X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fmarkdown%2Freleases%2Frelease-2_11_3_0.md;h=5a9de38922d829d07e6f2b3364d7a85a2f1f4750;hb=fbdb24c3c8ad23e3966a8295bed2de3b05f60119;hp=e86d2efd3c157bccaabbc1464a6db78d1dbd784b;hpb=1c50c6dd5d8051bc76e6c243624c5e08693ee48a;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 e86d2ef..5a9de38 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: 2023-10-25 +date: 2023-11-03 channel: "release" --- @@ -18,13 +18,14 @@ channel: "release" - 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 +- 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 - 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 @@ -63,12 +64,14 @@ channel: "release" - 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. +- Overview display and hidden region visibility stored in Jalview projects ### 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) @@ -89,7 +92,7 @@ channel: "release" - 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 +- 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. @@ -102,6 +105,9 @@ channel: "release" - 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 - 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. @@ -109,11 +115,14 @@ channel: "release" - 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 +- 'Reload' for a jalview project results in all windows being duplicated (since 2.11.2.6, more severe in 2.11.3.0) +- Annotation colouring dialog box doesn't remember 'use original colours' settings when opened via the Colour menu