James Procter <j.procter@dundee.ac.uk>: Author Summary
| Build | Completed | Code commits | Tests |
|---|---|---|---|
| JB › GDBI › #21 | 4 months ago |
Merge branch 'bug/JAL-4186_space_in_sequence_name_causes_empty_modal' into develop
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Testless build |
| JB › GPC › #244 | 1 day ago |
JAL-3858 fix check annotation row and column positioning in case we have been called during an annotation height change operation
JAL-3858 improved contactInterval computation and added detailed test coverage for ContactGeometry - contactInterval.cStart/cEnd and pStart/pEnd are now base-0 inclusive ranges, always less than contactHeight and graphHeight - change in mapFor behaviour so cStart/cEnd and pStart/pEnd are always just one mapped range, not as many as requested to cover mapFor(pFrom,pTo)
JAL-3858 javadoc and slightly revised green linear shading - still not a perfect match to EBI AlphaFold
JAL-4090 figures in paematrix doc
Merge branch 'bug/JAL-244_interactingpngexportnotwysiwig' into develop
JAL-3858 minimum value for a range is used to shade ranges in PAE map
JAL-4153 move JvCacheableInputBoxTest to testTask2
JAL-629 JAL-4265 JAL-4286 report the filename for the exported structure image like we do for exported alignment images
JAL-4090 fix url to new cli docs
JAL-3858 report PAE range with sensible precision
JAL-3858 check annotation row and column positioning in case we have been called during an annotation height change operation
JAL-3858 don’t divide if we only had one value to count
JAL-4288 fix up gradle generated getdown launch jvl for bamboo channel builds
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Testless build |
| JB › GDB › #563 | 1 day ago |
Merge branch 'bug/JAL-244_interactingpngexportnotwysiwig' into develop
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1676 passed |
| JB › GJB › #342 | 1 day ago | Testless build | |
| JB › GJB › #341 | 1 day ago |
JAL-3858 don’t divide if we only had one value to count
JAL-4090 figures in paematrix doc
JAL-3858 fix check annotation row and column positioning in case we have been called during an annotation height change operation
JAL-3858 improved contactInterval computation and added detailed test coverage for ContactGeometry - contactInterval.cStart/cEnd and pStart/pEnd are now base-0 inclusive ranges, always less than contactHeight and graphHeight - change in mapFor behaviour so cStart/cEnd and pStart/pEnd are always just one mapped range, not as many as requested to cover mapFor(pFrom,pTo)
JAL-3858 javadoc and slightly revised green linear shading - still not a perfect match to EBI AlphaFold
JAL-4090 fix url to new cli docs
JAL-3858 report PAE range with sensible precision
JAL-4153 move JvCacheableInputBoxTest to testTask2
JAL-4288 fix up gradle generated getdown launch jvl for bamboo channel builds
JAL-3858 minimum value for a range is used to shade ranges in PAE map
JAL-3858 check annotation row and column positioning in case we have been called during an annotation height change operation
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Testless build |
| JB › GDC › #171 | 5 days ago |
JAL-4090 fix link...
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Testless build |
| JB › GPC › #243 | 5 days ago | Testless build | |
| JB › GDC › #170 | 6 days ago |
JAL-4265 bail early when attempting to export a view from other viewers than Jmol, and use viewType independent methods as much as possible.
JAL-4265 JAL-4286 reinstated explicit restoreSession method because Jmol’s LOAD files command does not behave the same way as restore STATE. Also added defensive check for unexpected exceptions if the state restore trashes the Jmol/Jalview binding
JAL-3858 JAL-3855 documentation for import and display PAE from alphafold and JSON format flat files for Import 3D structure from file
JAL-4217 - try to invokeAndWait on Desktop.closeAll() to avoid Jmol redraw blocking close
fix link...
JAL-3855 disable the AlphaFold DB entry in Sequence Fetcher - see JAL-4287 for an alternative (and perhaps preferred way) of fetching proteins with alphafold structures.
JAL-4285 don’t say you are reporting warnings/errors when there are none..
JAL-4265 back out redundant ‘saveState’ and ‘restoreState’ StructureCommandsI methods.
JAL-4274 fix test failure message typo
JAL-4265 JAL-4267 added a ‘restoreSession’ StructureViewer.getBinding() method that allows a snapshot to be explicitly reloaded in place.
JAL-1551 javadoc for mapUtils
JAL-4090 smaller associate PDB file panel image in docs
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Testless build |
| JB › GTC › #6 | 2 months ago |
JAL-4196 structure view cli tests wait using new jalview.Desktop.instance.operationsAreInProgress() returns true if any desktop windows have a progress indicator still active
JAL-3855 auto select clusters and fix up colouring/propagation on calculation & tree display
Merge branch 'patch/JAL-2292_caseSensitivePAE' into develop
Merge branch 'patch/JAL-4195_cli_eps_export_npe' into develop
Merge branch 'patch/JAL-4196_structure_viewer_synchronising' into develop
JAL-4090 update 2.11.3.0 release notes (with in-progress bits too) and what's new
JAL-629 make —structure image work again after threading it off
Merge branch 'task/JAL-4001_Plausible_API' into develop
JAL-4243 Jalview 2.11.2.7’s biotool record as JSON complete with update instructions as a README
JAL-4217 move Commands.structureImageTest to testTask1
JAL-2292 - ensure mapping is built for equal symbols with mismatched case
JAL-4223 - test and patch to ensure numbering matches sequence data from RNAML file
JAL-4223 add testdata for test
Merge branch 'develop' into patch/JAL-4195_cli_eps_export_npe
Merge branch 'patch/JAL-4119_sifts_ftp_split' into develop
JAL-3858 fix off-by-one in matrix visualisation and interactive tooltip
JAL-4195 add exception handling for all other CommandsTest tests and remove errant class-level @Test tag
JAL-629 even more console debug for --structureviewer opening arguments
Merge branch 'patch/JAL-4213_addref_with_selection' into develop
JAL-3858 flip diagonal so matrix visualisation is top left to bottom right
Merge branch 'merge/from_2_11_2_7_to_2_11_3_0' into develop
JAL-4001 analytics url provided by https://www.jalview.org/services/config/analytics/url
JAL-629 liberal defensive coding, comments about refactoring and DEBUG output for --structureimage
JAL-4217 wrap imageExport CLI method's call to imageExport in an invokeAndWait
JAL-2292 verify mixed case alignment actually aligns
JAL-3855 tree title for PAE matrix tree is PAE Matrix (method) for (structure) (sequence)
JAL-4196 report an error if structure view doesn’t get created (for whatever reason) during CLI arg processing, and wait around until the viewer has finished importing before doing anything
Merge branch 'task/JAL-4001_Plausible_API' into develop
JAL-3855 PAE matrices are transposed on import from JSON so returned contact vectors correspond to errors predicted when superposing at a given column position
JAL-4216 compute size of annotation using start/end of sequence and given length. This might not work...
JAL-4217 try really hard to shut down and dispose of Desktop resources and any lurking threads
Merge branch 'develop' into patch/JAL-4196_structure_viewer_synchronising
JAL-3858 annotation .height is bigger than graphHeight so adjacent PAE matrices are clearly separated
JAL-4217 wrap imageExport CLI method's call to imageExport in a separate thread and hang around until it completes…
JAL-4217 interruptedExceptions should also break any wait loops
JAL-4213 - document the addReferenceAnnotations method’s behaviour when given a selection
JAL-4221 update description when transferring annotation and no description already set
Merge branch 'develop' into patch/JAL-3855_fixup_pae
Merge branch 'patch/JAL-3855_fixup_pae' into develop
JAL-4196 make very sure we avoid CME by defensively copying the Map.values() to another list and synchronising on it
JAL-4213 don’t pass active selection when actioning the addReferenceAnnotation
JAL-4217 JAL-629 built in 25s time out waiting for structure viewer to load data before attempting to grab an image.
JAL-4119 TRACE level console message reporting download URL for sifts. Also more informative message when ‘Sifts Mapping Failed’ is reported as an exception - since this message can be reported when some chains in the PDB file do not match sequences being associated (but others do!!).
JAL-4217 catch case when the structure viewer doesn't get added to the desktop window (possible knock on for flatlaf JAL-3416)
JAL-4117 Fri June 30th release of 2.11.2.7 with Jalview Plausible analytics
JAL-4216 release notes
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Testless build |
| JB › GGR › #7 | 6 months 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 |
|---|---|---|---|
| JB › GGR › #7 | 6 months 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 |
|---|---|---|---|
| JB › GPC › #244 | 1 day ago |
JAL-3858 fix check annotation row and column positioning in case we have been called during an annotation height change operation
JAL-3858 improved contactInterval computation and added detailed test coverage for ContactGeometry - contactInterval.cStart/cEnd and pStart/pEnd are now base-0 inclusive ranges, always less than contactHeight and graphHeight - change in mapFor behaviour so cStart/cEnd and pStart/pEnd are always just one mapped range, not as many as requested to cover mapFor(pFrom,pTo)
JAL-3858 javadoc and slightly revised green linear shading - still not a perfect match to EBI AlphaFold
JAL-4090 figures in paematrix doc
Merge branch 'bug/JAL-244_interactingpngexportnotwysiwig' into develop
JAL-3858 minimum value for a range is used to shade ranges in PAE map
JAL-4153 move JvCacheableInputBoxTest to testTask2
JAL-629 JAL-4265 JAL-4286 report the filename for the exported structure image like we do for exported alignment images
JAL-4090 fix url to new cli docs
JAL-3858 report PAE range with sensible precision
JAL-3858 check annotation row and column positioning in case we have been called during an annotation height change operation
JAL-3858 don’t divide if we only had one value to count
JAL-4288 fix up gradle generated getdown launch jvl for bamboo channel builds
|
Testless build |