Jalview Git

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  Gitlab User 11 Nov 2024 416aad339a728afd5ca4c2a558b6a395dd53a3ac

  JAL-4490 JAL-4474 release notes (preemptive but hopeful that it works!)

  • help/markdown/releases/release-2_11_4_2.md (version 416aad339a728afd5ca4c2a558b6a395dd53a3ac) (diffs)
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  Gitlab User 11 Nov 2024 73199534925586fef0b3a346f6ac2b34024061b1

  Merge branch 'JAL-4474_jalview.ps1_not_working' into develop
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  Gitlab User 11 Nov 2024 67eb1f5444c58924bb3af2dbe9c98b1158032b14

  JAL-4490 release notes for JAL-4485 et al.

  • help/markdown/releases/release-2_11_4_2.md (version 67eb1f5444c58924bb3af2dbe9c98b1158032b14) (diffs)
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  Gitlab User 11 Nov 2024 9091bdd6ce0942ab8837905c03d5ca9ec7d3743c

  Merge branch 'improvement/JAL-4485_not_finding_chimerax_on_managed_desktop' into develop
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  Gitlab User 11 Nov 2024 6741c082e78e332b5de93efe41a87f30e9bda657

  JAL-4490 bump version and release notes

  • help/markdown/releases/release-2_11_4_2.md (version 6741c082e78e332b5de93efe41a87f30e9bda657) (diffs)
  • RELEASE (version 6741c082e78e332b5de93efe41a87f30e9bda657) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 06 Nov 2024 c6c46de559211c83d7e8bdf450d17628ae534af4

  JAL-4485 Tests for FileUtils.getMatchingVersionedFilesTest()

  • test/jalview/util/FileUtilsTest.java (version c6c46de559211c83d7e8bdf450d17628ae534af4) (diffs)
  • src/jalview/util/FileUtils.java (version c6c46de559211c83d7e8bdf450d17628ae534af4) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 06 Nov 2024 f3bd577f8e6edd657c951157b41a2cd0455429e9

  JAL-4485 Not using whitelist, just file glob and blacklist

  • src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java (version f3bd577f8e6edd657c951157b41a2cd0455429e9) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 06 Nov 2024 8c5dec3ff3d7d6ebf79233499836e601e0f9fadd

  JAL-4485 Better var name and using FileUtils method in StructureManager

  • src/jalview/util/FileUtils.java (version 8c5dec3ff3d7d6ebf79233499836e601e0f9fadd) (diffs)
  • src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java (version 8c5dec3ff3d7d6ebf79233499836e601e0f9fadd) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 06 Nov 2024 c33f378461cc617d47f30d6e4bb426724d338d8f

  JAL-4485 Extracted the whitelist/blacklist fileglob finding code into FileUtils for more generic use

  • src/jalview/util/FileUtils.java (version c33f378461cc617d47f30d6e4bb426724d338d8f) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 06 Nov 2024 5ef2e9ac9664438c3ffd47762e83a296b2b3b01c

  JAL-4485 Fix the template path for Windows Chimera/X executable. Added more debugging for path finding.

  • src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java (version 5ef2e9ac9664438c3ffd47762e83a296b2b3b01c) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 06 Nov 2024 7dd2e65dd82f622ef447070256e4c3659fe636ca

  JAL-4487 Escape backslash file separators when looking for file globs. Fixed a CLI and a debugging NPE.

  • src/jalview/util/FileUtils.java (version 7dd2e65dd82f622ef447070256e4c3659fe636ca) (diffs)
  • src/jalview/gui/Preferences.java (version 7dd2e65dd82f622ef447070256e4c3659fe636ca) (diffs)
  • src/jalview/bin/Commands.java (version 7dd2e65dd82f622ef447070256e4c3659fe636ca) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 05 Nov 2024 d96be07c64432e609182c3bf09c629a6163c28de

  JAL-4485 Path fix for macOS Application*s*

  • src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java (version d96be07c64432e609182c3bf09c629a6163c28de) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 05 Nov 2024 11f6950ab4b5f8aa2a2e16f2f46d61fc9ea3aca2

  JAL-4485 Initially look for all installations of Chimera/X and add to the pathlist if version is not in the blacklist

  • src/jalview/gui/Preferences.java (version 11f6950ab4b5f8aa2a2e16f2f46d61fc9ea3aca2) (diffs)
  • src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java (version 11f6950ab4b5f8aa2a2e16f2f46d61fc9ea3aca2) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 01 Nov 2024 df635455b3ff798e54f8a4c927a14e1e0e2d8260

  JAL-4485 Extra debugging for Chimera/X and PyMol launches

  • src/jalview/ext/pymol/PymolManager.java (version df635455b3ff798e54f8a4c927a14e1e0e2d8260) (diffs)
  • src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java (version df635455b3ff798e54f8a4c927a14e1e0e2d8260) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 01 Nov 2024 1da3b80194892879ba275911738cdb4372a29ad4

  JAL-4474 Added -Force option to all Get-Item calls in Readlink-f function in jalview.ps1

  • utils/getdown/bin/jalview.ps1 (version 1da3b80194892879ba275911738cdb4372a29ad4) (diffs)