X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fmarkdown%2Freleases%2Frelease-2_11_3_0.md;h=8eba74aa4450c024a8a0055e18ba13c0e076dd40;hb=507114c6c8a2735953006dd9973ff7fad4bb5600;hp=fbd7b9fcce3d7c40e99dc04aa739ffcf204a8e12;hpb=7c40be8c2aed396b01242811c74d90c6cf3f5ccd;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 fbd7b9f..8eba74a 100644 --- a/help/markdown/releases/release-2_11_3_0.md +++ b/help/markdown/releases/release-2_11_3_0.md @@ -8,7 +8,7 @@ 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 @@ -21,7 +21,10 @@ channel: "release" - 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 @@ -43,11 +46,18 @@ channel: "release" ### 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 +- 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. - 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 @@ -64,7 +74,11 @@ known issue ? 'Reload' for a jalview project results in all wi - 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 @@ -74,7 +88,10 @@ known issue ? 'Reload' for a jalview project results in all wi ### 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 @@ -95,3 +112,19 @@ known issue ? 'Reload' for a jalview project results in all wi - 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) +- Test coverage for ID width adjustment disabled pending fix for new annotation label geometry and width calculation + + + +