X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fmarkdown%2Freleases%2Frelease-2_11_3_0.md;h=0fa114dfd0eeb6055b414d6f7a79f25f6084d7dc;hb=471cfb5b0f6bb249e478f0c02d80eeea6a834383;hp=31cabd705fc9b02d77e2678c1c4aaf7f66d64191;hpb=1507992e2491be9bce5047d65e77e6a49c3bc068;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 31cabd7..0fa114d 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: 2023-07-19 channel: "release" --- @@ -8,41 +8,92 @@ channel: "release" - 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 ? +- FlatLAF default look and feel 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 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 +- 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 -- 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 +- Multiple residue sidechain highlighting in structure viewers from PAE mouseovers -- Overview window is saved in project file, and state of 'show hidden regions' is preserved. +### Jalview on the command line + +- 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 +- Automatically adjust Left margin on import to avoid cropping of annotation labels & sequence IDs +- Specify alignment title on import via --title argument + +### 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 +- 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 +- "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 -- 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 +- 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 +### Development and Deployment + +- 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. - Unsaved Alignment windows close without prompting to save, individually or at application quit. - Can quit Jalview while 'save project' is in progress @@ -52,3 +103,26 @@ 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 +- SLF4J produces an error to STDERR at Jalview startup due to missing class +- 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 +- 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) + + + +