JAL-4090 update 2.11.3.0 release notes for recent merges

diff --git a/help/markdown/releases/release-2_11_3_0.md b/help/markdown/releases/release-2_11_3_0.md
index 31cabd7..1309483 100644 (file)
--- 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: 2023-03-07
+date: 2023-06-07
 channel: "release"
 ---
 
@@ -13,26 +13,37 @@ 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-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
+
 - <!-- JAL-4089 --> Use selected columns for superposition
 - <!-- JAL-4086 --> Highlight aligned positions on all associated structures when mousing over a column
 
+### Improved support for working with computationally determined models
+
 - <!-- JAL-3895 --> Alphafold red/orange/yellow/green colourscheme for structures
 - <!-- JAL-4095 --> Interactive picking of low pAE score regions
 - <!-- JAL-4027 --> contact matrix datatype in Jalview
 - <!-- JAL-4033 --> Selections with visual feedback via contact matrix annotation
 
-- <!-- JAL-4075 --> Don't add string label version of DSSP secondary structure codes in secondary structure annotation rows
 - <!-- JAL-3855 --> Discover and import alphafold2 models and metadata from https://alphafold.ebi.ac.uk/
 
-- <!-- JAL-2961 --> Jmol view not always centred on structures when multiple structures are viewed
+- <!-- JAL-4091 --> Visual indication of relationship with associated sequence to distinguish different sequence associated annotation rows
+- <!-- JAL-4123 --> GUI and command line allows configuration of how temperature factor in imported 3D structure data should be interpreted
+- <!-- JAL-3914 --> Import model reliability scores encoded as temperature factor annotation with their correct name and semantics
+- <!-- JAL-3858 --> Import and display alphafold alignment uncertainty matrices from JSON
+- <!-- JAL-4134,JAL-4158 --> Column-wise alignment groups and selections and interactive tree viewer for PAE matrices
+- <!-- JAL-4124 --> Store/Restore PAE data and visualisation settings from Jalview Project
 
-- <!-- JAL-2528, JAL-1713 --> Overview window is saved in project file, and state of 'show hidden regions' is preserved.
+### Jalview on the command line
 
-- <!-- JAL-3119 --> Name of alignment and view included in overview window's title
+- <!-- 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-4121 --> Assume --headless when jalview is run with a command line argument that generates output
 
-- <!-- JAL-4091 --> Visual indication of relationship with associated sequence to distinguish different sequence associated annotation rows
-- <!-- JAL-4094 --> Shift+Click+Drag to adjust height of all annotation tracks of same type
+### Other improvements
 
+- <!-- JAL-3119 --> Name of alignment and view included in overview window's title
 
 ## Still in progress (delete on release)
 
@@ -40,9 +51,13 @@ channel: "release"
 - <!-- JAL-2349 --> Contact prediction visualisation
 - <!-- JAL-2348 --> modularise annotation renderer
 
+### Development and Deployment
 
+- <!-- JAL-4167 --> Create separate gradle test task for some tests
+- <!-- JAL-4111 --> Allow gradle build to create suffixed DEVELOP-... builds with channel appbase
 
 ## 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.
 - <!-- JAL-3772 --> Unsaved Alignment windows close without prompting to save, individually or at application quit.
 - <!-- JAL-1988 --> Can quit Jalview while 'save project' is in progress
@@ -52,3 +67,11 @@ channel: "release"
 - <!-- JAL-3785 --> Overview windows opened automatically (due to preferences settings) lack title
 - <!-- JAL-2353 --> Show Crossrefs fails to retrieve CDS from ENA or Ensembl for sequences retrieved from Uniprot due to version numbers in cross-reference accession
 - <!-- JAL-4184 --> Stockholm export does not include sequence descriptions
+- <!-- JAL-4075 --> Don't add string label version of DSSP secondary structure codes in secondary structure annotation rows
+- <!-- JAL-4182 --> reference annotation not correctly transferred to alignment containing a sub-sequence when a selection is active
+- <!-- JAL-4177 --> Can press 'Add' or 'New View' multiple times when manually adding and viewing a 3D structure via structure chooser
+- <!-- JAL-4133 --> Jalview project does not preserve font aspect ratio when Viewport is zoomed with mouse
+- <!-- JAL-4128 --> Resizing overview quickly with solid-drags enabled causes exception
+- <!-- 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