Build: #188 was successful Changes by Ben Soares <b.soares@dundee.ac.uk> and James Procter <j.procter@dundee.ac.uk>
Code commits
Jalview Git
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James Procter <j.procter@dundee.ac.uk> c4d23061be96300cc0af4c25d8628665a9c2a155
JAL-4356 release notes
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James Procter <j.procter@dundee.ac.uk> 26ac9a5b81dff731ffb988fdb7e7df2f8ee99747
JAL-4356 update release notes for 2.11.3.3
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Ben Soares <b.soares@dundee.ac.uk> 7485177a17e47a8107ed99c87e57e4b82e014fe1
JAL-4290 fixed tests
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James Procter <j.procter@dundee.ac.uk> 696c16c4ffcf743263e546ac8fc47e66e1951e11 m
JAL-4353 singleThread all tests
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James Procter <j.procter@dundee.ac.uk> ca9a7a8387cb17ea0a4511d1ce3c4c0c45e50db4
Merge branch 'bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor' into develop
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Ben Soares <b.soares@dundee.ac.uk> 2142ec8f18749862556286fe89f57e46e4747c40
JAL-4290 Fix image comparison between gui and headless output. Images are now the same
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Ben Soares <b.soares@dundee.ac.uk> ea920b2f6a5fb611397ec1fd51bc12402c5a8d09
JAL-4367 Limit right and top adjustments
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James Procter <j.procter@dundee.ac.uk> d1d89672d38fb328eca3495177d651c396970fd1
Merge branch 'develop' into bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor
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Ben Soares <b.soares@dundee.ac.uk> ef0960a1dbe3e3b5050d75cd43279ae9a9f7b922
Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment' into bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor
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Ben Soares <b.soares@dundee.ac.uk> 6caf8e67439a4ea034d8f3575d3f6167c86784d0
Merge branch 'develop' into bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment
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James Procter <j.procter@dundee.ac.uk> bb7a72429d195f54e3ea6df1b602732a952a1cb1 m
Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment_with_renderpatch' into bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment
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James Procter <j.procter@dundee.ac.uk> 360ef45fd26bf78323fff8f0a3f7a8632cd9db8e m
JAL-4353 wait for files to be written fully before comparing size with older file
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James Procter <j.procter@dundee.ac.uk> a2f16af6d565a7535083ff87da9be198b31d95c0
JAL-4369 invokeAndWait to avoid hang whilst calling getFiles if a Jmol redraw is in progress
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James Procter <j.procter@dundee.ac.uk> 7ccce06a54f5d49154f808e82fbb46742d024d23
JAL-4369 use rest.uniprot.org as fetch domain t pu# Please enter the commit message for your changes. Lines starting
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James Procter <j.procter@dundee.ac.uk> 78ab9489fc08f66f7a11dc587c042bd4d0c64e54
JAL-4369 uniprotkb - try to avoid another redirect response
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James Procter <j.procter@dundee.ac.uk> 3dcec29e9be7607122fb981050ff2198cef2a746
Merge branch 'bug/JAL-4373_jvmmemmax_and_jvmmempc_ignored_on_command_line_for_executable_jar_launch' into develop
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James Procter <j.procter@dundee.ac.uk> cc58c69c02ae426819761564b54161d05e6f94e9
Merge branch 'bug/JAL-4368_default_colourscheme_applied_to_JVP_inappropriately' into develop
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Ben Soares <b.soares@dundee.ac.uk> fc3c0910b7086411d72104c0a2cf4b8b45a95015
JAL-4373 Setting the jvmmempc and jvmmemmax strings from the Arg.getName() for consistency. Updated some comments.
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Ben Soares <b.soares@dundee.ac.uk> d6a4f39f26548ff14e96609b40e5ac4d35fc8448
JAL-4373 Fix Main-Class and other attribute settings in the shadowJar manifest. It requires a 'dummy' Jar task with the correct settings.
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Ben Soares <b.soares@dundee.ac.uk> 69827911885f6e7ed824b5e6f2f802e0a23c25f0
JAL-4368 Only set a colour scheme if --colour is given or it's not a JVP file
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Ben Soares <b.soares@dundee.ac.uk> 334013f9dc7b599af9062ca053d9d091a474472e
JAL-4290 Fixed one test
- src/jalview/bin/argparser/ArgValuesMap.java (version 334013f9dc7b599af9062ca053d9d091a474472e) (diffs)
- src/jalview/gui/AlignmentPanel.java (version 334013f9dc7b599af9062ca053d9d091a474472e) (diffs)
- src/jalview/gui/AnnotationLabels.java (version 334013f9dc7b599af9062ca053d9d091a474472e) (diffs)
- test/jalview/bin/CommandsTest.java (version 334013f9dc7b599af9062ca053d9d091a474472e) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> c67cd4c55333e4ed3928a86f23d9e291789b1ec4
JAL-4290 not quite working tests
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Ben Soares <b.soares@dundee.ac.uk> 606873e647ea10d3784ac03e98d16e51d77c3e40
JAL-4290 incorrect usage of main()
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Ben Soares <b.soares@dundee.ac.uk> cb3f31e3aacf81fa2b33f9eab9657ed40a66161e
Merge branch 'bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor' of https://source.jalview.org/git/jalview into bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor
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Ben Soares <b.soares@dundee.ac.uk> 89f6194d4bba6f8c9efa916e02e6fba2130c5e0f
JAL-4290 Add method to allow for specific settings. Revert setting show annotations.
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Ben Soares <b.soares@dundee.ac.uk> faf491e024f9835435f5dd6c20a033250dd9297d
JAL-4290 Set structureSelectionManager settings more generically and when no desktop exists
- src/jalview/bin/Commands.java (version faf491e024f9835435f5dd6c20a033250dd9297d) (diffs)
- src/jalview/gui/Desktop.java (version faf491e024f9835435f5dd6c20a033250dd9297d) (diffs)
- src/jalview/gui/StructureChooser.java (version faf491e024f9835435f5dd6c20a033250dd9297d) (diffs)
- src/jalview/structure/StructureSelectionManager.java (version faf491e024f9835435f5dd6c20a033250dd9297d) (diffs)
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James Procter <j.procter@dundee.ac.uk> 25513f2ce9d341344e29677335022a94e7822202
Merge branch 'bug/JAL-4290_headless_alignment_figure_with_sse' into bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor
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James Procter <j.procter@dundee.ac.uk> aabbea350930b8c2904e4f1544f0d786e7d59792
JAL-4290 new CommandsTest.headlessOrGuiImageOutputTest - uses CommandLineOperations.Worker to run jalview as a separate process to verify headless alignment image export should be same size as when launched with —gui
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Ben Soares <b.soares@dundee.ac.uk> 0a871d8258ce41f9293615771b1c3dcf447f0eb6
JAL-4290 Move some annotation visibility settings to after opening a structure. Set synchronously if in headless mode.