X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fmarkdown%2Freleases%2Frelease-2_11_3_0.md;h=bce9435b25900a9022670664cc3daf754ff3a1cd;hb=6fb31e80680c47ed613ca84779be5604d027bdc1;hp=46de783d6d43e8f7e3e22d8d63f75c65a1e74f27;hpb=17863d983fe946ec642e3d6d86cabd2e01be3b19;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 46de783..bce9435 100644 --- a/help/markdown/releases/release-2_11_3_0.md +++ b/help/markdown/releases/release-2_11_3_0.md @@ -1,48 +1,82 @@ --- version: 2.11.3.0 -date: 2023-03-07 +date: 2023-11-03 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 (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 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 - -- 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 - -- Overview window is saved in project file, and state of 'show hidden regions' is preserved. - -- Name of alignment and view included in overview window's title - - 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 - +- 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 +- 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. -## Still in progress (delete on release) -- Import and display sequence-associated contact predictions in CASP-RR format -- Contact prediction visualisation -- modularise annotation renderer +### 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 +- 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 +- EMBL-EBI SIFTS file downloads now use split directories +- 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 +- 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 +- Upgrade bundled groovy to v4.0.15 and regularised interface for groovy scripts run from CLI, interactively and headlessly. +### 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 @@ -50,4 +84,42 @@ channel: "release" - PDB structures slow to view when Jalview Java Console is open (2.11.2.7 patch) - 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 \ No newline at end of file +- 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 +- 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 +- 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 + +## New Known defects +- 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. +- 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 +- 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 + +