From 445dbb25230b1b9b6c3ac65b4e79e3ba052ba87c Mon Sep 17 00:00:00 2001 From: James Procter Date: Tue, 3 Oct 2023 13:18:02 +0100 Subject: [PATCH] =?utf8?q?JAL-4090=20fix=20up=20release=20notes=20and=20what?= =?utf8?q?=E2=80=99s=20new=20(inc=20removing=202.11.2=20cruft=20from=20templ?= =?utf8?q?ate)?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- help/markdown/releases/release-2_11_3_0.md | 47 ++++---------------- help/markdown/whatsnew/whatsnew-2_11_3_0.md | 2 +- help/templates/whatsNew.html | 64 --------------------------- 3 files changed, 10 insertions(+), 103 deletions(-) diff --git a/help/markdown/releases/release-2_11_3_0.md b/help/markdown/releases/release-2_11_3_0.md index 01a54f6..80f8cf4 100644 --- a/help/markdown/releases/release-2_11_3_0.md +++ b/help/markdown/releases/release-2_11_3_0.md @@ -1,40 +1,31 @@ --- version: 2.11.3.0 -date: 2023-07-19 +date: 2023-10-03 channel: "release" --- ## New Features - Native M1 build for macOS using Adoptium JRE 11 macos-aarch64 -- Installers built with install4j10 -- Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button -- FlatLAF default look and feel on Linux, OSX and everywhere else - +- Jalview now uses a standard 'look and feel' (FlatLaf) on Linux, OSX and everywhere else - Ambiguous Base Colourscheme - Find can search sequence features' type and description - Hold down Shift + CMD/CTRL C to copy highlighted regions as new sequences - Quickly enable select and/or colour by for displayed annotation row via annotation panel popup menu - Shift+Click+Drag to adjust height of all annotation tracks of same type - Pressing escape in tree panel clears any current selection - - 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 - Adjustable ID margin when alignment is wrapped - - Command line options and configurable bitmap export preferences for height, width and scale factor ### Improved support for working with computationally determined models - - Alphafold red/orange/yellow/green colourscheme for structures - Interactive picking of low pAE score regions - contact matrix datatype in Jalview - Selections with visual feedback via contact matrix annotation - - Discover and import alphafold2 models and metadata from https://alphafold.ebi.ac.uk/ - - Visual indication of relationship with associated sequence to distinguish different sequence associated annotation rows - GUI and command line allows configuration of how temperature factor in imported 3D structure data should be interpreted - Import model reliability scores encoded as temperature factor annotation with their correct name and semantics @@ -43,17 +34,17 @@ channel: "release" - Store/Restore PAE data and visualisation settings from Jalview Project - Multiple residue sidechain highlighting in structure viewers from PAE mouseovers - ### Jalview on the command line - - New command line argument framework allowing flexible batch processing, import of structures, pae matrices and other sequence associated data, and alignment and structure figure generation. +- Command-line wrapper script for macOS bundle, linux and Windows installations (bash, powershell and .bat wrappers) - 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 ### 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 - Lower line of the sequence group border does not align with vertical and background residue box @@ -61,38 +52,18 @@ channel: "release" - Name of alignment and view included in overview window's title - "add reference annotation" add all positions in reference annotation tracks, not just positions in the currently highlighted columns/selection range - EMBL-EBI SIFTS file downloads now use split directories - -- 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 - - -JAL-4187 Powershell launcher script fails when given no arguments with the old ArgsParser - -known issue ? 'Reload' for a jalview project results in all windows being duplicated - - -- Command-line wrapper script for macOS bundle, linux and Windows installations (bash, powershell and .bat wrappers) - In Linux desktops' task-managers, the grouped Jalview windows get a generic name - Improved file chooser's 'recent files' view and added filter for 'All known alignment files' - Relative files added to recent files list via import from command line are selected when Jalview opened from same location - - - -## Still in progress (delete on release) - -- Import and display sequence-associated contact predictions in CASP-RR format -- Contact prediction visualisation -- modularise annotation renderer +- Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button ### Development and Deployment - +- Installers built with install4j10 - Create separate gradle test task for some tests - Prevent gradle test on macOS continuously grabbing focus - Allow gradle build to create suffixed DEVELOP-... builds with channel appbase - Jalview bio.tools description maintained under jalview's git repo and bundled with source release - ## Issues Resolved - Jmol view not always centred on structures when multiple structures are viewed - Cancelling interactive calculation leaves empty progress bar. @@ -116,10 +87,10 @@ known issue ? 'Reload' for a jalview project results in all wi - macOS Dock and KDE taskbar names Jalview icon "java" when running - HeadlessException in console in headless mode (actually fixed in 2.11.{0,1,2)) - ## New Known defects - 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 - 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 - Files opened via command line with a relative path are added as relative paths to Recent files list (since 2.0.x) diff --git a/help/markdown/whatsnew/whatsnew-2_11_3_0.md b/help/markdown/whatsnew/whatsnew-2_11_3_0.md index cf91e3a..b6c1b0d 100644 --- a/help/markdown/whatsnew/whatsnew-2_11_3_0.md +++ b/help/markdown/whatsnew/whatsnew-2_11_3_0.md @@ -1,4 +1,4 @@ -The 2.11.3 Jalview release features a new and more powerful command line interface, support for in-depth exploration of predicted alignment error (PAE) matrices from AlphaFold in the context of multiple alignments, AlphaFold's standard Blue-Orange-Red confidence colourscheme, and a host of minor improvements and bug fixes. +The 2.11.3 Jalview release features a new and more powerful command line interface, support for in-depth exploration of predicted alignment error (PAE) matrices from AlphaFold in the context of multiple alignments, AlphaFold's standard Blue-Orange-Red confidence colourscheme, and a host of [minor improvements and bug fixes](releases.html#Jalview.2.11.3.0) **Interactive exploration of AlphaFold Predicted Alignment Error Matrices** diff --git a/help/templates/whatsNew.html b/help/templates/whatsNew.html index 70deea4..301ea4b 100755 --- a/help/templates/whatsNew.html +++ b/help/templates/whatsNew.html @@ -27,69 +27,5 @@ Welcome to Jalview Version __VERSION__ (released __DISPLAY_DATE__)!!

__WHATS_NEW__ -

- The 2.11.2 release series provides support for two popular 3D - structure visualisation tools, new features for discovery of 3D - structures, improved platform integration and a new command line - tool allowing Jalview to be more easily called from scripts.

- -

- View predicted protein structures via 3D-Beacons
- Jalview 2.11.2's Structure - Chooser includes a client for the 3D-Beacons Network. Launched in - 2021, the 3D-Beacons network (www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/) - provides a central point for the retrieval of predicted and observed - 3D structures for sequences in Uniprot, including homology models - from Swiss-model and deep learning based predictions from the EBI's - Alphafold database (Orengo et al. 2020, doi:10.12688/f1000research.20559.1).
-

- -

- Support for viewing structures with ChimeraX and - Pymol
Jalview's 3D structure viewer system has been - re-architected to allow easier integration of external structure - viewers, and takes advantage of the strucViz2 Chimera communications - library developed by Scooter Morris (doi:10.1093/bioinformatics/btm329).

- The Structures - Preferences tab provides new options allowing ChimeraX and - Pymol to be used for visualising external 3D structures. Views - from all structure viewers are saved in Jalview Projects, allowing - them to be shared with others using Jalview 2.11.2 or later, - providing they have the same viewer installed and configured to be - used with Jalview.

Jalview - 2.11.2 has been tested with Pymol 2.5.0 (community) and 2.5.2 - (incentive). For ChimeraX, we recommend using v1.3 or later. -

-

Other highlights include:

- - - -

- For the full details, see the Jalview 2.11.2 series - release notes. -

-

- Known Issues
The following known issues will - be addressed in a minor patch release. - -

-

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