From 1508ecb803ac8c2df32f7832621c1be502dea535 Mon Sep 17 00:00:00 2001 From: James Procter Date: Wed, 15 Nov 2023 15:24:40 +0000 Subject: [PATCH] JAL-4090 fix up release notes new known issues --- help/markdown/releases/release-2_11_3_0.md | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/help/markdown/releases/release-2_11_3_0.md b/help/markdown/releases/release-2_11_3_0.md index 5299026..47b3778 100644 --- a/help/markdown/releases/release-2_11_3_0.md +++ b/help/markdown/releases/release-2_11_3_0.md @@ -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. @@ -110,13 +111,14 @@ 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 @@ -124,7 +126,7 @@ 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) -- 1.7.10.2