X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fmarkdown%2Freleases%2Frelease-2_11_3_0.md;h=c732130423ad888b4efa3e347491c065f44b259d;hb=c8d80485038ab96fb06bd0885c323803646d8e57;hp=cdd74eb620c0fb4599db996430792f6741e34681;hpb=18bd007875813a328ed685f2d263c1cc0169f9d6;p=jalview.git diff --git a/help/markdown/releases/release-2_11_3_0.md b/help/markdown/releases/release-2_11_3_0.md index cdd74eb..c732130 100644 --- a/help/markdown/releases/release-2_11_3_0.md +++ b/help/markdown/releases/release-2_11_3_0.md @@ -1,6 +1,6 @@ --- version: 2.11.3.0 -date: 2023-11-03 +date: 2023-11-15 channel: "release" --- @@ -16,7 +16,7 @@ channel: "release" - Use selected columns for superposition - Highlight aligned positions on all associated structures when mousing over a column - sequence descriptions are updated from database reference sources if not already defined -- Visible adjuster marks to grab and adjust annotation panel height and id width +- Visible adjuster marks to grab and adjust annotation panel height and id width - Adjustable ID margin when alignment is wrapped - Command line options and configurable bitmap export (via preferences file) for height, width and scale factor - Show or hide ligands in a Jmol structure view via View Ligands submenu @@ -78,6 +78,7 @@ channel: "release" - Output stderr and stdout when running tests via gradle - New gradle task providing runtime acceptance test for JalviewJS based on Chromium for Tests (still work in progress) + ## Issues Resolved - Jmol view not always centred on structures when multiple structures are viewed - Unsaved Alignment windows close without prompting to save, individually or at application quit. @@ -87,6 +88,7 @@ channel: "release" - Multiple overview windows can be opened for a particular alignment view when multiple views are present - Overview windows opened automatically (due to preferences settings) lack title - Show Crossrefs fails to retrieve CDS from ENA or Ensembl for sequences retrieved from Uniprot due to version numbers in cross-reference accession +- Uniprot parser fails to import sequences with features that have 'unknown' start or end - Stockholm export does not include sequence descriptions - Don't add string label version of DSSP secondary structure codes in secondary structure annotation rows - reference annotation not correctly transferred to alignment containing a sub-sequence when a selection is active @@ -110,12 +112,14 @@ channel: "release" - Jalview source distribution unnecessarily includes dist directory with built jalview jar and dependencies - 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 - 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. - Tree renderer doesn't show bottom-most leaves of tree when Fit-To-Window is enabled. +- PAE partition not shown in the same place when tree is closed and reopened - Cannot cancel structure view open action once it has been started via the structure chooser dialog - Example project's multiple views do not open in distinct locations when eXpand views is used to show them all separately -- 'Reload' for a jalview project results in all windows being duplicated (since 2.11.2.6, more severe in 2.11.3.0 +- 'Reload' for a jalview project results in all windows being duplicated (since 2.11.2.6, more severe in 2.11.3.0) - Overview shown and then closed when importing legacy jalview projects without overview store/restore information - Missing last letter when copying consensus sequence from alignment if first column is hidden - Last sequence ID in alignment not shown and annotation labels are misaligned in HTML export @@ -123,7 +127,7 @@ channel: "release" - Test coverage for ID width adjustment disabled pending fix for new annotation label geometry and width calculation - scripts adding new fileformats or colourschemes do not work when run via command line - Headless alignment export with structure annotations doesn't include secondary structure and temperature factor -- Copy sequences from one alignment and Pasting as new window in another alignment doesn't propagate title from original alignment's window) +- Copy sequences from one alignment and Pasting as new window in another alignment doesn't propagate title from original alignment's window - Annotation colouring dialog box doesn't remember 'use original colours' settings when opened via the Colour menu - When the Groovy console is open Jalview does not prompt to save before quitting - Jalview works with but is not fully compatible with latest Ensembl REST API (15.6)