Jalview Git

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  Gitlab User 29 Aug 2024 f40edd5d97571d331bd03489ef67858bbb2595bf

  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)
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  Gitlab User 29 Aug 2024 30c13c1638967753f7b1f9c880a92cc7308b1278

  JAL-4446 refactor progress listener handler code for reuse

  • src/jalview/gui/PaSiMapPanel.java (version 30c13c1638967753f7b1f9c880a92cc7308b1278) (diffs)
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  Gitlab User 29 Aug 2024 6ec1491ad65b1a0d63eff8277677a8ecd5ab354d

  Merge branch 'develop' into feature/JAL-4446_cancellable_pasimap_etal
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  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)
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  Gitlab User 28 Aug 2024 6a6a1654226d5c75406c3bcd95f646d0d9996f61 m

  Merge branch 'feature/JAL-3631_allow_jalview_to_work_from_user-space_directory' into develop
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  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)
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  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)
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  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)
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  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)
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  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)
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  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)
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  Gitlab User 26 Aug 2024 88be27652649d3404aa05326e6a54fc221b65ab5 m

  Merge branch 'jims/JAL-4420_review_redo' into develop
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  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)
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  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)
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  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)
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  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)
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  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)
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  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)
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  Gitlab User 26 Aug 2024 7e3271b6887c1674671dfc13725df09251177946 m

  Merge branch 'bug/JAL-4398_Window_menu_font_rendering' into develop
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  Gitlab User 23 Aug 2024 be1250ac8d031ee2501458377a6672b5dd4a4941 m

  Merge branch 'develop' into bug/JAL-4449_ensembl_sequence_retrieval_broken
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  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)
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  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)
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  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)
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  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)
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  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)
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  Ben Soares <b.soares@dundee.ac.uk> 19 Aug 2024 b3aa009895567ae6c7131c2c09aefb7def40fc7a m

  JAL-3631 Change macos-install-jalview.sh to use ditto instead of rsync. Localise function vars.

  • utils/install4j/macos-install-jalview.sh (version b3aa009895567ae6c7131c2c09aefb7def40fc7a) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 16 Aug 2024 30246584379baffaa0d7467f4362104a7187d074 m

  JAL-3631 Fix EnvConfig.getUserAppdir() in getdown when running the getdown-launcher.jar update

  • getdown/lib/FJVL_VERSION (version 30246584379baffaa0d7467f4362104a7187d074) (diffs)
  • getdown/lib/JVL_VERSION (version 30246584379baffaa0d7467f4362104a7187d074) (diffs)
  • getdown/lib/getdown-core.jar (version 30246584379baffaa0d7467f4362104a7187d074) (diffs)
  • getdown/lib/getdown-launcher-local.jar (version 30246584379baffaa0d7467f4362104a7187d074) (diffs)
  • getdown/lib/getdown-launcher.jar (version 30246584379baffaa0d7467f4362104a7187d074) (diffs)
  • getdown/src/getdown/ant/pom.xml (version 30246584379baffaa0d7467f4362104a7187d074) (diffs)
  • getdown/src/getdown/core/pom.xml (version 30246584379baffaa0d7467f4362104a7187d074) (diffs)
  • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java (version 30246584379baffaa0d7467f4362104a7187d074) (diffs)
  • getdown/src/getdown/core/src/main/java/jalview/bin/GetdownLauncherUpdate.java (version 30246584379baffaa0d7467f4362104a7187d074) (diffs)
  • getdown/src/getdown/core/src/main/java/jalview/util/ErrorLog.java (version 30246584379baffaa0d7467f4362104a7187d074) (diffs)
  • getdown/src/getdown/core/src/main/java/jalview/util/LaunchUtils.java (version 30246584379baffaa0d7467f4362104a7187d074) (diffs)
  • getdown/src/getdown/launcher/pom.xml (version 30246584379baffaa0d7467f4362104a7187d074) (diffs)
  • getdown/src/getdown/mvn_cmd (version 30246584379baffaa0d7467f4362104a7187d074) (diffs)
  • getdown/src/getdown/pom.xml (version 30246584379baffaa0d7467f4362104a7187d074) (diffs)
  • j11lib/getdown-core.jar (version 30246584379baffaa0d7467f4362104a7187d074) (diffs)
  • j8lib/getdown-core.jar (version 30246584379baffaa0d7467f4362104a7187d074) (diffs)
  • src/jalview/bin/GetdownLauncherUpdate.java (version 30246584379baffaa0d7467f4362104a7187d074) (diffs)
  • src/jalview/util/LaunchUtils.java (version 30246584379baffaa0d7467f4362104a7187d074) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 15 Aug 2024 178aa13090b05c788cd00a580989c2528b47be7d m

  JAL-3631 Create a jalview_x_update link in appdir/bin alongside jalview_x in install4j wizard

  • utils/install4j/install4j10_template.install4j (version 178aa13090b05c788cd00a580989c2528b47be7d) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 15 Aug 2024 f13e674270b352c13e89a390e3cb613dc022358c m

  Merge branch 'develop' into feature/JAL-3631_allow_jalview_to_work_from_user-space_directory
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  Ben Soares <b.soares@dundee.ac.uk> 12 Aug 2024 614431e4e8a5c49c71a22444b2b2a352cab6b592 m

  Merge branch 'develop' into feature/JAL-3631_allow_jalview_to_work_from_user-space_directory
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  Ben Soares <b.soares@dundee.ac.uk> 08 Aug 2024 0f805a31db48d5fa56f53bb6f7da5efd81b70992 m

  JAL-3631 Better messaging and a root check on updating the --installation

  • utils/getdown/bin/update.sh (version 0f805a31db48d5fa56f53bb6f7da5efd81b70992) (diffs)
  • utils/install4j/macos-install-jalview.sh (version 0f805a31db48d5fa56f53bb6f7da5efd81b70992) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 08 Aug 2024 e3900f3622434ea40131b00e0c3562d31cfdeaf8 m

  JAL-3631 Change name of update link in DMGs. Correct wrong message in macos installer script.  Adding build_properties and channel.props into hidden folder on DMG. I'm sure they will be useful!

  • utils/install4j/install4j10_template.install4j (version e3900f3622434ea40131b00e0c3562d31cfdeaf8) (diffs)
  • utils/install4j/macos-install-jalview.sh (version e3900f3622434ea40131b00e0c3562d31cfdeaf8) (diffs)
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  Ben Soares <b.soares@dundee.ac.uk> 29 Apr 2024 8183ef1205ddc7ddc2aa40def6e81917c9c23940 m

  JAL-4398 Instantiate (static) JMenu windowMenu at the same time as the other (instance) JMenus for same context (FlatLaf?) settings

  • src/jalview/jbgui/GDesktop.java (version 8183ef1205ddc7ddc2aa40def6e81917c9c23940) (diffs)