James Procter <j.procter@dundee.ac.uk>: Author Summary
| Build | Completed | Code commits | Tests |
|---|---|---|---|
| JB › GDBI › #21 | 11 months ago |
Merge branch 'bug/JAL-4186_space_in_sequence_name_causes_empty_modal' into develop
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Testless build |
| JB › GDC › #188 | 3 months ago |
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
JAL-4353 wait for files to be written fully before comparing size with older file
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
Merge branch 'develop' into bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor
JAL-4369 uniprotkb - try to avoid another redirect response
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
Merge branch 'bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor' into develop
JAL-4353 singleThread all tests
Merge branch 'bug/JAL-4373_jvmmemmax_and_jvmmempc_ignored_on_command_line_for_executable_jar_launch' into develop
Merge branch 'bug/JAL-4368_default_colourscheme_applied_to_JVP_inappropriately' into develop
JAL-4356 update release notes for 2.11.3.3
JAL-4369 invokeAndWait to avoid hang whilst calling getFiles if a Jmol redraw is in progress
JAL-4369 use rest.uniprot.org as fetch domain t pu# Please enter the commit message for your changes. Lines starting
JAL-4356 release notes
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Testless build |
| JB › GGR › #7 | 1 year ago |
JAL-629 JAL-4124 JAL-3855 test to check we can import PAE matrices in a variety of formats - and fix up a casting issue (again?)
Merge branch 'develop' into feature/JAL-1713_overviewInProject
JAL-4133 store/restore alignment view’s charWidth and charHeight in Jalview project
Merge branch 'features/JAL-3858_PAEsInProjects' into develop
Merge branch 'new_feature/JAL-4019_ambiguous_base_colourscheme' into develop
JAL-3858 construct a PAE direct from float array
JAL-3858 JAL-2381 allow different linear shading schemes for selected/non-selected regions of contact matrix heat map
JAL-4090 Release 2.11.3.0 release notes and version bump
JAL-1713 update from Jalview 2.11.3 develop Merge branch 'develop' into feature/JAL-1713_overviewInProject regenerated jaxb classes to resolve conflicts
JAL-4027 JAL-3858 rename CUSTOM_RENDERER to CONTACT_MATRIX annotation.graph type, with actual matrix type stored in calcId
JAL-629 don’t complain for Unary args
JAL-4090 move 2.11.3 series release notes to 2.11.3.0 release and premptively list issues already or nearly addressed in this version
JAL-4095 slightly better threshold setting and todos for improvement
JAL-629 suggest not breaking out of the structure processing loop if just one structure has a bunk sequence association..
JAL-4133 update validChar width when font is changed so characters are suppressed for small widths
Fix for JAL-4126 - don’t automatically create a threshold line when no threshold line is needed when reconstructing the annotation colour scheme from a project file
Merge branch 'develop' (JAL-4102 2.11.2.6 patch release) into features/r2_11_2_alphafold/JAL-2349_JAL-3855
JAL-1551 source formatting
JAL-629 hacked in --tempfac-shading - hardcoded to use existing colours in per-sequence annotation
JAL-3077 broken conflict resolve resulted in failing test (nb - still not resolved the issue of (promoted) dbrefs!)
JAL-629 labelled breaks are frowned upon by everyone
JAL-3858 new MatrixType JAX-RI POJO
JAL-3858 persist PAE matrix (only so far) as serialised floats in element on dataset sequence annotation. Rudimentary tests.
Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects
Conflicts: src/jalview/bin/Jalview.java JAL-1713 don’t close an automatically created overview window for projects from Jalview versions older than 2.11.3
JAL-4126 comment out closeAll - so we can visually check the alignment frame as it is restored
JAL-629 don’t trash user’s system property file when adjusting settings to process CL args
JAL-4116 relegate the failed to promote warning to Console.debug so most users won’t even see it (or be slowed down by it).
JAL-629 need to delay call to AlignFile.parse() if StructureFile needs to configure itself at construction time
Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects
Conflicts: src/jalview/bin/Jalview.java Merge branch 'develop' into feature/JAL-1713_overviewInProject
JAL-4126 failing test - colour scheme appears to be being created and configured, but the renderer is not actually using the colour scheme to shade the sequence when the project is restored.
JAL-629 JAL-4124 JAL-3855 test to check we can import PAE matrices in a variety of formats - additional test case
JAL-3858 simple test for PAE matrix recovery
JAL-1551 remove temp file in src
JAL-629 make sure we show GUI when not driven programmatically
JAL-4095 magic fill behaviour is PAE specific
JAL-629 don’t carry on Jalview.main if we’ve already processed command line args another way
|
Testless build |
| JB › GDI › #11 | 1 year ago |
JAL-1713 don’t close an automatically created overview window for projects from Jalview versions older than 2.11.3
JAL-4116 relegate the failed to promote warning to Console.debug so most users won’t even see it (or be slowed down by it).
JAL-4126 comment out closeAll - so we can visually check the alignment frame as it is restored
JAL-3077 broken conflict resolve resulted in failing test (nb - still not resolved the issue of (promoted) dbrefs!)
JAL-4126 failing test - colour scheme appears to be being created and configured, but the renderer is not actually using the colour scheme to shade the sequence when the project is restored.
Merge branch 'develop' into feature/JAL-1713_overviewInProject
Merge branch 'new_feature/JAL-4019_ambiguous_base_colourscheme' into develop
Merge branch 'develop' into feature/JAL-1713_overviewInProject
JAL-1551 remove temp file in src
JAL-4090 move 2.11.3 series release notes to 2.11.3.0 release and premptively list issues already or nearly addressed in this version
JAL-1713 update from Jalview 2.11.3 develop Merge branch 'develop' into feature/JAL-1713_overviewInProject regenerated jaxb classes to resolve conflicts
JAL-4090 Release 2.11.3.0 release notes and version bump
Merge branch 'develop' (JAL-4102 2.11.2.6 patch release) into features/r2_11_2_alphafold/JAL-2349_JAL-3855
Fix for JAL-4126 - don’t automatically create a threshold line when no threshold line is needed when reconstructing the annotation colour scheme from a project file
|
Testless build |
| Build | Completed | Code commits | Tests |
|---|---|---|---|
| JB › GGR › #7 | 1 year ago |
JAL-629 JAL-4124 JAL-3855 test to check we can import PAE matrices in a variety of formats - and fix up a casting issue (again?)
Merge branch 'develop' into feature/JAL-1713_overviewInProject
JAL-4133 store/restore alignment view’s charWidth and charHeight in Jalview project
Merge branch 'features/JAL-3858_PAEsInProjects' into develop
Merge branch 'new_feature/JAL-4019_ambiguous_base_colourscheme' into develop
JAL-3858 construct a PAE direct from float array
JAL-3858 JAL-2381 allow different linear shading schemes for selected/non-selected regions of contact matrix heat map
JAL-4090 Release 2.11.3.0 release notes and version bump
JAL-1713 update from Jalview 2.11.3 develop Merge branch 'develop' into feature/JAL-1713_overviewInProject regenerated jaxb classes to resolve conflicts
JAL-4027 JAL-3858 rename CUSTOM_RENDERER to CONTACT_MATRIX annotation.graph type, with actual matrix type stored in calcId
JAL-629 don’t complain for Unary args
JAL-4090 move 2.11.3 series release notes to 2.11.3.0 release and premptively list issues already or nearly addressed in this version
JAL-4095 slightly better threshold setting and todos for improvement
JAL-629 suggest not breaking out of the structure processing loop if just one structure has a bunk sequence association..
JAL-4133 update validChar width when font is changed so characters are suppressed for small widths
Fix for JAL-4126 - don’t automatically create a threshold line when no threshold line is needed when reconstructing the annotation colour scheme from a project file
Merge branch 'develop' (JAL-4102 2.11.2.6 patch release) into features/r2_11_2_alphafold/JAL-2349_JAL-3855
JAL-1551 source formatting
JAL-629 hacked in --tempfac-shading - hardcoded to use existing colours in per-sequence annotation
JAL-3077 broken conflict resolve resulted in failing test (nb - still not resolved the issue of (promoted) dbrefs!)
JAL-629 labelled breaks are frowned upon by everyone
JAL-3858 new MatrixType JAX-RI POJO
JAL-3858 persist PAE matrix (only so far) as serialised floats in element on dataset sequence annotation. Rudimentary tests.
Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects
Conflicts: src/jalview/bin/Jalview.java JAL-1713 don’t close an automatically created overview window for projects from Jalview versions older than 2.11.3
JAL-4126 comment out closeAll - so we can visually check the alignment frame as it is restored
JAL-629 don’t trash user’s system property file when adjusting settings to process CL args
JAL-4116 relegate the failed to promote warning to Console.debug so most users won’t even see it (or be slowed down by it).
JAL-629 need to delay call to AlignFile.parse() if StructureFile needs to configure itself at construction time
Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects
Conflicts: src/jalview/bin/Jalview.java Merge branch 'develop' into feature/JAL-1713_overviewInProject
JAL-4126 failing test - colour scheme appears to be being created and configured, but the renderer is not actually using the colour scheme to shade the sequence when the project is restored.
JAL-629 JAL-4124 JAL-3855 test to check we can import PAE matrices in a variety of formats - additional test case
JAL-3858 simple test for PAE matrix recovery
JAL-1551 remove temp file in src
JAL-629 make sure we show GUI when not driven programmatically
JAL-4095 magic fill behaviour is PAE specific
JAL-629 don’t carry on Jalview.main if we’ve already processed command line args another way
|
Testless build |
| Build | Completed | Code commits | Tests |
|---|