From a1b2001f5f89248bdaa2f1e10d4a7a2d6a1163d8 Mon Sep 17 00:00:00 2001 From: James Procter Date: Fri, 2 Jun 2023 12:13:36 +0100 Subject: [PATCH] JAL-4090 update 2.11.3.0 release notes for recent merges --- help/markdown/releases/release-2_11_3_0.md | 37 ++++++++++++++++++++++------ 1 file changed, 30 insertions(+), 7 deletions(-) diff --git a/help/markdown/releases/release-2_11_3_0.md b/help/markdown/releases/release-2_11_3_0.md index 31cabd7..1309483 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: 2023-03-07 +date: 2023-06-07 channel: "release" --- @@ -13,26 +13,37 @@ channel: "release" - 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 its 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 +### 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 -- Don't add string label version of DSSP secondary structure codes in secondary structure annotation rows - Discover and import alphafold2 models and metadata from https://alphafold.ebi.ac.uk/ -- Jmol view not always centred on structures when multiple structures are viewed +- 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 +- Import and display alphafold alignment uncertainty matrices from JSON +- Column-wise alignment groups and selections and interactive tree viewer for PAE matrices +- Store/Restore PAE data and visualisation settings from Jalview Project -- Overview window is saved in project file, and state of 'show hidden regions' is preserved. +### Jalview on the command line -- Name of alignment and view included in overview window's title +- New command line argument framework allowing flexible batch processing, figure generation, and import of structures, pae matrices and other sequence associated data +- Assume --headless when jalview is run with a command line argument that generates output -- Visual indication of relationship with associated sequence to distinguish different sequence associated annotation rows -- Shift+Click+Drag to adjust height of all annotation tracks of same type +### Other improvements +- Name of alignment and view included in overview window's title ## Still in progress (delete on release) @@ -40,9 +51,13 @@ channel: "release" - Contact prediction visualisation - modularise annotation renderer +### Development and Deployment +- Create separate gradle test task for some tests +- Allow gradle build to create suffixed DEVELOP-... builds with channel appbase ## 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 @@ -52,3 +67,11 @@ channel: "release" - 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 - 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 +- Can press 'Add' or 'New View' multiple times when manually adding and viewing a 3D structure via structure chooser +- Jalview project does not preserve font aspect ratio when Viewport is zoomed with mouse +- Resizing overview quickly with solid-drags enabled causes exception +- Sequences copied to clipboard from within Jalview cannot be pasted via the desktop's popup menu to a new alignment window +- Overview window is saved in project file, and state of 'show hidden regions' is preserved. +- JvCacheableInputBoxTest flaky on build server -- 1.7.10.2