---
version: 2.11.4.0
-date: 2024-06-30
+date: 2024-08-13
channel: "develop"
---
## New Features
+- <!-- JAL-4159,JAL-4390 --> Calculate PASiMap projection for sequences - ported by Thomas Morell ( U. Konstanz)
- <!-- JAL-4392 --> Consensus secondary structure visualization for alignments
+- <!-- JAL-4411 --> Show data source for 'reference annotation' from 3D structure (e.g. Secondary Structure)
- <!-- JAL-4386 --> Calculate tree or PCA using secondary structure annotation
-- <!-- JAL-4159 --> Calculate PASiMap projection for sequences - ported by Thomas Morell ( U. Konstanz)
- <!-- JAL-789,JAL-4257 --> allow adjustment of gap opening, extension, and score model for built in pairwise alignment
-
+- <!-- JAL-4420 --> Jalview sensibly handles opening or a drag'n'drop of several .features, .annotations and .newick files onto an alignment
+<!-- not yet! - -- JAL-4366 Linked visualisation of Foldseek 3Di MSAs with corresponding 3D structures -->
### development and deployment
+- <!-- JAL-3830 --> Add a command-line wrapper script to macOS bundle, linux and Windows installations (bash, powershell and .bat wrappers)
+- <!-- JAL-3384 --> Redirect stdout and stderr to file when launched from getdown
+- <!-- JAL-3845 --> Add error message when launched directly from Jalview Installer DMG volume
+- <!-- JAL-3631,JAL-4104 --> Allow jalview auto-updates to download to and work from separate user-space directory
+- <!-- JAL-3978, JAL-3196 --> Gradle build with install4j launchers
+- <!-- JAL-4409, JAL-4160 --> Implement in Jalview (and getdown for JVL) the use of specific scheme names for different channels (e.g. jalviewd://)
+- <!-- JAL-4428 --> integrate OSX codesigning scripts in jalview's repository
+- <!-- JAL-4397 --> fixed inconsistencies in test suite on different platforms
## Issues Resolved
-
+- <!-- JAL-1054 --> jalview does not fetch from a URL containing a redirect
+- <!-- JAL-4414 --> HTTP errors are often interpreted to the user as a file format error - and FileNotFound errors are not propagated from Web or Local file import
+- <!-- JAL-3409 --> launcher.log from jalview runtime missing newlines and also lacks stdout/stderr reported in Jalview Console
+- <!-- JAL-4072 --> Possible "Zip Slip Vulnerability" in getdown
+- <!-- JAL-4417 --> jalview.bin.CommandsTest.headlessOrGuiImageOutputTest produces different images for --gui and --headless when using certain .jalview_properties
+- <!-- JAL-4421 --> Release installer DMG does not display the background image
+- <!-- JAL-4358 --> Getdown splash screen should disappear as soon as the Jalview Desktop is created/visible
### New Known Issues