Build: #3 was successful Changes by Gitlab User
Code commits
Jalview Git
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Gitlab User 03ba07a5429bb19cc81bbfd44d240e002481877b
Merge branch 'feature/JAL-4386_JAL-4435_trees_from_annotations_on_alignment_2114_update' into trial_merge_JAL-4386
# Conflicts:
# src/jalview/analysis/AAFrequency.java
# src/jalview/analysis/AlignmentUtils.java
# src/jalview/analysis/PaSiMap.java
# src/jalview/analysis/ccAnalysis.java
# src/jalview/analysis/scoremodels/ScoreModels.java
# src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
# src/jalview/api/AlignViewportI.java
# src/jalview/datamodel/SequenceGroup.java
# src/jalview/gui/PaSiMapPanel.java
# src/jalview/gui/PairwiseAlignPanel.java
# src/jalview/gui/PopupMenu.java
# src/jalview/gui/SliderPanel.java
# src/jalview/jbgui/GAlignFrame.java
# src/jalview/jbgui/GPaSiMapPanel.java
# src/jalview/project/Jalview2XML.java
# src/jalview/renderer/AnnotationRenderer.java
# src/jalview/renderer/ResidueShader.java
# src/jalview/util/Constants.java
# src/jalview/viewmodel/AlignmentViewport.java
# test/jalview/analysis/AlignmentUtilsTests.java -
Gitlab User e6d7db13cbe8bc862bd669d138e84d5200673a96 m
Merge branch 'develop' into feature/JAL-4386_calculate_tree_using_secondary_structure_annotation
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Gitlab User be288e5f7036e8a55928ac18820fc47572d6b0ff m
JAL-4418 sign off JAL-4454 and convert markdown header to html for whatsNew 'experimental'
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Gitlab User 8e8ae2a3b94b347f7fd6dee43d5952c8d116662f m
Merge branch 'bug/JAL-4427_HTML_code_in_sequence_ID_text' into develop
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Gitlab User 3d816f4854b3283c2764327065f63fc2d46e50ff m
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Gitlab User 47cde5d652a565b540c345825c638fc4c167c4d7 m
Merge branch 'bug/JAL-4427_HTML_code_in_sequence_ID_text' into develop
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Gitlab User e87c7127294709e3eb3f6e2ee6582c6a6890d788 m
JAL-4454 make sure 2.11.4.0-test is stripped - *for reals*
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Gitlab User 50cf1b0f1c8ca0f99f35c33fb5f6556a200ef057 m
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Gitlab User d9bc459a175e6fc2d3806adfa71aea35e59027a9 m
Merge branch 'bug/JAL-4460_alignment_save_as_format_not_registering' into develop
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Gitlab User 96e15273c58ad93f09a18d52e7eadcf6901012aa m
JAL-4454 make sure 2.11.4.0-test is stripped
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Ben Soares <b.soares@dundee.ac.uk> 8003658d5abb83eb5d42a1a7b957b0686c852a26 m
JAL-4460 In save as, set format from file extension if a multi-format file filter is selected
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Ben Soares <b.soares@dundee.ac.uk> 983bf691df367eef3dff83ec809bb236f7e021af m
JAL-4460 Don't add .aln for an 'All known formats...' filename
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Ben Soares <b.soares@dundee.ac.uk> 4dd649b088b13205d9eff79b494158d67c63dc16 m
JAL-4460 Update currentFileFormat /after/ new format selection
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Gitlab User 4d60d8b917a3cfe7202c9ff2e301eeb5e14ff1be m
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Gitlab User 4da518baaf1ad5a8e19243e8fe98cbb162d797f9 m
Merge branch 'patch/JAL-4428_osx_codesigning_scripts' into develop
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Gitlab User e428c76d94fdfb3c8d3783b62c14ef555e693adc m
JAL-4428 codesign jnilibs
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Gitlab User 8b9105836b3e771c2bad52b567a8cbdad2404cfa m
JAL-4428 informational output (possibly needs verbosity control)
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Gitlab User 6ca157ff447d81c2f38fc17b51cffa484afed9ba m
JAL-4428 giving another XXX
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Gitlab User 7513043ef659cee485e54ec0939c64a36cd031cc m
JAL-4428 add some XXXX for mktemp -t
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Ben Soares <b.soares@dundee.ac.uk> 619551ed8a68b6f9d5cedd08cc67945150cc9d9d m
JAL-4428 Fixes to -z's and mktemp
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Gitlab User 2ab8dec60f0beca5e33ba4c9f348c45227d0ffd1 m
Merge branch 'patch/JAL-4428_osx_codesigning_scripts' into develop
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Gitlab User 08ed00519c5f652f91e8403ae1ea2790a479394f m
JAL-4454 allow channels to pick up most recent 'whatsNew' and releasenotes for their associated version
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Gitlab User 84393a0dcdd5056f3b75b28ecce838c409d9b6ff m
JAL-4418 initial pasimap documentation and updated release notes for recent merges
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Gitlab User bcd1fb33af892cbbaea5162e7a9da57e385d9e8a m
JAL-4418 postpone release to Thursday 12th Sept 2024
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Renia Correya c52a3a6cdf7d0e05ff3ca5e11ab60e95038c73fe m
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 8a347b5268314778b49c80737058679cb3ec4827 m
JAL-4386 remove magic string in registerScoreModel...
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Gitlab User e7bfd7141229e93961d676431233487da4e7789b m
JAL-4418 fix linkCheck
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Gitlab User e937933118a48e607805629f9581c6fd6d274a33 m
JAL-4418 release 10th September
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Gitlab User e386ab351a5fae6088dc95e3be00cc70c17d8cee m
Merge branch 'documentation/JAL-4418_2_11_4_0_docs' into develop
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Gitlab User 3296f8cb9d9f4c9f01f197e971ff625cd3be3ed7 m
Merge branch 'feature/JAL-4446_cancellable_pasimap_etal' into develop
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Gitlab User 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)
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Renia Correya 621f426fa1cd84aa41ab94581fecf0b4b659da50 m
Fix for JAL-4427
Sequence ID text showing html code - protein disorder. -
Renia Correya 391348cbefa931101392b98c60d0494f3f382ef3 m
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. -
Gitlab User 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)
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Gitlab User 30c13c1638967753f7b1f9c880a92cc7308b1278 m
JAL-4446 refactor progress listener handler code for reuse
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Gitlab User 6ec1491ad65b1a0d63eff8277677a8ecd5ab354d m
Merge branch 'develop' into feature/JAL-4446_cancellable_pasimap_etal
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Gitlab User 356477aa523d0422c42e34c60cb98c9249ac4ed3 m
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Gitlab User 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> b9a24a3b7bacdc1f653b5de8b696e0892fa8f5c5 m
JAL-3631 Allow use of ~/ for unixBinDir specified in response.varfile
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Ben Soares <b.soares@dundee.ac.uk> 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.
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Ben Soares <b.soares@dundee.ac.uk> db28770c295fa1f8d4d2ae16931ee0bc2bfeb46e m
JAL-3631 Configuration tweaks if using the response.varfile
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Ben Soares <b.soares@dundee.ac.uk> 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.
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Ben Soares <b.soares@dundee.ac.uk> 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.
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Ben Soares <b.soares@dundee.ac.uk> b28a43feb85d380c9912cf67a80761f2ccd7fa9b m
JAL-3631 Fix interpolative quotation marks in new grep
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Gitlab User 88be27652649d3404aa05326e6a54fc221b65ab5 m
Merge branch 'jims/JAL-4420_review_redo' into develop
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Ben Soares <b.soares@dundee.ac.uk> 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
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Ben Soares <b.soares@dundee.ac.uk> 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 85e30a861f26369f9be8cffa4a1345c79092a895 m
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Gitlab User 1b68541c7d4b464f8165ca3dbdc5916ef6cf8c19 m
JAL-4420 new drag'n'drop behaviour is now an 'Experimental Feature'
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Gitlab User ee4305f7cad84f8c254c8709b9da8621a2f18872 m
JAL-4420 report exceptions raised during a drop rather than swallowing them
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Gitlab User 6ce6f76a29779263ce810e0875b8050d25cbd0bb m
JAL-4418 release notes for JAL-4398 and rejigged order a bit
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Gitlab User 7e3271b6887c1674671dfc13725df09251177946 m
Merge branch 'bug/JAL-4398_Window_menu_font_rendering' into develop
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Gitlab User be1250ac8d031ee2501458377a6672b5dd4a4941 m
Merge branch 'develop' into bug/JAL-4449_ensembl_sequence_retrieval_broken
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Gitlab User ab788613300c36da80e7d37f946d699b19d562dd m
JAL-4449 signed off and also updated Ensembl REST API version after fixing the EnsemblGene BRAF query test: JAL-3018
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Gitlab User a7218e71d8f55d564051673bc4ba8519315220aa m
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Ben Soares <b.soares@dundee.ac.uk> 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
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Gitlab User cec9228733938df22e2332849ce72dccaec3c89c m
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Gitlab User 894e28b96fbe246ffeba3f834f2b30f06a4ec0f8 m
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Ben Soares <b.soares@dundee.ac.uk> 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)
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Gitlab User e69db6fc850b0e89328bb2dbc3d371930fa6c595 m
JAL-789 limit applicable score models to substitution matrix based ones
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Ben Soares <b.soares@dundee.ac.uk> b3aa009895567ae6c7131c2c09aefb7def40fc7a m
JAL-3631 Change macos-install-jalview.sh to use ditto instead of rsync. Localise function vars.
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Gitlab User 23eabe997df728d46b1333cbfd01407acba70908 m
JAL-4446 allow progress bar to become indeterminate after pairwise alignment step
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Gitlab User 695d7f4c7259087a58d01bdf3bbddd11aa59de79 m
Merge branch 'develop' into feature/JAL-4446_cancellable_pasimap_etal
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Ben Soares <b.soares@dundee.ac.uk> 44a4e6d8ab25553d72ddbb214f3fc8abfb9dd3a0 m
JAL-4428 localise function vars. Add -q -q option. Fix detaching volumes for cleanup -C
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Ben Soares <b.soares@dundee.ac.uk> 08791dd0d5c3293554d3d65ba41a22d2954edf81 m
JAL-4428 More coherent command line options and better 'running command' stdout management
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Ben Soares <b.soares@dundee.ac.uk> 3264c552a4fe29835a10f38ca92244253f305bb0 m
JAL-4428 Added in stapling into (now) sign_and_staple_dmg.sh. Some other small improvements to the script.
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Ben Soares <b.soares@dundee.ac.uk> 8204755d1364be5cfbdbb1695803e8c1f2ea24f6 m
JAL-4428 sign_dmg.sh with bells on
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Ben Soares <b.soares@dundee.ac.uk> 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> 178aa13090b05c788cd00a580989c2528b47be7d m
JAL-3631 Create a jalview_x_update link in appdir/bin alongside jalview_x in install4j wizard
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Ben Soares <b.soares@dundee.ac.uk> 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> be110b0de54d8e840c1468fa06441d42a44edd87 m
JAL-4111 Remove unnecessary dependency on gradle-imagemagick plugin, as causing problems in repo on Windows
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Ben Soares <b.soares@dundee.ac.uk> 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> 0f805a31db48d5fa56f53bb6f7da5efd81b70992 m
JAL-3631 Better messaging and a root check on updating the --installation
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Ben Soares <b.soares@dundee.ac.uk> 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!
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Gitlab User 4af2311cac6864a2879463213930dc46ce83c626 m
Merge branch 'feature/JAL-3631_allow_jalview_to_work_from_user-space_directory' into develop
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Gitlab User a51b5f709d28d8a25a3c2c4596cbe086aa34ea43 m
JAL-4447 standardised title formula for reporting score model and other parameters for pairwise alignment, PCA, tree, and Pasimap
- src/jalview/gui/AlignFrame.java (version a51b5f709d28d8a25a3c2c4596cbe086aa34ea43) (diffs)
- src/jalview/gui/CalculationChooser.java (version a51b5f709d28d8a25a3c2c4596cbe086aa34ea43) (diffs)
- src/jalview/gui/PCAPanel.java (version a51b5f709d28d8a25a3c2c4596cbe086aa34ea43) (diffs)
- src/jalview/gui/PaSiMapPanel.java (version a51b5f709d28d8a25a3c2c4596cbe086aa34ea43) (diffs)
- src/jalview/gui/PairwiseAlignPanel.java (version a51b5f709d28d8a25a3c2c4596cbe086aa34ea43) (diffs)
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Gitlab User a74f2604de0825eeeeda41158e9b9c1a32a2dd3c m
JAL-4446 reuse lasteta value
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Gitlab User 11cfa06b3572d711c3441c965e6340abcf20a4a2 m
JAL-4159 JAL-789 report pasimap and pairwise alignment parameters in window title
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Gitlab User 0c8213058cfc306cf459355543bcb93c546047dc m
JAL-4159 suppress pairwise alignment display options when not available from pasimap
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Gitlab User 39ef2c483d62e04129703d6acff8a594cc7e9b16 m
JAL-4446 better reporting of ETA estimation - particularly for large alignments
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Ben Soares <b.soares@dundee.ac.uk> 517f3b0fe55f619fa02db7021c6622cfea37e1f3 m
JAL-3631 Made bespoke command line arguments for console or unattended installs only (i.e. not GUI install mode), and work consistently with macos-install-jalview.sh
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Ben Soares <b.soares@dundee.ac.uk> d2b2b24f81eaf1aac20a66012961bfe3aefc63dd m
JAL-3631 Added install4j installer command line options -a -u -U and -S to match the macos-install-jalview.sh script
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Ben Soares <b.soares@dundee.ac.uk> 99449c096aed862fb24e97fc8585d928887ab33a m
JAL-3631 Important change to Execution Level in Windows. Some disabled attempts at File Association Reset.
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Ben Soares <b.soares@dundee.ac.uk> 4d482e435ef04f347a2b8933e4d6cc44708e86f9 m
JAL-3631 Short sleep added to 100% progress on installer wizard
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Ben Soares <b.soares@dundee.ac.uk> 7216fb878dfea790b1a14bc471a22e574106ad78 m
JAL-3631 An attempt to add a Reset to defaults button on the File Associations screen, but no joy (yet). Useful changes to customizedIds left in
- utils/install4j/file_associations_auto-install4j10.xml (version 7216fb878dfea790b1a14bc471a22e574106ad78) (diffs)
- utils/install4j/file_associations_template-install4j10.xml (version 7216fb878dfea790b1a14bc471a22e574106ad78) (diffs)
- utils/install4j/install4j10_template.install4j (version 7216fb878dfea790b1a14bc471a22e574106ad78) (diffs)
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Gitlab User df8c5515d51b26ef229cd2916a30d6a27f46c236 m
JAL-4446 avoid NPE when progress bar message is null
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Ben Soares <b.soares@dundee.ac.uk> 9375a2a68ed9258e68d6b70c6d3290a6da9da91e m
JAL-3631 Some small but important changes to run_other_script.ps1
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Ben Soares <b.soares@dundee.ac.uk> 87e83efdb057cb0761a7be1fc09fa3bbb2f72c42 m
JAL-3631 JAL-4444 Change way we add the jalview_x and jalview_x_update PS1 and BAT files, moved into build.gradle and removed from install4j. Add title icon to install4j.
- build.gradle (version 87e83efdb057cb0761a7be1fc09fa3bbb2f72c42) (diffs)
- gradle.properties (version 87e83efdb057cb0761a7be1fc09fa3bbb2f72c42) (diffs)
- utils/getdown/bin/jalview.bat (version 87e83efdb057cb0761a7be1fc09fa3bbb2f72c42) (diffs)
- utils/getdown/bin/jalview.ps1 (version 87e83efdb057cb0761a7be1fc09fa3bbb2f72c42) (diffs)
- utils/getdown/bin/run_other_script.ps1 (version 87e83efdb057cb0761a7be1fc09fa3bbb2f72c42) (diffs)
- utils/getdown/bin/run_powershell.bat (version 87e83efdb057cb0761a7be1fc09fa3bbb2f72c42) (diffs)
- utils/getdown/bin/update.bat (version 87e83efdb057cb0761a7be1fc09fa3bbb2f72c42) (diffs)
- utils/getdown/bin/update.ps1 (version 87e83efdb057cb0761a7be1fc09fa3bbb2f72c42) (diffs)
- utils/install4j/install4j10_template.install4j (version 87e83efdb057cb0761a7be1fc09fa3bbb2f72c42) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> bf54b1601de726d6e5c811d0c0692ccefa90423c m
JAL-3631 Icons for installer wizard title bar
- utils/channels/default/channel_gradle.properties (version bf54b1601de726d6e5c811d0c0692ccefa90423c) (diffs)
- utils/channels/default/images/jalview_logo-64.png (version bf54b1601de726d6e5c811d0c0692ccefa90423c) (diffs)
- utils/channels/default/images/jalview_logo-64@2x.png (version bf54b1601de726d6e5c811d0c0692ccefa90423c) (diffs)
- utils/channels/develop-SUFFIX/channel_gradle.properties (version bf54b1601de726d6e5c811d0c0692ccefa90423c) (diffs)
- utils/channels/develop-SUFFIX/images/jalview_develop_logo-64.png (version bf54b1601de726d6e5c811d0c0692ccefa90423c) (diffs)
- utils/channels/develop-SUFFIX/images/jalview_develop_logo-64@2x.png (version bf54b1601de726d6e5c811d0c0692ccefa90423c) (diffs)
- utils/channels/develop/channel_gradle.properties (version bf54b1601de726d6e5c811d0c0692ccefa90423c) (diffs)
- utils/channels/develop/images/jalview_develop_logo-64.png (version bf54b1601de726d6e5c811d0c0692ccefa90423c) (diffs)
- utils/channels/develop/images/jalview_develop_logo-64@2x.png (version bf54b1601de726d6e5c811d0c0692ccefa90423c) (diffs)
- utils/channels/jalviewjs/channel_gradle.properties (version bf54b1601de726d6e5c811d0c0692ccefa90423c) (diffs)
- utils/channels/jalviewjs/images/jalview_logo-64.png (version bf54b1601de726d6e5c811d0c0692ccefa90423c) (diffs)
- utils/channels/jalviewjs/images/jalview_logo-64@2x.png (version bf54b1601de726d6e5c811d0c0692ccefa90423c) (diffs)
- utils/channels/release/channel_gradle.properties (version bf54b1601de726d6e5c811d0c0692ccefa90423c) (diffs)
- utils/channels/release/images/jalview_logo-64.png (version bf54b1601de726d6e5c811d0c0692ccefa90423c) (diffs)
- utils/channels/release/images/jalview_logo-64@2x.png (version bf54b1601de726d6e5c811d0c0692ccefa90423c) (diffs)
- utils/channels/test-release/channel_gradle.properties (version bf54b1601de726d6e5c811d0c0692ccefa90423c) (diffs)
- utils/channels/test-release/images/jalview_test-release_logo-64.png (version bf54b1601de726d6e5c811d0c0692ccefa90423c) (diffs)
- utils/channels/test-release/images/jalview_test-release_logo-64@2x.png (version bf54b1601de726d6e5c811d0c0692ccefa90423c) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> 47946f0b85344cf22fe86cbcbfd4f190fce990da m
JAL-3631 update.ps1 has fixed Readlink-f function, works across platforms
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Ben Soares <b.soares@dundee.ac.uk> 15d55d9eecd6541e461ed302c246b902898cfd2a m
JAL-3631 Revert the Jalview installer icon back to the Jalview icon
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Gitlab User 2d58512c094e647e9652b6b8b75e215fc0c223c4 m
JAL-1551 source formatting and header
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Gitlab User 1a09df2fbacbdaf9a76ee5fe3b25925742bc78d9 m
JAL-4446 .. missing methods for cancellable pasimap
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Gitlab User 2f15cb2f6239cf3a51d2528f5f873273cdcc7936 m
JAL-4446 cancellable Pasimap - still need to make the actual pasimap CCA calculation cancellable and report progress
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Gitlab User 01dd0eed037513b5b2dbcd499dfd0cdd957cf0bd m
JAL-4446 calculate and report PaSiMap ETA in progress bar
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Gitlab User 84126942cf15bed4109e81345e2412425cfa48ed m
JAL-4446 allow progress bar message to be changed whilst progress continues & todo re desktop's custom progress implementation
- src/jalview/gui/AlignFrame.java (version 84126942cf15bed4109e81345e2412425cfa48ed) (diffs)
- src/jalview/gui/Desktop.java (version 84126942cf15bed4109e81345e2412425cfa48ed) (diffs)
- src/jalview/gui/IProgressIndicator.java (version 84126942cf15bed4109e81345e2412425cfa48ed) (diffs)
- src/jalview/gui/PCAPanel.java (version 84126942cf15bed4109e81345e2412425cfa48ed) (diffs)
- src/jalview/gui/PaSiMapPanel.java (version 84126942cf15bed4109e81345e2412425cfa48ed) (diffs)
- src/jalview/gui/ProgressBar.java (version 84126942cf15bed4109e81345e2412425cfa48ed) (diffs)
- src/jalview/gui/StructureChooser.java (version 84126942cf15bed4109e81345e2412425cfa48ed) (diffs)
- src/jalview/gui/WebserviceInfo.java (version 84126942cf15bed4109e81345e2412425cfa48ed) (diffs)
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Gitlab User f0c27e637a00150d508fd8418dbe8a934fbc75bc m
JAL-1551 apply GPLv3 for source files
- src/jalview/datamodel/ContactMapHolder.java (version f0c27e637a00150d508fd8418dbe8a934fbc75bc) (diffs)
- src/jalview/datamodel/ContactMapHolderI.java (version f0c27e637a00150d508fd8418dbe8a934fbc75bc) (diffs)
- src/jalview/datamodel/GroupSetHolder.java (version f0c27e637a00150d508fd8418dbe8a934fbc75bc) (diffs)
- src/jalview/datamodel/annotations/AlphaFoldAnnotationRowBuilder.java (version f0c27e637a00150d508fd8418dbe8a934fbc75bc) (diffs)
- src/jalview/util/ArgParserUtils.java (version f0c27e637a00150d508fd8418dbe8a934fbc75bc) (diffs)
- src/jalview/util/ErrorLog.java (version f0c27e637a00150d508fd8418dbe8a934fbc75bc) (diffs)
- src/jalview/util/UserAgent.java (version f0c27e637a00150d508fd8418dbe8a934fbc75bc) (diffs)
- src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java (version f0c27e637a00150d508fd8418dbe8a934fbc75bc) (diffs)
- src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java (version f0c27e637a00150d508fd8418dbe8a934fbc75bc) (diffs)
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Gitlab User 8261f257af8a4a9509a6bb8054b0016dfeae4a55 m
JAL-1551 gradle spotlessApply and doc tweaks
- src/jalview/analysis/AAFrequency.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/analysis/AlignSeq.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/analysis/AlignmentUtils.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/analysis/ConnectivityException.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/analysis/Finder.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/analysis/PaSiMap.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/analysis/ccAnalysis.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/analysis/scoremodels/DistanceScoreModel.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/analysis/scoremodels/FeatureDistanceModel.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/analysis/scoremodels/ScoreModels.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/analysis/scoremodels/SimilarityParams.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/api/AlignViewControllerI.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/api/AlignViewportI.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/api/analysis/ScoreModelI.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/api/analysis/SimilarityParamsI.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/appletgui/AlignFrame.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/bin/Cache.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/bin/JalviewLite.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/commands/JustifyLeftOrRightCommand.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/controller/AlignViewController.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/datamodel/PDBEntry.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/datamodel/Profile.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/datamodel/ProfileI.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/datamodel/SecondaryStructureCount.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/datamodel/SequenceGroup.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/gui/AlignFrame.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/gui/AlignViewport.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/gui/AppJmol.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/gui/CalculationChooser.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/gui/CutAndPasteTransfer.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/gui/Desktop.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/gui/FontChooser.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/gui/PaSiMapPanel.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/gui/PairwiseAlignPanel.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/gui/PopupMenu.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/gui/ProgressBar.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/gui/RotatableCanvas.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/gui/StructureChooser.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/jbgui/GAlignFrame.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/jbgui/GCutAndPasteTransfer.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/jbgui/GPCAPanel.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/jbgui/GPaSiMapPanel.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/jbgui/GPreferences.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/math/Matrix.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/math/MatrixI.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/math/MiscMath.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/project/Jalview2XML.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/renderer/AnnotationRenderer.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/renderer/ResidueShader.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/renderer/ResidueShaderI.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/schemes/ClustalxColourScheme.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/schemes/ResidueProperties.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/util/Constants.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/viewmodel/AlignmentViewport.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/viewmodel/PaSiMapModel.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- src/jalview/workers/SecondaryStructureConsensusThread.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- test/jalview/analysis/AlignSeqTest.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- test/jalview/analysis/AlignmentUtilsTests.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- test/jalview/analysis/scoremodels/ScoreModelsTest.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- test/jalview/analysis/scoremodels/SecondaryStructureDistanceModelTest.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- test/jalview/commands/EditCommandTest.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- test/jalview/gui/AssociatePDBFileTest.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- test/jalview/gui/CalculationChooserTest.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- test/jalview/project/Jalview2xmlTests.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- test/jalview/renderer/ResidueShaderTest.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- test/jalview/schemes/ClustalxColourSchemeTest.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
- test/jalview/util/FileUtilsTest.java (version 8261f257af8a4a9509a6bb8054b0016dfeae4a55) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> f7546bfa60917a5153203cc9d3cdc9322f71b812 m
JAL-3631 Adjustment to wizard size (was too big in Windows) and add 'Administrator mode' label to installation progress screen
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Gitlab User b02e2539ae024c042885be9e3f03ed1262d708c9 m
Merge branch 'feature/JAL-3631_allow_jalview_to_work_from_user-space_directory' into develop
