Jalview Git

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  Gitlab User 18 Sep 2024 839b67dfeae7dc17cc31bfd9035f70b22655995b

  JAL-4418 release notes typos

  • help/markdown/whatsnew/whatsnew-2_11_4_0.md (version 839b67dfeae7dc17cc31bfd9035f70b22655995b) (diffs)
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  Gitlab User 18 Sep 2024 0e2404da165d38cb1dd9928c1680273e1f65ad2a

  JAL-4418 bump release date to 18th September 2024

  • help/markdown/releases/release-2_11_4_0.md (version 0e2404da165d38cb1dd9928c1680273e1f65ad2a) (diffs)
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  Gitlab User 18 Sep 2024 75660f8029c41b82da83db312ce4bc422e02f6ca

  JAL-4418 fix up help TOC copypaste error

  • help/help/helpTOC.xml (version 75660f8029c41b82da83db312ce4bc422e02f6ca) (diffs)
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  Gitlab User 17 Sep 2024 1a41af382c8f65c9eee85b18ab4fb6a6b712b6c3

  JAL-4418 more documentation tweaks - getting Jen Fleming's name correct

  • help/help/html/calculations/calculatedialog.png (version 1a41af382c8f65c9eee85b18ab4fb6a6b712b6c3) (diffs)
  • help/help/html/calculations/calculations.html (version 1a41af382c8f65c9eee85b18ab4fb6a6b712b6c3) (diffs)
  • help/help/html/calculations/pairwise.html (version 1a41af382c8f65c9eee85b18ab4fb6a6b712b6c3) (diffs)
  • help/help/html/calculations/pasimap.html (version 1a41af382c8f65c9eee85b18ab4fb6a6b712b6c3) (diffs)
  • help/help/html/calculations/pasimapviewer.png (version 1a41af382c8f65c9eee85b18ab4fb6a6b712b6c3) (diffs)
  • help/markdown/releases/release-2_11_4_0.md (version 1a41af382c8f65c9eee85b18ab4fb6a6b712b6c3) (diffs)
  • help/markdown/whatsnew/whatsnew-2_11_4_0.md (version 1a41af382c8f65c9eee85b18ab4fb6a6b712b6c3) (diffs)
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  Gitlab User 17 Sep 2024 588465477e702bfda9bb4470a6eb0d69f45388d4

  JAL-4418 JAL-4428 CHANNEL=RELEASE has a different path for the jni jars

  • utils/osx_signing/sign_and_staple_dmg.sh (version 588465477e702bfda9bb4470a6eb0d69f45388d4) (diffs)
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  Gitlab User 17 Sep 2024 ab3055b2ebd93e8265cb193e7b6a79f326732316

  JAL-4418 fix link case for linkcheck and window menu documentation update

  • help/help/html/menus/alignmentMenu.html (version ab3055b2ebd93e8265cb193e7b6a79f326732316) (diffs)
  • help/help/html/menus/alwannotation.html (version ab3055b2ebd93e8265cb193e7b6a79f326732316) (diffs)
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  Gitlab User 17 Sep 2024 17461ae91a48f78a582ba2566364e7c7d778c87e

  JAL-4159 pasimap viewer image for docs

  • help/help/html/calculations/pasimap.html (version 17461ae91a48f78a582ba2566364e7c7d778c87e) (diffs)
  • help/help/html/calculations/pasimapviewer.png (version 17461ae91a48f78a582ba2566364e7c7d778c87e) (diffs)
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  Gitlab User 17 Sep 2024 d51b30d583717a947882a377671db063d0f22b17

  JAL-4418 JAL-4090 known defect report for JAL-4349

  • help/markdown/releases/release-2_11_4_0.md (version d51b30d583717a947882a377671db063d0f22b17) (diffs)
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  Gitlab User 17 Sep 2024 d710fdd71f60fc6a6b3c31d1a3691c581654fd25

  JAL-4414 JAL-1054 fix irrelevant failing network test for JAL-4418 2.11.4.0 release

  • src/jalview/ws/DBRefFetcher.java (version d710fdd71f60fc6a6b3c31d1a3691c581654fd25) (diffs)
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  Gitlab User 17 Sep 2024 207feba719c878b68c6a3c656d5a91f282338d49

  Merge branch 'bug/JAL-1054_broken_test' into develop
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  Gitlab User 17 Sep 2024 d94e2889036b7ea99c36045cc6d73c4f497139a5

  JAL-4418 documentation for 4461

  • help/help/html/io/index.html (version d94e2889036b7ea99c36045cc6d73c4f497139a5) (diffs)
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  Gitlab User 17 Sep 2024 157385223801346ee6800b5eb1e0cecc33b12701

  JAL-4418 documentation for ss annotation row preference and auto show (JAL-4425 JAL-4392)

  • help/help/html/calculations/protssconsensus.html (version 157385223801346ee6800b5eb1e0cecc33b12701) (diffs)
  • help/help/html/features/preferences.html (version 157385223801346ee6800b5eb1e0cecc33b12701) (diffs)
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  Gitlab User 17 Sep 2024 29c1f7f296259f96fb0d1341f4381b83b8ea9788

  JAL-4418 JAL-4442 quit racecondition patch

  • help/markdown/releases/release-2_11_4_0.md (version 29c1f7f296259f96fb0d1341f4381b83b8ea9788) (diffs)
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  Gitlab User 17 Sep 2024 3b321ee3d6ec9ca63d37a1c5f63b491ec1e365a5

  Merge branch 'JAL-4442_cant_quit_jalview_on_windows_11' into develop
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  Gitlab User 17 Sep 2024 cc5c69bfd4a472470f18cf5652805899bc7a3551

  JAL-4418 release 2.11.4.0 today!

  • help/markdown/releases/release-2_11_4_0.md (version cc5c69bfd4a472470f18cf5652805899bc7a3551) (diffs)
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  Gitlab User 17 Sep 2024 20e70a8e299b3531d173285a2bd4de64e1ed9fc4

  JAL-4418 JAL-4392 show/hide group associated secondary structure consensus and document autohide of secondary structure consensus JAL-4464 also knowndefect for not storing/restoring group associated secondary structure consensus

  • help/help/html/calculations/protssconsensus.html (version 20e70a8e299b3531d173285a2bd4de64e1ed9fc4) (diffs)
  • help/help/html/menus/alwannotation.html (version 20e70a8e299b3531d173285a2bd4de64e1ed9fc4) (diffs)
  • resources/lang/Messages.properties (version 20e70a8e299b3531d173285a2bd4de64e1ed9fc4) (diffs)
  • src/jalview/gui/AlignFrame.java (version 20e70a8e299b3531d173285a2bd4de64e1ed9fc4) (diffs)
  • src/jalview/jbgui/GAlignFrame.java (version 20e70a8e299b3531d173285a2bd4de64e1ed9fc4) (diffs)
  • src/jalview/viewmodel/AlignmentViewport.java (version 20e70a8e299b3531d173285a2bd4de64e1ed9fc4) (diffs)
  • src/jalview/workers/SecondaryStructureConsensusThread.java (version 20e70a8e299b3531d173285a2bd4de64e1ed9fc4) (diffs)
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  Gitlab User 17 Sep 2024 1b0426d9c3091ecc80c8fdeb582c7945fb16cff1

  Merge branch 'improvement/JAL-4461_select_format_from_extension' into develop
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  Ben Soares <b.soares@dundee.ac.uk> 16 Sep 2024 82ffdea414be32b2fee43828940c0af3c0f17801 m

  JAL-4461 Move SwingUtils to darrylbu.util.SwingUtils, more appropriate

  • src/darrylbu/util/SwingUtils.java (version 82ffdea414be32b2fee43828940c0af3c0f17801) (diffs)
  • src/jalview/io/JalviewFileChooser.java (version 82ffdea414be32b2fee43828940c0af3c0f17801) (diffs)
  • src/jalview/util/SwingUtils.java (version 82ffdea414be32b2fee43828940c0af3c0f17801) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 02 Sep 2024 08a024937b60499b53a60024f9b40402f623ec8d m

  JAL-1054 Add option to always follow redirects and not just http->https ones in jalview.util.HttpUtils. Fix tests for HttpUtils.followConnection,openConnection,openStream by checking with the followAnyway flag true and false.

  • src/jalview/util/HttpUtils.java (version 08a024937b60499b53a60024f9b40402f623ec8d) (diffs)
  • test/jalview/util/HttpUtilsTest.java (version 08a024937b60499b53a60024f9b40402f623ec8d) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 26 Aug 2024 88ec5ec9e697a1a5ee9e2c3ede3e248e1a6d918e m

  JAL-4442 Removed debugging variables and a stray 'wait' boolean which is not used

  • src/jalview/gui/QuitHandler.java (version 88ec5ec9e697a1a5ee9e2c3ede3e248e1a6d918e) (diffs)
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  Gitlab User 26 Aug 2024 06bf5d0d823d53c6b6337cdf0ebb2c8897597b45 m

  Merge branch 'develop' into JAL-4442_cant_quit_jalview_on_windows_11
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  Gitlab User 21 Aug 2024 f599ef3e45d8bf3c247023f4156348a9d36a2d99 m

  Merge branch 'develop' into JAL-4442_cant_quit_jalview_on_windows_11
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  Gitlab User 21 Aug 2024 85d6c4e85b067e72af161cbe584ad8f247565055 m

  JAL-4442 reprioritise QuitHandler debug output to either trace, debug or warn

  • src/jalview/gui/QuitHandler.java (version 85d6c4e85b067e72af161cbe584ad8f247565055) (diffs)
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  Gitlab User 21 Aug 2024 b81cfff0a0c0a8ce6b1618ac9db65e553369eaef m

  JAL-4442 reprioritise JvOptionPane debug output to either trace, debug or warn

  • src/jalview/gui/JvOptionPane.java (version b81cfff0a0c0a8ce6b1618ac9db65e553369eaef) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 12 Aug 2024 df97c670f60a8dc0082b464ec542c43d0b6f16fd m

  JAL-4442 Add a wait for termination of button action handlers method

  • src/jalview/gui/JvOptionPane.java (version df97c670f60a8dc0082b464ec542c43d0b6f16fd) (diffs)
  • src/jalview/gui/QuitHandler.java (version df97c670f60a8dc0082b464ec542c43d0b6f16fd) (diffs)