X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fmarkdown%2Freleases%2Frelease-2_11_3_0.md;h=c732130423ad888b4efa3e347491c065f44b259d;hb=refs%2Fheads%2Fdevelop;hp=7ddd76f38746c25ab29cc5af3748b5c4da460f7a;hpb=bca92e34b044bba83a9e5a0284cd18b4029d0167;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 7ddd76f..c732130 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: 2023-10-03 +date: 2023-11-15 channel: "release" --- @@ -16,14 +16,16 @@ channel: "release" - 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 +- 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 +- Command line options and configurable bitmap export (via preferences file) for height, width and scale factor +- Show or hide ligands in a Jmol structure view via View Ligands submenu +- Jmol's display is antialiased by default (smoother, less pixellated) -### Improved support for working with computationally determined models +### Improved support for working with structures and computationally determined models - Alphafold red/orange/yellow/green colourscheme for structures - Interactive picking of low pAE score regions -- contact matrix datatype in Jalview +- Predicted Alignment Error annotation tracks for structures from AlphaFold DB - 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 @@ -32,7 +34,11 @@ channel: "release" - 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 +- 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 - 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. @@ -40,14 +46,14 @@ 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 -- Lower line of the sequence group border does not align with vertical and background residue box +- 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 - "add reference annotation" add all positions in reference annotation tracks, not just positions in the currently highlighted columns/selection range @@ -55,18 +61,26 @@ channel: "release" - 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 -- Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button +- Reduce number of database crossreferences shown in tooltip +- Drag and drop feature colours file on an alignment to quickly apply feature settings +- 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 - 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 +- Update .jvl generation in build.gradle for jalview branch builds - Jalview bio.tools description maintained under jalview's git repo and bundled with source 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 -- 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 @@ -74,29 +88,47 @@ channel: "release" - Multiple overview windows can be opened for a particular alignment view when multiple views are present - 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 +- Uniprot parser fails to import sequences with features that have 'unknown' start or end - 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 +- 3D beacons sources providing models scored with PLDDT and pTM not sorted against alphaFoldDB models - Jalview project does not preserve font aspect ratio when Viewport is zoomed with mouse +- Lower line of the sequence group border does not align with vertical and background residue box - 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 +- 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 +- Java Console opening at startup with the exampleFile_v2_7.jvp opening (nearly always) causes Jalview to hang +- automatic positioning of ID width for imported project can fail for certain font size configured in User preferences (affects most versions of Jalview prior to 2.11.3.0) +- RNAML import missing terminal residue +- RNA secondary structure annotation final-ending-solo-brace arrow points the wrong way +- 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 +- '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 - Files opened via command line with a relative path are added as relative paths to Recent files list (since 2.0.x) - 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 +- 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)