Jalview Git

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  Ben Soares <b.soares@dundee.ac.uk> 20 Nov 2024 72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9

  JAL-4491 Allow getdown to download missing cert-chain certificates if not in the cacerts bundle (Jalview already does this). Recompile.

  • getdown/lib/getdown-core.jar (version 72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version 72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9) (diffs)
  • getdown/lib/getdown-launcher.jar (version 72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9) (diffs)
  • j11lib/getdown-core.jar (version 72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9) (diffs)
  • j8lib/getdown-core.jar (version 72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 20 Nov 2024 0ad213ec71dc74a1c9964176da82941444a5374d

  JAL-4491 Allow getdown to download missing cert-chain certificates if not in the cacerts bundle (Jalview already does this).

  • getdown/lib/getdown-core.jar (version 0ad213ec71dc74a1c9964176da82941444a5374d) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version 0ad213ec71dc74a1c9964176da82941444a5374d) (diffs)
  • getdown/lib/getdown-launcher.jar (version 0ad213ec71dc74a1c9964176da82941444a5374d) (diffs)
  • getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/GetdownApp.java (version 0ad213ec71dc74a1c9964176da82941444a5374d) (diffs)
  • j11lib/getdown-core.jar (version 0ad213ec71dc74a1c9964176da82941444a5374d) (diffs)
  • j8lib/getdown-core.jar (version 0ad213ec71dc74a1c9964176da82941444a5374d) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 20 Nov 2024 160fe15b38e09fd37d11b2f6fd42f6e5d600c420

  JAL-4477 Re-work install4j and getdown to use the installer.appdir first or installer.original_appdir if installer.appdir doesn't exist. Fix FileUtils to workj with getdown.

  • getdown/lib/getdown-core.jar (version 160fe15b38e09fd37d11b2f6fd42f6e5d600c420) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version 160fe15b38e09fd37d11b2f6fd42f6e5d600c420) (diffs)
  • getdown/lib/getdown-launcher.jar (version 160fe15b38e09fd37d11b2f6fd42f6e5d600c420) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java (version 160fe15b38e09fd37d11b2f6fd42f6e5d600c420) (diffs)
  • getdown/src/getdown/core/src/main/java/jalview/util/FileUtils.java (version 160fe15b38e09fd37d11b2f6fd42f6e5d600c420) (diffs)
  • j11lib/getdown-core.jar (version 160fe15b38e09fd37d11b2f6fd42f6e5d600c420) (diffs)
  • j8lib/getdown-core.jar (version 160fe15b38e09fd37d11b2f6fd42f6e5d600c420) (diffs)
  • src/jalview/util/FileUtils.java (version 160fe15b38e09fd37d11b2f6fd42f6e5d600c420) (diffs)
  • utils/install4j/install4j11_template.install4j (version 160fe15b38e09fd37d11b2f6fd42f6e5d600c420) (diffs)
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  Gitlab User 11 Nov 2024 a8875a08d16716161d51d26824b551ddc79fca9b

  JAL-4477 missing import ?  not sure how I missed this !

  • src/jalview/util/FileUtils.java (version a8875a08d16716161d51d26824b551ddc79fca9b) (diffs)
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  Gitlab User 11 Nov 2024 d7c3dc79c05b6bcfb728e455ed8148650d00d551

  Merge branch 'develop' into bug/JAL-4477_unmapped_filename_characters
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  Gitlab User 11 Nov 2024 67eb1f5444c58924bb3af2dbe9c98b1158032b14 m

  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 m

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

  JAL-4490 bump version and release notes

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

  JAL-4485 Tests for FileUtils.getMatchingVersionedFilesTest()

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

  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 m

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

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

  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 m

  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 m

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

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

  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 m

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

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

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

  • src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java (version df635455b3ff798e54f8a4c927a14e1e0e2d8260) (diffs)
  • src/jalview/ext/pymol/PymolManager.java (version df635455b3ff798e54f8a4c927a14e1e0e2d8260) (diffs)