Jalview Git

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  Gitlab User 13 Nov 2024 544bd63f8e2c0122da4f309bdc415162fc1da737

  JAL-2275 JAL-3921 JAL-4077 release notes JAL-4090

  • help/markdown/releases/release-2_11_4_2.md (version 544bd63f8e2c0122da4f309bdc415162fc1da737) (diffs)
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  Gitlab User 13 Nov 2024 32b26331040cbf31cf842f059155c7f56560639b

  Merge branch 'patch/JAL-4077_jmolsaveloadwindows' into develop
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  Gitlab User 13 Nov 2024 c3c2fd13cbad21be9dd6529f6bf749fd90bcf844

  JAL-4077 JAL-3921 TRACE level reporting of Jmol modelfilenames

  • src/jalview/ext/jmol/JalviewJmolBinding.java (version c3c2fd13cbad21be9dd6529f6bf749fd90bcf844) (diffs)
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  Gitlab User 13 Nov 2024 278d4b2921b6cb58c3a6c15de0c0a4ed3c66b3f7

  JAL-4077 JAL-1551 formatting

  • src/jalview/ext/jmol/JalviewJmolBinding.java (version 278d4b2921b6cb58c3a6c15de0c0a4ed3c66b3f7) (diffs)
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  Gitlab User 13 Nov 2024 503685f9db9a9cd37212789dbd150dde18bcc529

  JAL-3921 escape and transform file paths for Jmol scripting environment

  • src/jalview/gui/AppJmol.java (version 503685f9db9a9cd37212789dbd150dde18bcc529) (diffs)
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  Gitlab User 13 Nov 2024 7e33a66f88f3a65467e849294202fdb273f45967

  JAL-4077 JAL-3921 match up transformed windows filepaths in Jmol's datamodel to original path in Jalview so associations work

  • src/jalview/ext/jmol/JalviewJmolBinding.java (version 7e33a66f88f3a65467e849294202fdb273f45967) (diffs)
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  Gitlab User 13 Nov 2024 cf1d19a283a24106e119d430685188a86e5a266f

  JAL-4077 translate between Java/windows and Jmol 14.31.53 script/internal model representation of local and network file paths

  • test/jalview/ext/jmol/JmolCommandsTest.java (version cf1d19a283a24106e119d430685188a86e5a266f) (diffs)
  • src/jalview/ext/jmol/JmolCommands.java (version cf1d19a283a24106e119d430685188a86e5a266f) (diffs)
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  Gitlab User 12 Nov 2024 5bb42b3567011fac02bc8b4bc2116d1b87af9763

  JAL-4077 additional trace output to help track down temporary files saved/loaded for sesions

  • src/jalview/structures/models/AAStructureBindingModel.java (version 5bb42b3567011fac02bc8b4bc2116d1b87af9763) (diffs)
  • src/jalview/project/Jalview2XML.java (version 5bb42b3567011fac02bc8b4bc2116d1b87af9763) (diffs)
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  Gitlab User 12 Nov 2024 f2b9dd1eb23246ad6c5447c2f49241d0306be68d

  JAL-4077 JAL-3921 even more generous incremental backoff and warnings to log and GUI if the saved structure session file was zero length

  • src/jalview/project/Jalview2XML.java (version f2b9dd1eb23246ad6c5447c2f49241d0306be68d) (diffs)
  • src/jalview/gui/StructureViewerBase.java (version f2b9dd1eb23246ad6c5447c2f49241d0306be68d) (diffs)
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  Gitlab User 12 Nov 2024 e27f752dfc9e7978827ab85cf4b5565cd13bd219

  JAL-4077 patched sessionSave(File ) command and test for Jmol so it actually escapes backslashes

  • test/jalview/ext/jmol/JmolCommandsTest.java (version e27f752dfc9e7978827ab85cf4b5565cd13bd219) (diffs)
  • src/jalview/ext/jmol/JmolCommands.java (version e27f752dfc9e7978827ab85cf4b5565cd13bd219) (diffs)