Jalview Git

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  Renia Correya 25 Sep 2024 2940d9c01539dd10962eb201ec7f0cb0eb905be9

  Merge develop into feature/JAL-4386_calculate_tree_using_secondary_structure_annotation
  Resolved merge conflicts in Messages.properties, GAlignFrame.java, AlignmentViewport.java, and SecondaryStructureConsensusThread.java
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  Gitlab User 18 Sep 2024 839b67dfeae7dc17cc31bfd9035f70b22655995b m

  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 m

  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 m

  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 m

  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 m

  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 m

  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 m

  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 m

  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 m

  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 m

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

  JAL-4418 documentation for 4461

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

  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 m

  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 m

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

  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 m

  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 m

  Merge branch 'improvement/JAL-4461_select_format_from_extension' into develop
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  Gitlab User 16 Sep 2024 e90033c6fcd1a828068690963fbb34e2b8d3631c m

  JAL-4392 JAL-4425 commented out code to allow consensus to be hidden automatically when just one sequence is shown

  • src/jalview/workers/ConsensusThread.java (version e90033c6fcd1a828068690963fbb34e2b8d3631c) (diffs)
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  Gitlab User 16 Sep 2024 f041ddeee56a2cb01ebd91b619b5ba9298a5f902 m

  Merge branch 'patch/JAL-4392_hide_ssconsensus_if_no_data' into develop
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  Gitlab User 16 Sep 2024 d764d838a8e1c2ef752825a6e209990f8c9de9f7 m

  Merge branch 'bug/JAL-4427_HTML_code_in_sequence_ID_text' into develop
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  Gitlab User 16 Sep 2024 9e2fa8ea576657fb12aed3ad639b221c4354b000 m

  JAL-4392 autohide the secondary structure consensus annotation by setting AlignmentAnnotation.hasData to false so it is not displayed in view

  • src/jalview/analysis/AAFrequency.java (version 9e2fa8ea576657fb12aed3ad639b221c4354b000) (diffs)
  • src/jalview/analysis/AlignmentAnnotationUtils.java (version 9e2fa8ea576657fb12aed3ad639b221c4354b000) (diffs)
  • src/jalview/analysis/AlignmentUtils.java (version 9e2fa8ea576657fb12aed3ad639b221c4354b000) (diffs)
  • src/jalview/analysis/Dna.java (version 9e2fa8ea576657fb12aed3ad639b221c4354b000) (diffs)
  • src/jalview/datamodel/AlignmentAnnotation.java (version 9e2fa8ea576657fb12aed3ad639b221c4354b000) (diffs)
  • src/jalview/datamodel/Profiles.java (version 9e2fa8ea576657fb12aed3ad639b221c4354b000) (diffs)
  • src/jalview/datamodel/ProfilesI.java (version 9e2fa8ea576657fb12aed3ad639b221c4354b000) (diffs)
  • src/jalview/gui/AlignmentPanel.java (version 9e2fa8ea576657fb12aed3ad639b221c4354b000) (diffs)
  • src/jalview/gui/AnnotationLabels.java (version 9e2fa8ea576657fb12aed3ad639b221c4354b000) (diffs)
  • src/jalview/gui/AnnotationPanel.java (version 9e2fa8ea576657fb12aed3ad639b221c4354b000) (diffs)
  • src/jalview/renderer/AnnotationRenderer.java (version 9e2fa8ea576657fb12aed3ad639b221c4354b000) (diffs)
  • src/jalview/schemes/RNAHelicesColour.java (version 9e2fa8ea576657fb12aed3ad639b221c4354b000) (diffs)
  • src/jalview/viewmodel/AlignmentViewport.java (version 9e2fa8ea576657fb12aed3ad639b221c4354b000) (diffs)
  • src/jalview/workers/SecondaryStructureConsensusThread.java (version 9e2fa8ea576657fb12aed3ad639b221c4354b000) (diffs)
  • src/jalview/workers/StrucConsensusThread.java (version 9e2fa8ea576657fb12aed3ad639b221c4354b000) (diffs)
  • test/jalview/datamodel/SequenceGroupTest.java (version 9e2fa8ea576657fb12aed3ad639b221c4354b000) (diffs)
  • test/jalview/renderer/ResidueShaderTest.java (version 9e2fa8ea576657fb12aed3ad639b221c4354b000) (diffs)
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  Renia Correya 16 Sep 2024 13190d3a1ce589bfb7bd24e81e2c8660a88ff161 m

  JAL-4427 Added test cases and a minor correction

  • src/jalview/gui/AnnotationLabels.java (version 13190d3a1ce589bfb7bd24e81e2c8660a88ff161) (diffs)
  • test/jalview/gui/AnnotationLabelsTest.java (version 13190d3a1ce589bfb7bd24e81e2c8660a88ff161) (diffs)
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  Gitlab User 16 Sep 2024 41e8b795a5d6f6192ff0610b9b438140b27a1137 m

  JAL-4392 don't show SS consensus for DNA alignments

  • src/jalview/viewmodel/AlignmentViewport.java (version 41e8b795a5d6f6192ff0610b9b438140b27a1137) (diffs)
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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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  Gitlab User 13 Sep 2024 269db78d89891e592bae2c32979d8788e3a66667 m

  JAL-4418 release notes for JAL-4461 - nb need to document the new option in the built in help

  • help/markdown/releases/release-2_11_4_0.md (version 269db78d89891e592bae2c32979d8788e3a66667) (diffs)
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  Gitlab User 13 Sep 2024 662f5482e6120e839c90bc88f5b7bd3d82eaf42e m

  Merge branch 'improvement/JAL-4461_select_format_from_extension' into develop
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  Ben Soares <b.soares@dundee.ac.uk> 13 Sep 2024 1a53fb93612a57a847ce8416362a7b00b8d862d7 m

  JAL-4461 Tests for JalviewFileChooser.defaultSaveFileFormat() and a slight fix to the code

  • src/jalview/gui/AlignFrame.java (version 1a53fb93612a57a847ce8416362a7b00b8d862d7) (diffs)
  • src/jalview/io/JalviewFileChooser.java (version 1a53fb93612a57a847ce8416362a7b00b8d862d7) (diffs)
  • test/jalview/io/JalviewFileChooserTest.java (version 1a53fb93612a57a847ce8416362a7b00b8d862d7) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 13 Sep 2024 b2ba3f351c30380ae7a0dd204757d7c3b54dad7f m

  JAL-4461 Adding in a number of properties that control the default save_as format. See issue for details.

  • resources/lang/Messages.properties (version b2ba3f351c30380ae7a0dd204757d7c3b54dad7f) (diffs)
  • resources/lang/Messages_es.properties (version b2ba3f351c30380ae7a0dd204757d7c3b54dad7f) (diffs)
  • src/jalview/gui/AlignFrame.java (version b2ba3f351c30380ae7a0dd204757d7c3b54dad7f) (diffs)
  • src/jalview/gui/Desktop.java (version b2ba3f351c30380ae7a0dd204757d7c3b54dad7f) (diffs)
  • src/jalview/gui/Preferences.java (version b2ba3f351c30380ae7a0dd204757d7c3b54dad7f) (diffs)
  • src/jalview/io/JalviewFileChooser.java (version b2ba3f351c30380ae7a0dd204757d7c3b54dad7f) (diffs)
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  Gitlab User 13 Sep 2024 e6d7db13cbe8bc862bd669d138e84d5200673a96

  Merge branch 'develop' into feature/JAL-4386_calculate_tree_using_secondary_structure_annotation
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  Gitlab User 13 Sep 2024 be288e5f7036e8a55928ac18820fc47572d6b0ff m

  JAL-4418 sign off JAL-4454 and convert markdown header to html for whatsNew 'experimental'

  • help/markdown/releases/release-2_11_4_0.md (version be288e5f7036e8a55928ac18820fc47572d6b0ff) (diffs)
  • help/markdown/whatsnew/whatsnew-2_11_4_0.md (version be288e5f7036e8a55928ac18820fc47572d6b0ff) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 13 Sep 2024 8ede146f4d51eca8d440e1c1a6fa081029b4cd1c m

  JAL-4461 Change JalviewFileFilter to use LinkedHashSet for extensions. Add list of extensions to 'By extensions' tooltip.

  • src/jalview/io/JalviewFileChooser.java (version 8ede146f4d51eca8d440e1c1a6fa081029b4cd1c) (diffs)
  • src/jalview/io/JalviewFileFilter.java (version 8ede146f4d51eca8d440e1c1a6fa081029b4cd1c) (diffs)
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  Gitlab User 12 Sep 2024 8e8ae2a3b94b347f7fd6dee43d5952c8d116662f m

  Merge branch 'bug/JAL-4427_HTML_code_in_sequence_ID_text' into develop
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  Gitlab User 12 Sep 2024 3d816f4854b3283c2764327065f63fc2d46e50ff m

  JAL-4418 sign off JAL-4427 JAL-4451 fix

  • help/markdown/releases/release-2_11_4_0.md (version 3d816f4854b3283c2764327065f63fc2d46e50ff) (diffs)
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  Gitlab User 12 Sep 2024 47cde5d652a565b540c345825c638fc4c167c4d7 m

  Merge branch 'bug/JAL-4427_HTML_code_in_sequence_ID_text' into develop
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  Ben Soares <b.soares@dundee.ac.uk> 12 Sep 2024 cea846e6b899fb5903011acc67004d73f59c3ba1 m

  JAL-4461 Added a dynamic tooltip to give more information when 'By extension' is the selected File Type.  Utilising MIT licensed SwingUtils.getDescendantsByClass() to delve into the JFileChooser.

  • resources/lang/Messages.properties (version cea846e6b899fb5903011acc67004d73f59c3ba1) (diffs)
  • resources/lang/Messages_es.properties (version cea846e6b899fb5903011acc67004d73f59c3ba1) (diffs)
  • src/jalview/io/JalviewFileChooser.java (version cea846e6b899fb5903011acc67004d73f59c3ba1) (diffs)
  • src/jalview/util/SwingUtils.java (version cea846e6b899fb5903011acc67004d73f59c3ba1) (diffs)
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  Gitlab User 12 Sep 2024 67cc778b79c2cca83b6c746bbc52a9d9166743fb m

  JAL-4461 fix up formatting and remove old comment

  • src/jalview/gui/AlignFrame.java (version 67cc778b79c2cca83b6c746bbc52a9d9166743fb) (diffs)
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  Gitlab User 12 Sep 2024 f9644737ff404d376d442fd21b2748ec9894ea2d m

  JAL-4461 after autodetection, update the filechooser dialog and let the user hit OK again to confirm the autodetected format

  • src/jalview/io/JalviewFileChooser.java (version f9644737ff404d376d442fd21b2748ec9894ea2d) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 12 Sep 2024 335d8b6b184c60944edf609bb86e08a12a355a73 m

  JAL-4461 Change labelling of All-known-alignment-files to Select-format-from-extension for Save-as file chooser

  • resources/lang/Messages.properties (version 335d8b6b184c60944edf609bb86e08a12a355a73) (diffs)
  • resources/lang/Messages_es.properties (version 335d8b6b184c60944edf609bb86e08a12a355a73) (diffs)
  • src/jalview/gui/AlignFrame.java (version 335d8b6b184c60944edf609bb86e08a12a355a73) (diffs)
  • src/jalview/io/JalviewFileChooser.java (version 335d8b6b184c60944edf609bb86e08a12a355a73) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 12 Sep 2024 efcc858be7c5023e58786f8117092b5879e573d7 m

  JAL-4460  Don't display the All-known-alignment-files format when a JalviewFileChooser is made with acceptAny set to false (usually a Save-as dialog)

  • src/jalview/io/JalviewFileChooser.java (version efcc858be7c5023e58786f8117092b5879e573d7) (diffs)
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  Gitlab User 12 Sep 2024 e87c7127294709e3eb3f6e2ee6582c6a6890d788 m

  JAL-4454 make sure 2.11.4.0-test is stripped - *for reals*

  • build.gradle (version e87c7127294709e3eb3f6e2ee6582c6a6890d788) (diffs)
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  Gitlab User 11 Sep 2024 50cf1b0f1c8ca0f99f35c33fb5f6556a200ef057 m

  JAL-4418 release notes for JAL-4460

  • help/markdown/releases/release-2_11_4_0.md (version 50cf1b0f1c8ca0f99f35c33fb5f6556a200ef057) (diffs)
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  Gitlab User 11 Sep 2024 d9bc459a175e6fc2d3806adfa71aea35e59027a9 m

  Merge branch 'bug/JAL-4460_alignment_save_as_format_not_registering' into develop
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  Gitlab User 11 Sep 2024 96e15273c58ad93f09a18d52e7eadcf6901012aa m

  JAL-4454 make sure 2.11.4.0-test is stripped

  • build.gradle (version 96e15273c58ad93f09a18d52e7eadcf6901012aa) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 11 Sep 2024 8003658d5abb83eb5d42a1a7b957b0686c852a26 m

  JAL-4460 In save as, set format from file extension if a multi-format file filter is selected

  • src/jalview/io/JalviewFileChooser.java (version 8003658d5abb83eb5d42a1a7b957b0686c852a26) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 11 Sep 2024 983bf691df367eef3dff83ec809bb236f7e021af m

  JAL-4460 Don't add .aln for an 'All known formats...' filename

  • src/jalview/io/JalviewFileChooser.java (version 983bf691df367eef3dff83ec809bb236f7e021af) (diffs)
  • src/jalview/io/JalviewFileFilter.java (version 983bf691df367eef3dff83ec809bb236f7e021af) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 11 Sep 2024 4dd649b088b13205d9eff79b494158d67c63dc16 m

  JAL-4460 Update currentFileFormat /after/ new format selection

  • src/jalview/gui/AlignFrame.java (version 4dd649b088b13205d9eff79b494158d67c63dc16) (diffs)
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  Gitlab User 11 Sep 2024 4d60d8b917a3cfe7202c9ff2e301eeb5e14ff1be m

  JAL-4418  JAL-4428,JAL-4421,JAL-3393 release notes

  • help/markdown/releases/release-2_11_4_0.md (version 4d60d8b917a3cfe7202c9ff2e301eeb5e14ff1be) (diffs)
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  Gitlab User 11 Sep 2024 4da518baaf1ad5a8e19243e8fe98cbb162d797f9 m

  Merge branch 'patch/JAL-4428_osx_codesigning_scripts' into develop
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  Gitlab User 11 Sep 2024 e428c76d94fdfb3c8d3783b62c14ef555e693adc m

  JAL-4428 codesign jnilibs

  • utils/osx_signing/sign_and_staple_dmg.sh (version e428c76d94fdfb3c8d3783b62c14ef555e693adc) (diffs)
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  Gitlab User 11 Sep 2024 8b9105836b3e771c2bad52b567a8cbdad2404cfa m

  JAL-4428 informational output (possibly needs verbosity control)

  • utils/osx_signing/sign_and_staple_dmg.sh (version 8b9105836b3e771c2bad52b567a8cbdad2404cfa) (diffs)
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  Gitlab User 11 Sep 2024 6ca157ff447d81c2f38fc17b51cffa484afed9ba m

  JAL-4428 giving another XXX

  • utils/osx_signing/sign_and_staple_dmg.sh (version 6ca157ff447d81c2f38fc17b51cffa484afed9ba) (diffs)
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  Gitlab User 11 Sep 2024 7513043ef659cee485e54ec0939c64a36cd031cc m

  JAL-4428 add some XXXX for mktemp -t

  • utils/osx_signing/sign_and_staple_dmg.sh (version 7513043ef659cee485e54ec0939c64a36cd031cc) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 11 Sep 2024 619551ed8a68b6f9d5cedd08cc67945150cc9d9d m

  JAL-4428 Fixes to -z's and mktemp

  • utils/osx_signing/sign_and_staple_dmg.sh (version 619551ed8a68b6f9d5cedd08cc67945150cc9d9d) (diffs)
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  Gitlab User 10 Sep 2024 2ab8dec60f0beca5e33ba4c9f348c45227d0ffd1 m

  Merge branch 'patch/JAL-4428_osx_codesigning_scripts' into develop
• 

  Gitlab User 10 Sep 2024 08ed00519c5f652f91e8403ae1ea2790a479394f m

  JAL-4454 allow channels to pick up most recent 'whatsNew' and releasenotes for their associated version

  • build.gradle (version 08ed00519c5f652f91e8403ae1ea2790a479394f) (diffs)
• 

  Gitlab User 09 Sep 2024 84393a0dcdd5056f3b75b28ecce838c409d9b6ff m

  JAL-4418 initial pasimap documentation and updated release notes for recent merges

  • help/help/html/calculations/pasimap.html (version 84393a0dcdd5056f3b75b28ecce838c409d9b6ff) (diffs)
  • help/markdown/releases/release-2_11_4_0.md (version 84393a0dcdd5056f3b75b28ecce838c409d9b6ff) (diffs)
• 

  Gitlab User 09 Sep 2024 bcd1fb33af892cbbaea5162e7a9da57e385d9e8a m

  JAL-4418 postpone release to Thursday 12th Sept 2024

  • help/markdown/releases/release-2_11_4_0.md (version bcd1fb33af892cbbaea5162e7a9da57e385d9e8a) (diffs)
• 

  Renia Correya 03 Sep 2024 c52a3a6cdf7d0e05ff3ca5e11ab60e95038c73fe

  Merge branch 'develop' into feature/JAL-4386_calculate_tree_using_secondary_structure_annotation
  # Conflicts:
  #        src/jalview/analysis/AAFrequency.java
  #        src/jalview/analysis/AlignmentUtils.java
  #        src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
  #        src/jalview/api/AlignViewportI.java
  #        src/jalview/datamodel/Profile.java
  #        src/jalview/datamodel/SequenceGroup.java
  #        src/jalview/gui/AlignFrame.java
  #        src/jalview/gui/AlignViewport.java
  #        src/jalview/gui/PopupMenu.java
  #        src/jalview/jbgui/GAlignFrame.java
  #        src/jalview/project/Jalview2XML.java
  #        src/jalview/renderer/AnnotationRenderer.java
  #        src/jalview/renderer/ResidueShader.java
  #        src/jalview/renderer/ResidueShaderI.java
  #        src/jalview/util/Constants.java
  #        src/jalview/viewmodel/AlignmentViewport.java
  #        src/jalview/workers/SecondaryStructureConsensusThread.java
  #        test/jalview/analysis/AlignmentUtilsTests.java
• 

  Gitlab User 03 Sep 2024 8a347b5268314778b49c80737058679cb3ec4827 m

  JAL-4386 remove magic string in registerScoreModel...

  • src/jalview/analysis/scoremodels/ScoreModels.java (version 8a347b5268314778b49c80737058679cb3ec4827) (diffs)
• 

  Gitlab User 02 Sep 2024 e7bfd7141229e93961d676431233487da4e7789b m

  JAL-4418 fix linkCheck

  • help/help/helpTOC.xml (version e7bfd7141229e93961d676431233487da4e7789b) (diffs)
  • help/markdown/whatsnew/whatsnew-2_11_4_0.md (version e7bfd7141229e93961d676431233487da4e7789b) (diffs)
• 

  Gitlab User 02 Sep 2024 e937933118a48e607805629f9581c6fd6d274a33 m

  JAL-4418 release 10th September

  • help/markdown/releases/release-2_11_4_0.md (version e937933118a48e607805629f9581c6fd6d274a33) (diffs)
• 

  Gitlab User 02 Sep 2024 e386ab351a5fae6088dc95e3be00cc70c17d8cee m

  Merge branch 'documentation/JAL-4418_2_11_4_0_docs' into develop
• 

  Gitlab User 02 Sep 2024 3296f8cb9d9f4c9f01f197e971ff625cd3be3ed7 m

  Merge branch 'feature/JAL-4446_cancellable_pasimap_etal' into develop
• 

  Gitlab User 02 Sep 2024 69e9cb3c4b9297c19411876e32604822f7f909de m

  JAL-4418 first pass at updating docs with pasimap, ssconservation, etc

  • help/help/help.jhm (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
  • help/help/helpTOC.xml (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
  • help/help/html/calculations/calculations.html (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
  • help/help/html/calculations/pasimap.html (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
  • help/help/html/calculations/protssconsensus.html (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
  • help/help/html/calculations/tree.html (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
  • help/help/html/menus/alignmentMenu.html (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
  • help/help/html/menus/alwannotation.html (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
  • help/help/html/menus/alwannotationpanel.html (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
  • help/help/html/menus/alwcalculate.html (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
  • help/help/html/menus/alwcolour.html (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
  • help/help/html/menus/alwformat.html (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
  • help/help/html/menus/desktopMenu.html (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
  • help/help/html/menus/wsmenu.html (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
  • help/markdown/whatsnew/whatsnew-2_11_4_0.md (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
• 

  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)
• 

  Renia Correya 30 Aug 2024 621f426fa1cd84aa41ab94581fecf0b4b659da50 m

  Fix for JAL-4427
  Sequence ID text showing html code - protein disorder.

  • src/jalview/gui/AnnotationLabels.java (version 621f426fa1cd84aa41ab94581fecf0b4b659da50) (diffs)
• 

  Renia Correya 30 Aug 2024 391348cbefa931101392b98c60d0494f3f382ef3

  JAL-4436 Colour by secondary structure conservation
  Corrected the labels as secondary structure conservation increment.
  Added a check for secondary structure in Colour by Above identity
  threshold feature.

  • resources/lang/Messages.properties (version 391348cbefa931101392b98c60d0494f3f382ef3) (diffs)
  • src/jalview/gui/SliderPanel.java (version 391348cbefa931101392b98c60d0494f3f382ef3) (diffs)
  • src/jalview/renderer/ResidueShader.java (version 391348cbefa931101392b98c60d0494f3f382ef3) (diffs)
• 

  Gitlab User 29 Aug 2024 f40edd5d97571d331bd03489ef67858bbb2595bf m

  JAL-4446 improved reporting of progress, and transition between cancelable and non-cancelable phases of pasimap calculation

  • src/jalview/analysis/PaSiMap.java (version f40edd5d97571d331bd03489ef67858bbb2595bf) (diffs)
  • src/jalview/gui/PaSiMapPanel.java (version f40edd5d97571d331bd03489ef67858bbb2595bf) (diffs)
  • src/jalview/gui/PairwiseAlignPanel.java (version f40edd5d97571d331bd03489ef67858bbb2595bf) (diffs)
  • src/jalview/gui/ProgressBar.java (version f40edd5d97571d331bd03489ef67858bbb2595bf) (diffs)
  • src/jalview/viewmodel/PaSiMapModel.java (version f40edd5d97571d331bd03489ef67858bbb2595bf) (diffs)
• 

  Gitlab User 29 Aug 2024 30c13c1638967753f7b1f9c880a92cc7308b1278 m

  JAL-4446 refactor progress listener handler code for reuse

  • src/jalview/gui/PaSiMapPanel.java (version 30c13c1638967753f7b1f9c880a92cc7308b1278) (diffs)
• 

  Gitlab User 29 Aug 2024 6ec1491ad65b1a0d63eff8277677a8ecd5ab354d m

  Merge branch 'develop' into feature/JAL-4446_cancellable_pasimap_etal
• 

  Gitlab User 28 Aug 2024 356477aa523d0422c42e34c60cb98c9249ac4ed3 m

  JAL-4418 tweak release notes for JAL-4328

  • help/markdown/releases/release-2_11_4_0.md (version 356477aa523d0422c42e34c60cb98c9249ac4ed3) (diffs)
• 

  Gitlab User 28 Aug 2024 6a6a1654226d5c75406c3bcd95f646d0d9996f61 m

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

  Ben Soares <b.soares@dundee.ac.uk> 28 Aug 2024 b9a24a3b7bacdc1f653b5de8b696e0892fa8f5c5 m

  JAL-3631 Allow use of ~/ for unixBinDir specified in response.varfile

  • utils/install4j/install4j10_template.install4j (version b9a24a3b7bacdc1f653b5de8b696e0892fa8f5c5) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 28 Aug 2024 0f709498e152ee504198a378472a348a1d91590d m

  JAL-3631 Allow unixBinDir (where a symbolic link gets made) to be set in response.varfile.  If it's not set or empty then the usual (dynamic) default will be ascertained.  Disallow reading in certain variables from the response.varfile that would just mess up the installation if changed.

  • utils/install4j/install4j10_template.install4j (version 0f709498e152ee504198a378472a348a1d91590d) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 28 Aug 2024 db28770c295fa1f8d4d2ae16931ee0bc2bfeb46e m

  JAL-3631 Configuration tweaks if using the response.varfile

  • utils/install4j/install4j10_template.install4j (version db28770c295fa1f8d4d2ae16931ee0bc2bfeb46e) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 28 Aug 2024 acb90325e4fde76fbe1d67b80f451a76353908bd m

  JAL-3631 Adjustments to allow setting the Advanced options in the response.varfile. Also big improvement on setting sys.fileAssociation.launchers automatically so only sys.fileAssociation.extensions needs to be set in a response.varfile.

  • utils/install4j/install4j10_template.install4j (version acb90325e4fde76fbe1d67b80f451a76353908bd) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 26 Aug 2024 ac69832b3a877a4b43b9a75a1f1f9b31cb55abee m

  JAL-3631 Fix interpolatove quotation marks in grep in jalview.sh.  Fix some folder name trailing slash checks in macos_install_jalview.sh, add ditto -v and more informative output.

  • utils/getdown/bin/jalview.sh (version ac69832b3a877a4b43b9a75a1f1f9b31cb55abee) (diffs)
  • utils/install4j/macos-install-jalview.sh (version ac69832b3a877a4b43b9a75a1f1f9b31cb55abee) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 26 Aug 2024 b28a43feb85d380c9912cf67a80761f2ccd7fa9b m

  JAL-3631 Fix interpolative quotation marks in new grep

  • utils/install4j/macos-install-jalview.sh (version b28a43feb85d380c9912cf67a80761f2ccd7fa9b) (diffs)
• 

  Gitlab User 26 Aug 2024 88be27652649d3404aa05326e6a54fc221b65ab5 m

  Merge branch 'jims/JAL-4420_review_redo' into develop
• 

  Ben Soares <b.soares@dundee.ac.uk> 26 Aug 2024 87ab843ae2e9afa891535b885d49d16ce6d1fce5 m

  JAL-3631 When appdir/jre can't be found, look for the installer.appdir found in installer.properties (if it exists) and use jre dir in installer.appdir

  • utils/getdown/bin/jalview.sh (version 87ab843ae2e9afa891535b885d49d16ce6d1fce5) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 26 Aug 2024 451d5c6724dd5ed4c42f8546553f97e2e9b686da m

  JAL-3631 Create an installer.properties file in the userappdir

  • getdown/lib/getdown-core.jar (version 451d5c6724dd5ed4c42f8546553f97e2e9b686da) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version 451d5c6724dd5ed4c42f8546553f97e2e9b686da) (diffs)
  • getdown/lib/getdown-launcher.jar (version 451d5c6724dd5ed4c42f8546553f97e2e9b686da) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java (version 451d5c6724dd5ed4c42f8546553f97e2e9b686da) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java (version 451d5c6724dd5ed4c42f8546553f97e2e9b686da) (diffs)
  • j11lib/getdown-core.jar (version 451d5c6724dd5ed4c42f8546553f97e2e9b686da) (diffs)
  • j8lib/getdown-core.jar (version 451d5c6724dd5ed4c42f8546553f97e2e9b686da) (diffs)
• 

  Gitlab User 26 Aug 2024 85e30a861f26369f9be8cffa4a1345c79092a895 m

  JAL-4418 JAL-4420 is experimental feature

  • help/markdown/releases/release-2_11_4_0.md (version 85e30a861f26369f9be8cffa4a1345c79092a895) (diffs)
• 

  Gitlab User 26 Aug 2024 1b68541c7d4b464f8165ca3dbdc5916ef6cf8c19 m

  JAL-4420 new drag'n'drop behaviour is now an 'Experimental Feature'

  • src/jalview/gui/Desktop.java (version 1b68541c7d4b464f8165ca3dbdc5916ef6cf8c19) (diffs)
• 

  Gitlab User 26 Aug 2024 ee4305f7cad84f8c254c8709b9da8621a2f18872 m

  JAL-4420 report exceptions raised during a drop rather than swallowing them

  • src/jalview/gui/Desktop.java (version ee4305f7cad84f8c254c8709b9da8621a2f18872) (diffs)
• 

  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)
• 

  Gitlab User 26 Aug 2024 6ce6f76a29779263ce810e0875b8050d25cbd0bb m

  JAL-4418 release notes for JAL-4398 and rejigged order a bit

  • help/markdown/releases/release-2_11_4_0.md (version 6ce6f76a29779263ce810e0875b8050d25cbd0bb) (diffs)
• 

  Gitlab User 26 Aug 2024 7e3271b6887c1674671dfc13725df09251177946 m

  Merge branch 'bug/JAL-4398_Window_menu_font_rendering' into develop
• 

  Gitlab User 26 Aug 2024 06bf5d0d823d53c6b6337cdf0ebb2c8897597b45 m

  Merge branch 'develop' into JAL-4442_cant_quit_jalview_on_windows_11
• 

  Gitlab User 23 Aug 2024 be1250ac8d031ee2501458377a6672b5dd4a4941 m

  Merge branch 'develop' into bug/JAL-4449_ensembl_sequence_retrieval_broken
• 

  Gitlab User 23 Aug 2024 ab788613300c36da80e7d37f946d699b19d562dd m

  JAL-4449 signed off and also updated Ensembl REST API version after fixing the EnsemblGene BRAF query test: JAL-3018

  • src/jalview/ext/ensembl/EnsemblRestClient.java (version ab788613300c36da80e7d37f946d699b19d562dd) (diffs)
  • test/jalview/ext/ensembl/EnsemblGeneTest.java (version ab788613300c36da80e7d37f946d699b19d562dd) (diffs)
• 

  Gitlab User 23 Aug 2024 a7218e71d8f55d564051673bc4ba8519315220aa m

  JAL-4418 JAL-3064 JAL-4111 release notes

  • help/markdown/releases/release-2_11_4_0.md (version a7218e71d8f55d564051673bc4ba8519315220aa) (diffs)
• 

  Ben Soares <b.soares@dundee.ac.uk> 22 Aug 2024 d575022e7f98391bca61ec8e70d01b7b61d5efd5 m

  JAL-4449 Changed HttpUtils.followConnection(conn0) to return conn0 unused when there is not a redirect from http to https, otherwise to return a new unused connection directly to the new https URL

  • src/jalview/util/HttpUtils.java (version d575022e7f98391bca61ec8e70d01b7b61d5efd5) (diffs)
• 

  Gitlab User 22 Aug 2024 cec9228733938df22e2332849ce72dccaec3c89c m

  JAL-4418 JAL-4450 known issue for 2.11.4 and 2.11.3.3

  • help/markdown/releases/release-2_11_4_0.md (version cec9228733938df22e2332849ce72dccaec3c89c) (diffs)
• 

  Gitlab User 22 Aug 2024 894e28b96fbe246ffeba3f834f2b30f06a4ec0f8 m

  JAL-4418 JAL-4100 ncrna genbank as known issue

  • help/markdown/releases/release-2_11_4_0.md (version 894e28b96fbe246ffeba3f834f2b30f06a4ec0f8) (diffs)
• 

  Gitlab User 21 Aug 2024 f599ef3e45d8bf3c247023f4156348a9d36a2d99 m

  Merge branch 'develop' into JAL-4442_cant_quit_jalview_on_windows_11
• 

  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)
• 

  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)
• 

  Ben Soares <b.soares@dundee.ac.uk> 19 Aug 2024 518abfdf0b3d2028617b781219086ad932c6f40a m

  JAL-4428 README.md file for sign_and_stapled_dmg.sh

  • utils/osx_signing/README (version 518abfdf0b3d2028617b781219086ad932c6f40a) (diffs)
  • utils/osx_signing/README.md (version 518abfdf0b3d2028617b781219086ad932c6f40a) (diffs)
  • utils/osx_signing/README.old (version 518abfdf0b3d2028617b781219086ad932c6f40a) (diffs)
  • utils/osx_signing/staple_dmg.sh (version 518abfdf0b3d2028617b781219086ad932c6f40a) (diffs)
• 

  Gitlab User 19 Aug 2024 e69db6fc850b0e89328bb2dbc3d371930fa6c595 m

  JAL-789 limit applicable score models to substitution matrix based ones

  • src/jalview/gui/CalculationChooser.java (version e69db6fc850b0e89328bb2dbc3d371930fa6c595) (diffs)