Merge branch 'develop' into releases/Release_2_11_3_Branch

[jalview.git] / help / markdown / releases / release-2_11_3_0.md

diff --git a/help/markdown/releases/release-2_11_3_0.md b/help/markdown/releases/release-2_11_3_0.md
index 0fa114d..4904c4c 100644 (file)
--- a/help/markdown/releases/release-2_11_3_0.md
+++ b/help/markdown/releases/release-2_11_3_0.md
@@ -13,7 +13,7 @@ channel: "release"
 - <!-- JAL-4019 --> Ambiguous Base Colourscheme
 - <!-- JAL-4061 --> Find can search sequence features' type and description
 - <!-- JAL-4062 --> Hold down Shift + CMD/CTRL C to copy highlighted regions as new sequences
-- <!-- JAL-1556 --> Quickly enable select and/or colour by for displayed annotation row via its popup menu
+- <!-- JAL-1556 --> Quickly enable select and/or colour by for displayed annotation row via annotation panel popup menu
 - <!-- JAL-4094 --> Shift+Click+Drag to adjust height of all annotation tracks of same type
 - <!-- JAL-4190 --> Pressing escape in tree panel clears any current selection
 
@@ -46,7 +46,7 @@ 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
@@ -77,6 +77,7 @@ known issue ? <!-- JAL-4127   --> 'Reload' for a jalview project results in all wi
 - <!-- 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)
 
@@ -91,7 +92,6 @@ known issue ? <!-- JAL-4127   --> 'Reload' for a jalview project results in all wi
 - <!-- 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.
@@ -122,6 +122,7 @@ known issue ? <!-- JAL-4127 --> 'Reload' for a jalview project results in all wi
 - <!-- 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