErrorLog.java (version d2145b21b3be14def63b9623953eb7be88fe3fd1) (diffs)
  • src/jalview/util/LaunchUtils.java (version d2145b21b3be14def63b9623953eb7be88fe3fd1) (diffs)
  • utils/install4j/install4j10_template.install4j (version d2145b21b3be14def63b9623953eb7be88fe3fd1) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 17 Jun 2024 d5ab8c4abf125fbb7ed49326f7aab5ee2bd0cebe m

  JAL-3631 Allow quick deployment of gradle build on linux and macos

  • utils/dev_install.sh (version d5ab8c4abf125fbb7ed49326f7aab5ee2bd0cebe) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 14 Jun 2024 7c9eaa13d7ef664ebe57c40b2af20bc830596ca2 m

  Merge branch 'develop' into feature/JAL-3631_allow_jalview_to_work_from_user-space_directory
• 

  Ben Soares <b.soares@dundee.ac.uk> 14 Jun 2024 63e1d6a7a87f084e3950d8cf6c535c0c62eaf3ee m

  JAL-3631 Got rid of the USER_EXECUTABLE_NAME as it's no longer needed since getting rid of the old Launcher in install4j

  • build.gradle (version 63e1d6a7a87f084e3950d8cf6c535c0c62eaf3ee) (diffs)
  • gradle.properties (version 63e1d6a7a87f084e3950d8cf6c535c0c62eaf3ee) (diffs)
  • utils/install4j/install4j10_template.install4j (version 63e1d6a7a87f084e3950d8cf6c535c0c62eaf3ee) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 14 Jun 2024 297ea17e43543bd55182dbd258f06f05d25b094b m

  JAL-3631 Removed old non-user launcher. Labelled USERSPACE actions.

  • utils/install4j/install4j10_template.install4j (version 297ea17e43543bd55182dbd258f06f05d25b094b) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 14 Jun 2024 34b787f756e949ca714ebbe6b9ee8c61ec407002 m

  JAL-3631 JAL-4104 More consistent system property names passing through getdown. Add nousedefaultappdir property to allow non-updating system installation of Jalview.

  • getdown/lib/getdown-core.jar (version 34b787f756e949ca714ebbe6b9ee8c61ec407002) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version 34b787f756e949ca714ebbe6b9ee8c61ec407002) (diffs)
  • getdown/lib/getdown-launcher.jar (version 34b787f756e949ca714ebbe6b9ee8c61ec407002) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java (version 34b787f756e949ca714ebbe6b9ee8c61ec407002) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java (version 34b787f756e949ca714ebbe6b9ee8c61ec407002) (diffs)
  • j11lib/getdown-core.jar (version 34b787f756e949ca714ebbe6b9ee8c61ec407002) (diffs)
  • j8lib/getdown-core.jar (version 34b787f756e949ca714ebbe6b9ee8c61ec407002) (diffs)
  • src/jalview/analytics/Plausible.java (version 34b787f756e949ca714ebbe6b9ee8c61ec407002) (diffs)
  • src/jalview/bin/Cache.java (version 34b787f756e949ca714ebbe6b9ee8c61ec407002) (diffs)
  • src/jalview/bin/Jalview.java (version 34b787f756e949ca714ebbe6b9ee8c61ec407002) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 14 Jun 2024 ef0a42b569349499f859001b5ca1d85ea7af8904 m

  JAL-3631 Allow -Pinstall4j_build_ids=MACOS-AARCH64-DMG for specific installer build. Fix installer icons (PNGs and paths).

  • build.gradle (version ef0a42b569349499f859001b5ca1d85ea7af8904) (diffs)
  • gradle.properties (version ef0a42b569349499f859001b5ca1d85ea7af8904) (diffs)
  • utils/channels/default/images/jalview_installer.png (version ef0a42b569349499f859001b5ca1d85ea7af8904) (diffs)
  • utils/channels/develop/images/jalview_develop_installer.png (version ef0a42b569349499f859001b5ca1d85ea7af8904) (diffs)
  • utils/channels/release/images/jalview_installer.png (version ef0a42b569349499f859001b5ca1d85ea7af8904) (diffs)
  • utils/channels/test-release/images/jalview_installer.png (version ef0a42b569349499f859001b5ca1d85ea7af8904) (diffs)
  • utils/dev_macos_install.sh (version ef0a42b569349499f859001b5ca1d85ea7af8904) (diffs)
  • utils/install4j/install4j10_template.install4j (version ef0a42b569349499f859001b5ca1d85ea7af8904) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 13 Jun 2024 1a5f7cbd4317ce285a94f064c23ce982fccd2a85 m

  JAL-3845 Add a popup error message, with instructions, when Jalview launched from the Installer Volume

  • src/jalview/bin/Jalview.java (version 1a5f7cbd4317ce285a94f064c23ce982fccd2a85) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 13 Jun 2024 0112f6d85c67b26ed08a03d71a16fecddfba4b3f m

  JAL-3631 New Installer icons. Getdown check that the application appdir is different from the user default appdir before copying files. Also copy gedown-launcher.jar.

  • build.gradle (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • getdown/lib/getdown-core.jar (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • getdown/lib/getdown-launcher.jar (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • gradle.properties (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • j11lib/getdown-core.jar (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • j8lib/getdown-core.jar (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • resources/lang/Messages.properties (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • resources/lang/Messages_es.properties (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • utils/channels/default/channel_gradle.properties (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • utils/channels/default/images/jalview_installer.icns (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • utils/channels/default/images/jalview_installer.ico (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • utils/channels/default/images/jalview_installer.png (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • utils/channels/develop-SUFFIX/channel_gradle.properties (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • utils/channels/develop-SUFFIX/images/jalview_develop_installer.icns (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • utils/channels/develop-SUFFIX/images/jalview_develop_installer.ico (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • utils/channels/develop-SUFFIX/images/jalview_develop_installer.png (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • utils/channels/develop/channel_gradle.properties (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • utils/channels/develop/images/jalview_develop_installer.icns (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • utils/channels/develop/images/jalview_develop_installer.ico (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • utils/channels/develop/images/jalview_develop_installer.png (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • utils/channels/develop/images/jalview_develop_logo.icns (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • utils/channels/release/channel_gradle.properties (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • utils/channels/release/images/jalview_installer.icns (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • utils/channels/release/images/jalview_installer.ico (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • utils/channels/release/images/jalview_installer.png (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • utils/channels/test-release/channel_gradle.properties (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • utils/channels/test-release/images/jalview_installer.icns (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • utils/channels/test-release/images/jalview_installer.ico (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • utils/channels/test-release/images/jalview_installer.png (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
  • utils/install4j/install4j10_template.install4j (version 0112f6d85c67b26ed08a03d71a16fecddfba4b3f) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 12 Jun 2024 f967059dbaa4dff1396364a999309f1f218b697f m

  JAL-3631 Name changes to system properties and a fallback App name to avoid hard-coded name in getdown

  • src/jalview/analytics/Plausible.java (version f967059dbaa4dff1396364a999309f1f218b697f) (diffs)
  • src/jalview/bin/Cache.java (version f967059dbaa4dff1396364a999309f1f218b697f) (diffs)
  • src/jalview/bin/Jalview.java (version f967059dbaa4dff1396364a999309f1f218b697f) (diffs)
  • src/jalview/util/ChannelProperties.java (version f967059dbaa4dff1396364a999309f1f218b697f) (diffs)
  • src/jalview/util/LaunchUtils.java (version f967059dbaa4dff1396364a999309f1f218b697f) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 12 Jun 2024 ddcbcdbcbf276a40b074374ce69f7f02eaa2705a m

  JAL-3631 Spot system property triggers in getdown to create/activate using a user-space location (dependent on OS), and copy digest-tested files from the Application's app dir to the user's new app dir.  Debugging statements left in for testing on other OSes.

  • getdown/lib/getdown-core.jar (version ddcbcdbcbf276a40b074374ce69f7f02eaa2705a) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version ddcbcdbcbf276a40b074374ce69f7f02eaa2705a) (diffs)
  • getdown/lib/getdown-launcher.jar (version ddcbcdbcbf276a40b074374ce69f7f02eaa2705a) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java (version ddcbcdbcbf276a40b074374ce69f7f02eaa2705a) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Digest.java (version ddcbcdbcbf276a40b074374ce69f7f02eaa2705a) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java (version ddcbcdbcbf276a40b074374ce69f7f02eaa2705a) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/LaunchUtil.java (version ddcbcdbcbf276a40b074374ce69f7f02eaa2705a) (diffs)
  • getdown/src/getdown/core/src/main/java/jalview/util/ChannelProperties.java (version ddcbcdbcbf276a40b074374ce69f7f02eaa2705a) (diffs)
  • getdown/src/getdown/core/src/main/java/jalview/util/LaunchUtils.java (version ddcbcdbcbf276a40b074374ce69f7f02eaa2705a) (diffs)
  • getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/GetdownApp.java (version ddcbcdbcbf276a40b074374ce69f7f02eaa2705a) (diffs)
  • getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/StatusPanel.java (version ddcbcdbcbf276a40b074374ce69f7f02eaa2705a) (diffs)
  • j11lib/getdown-core.jar (version ddcbcdbcbf276a40b074374ce69f7f02eaa2705a) (diffs)
  • j8lib/getdown-core.jar (version ddcbcdbcbf276a40b074374ce69f7f02eaa2705a) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 12 Jun 2024 72e0c69f1cf47fd8422b80470e7e60e508d67e40 m

  JAL-3631 Add a new launcher in install4j to pass new system properties to getdown, triggering the user-space appdir creation

  • build.gradle (version 72e0c69f1cf47fd8422b80470e7e60e508d67e40) (diffs)
  • gradle.properties (version 72e0c69f1cf47fd8422b80470e7e60e508d67e40) (diffs)
  • utils/install4j/install4j10_template.install4j (version 72e0c69f1cf47fd8422b80470e7e60e508d67e40) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 10 Jun 2024 2923f8b7cc30a79c79019ec69b2cd2a54615c0de m

  Merge branch 'bug/JAL-4421_customise_volume_name_of_DMG_installers' into feature/JAL-3631_allow_jalview_to_work_from_user-space_directory
• 

  Gitlab User 10 Jun 2024 40db1508dd0c582952275fb4d6fb021a5307e3e0 m

  JAL-4159 remove errant jalview source .zip

  • .zip (version 40db1508dd0c582952275fb4d6fb021a5307e3e0) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 07 Jun 2024 0fd0b1dfca59b32bfa28acf7932e84dac5fd774b m

  Merge branch 'develop' into improvement/JAL-4409_implement_extra_schemes_in_getdown
• 

  Ben Soares <b.soares@dundee.ac.uk> 07 Jun 2024 fe6e1a5e8e7b69ed17cbe917250acf41c2eb12a3 m

  JAL-4421 Update the dev_masos_installer.sh to use new Volume name

  • utils/dev_macos_install.sh (version fe6e1a5e8e7b69ed17cbe917250acf41c2eb12a3) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 06 Jun 2024 98ac89f0dd7993401aea5adbbd124bb970a98ad9 m

  JAL-4420 Added some more filename extensions

  • src/jalview/util/ArgParserUtils.java (version 98ac89f0dd7993401aea5adbbd124bb970a98ad9) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 06 Jun 2024 58d8d12ca3bcc48b6aa0e766a3f56c250e13d1dc m

  JAL-4072 Add zip-slip check in getdown

  • getdown/lib/getdown-core.jar (version 58d8d12ca3bcc48b6aa0e766a3f56c250e13d1dc) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version 58d8d12ca3bcc48b6aa0e766a3f56c250e13d1dc) (diffs)
  • getdown/lib/getdown-launcher.jar (version 58d8d12ca3bcc48b6aa0e766a3f56c250e13d1dc) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/tools/Patcher.java (version 58d8d12ca3bcc48b6aa0e766a3f56c250e13d1dc) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/FileUtil.java (version 58d8d12ca3bcc48b6aa0e766a3f56c250e13d1dc) (diffs)
  • j11lib/getdown-core.jar (version 58d8d12ca3bcc48b6aa0e766a3f56c250e13d1dc) (diffs)
  • j8lib/getdown-core.jar (version 58d8d12ca3bcc48b6aa0e766a3f56c250e13d1dc) (diffs)
• 

  Gitlab User 06 Jun 2024 c5af67123917341b830038da89ba65add8272974 m

  Merge branch 'bug/JAL-4421_customise_volume_name_of_DMG_installers' into develop
• 

  Ben Soares <b.soares@dundee.ac.uk> 06 Jun 2024 80c10300e59a40ced95d54e85c5cbbc40e5d3f34 m

  JAL-4358 Add the JALVIEW: CREATED DESKTOP line to java app and look out for it in Getdown to close the splash screen

  • getdown/lib/getdown-core.jar (version 80c10300e59a40ced95d54e85c5cbbc40e5d3f34) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version 80c10300e59a40ced95d54e85c5cbbc40e5d3f34) (diffs)
  • getdown/lib/getdown-launcher.jar (version 80c10300e59a40ced95d54e85c5cbbc40e5d3f34) (diffs)
  • getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/Getdown.java (version 80c10300e59a40ced95d54e85c5cbbc40e5d3f34) (diffs)
  • getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/GetdownApp.java (version 80c10300e59a40ced95d54e85c5cbbc40e5d3f34) (diffs)
  • j11lib/getdown-core.jar (version 80c10300e59a40ced95d54e85c5cbbc40e5d3f34) (diffs)
  • j8lib/getdown-core.jar (version 80c10300e59a40ced95d54e85c5cbbc40e5d3f34) (diffs)
  • src/jalview/gui/Desktop.java (version 80c10300e59a40ced95d54e85c5cbbc40e5d3f34) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 05 Jun 2024 6151b89badff956d951326011424c08ccabb5e99 m

  JAL-4420 Allow associated files to be dragged on separately from the alignment (but afterwards).

  • src/jalview/gui/Desktop.java (version 6151b89badff956d951326011424c08ccabb5e99) (diffs)
  • src/jalview/util/ArgParserUtils.java (version 6151b89badff956d951326011424c08ccabb5e99) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 05 Jun 2024 3e428f447c03ff771ab6a82632acc274f640aeb5 m

  JAL-4409 Small refactoring of ArgParserUtils to allow processFiles to work on drag-and-dropped files list.

  • src/jalview/gui/Desktop.java (version 3e428f447c03ff771ab6a82632acc274f640aeb5) (diffs)
  • src/jalview/util/ArgParserUtils.java (version 3e428f447c03ff771ab6a82632acc274f640aeb5) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 05 Jun 2024 965c8af33ac58a3b5b940e52f04a7bfc16d83e98 m

  Merge branch 'develop' into bug/JAL-4421_customise_volume_name_of_DMG_installers
• 

  Ben Soares <b.soares@dundee.ac.uk> 05 Jun 2024 f5a1843eb07107c5e196fe348d75e785c11562d6 m

  JAL-4421 Downgrading ds_store to 1.3.0 for build server limitations

  • build.gradle (version f5a1843eb07107c5e196fe348d75e785c11562d6) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 05 Jun 2024 d50db8c31e09462ef215880f156764d843e69648 m

  JAL-4421 Configuration for positioning icons in DMG

  • utils/channels/default/channel_gradle.properties (version d50db8c31e09462ef215880f156764d843e69648) (diffs)
  • utils/channels/default/images/jalview_default_dmg_DS_Store.json (version d50db8c31e09462ef215880f156764d843e69648) (diffs)
  • utils/channels/develop-SUFFIX/images/jalview_develop_dmg_DS_Store.json (version d50db8c31e09462ef215880f156764d843e69648) (diffs)
  • utils/channels/release/images/jalview_dmg_DS_Store.json (version d50db8c31e09462ef215880f156764d843e69648) (diffs)
  • utils/channels/test-release/images/jalview_test-release_dmg_DS_Store.json (version d50db8c31e09462ef215880f156764d843e69648) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 05 Jun 2024 cbee9978721e4efff9e0741ba6933fb090d3aa23 m

  JAL-4421 Add --appname --appxpos --appypos to position variable application name icons, or read from config[app]

  • build.gradle (version cbee9978721e4efff9e0741ba6933fb090d3aa23) (diffs)
  • utils/macos_dmg/jalview_customise_dsstore.py (version cbee9978721e4efff9e0741ba6933fb090d3aa23) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 04 Jun 2024 72e22d79767010318a6de03d9f30d9ec8768dc45 m

  JAL-4421 Remove the disk_image_alias from the backgroundImageAlias altogether as it isn't needed and doesn't even make sense for a downloaded DMG

  • utils/macos_dmg/jalview_customise_dsstore.py (version 72e22d79767010318a6de03d9f30d9ec8768dc45) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 04 Jun 2024 b0f894660c05056490bf14ada8c64106d842ee17 m

  JAL-4421 Allow JSON config file to be options (no icon positioning for default or develop-SUFFIX). Allow .VolumeIcons.icns to be optional -- must remove <file> node from install4j template

  • build.gradle (version b0f894660c05056490bf14ada8c64106d842ee17) (diffs)
  • utils/channels/develop-SUFFIX/channel_gradle.properties (version b0f894660c05056490bf14ada8c64106d842ee17) (diffs)
  • utils/channels/develop/channel_gradle.properties (version b0f894660c05056490bf14ada8c64106d842ee17) (diffs)
  • utils/channels/develop/images/jalview_develop_dmg_DS_Store.json (version b0f894660c05056490bf14ada8c64106d842ee17) (diffs)
  • utils/channels/test-release/images/jalview_test-release_dmg_DS_Store.json (version b0f894660c05056490bf14ada8c64106d842ee17) (diffs)
  • utils/macos_dmg/jalview_customise_dsstore.py (version b0f894660c05056490bf14ada8c64106d842ee17) (diffs)
• 

  Gitlab User 04 Jun 2024 22bca29df20181576ca89862298468ed84c84bbb m

  Merge branch 'improvement/JAL-4409_implement_extra_schemes_in_getdown' into develop
• 

  Gitlab User 04 Jun 2024 55f81e9a949fa83107f5329131d344a4fe83b614 m

  JAL-4409 don't ignore gitignore !

  • .gitignore (version 55f81e9a949fa83107f5329131d344a4fe83b614) (diffs)
• 

  Gitlab User 04 Jun 2024 a604feb0d8241649ead385602bd03e092809b945 m

  JAL-4418 first development release for 2.11.4.0 - release notes for JAL-4159,JAL-4257,JAL-4386,JAL-4392,JAL-789

  • help/markdown/releases/release-2_11_4_0.md (version a604feb0d8241649ead385602bd03e092809b945) (diffs)
  • help/markdown/whatsnew/whatsnew-2_11_4_0.md (version a604feb0d8241649ead385602bd03e092809b945) (diffs)
• 

  Gitlab User 04 Jun 2024 ce59cf0845b1420b9382d91e4df1de78c00885d1 m

  Merge branch 'feature/JAL-4159_pasimap' into develop
   Conflicts:
          help/markdown/releases/release-2_11_3_0.md
• 

  Gitlab User 04 Jun 2024 8b4b6dc36c3f57292ce9d8484ce5005eaec77262 m

  Merge branch 'releases/Release_2_11_3_Branch' into develop
• 

  Ben Soares <b.soares@dundee.ac.uk> 04 Jun 2024 20432ca28c59b733a0b2c25577701a50800aab86 m

  JAL-4421 Put correct VolumeIcon.icns file onto DMG volume as /.VolumeIcon.icns

  • build.gradle (version 20432ca28c59b733a0b2c25577701a50800aab86) (diffs)
  • gradle.properties (version 20432ca28c59b733a0b2c25577701a50800aab86) (diffs)
  • utils/channels/default/images/jalview_default-VolumeIcon.icns (version 20432ca28c59b733a0b2c25577701a50800aab86) (diffs)
  • utils/channels/develop-SUFFIX/channel_gradle.properties (version 20432ca28c59b733a0b2c25577701a50800aab86) (diffs)
  • utils/channels/develop-SUFFIX/images/jalview_develop-VolumeIcon.icns (version 20432ca28c59b733a0b2c25577701a50800aab86) (diffs)
  • utils/channels/develop/channel_gradle.properties (version 20432ca28c59b733a0b2c25577701a50800aab86) (diffs)
  • utils/channels/release/channel_gradle.properties (version 20432ca28c59b733a0b2c25577701a50800aab86) (diffs)
  • utils/channels/test-release/channel_gradle.properties (version 20432ca28c59b733a0b2c25577701a50800aab86) (diffs)
  • utils/install4j/install4j10_template.install4j (version 20432ca28c59b733a0b2c25577701a50800aab86) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 04 Jun 2024 7e626def0fe318fd6ef8163a38deeba86f7dbc60 m

  JAL-4421 Icns to use as .VolumeIcon.icns in DMG volumes.  See comment with SetFile

  • utils/channels/develop/images/jalview_develop-VolumeIcon.icns (version 7e626def0fe318fd6ef8163a38deeba86f7dbc60) (diffs)
  • utils/channels/release/images/jalview-VolumeIcon.icns (version 7e626def0fe318fd6ef8163a38deeba86f7dbc60) (diffs)
  • utils/channels/test-release/images/jalview_test-release-VolumeIcon.icns (version 7e626def0fe318fd6ef8163a38deeba86f7dbc60) (diffs)
  • utils/macos_dmg/jalview_customise_dsstore.py (version 7e626def0fe318fd6ef8163a38deeba86f7dbc60) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 03 Jun 2024 7e2fee4899d9f351cfc9eb6f58d7ec0bd3152138 m

  JAL-4421 Also add DMG filename to python script. Necessitates DS_Store for x64 and aarch64 versions, with changes in build.gradle and install4j10_template.install4j. Ensure all x64 references are x64 and not the (more correct) x86 -- java uses x64.

  • build.gradle (version 7e2fee4899d9f351cfc9eb6f58d7ec0bd3152138) (diffs)
  • utils/install4j/install4j10_template.install4j (version 7e2fee4899d9f351cfc9eb6f58d7ec0bd3152138) (diffs)
  • utils/macos_dmg/jalview_customise_dsstore.py (version 7e2fee4899d9f351cfc9eb6f58d7ec0bd3152138) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 01 Jun 2024 b96091ff32d202126e5fe30eddb5ad32016f0e1b m

  JAL-4421 Add DS_Store customisation to gradle. Add backgroundImage alias dump to --dump

  • build.gradle (version b96091ff32d202126e5fe30eddb5ad32016f0e1b) (diffs)
  • gradle.properties (version b96091ff32d202126e5fe30eddb5ad32016f0e1b) (diffs)
  • utils/channels/test-release/channel_gradle.properties (version b96091ff32d202126e5fe30eddb5ad32016f0e1b) (diffs)
  • utils/channels/test-release/images/jalview_test-release_dmg_DS_Store.json (version b96091ff32d202126e5fe30eddb5ad32016f0e1b) (diffs)
  • utils/macos_dmg/jalview_custom_dsstore.py (version b96091ff32d202126e5fe30eddb5ad32016f0e1b) (diffs)
  • utils/macos_dmg/jalview_customise_dsstore.py (version b96091ff32d202126e5fe30eddb5ad32016f0e1b) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 31 May 2024 b5375e3f77b77e453e4d62e3846cb40c6dedf798 m

  JAL-4421 Python script for customising DS_Store.  Separate out more names for DMG volumes in install4j and gradle.  Channel specific icon positioning for channel specific DMG background images.

  • build.gradle (version b5375e3f77b77e453e4d62e3846cb40c6dedf798) (diffs)
  • gradle.properties (version b5375e3f77b77e453e4d62e3846cb40c6dedf798) (diffs)
  • utils/channels/release/channel_gradle.properties (version b5375e3f77b77e453e4d62e3846cb40c6dedf798) (diffs)
  • utils/channels/release/images/jalview_dmg_DS_Store.json (version b5375e3f77b77e453e4d62e3846cb40c6dedf798) (diffs)
  • utils/install4j/install4j10_template.install4j (version b5375e3f77b77e453e4d62e3846cb40c6dedf798) (diffs)
  • utils/macos_dmg/jalview_custom_dsstore.py (version b5375e3f77b77e453e4d62e3846cb40c6dedf798) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 29 May 2024 5a9cb62d3054a07ad1233b13595e19266b3cc627 m

  JAL-4409 Allow more URI schemes (e.g. file) to be opened in Jalview

  • src/jalview/bin/Commands.java (version 5a9cb62d3054a07ad1233b13595e19266b3cc627) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 29 May 2024 fe88522a1771e72d1e21f81764b823a1f708cc1f m

  JAL-4409 Allow more URI schemes (e.g. file) to filter through to Jalview

  • getdown/lib/getdown-core.jar (version fe88522a1771e72d1e21f81764b823a1f708cc1f) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version fe88522a1771e72d1e21f81764b823a1f708cc1f) (diffs)
  • getdown/lib/getdown-launcher.jar (version fe88522a1771e72d1e21f81764b823a1f708cc1f) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java (version fe88522a1771e72d1e21f81764b823a1f708cc1f) (diffs)
  • getdown/src/getdown/core/src/main/java/jalview/util/HttpUtils.java (version fe88522a1771e72d1e21f81764b823a1f708cc1f) (diffs)
  • j11lib/getdown-core.jar (version fe88522a1771e72d1e21f81764b823a1f708cc1f) (diffs)
  • j8lib/getdown-core.jar (version fe88522a1771e72d1e21f81764b823a1f708cc1f) (diffs)
  • src/jalview/util/HttpUtils.java (version fe88522a1771e72d1e21f81764b823a1f708cc1f) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 29 May 2024 7bb6882463062279027fa73984328edc864fd047 m

  JAL-4414 Add SocketTimeoutException to exceptions that trigger File Not Found rather than Format Not Recognised

  • src/jalview/bin/Commands.java (version 7bb6882463062279027fa73984328edc864fd047) (diffs)
  • src/jalview/io/FileParse.java (version 7bb6882463062279027fa73984328edc864fd047) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 29 May 2024 bf9559a79163265ff3c07591491495808fc95e4e m

  JAL-3196 Need more memory for the install4j process run by gradle

  • build.gradle (version bf9559a79163265ff3c07591491495808fc95e4e) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 28 May 2024 ca3071875159ff8ab35d786f2c8e5359d0370e27 m

  JAL-4409 JAL-4160 Don't let getdown turn jalviewX:// URIs into absolute local file paths. Allow getdown CLI memory setting with double-dash --jvmmemX

  • getdown/lib/getdown-core.jar (version ca3071875159ff8ab35d786f2c8e5359d0370e27) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version ca3071875159ff8ab35d786f2c8e5359d0370e27) (diffs)
  • getdown/lib/getdown-launcher.jar (version ca3071875159ff8ab35d786f2c8e5359d0370e27) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java (version ca3071875159ff8ab35d786f2c8e5359d0370e27) (diffs)
  • getdown/src/getdown/core/src/main/java/jalview/util/HttpUtils.java (version ca3071875159ff8ab35d786f2c8e5359d0370e27) (diffs)
  • j11lib/getdown-core.jar (version ca3071875159ff8ab35d786f2c8e5359d0370e27) (diffs)
  • j8lib/getdown-core.jar (version ca3071875159ff8ab35d786f2c8e5359d0370e27) (diffs)
  • src/jalview/util/HttpUtils.java (version ca3071875159ff8ab35d786f2c8e5359d0370e27) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 28 May 2024 da3f2d8e8ed76c47a6a8853b0a2432a453333de9 m

  JAL-4417 Use a specified props file for consistent output

  • test/jalview/bin/CommandsTest.java (version da3f2d8e8ed76c47a6a8853b0a2432a453333de9) (diffs)
  • test/jalview/bin/commandsTest3.jvprops (version da3f2d8e8ed76c47a6a8853b0a2432a453333de9) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 28 May 2024 632d1f334d20b9af0a5959a1b85028d7ea292d84 m

  JAL-4409 TEMPORARY don't clean up image files from jalview.bin.CommandsTest.headlessOrGuiImageOutputTest failing on build server

  • test/jalview/bin/CommandsTest.java (version 632d1f334d20b9af0a5959a1b85028d7ea292d84) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 28 May 2024 e2c02bbe2633e41ca2ab13fbabc2c652007758ca m

  JAL-4409 Ensure the specific scheme jalviewx is only for the release version

  • build.gradle (version e2c02bbe2633e41ca2ab13fbabc2c652007758ca) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 28 May 2024 5be594c57aa6a0f39c7bc4fc3de67fa53f625cdb m

  JAL-4409 Don't insist on HttpURLConnection, allows for file:/ protocol connection

  • src/jalview/analytics/Plausible.java (version 5be594c57aa6a0f39c7bc4fc3de67fa53f625cdb) (diffs)
  • src/jalview/ext/ensembl/EnsemblRestClient.java (version 5be594c57aa6a0f39c7bc4fc3de67fa53f625cdb) (diffs)
  • src/jalview/ext/pymol/PymolManager.java (version 5be594c57aa6a0f39c7bc4fc3de67fa53f625cdb) (diffs)
  • src/jalview/util/HttpUtils.java (version 5be594c57aa6a0f39c7bc4fc3de67fa53f625cdb) (diffs)
  • src/jalview/ws/dbsources/Uniprot.java (version 5be594c57aa6a0f39c7bc4fc3de67fa53f625cdb) (diffs)
  • src/jalview/ws/ebi/EBIFetchClient.java (version 5be594c57aa6a0f39c7bc4fc3de67fa53f625cdb) (diffs)
  • test/jalview/util/HttpUtilsTest.java (version 5be594c57aa6a0f39c7bc4fc3de67fa53f625cdb) (diffs)