From f6c9a7777d4a2f97c18c5012a149d6dbffa5c667 Mon Sep 17 00:00:00 2001 From: James Procter Date: Thu, 2 Nov 2023 23:03:14 +0000 Subject: [PATCH] JAL-4090 fix up release notes - add notes or JAL-4216 JAL-4169 JAL-4250 JAL-4327 and remove erroneous note for JAL-3776 (targeted for 2.12 release not this one) --- help/markdown/releases/release-2_11_3_0.md | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/help/markdown/releases/release-2_11_3_0.md b/help/markdown/releases/release-2_11_3_0.md index 5a9de38..04aa1d5 100644 --- a/help/markdown/releases/release-2_11_3_0.md +++ b/help/markdown/releases/release-2_11_3_0.md @@ -37,6 +37,7 @@ channel: "release" - Store and restore adjustable ID margin and annotation panel height in Jalview projects - Multiple residue sidechain highlighting in structure viewers from PAE mouseovers - Per-structure and chain shown when annotation shown sorted by label enabling secondary structure and temperature factor scores from different chains and structures for the same sequence to be visually compared. +- PDB or mmCIF files with chains with negative RESNUMs for their whole sequence extent cannot be linked to alignments ### Jalview on the command line @@ -45,13 +46,13 @@ channel: "release" - Assume --headless when jalview is run with a command line argument that generates output - Automatically adjust Left margin on import to avoid cropping of annotation labels & sequence IDs - Specify alignment title on import via --title argument -- sensible responses from the CLI when things go wrong during image export -- Add a command line option to set Jalview properties for this session only -- Add a command line option to suppress opening the startup file for this session +- Sensible responses from the CLI when things go wrong during image export +- Add a command line option to set Jalview properties for this session only +- Add a command line option to suppress opening the startup file for this session ### Other improvements - Secondary structure annotation glyphs are rendered anti-aliasing when enabled -- Helix and Sheet glyphs vertically centered with respect to grey coil secondary structure annotation track +- Helix and Sheet glyphs vertically centred with respect to grey coil secondary structure annotation track - feature should be displayed when its rendering and filtering settings are adjusted - Updated JFreeSVG (https://www.jfree.org/jfreesvg) from 2.1 to 3.4.3 - Name of alignment and view included in overview window's title @@ -62,9 +63,10 @@ channel: "release" - Relative files added to recent files list via import from command line are selected when Jalview opened from same location - Reduce number of database crossreferences shown in tooltip - Drag and drop feature colours file on an alignment to quickly apply feature settings -- Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button +- Improved startup info in console output: which properties file was being used and slight revisions to the formatting of platform information. - Upgrade bundled groovy to v4.0.15 and regularised interface for groovy scripts run from CLI, interactively and headlessly. - Overview display and hidden region visibility stored in Jalview projects +- Updated faq and documentation urls in splashscreen and help documentation ### Development and Deployment - Installers built with install4j10 @@ -78,7 +80,6 @@ channel: "release" ## Issues Resolved - Jmol view not always centred on structures when multiple structures are viewed -- Cancelling interactive calculation leaves empty progress bar. - Unsaved Alignment windows close without prompting to save, individually or at application quit. - Can quit Jalview while 'save project' is in progress - 'Use original colours' option of colour by annotation not honoured when restoring view from project @@ -98,7 +99,7 @@ channel: "release" - Overview window is saved in project file, and state of 'show hidden regions' is preserved. - JvCacheableInputBoxTest flaky on build server - SLF4J produces an error to STDERR at Jalview startup due to missing class -- macOS Dock and KDE taskbar names Jalview icon "java" when running +- macOS Dock and KDE taskbar names Jalview icon "java" when running jalview via the getdown app launcher - HeadlessException in console in headless mode (actually fixed in 2.11.{0,1,2)) - Groovy console does not open when Jalview launched from jalview's Java 11 executable jar (available via conda) for recent versions of groovy - Don't offer View model page for sources that do not have model pages @@ -114,7 +115,7 @@ channel: "release" - Tree renderer doesn't show bottom-most leaves of tree when Fit-To-Window is enabled. - 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 +- '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 @@ -122,7 +123,7 @@ 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 -- 'Reload' for a jalview project results in all windows being duplicated (since 2.11.2.6, more severe in 2.11.3.0) +- 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 -- 1.7.10.2