- <!-- JAL-4110 --> Output stderr and stdout when running tests via gradle
- <!-- JAL-3599 --> New gradle task providing runtime acceptance test for JalviewJS based on Chromium for Tests (still work in progress)
+
## Issues Resolved
- <!-- JAL-2961 --> Jmol view not always centred on structures when multiple structures are viewed
- <!-- JAL-3772 --> Unsaved Alignment windows close without prompting to save, individually or at application quit.
- <!-- JAL-3784 --> Multiple overview windows can be opened for a particular alignment view when multiple views are present
- <!-- JAL-3785 --> Overview windows opened automatically (due to preferences settings) lack title
- <!-- JAL-2353 --> Show Crossrefs fails to retrieve CDS from ENA or Ensembl for sequences retrieved from Uniprot due to version numbers in cross-reference accession
+- <!-- JAL-4334 --> Uniprot parser fails to import sequences with features that have 'unknown' start or end
- <!-- JAL-4184 --> Stockholm export does not include sequence descriptions
- <!-- JAL-4075 --> Don't add string label version of DSSP secondary structure codes in secondary structure annotation rows
- <!-- JAL-4182 --> reference annotation not correctly transferred to alignment containing a sub-sequence when a selection is active
- <!-- JAL-4218 --> Jalview source distribution unnecessarily includes dist directory with built jalview jar and dependencies
- <!-- JAL-3921 --> Jmol sessions involving large molecules may not be fully saved in Jalview project files (known defect in 2.11.2.x)
-## New Known defects
+
+### New Known Issues
- <!-- JAL-4303 --> EBI-AlphaFold PLDDT colours cannot be overlaid on alignment via 'Colour by annotation' unless the alignment's colourscheme has been set to 'None' via the Colours menu.
- <!-- JAL-4302 --> Tree renderer doesn't show bottom-most leaves of tree when Fit-To-Window is enabled.
- <!-- JAL-4338 --> PAE partition not shown in the same place when tree is closed and reopened
- <!-- JAL-4178 --> Cannot cancel structure view open action once it has been started via the structure chooser dialog
- <!-- JAL-4142 --> Example project's multiple views do not open in distinct locations when eXpand views is used to show them all separately
-- <!-- JAL-4127 --> 'Reload' for a jalview project results in all windows being duplicated (since 2.11.2.6, more severe in 2.11.3.0
+- <!-- JAL-4127 --> 'Reload' for a jalview project results in all windows being duplicated (since 2.11.2.6, more severe in 2.11.3.0)
- <!-- JAL-4325 --> Overview shown and then closed when importing legacy jalview projects without overview store/restore information
- <!-- JAL-4165 --> Missing last letter when copying consensus sequence from alignment if first column is hidden
- <!-- JAL-4261 --> Last sequence ID in alignment not shown and annotation labels are misaligned in HTML export
- <!-- JAL-4291 --> Test coverage for ID width adjustment disabled pending fix for new annotation label geometry and width calculation
- <!-- JAL-4323 --> scripts adding new fileformats or colourschemes do not work when run via command line
- <!-- JAL-4290 --> Headless alignment export with structure annotations doesn't include secondary structure and temperature factor
-- <!-- JAL-4151 --> Copy sequences from one alignment and Pasting as new window in another alignment doesn't propagate title from original alignment's window)
+- <!-- JAL-4151 --> Copy sequences from one alignment and Pasting as new window in another alignment doesn't propagate title from original alignment's window
- <!-- JAL-4157 --> Annotation colouring dialog box doesn't remember 'use original colours' settings when opened via the Colour menu
- <!-- JAL-4327 --> When the Groovy console is open Jalview does not prompt to save before quitting
- <!-- JAL-4328 --> Jalview works with but is not fully compatible with latest Ensembl REST API (15.6)
git://source.jalview.org / jalview.git / blobdiff