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=fdfa3a59c9446fdd9c6a4a08945c5f92a630fefb;hpb=772387bbccde43cd52ccfadb854d45b1c27f3324;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 fdfa3a5..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"
 - <!-- JAL-4064 --> Native M1 build for macOS using Adoptium JRE 11 macos-aarch64
 - <!-- JAL-4054 --> Installers built with install4j10
 - <!-- JAL-3676 --> Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button
-- <!-- JAL-3416 --> FlatLAF default look and feel on Linux, OSX and everywhere else ?
+- <!-- JAL-3416 --> FlatLAF default look and feel on Linux, OSX and everywhere else
 
 - <!-- JAL-4019 --> Ambiguous Base Colourscheme
 - <!-- JAL-4061 --> Find can search sequence features' type and description
@@ -22,7 +22,9 @@ channel: "release"
 
 - <!-- JAL-4221 --> sequence descriptions are updated from database reference sources if not already defined
 - <!-- JAL-4273 --> Visible adjuster marks to grab and adjust annotation panel height and id width
+- <!-- JAL-4260 --> Adjustable ID margin when alignment is wrapped
 
+- <!-- JAL-4274 --> Command line options and configurable bitmap export preferences for height, width and scale factor
 
 ### Improved support for working with computationally determined models
 
@@ -44,8 +46,10 @@ channel: "release"
 
 ### Jalview on the command line
 
-- <!-- JAL-4160,JAL-629 --> New command line argument framework allowing flexible batch processing, figure generation, and import of structures, pae matrices and other sequence associated data
+- <!-- JAL-4160,JAL-629,JAL-4262,JAL-4265, --> 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.
 - <!-- JAL-4121 --> Assume --headless when jalview is run with a command line argument that generates output
+- <!-- JAL-244 --> Automatically adjust Left margin on import to avoid cropping of annotation labels & sequence IDs
+- <!-- JAL-901 --> Specify alignment title on import via --title argument
 
 ### Other improvements
 
@@ -70,7 +74,11 @@ known issue ? <!-- JAL-4127	--> 'Reload' for a jalview project results in all wi
 
 - <!-- JAL-3830 --> Command-line wrapper script for macOS bundle, linux and Windows installations (bash, powershell and .bat wrappers)
 - <!-- JAL-3820 --> In Linux desktops' task-managers, the grouped Jalview windows get a generic name
+- <!-- JAL-4206 --> Improved file chooser's 'recent files' view and added filter for 'All known alignment files'
+- <!-- JAL-4206 --> 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)
 
 - <!-- JAL-2382 --> Import and display sequence-associated contact predictions in CASP-RR format
@@ -80,9 +88,11 @@ known issue ? <!-- JAL-4127	--> 'Reload' for a jalview project results in all wi
 ### Development and Deployment
 
 - <!-- JAL-4167 --> Create separate gradle test task for some tests
+- <!-- JAL-4212 --> Prevent gradle test on macOS continuously grabbing focus
 - <!-- JAL-4111 --> Allow gradle build to create suffixed DEVELOP-... builds with channel appbase
 - <!-- JAL-4243 --> Jalview bio.tools description maintained under jalview's git repo and bundled with source release
 
+
 ## Issues Resolved
 - <!-- JAL-2961 --> Jmol view not always centred on structures when multiple structures are viewed
 - <!-- JAL-3776 --> Cancelling interactive calculation leaves empty progress bar.
@@ -102,12 +112,19 @@ known issue ? <!-- JAL-4127	--> 'Reload' for a jalview project results in all wi
 - <!-- JAL-4150 --> Sequences copied to clipboard from within Jalview cannot be pasted via the desktop's popup menu to a new alignment window
 - <!-- JAL-2528, JAL-1713 --> Overview window is saved in project file, and state of 'show hidden regions' is preserved.
 - <!-- JAL-4153 --> JvCacheableInputBoxTest flaky on build server
+- <!-- JAL-4255 --> SLF4J produces an error to STDERR at Jalview startup due to missing class
+- <!-- JAL-4189 --> macOS Dock and KDE taskbar names Jalview icon "java" when running
+- <!-- JAL-2910 --> HeadlessException in console in headless mode (actually fixed in 2.11.{0,1,2))
+
 
 ## New Known defects
 - <!-- JAL-4178 --> Cannot cancel structure view open action once it has been started via the structure chooser dialog
 - <!-- JAL-4142 --> Example project's multiple views do not open in distinct locations when eXpand views is used to show them all separately
 - <!-- JAL-4165 --> Missing last letter when copying consensus sequence from alignment if first column is hidden
 - <!-- JAL-4261 --> Last sequence ID in alignment not shown and annotation labels are misaligned in HTML export
+- <!-- JAL-3024 --> Files opened via command line with a relative path are added as relative paths to Recent files list (since 2.0.x)
+- <!-- JAL-4291 --> Test coverage for ID width adjustment disabled pending fix for new annotation label geometry and width calculation
+