--- /dev/null
+---
+channel: release
+version: 2.11.1.1
+date: 2020-09-17
+---
+
+## New Features
+
+- <!-- JAL-3638 --> Shift+arrow keys navigate to next gap or residue in cursor mode
+- <!-- JAL-3695 --> Support import of VCF 4.3 by updating HTSJDK from 2.12 to 2.23
+- <!-- JAL-3621 --> IntervalStore library updated to v.1.1: optimisations and improvements suggested by Bob Hanson and improved compatibility with JalviewJS
+- <!-- JAL-3615 --> Retrieve GZipped stockholm formatted alignments from Pfam and Rfam
+- <!-- JAL-2656 --> Recognise GZipped content for URLs and File import (no longer based on .gz extension)
+- <!-- JAL-3570 --> Updated Spanish Translation for 2.11.1
+- <!-- JAL-3692 --> Migrate EMBL record retrieval to use latest ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and EMBL flat file
+- <!-- JAL-3667 --> Improved warning messages, debug logging and fixed Retry action when Jalview encounters errors when saving or making backup files.
+- <!-- JAL-3676 --> Enhanced Jalview Java Console:
+ - Jalview's logging level can be configured
+ - Copy to Clipboard Buttion
+- <!-- JAL-3541 --> Improved support for Hi-DPI (4K) screens when running on Linux (Requires Java 11+)
+- <!-- JAL-1842 JAL-3509 --> RESNUM sequence features (the green ones) are not automatically displayed when associated structures are displayed or for sequences retrieved from the PDB.
+
+
+### Launching Jalview
+- <!-- JAL-3608 --> Configure Jalview Desktop's look and feel through a system property
+- <!-- JAL-3477 --> Improved built-in documentation and command line help for configuring Jalview's memory
+
+
+## Issues Resolved
+
+- <!-- JAL-3691 --> Conservation and Quality tracks are shown but not calculated and no protein or DNA score models are available for tree/PCA calculation when launched with Turkish language locale
+- <!-- JAL-3493 --> Escape does not clear highlights on the alignment (Since Jalview 2.10.3)
+- <!-- JAL-3680 --> Alt+Left or Right arrow in cursor mode doesn't slide selected sequences, just sequence under cursor
+- <!-- JAL-3732 --> Alt+Up/Down in cursor mode doesn't move sequence under the cursor
+- <!-- JAL-3613 --> Peptide-to-CDS tracking broken when multiple EMBL gene products shown for a single contig
+- <!-- JAL-3696 --> Errors encountered when processing variants from VCF files yield "Error processing VCF: Format specifier '%s'" on the console
+- <!-- JAL-3697 --> Count of features not shown can be wrong when there are both local and complementary features mapped to the position under the cursor
+- <!-- JAL-3673 --> Sequence ID for reference sequence is clipped when Right align Sequence IDs enabled
+- <!-- JAL-2983 --> Slider with negative range values not rendered correctly in VAqua4 (Since 2.10.4)
+- <!-- JAL-3685 --> Single quotes not displayed correctly in internationalised text for some messages and log output
+- <!-- JAL-3490 --> Find doesn't report matches that span hidden gapped columns
+- <!-- JAL-3597 --> Resolved memory leaks in Tree and PCA panels, Alignment viewport and annotation renderer.
+- <!-- JAL-3561 --> Jalview ignores file format parameter specifying output format when exporting an alignment via the command line
+- <!-- JAL-3667 --> Windows 10: For a minority of users, if backups are not enabled, Jalview sometimes fails to overwrite an existing file and raises a warning dialog. (in 2.11.0, and 2.11.1.0, the workaround is to try to save the file again, and if that fails, delete the original file and save in place.)
+- <!-- JAL-3509 --> Dragging a PDB file onto an alignment with sequence features displayed causes displayed features to be hidden.
+- <!-- JAL-3750 --> Cannot process alignments from HTTPS urls via command line
+- <!-- JAL-3741 --> References to http://www.jalview.org in program and documentation
+
+
+### Launching Jalview
+- <!-- JAL-3718 --> Jalview application fails when launched the first time for a version that has different jars to the previous launched version.
+
+
+### Developing Jalview
+- <!-- JAL-3541 --> Fixed issue with cleaning up old coverage data, causing cloverReport gradle task to fail with an OutOfMemory error.
+- <!-- JAL-3280 --> Migrated the Jalview Version Checker to monitor the release channel
+
+
+### New Known defects
+- <!-- JAL-3748 --> CDS shown in result of submitting proteins in a CDS/Protein alignment to a web service is wrong when proteins share a common transcript sequence (e.g. genome of RNA viruses)
+- <!-- JAL-3576 --> Co-located features exported and re-imported are ordered differently when shown on alignment and in tooltips. (Also affects v2.11.1.0)
+- <!-- JAL-3702 --> Drag and drop of alignment file onto alignment window when in a HiDPI scaled mode in Linux only works for the top left quadrant of the alignment window
+- <!-- JAL-3701 --> Stale build data in jalview standalone jar builds (only affects 2.11.1.1 branch)
+- <!-- JAL-3127 --> Sequence ID colourscheme not re-applied when alignment view restored from project (since Jalview 2.11.0)
+- <!-- JAL-3749 --> Duplicate CDS sequences are generated when protein products for certain ENA records are repeatedly shown via Calculate->Show Cross Refs
git://source.jalview.org / jalview.git / blobdiff