X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=help%2Fmarkdown%2Freleases%2Frelease-2_11_1_1.md;fp=help%2Fmarkdown%2Freleases%2Frelease-2_11_1_1.md;h=6d66acbc7a73f7a903bdce51d1266611532f77eb;hp=0000000000000000000000000000000000000000;hb=07727bb7e06eb681af51a95e941cb035ac637d10;hpb=ce916cd46bbe1ec0446d8672b7341f5af7471b6e diff --git a/help/markdown/releases/release-2_11_1_1.md b/help/markdown/releases/release-2_11_1_1.md new file mode 100644 index 0000000..6d66acb --- /dev/null +++ b/help/markdown/releases/release-2_11_1_1.md @@ -0,0 +1,65 @@ +--- +channel: release +version: 2.11.1.1 +date: 2020-09-17 +--- + +## New Features + +- Shift+arrow keys navigate to next gap or residue in cursor mode +- Support import of VCF 4.3 by updating HTSJDK from 2.12 to 2.23 +- IntervalStore library updated to v.1.1: optimisations and improvements suggested by Bob Hanson and improved compatibility with JalviewJS +- Retrieve GZipped stockholm formatted alignments from Pfam and Rfam +- Recognise GZipped content for URLs and File import (no longer based on .gz extension) +- Updated Spanish Translation for 2.11.1 +- Migrate EMBL record retrieval to use latest ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and EMBL flat file +- Improved warning messages, debug logging and fixed Retry action when Jalview encounters errors when saving or making backup files. +- Enhanced Jalview Java Console: + - Jalview's logging level can be configured + - Copy to Clipboard Buttion +- Improved support for Hi-DPI (4K) screens when running on Linux (Requires Java 11+) +- RESNUM sequence features (the green ones) are not automatically displayed when associated structures are displayed or for sequences retrieved from the PDB. + + +### Launching Jalview +- Configure Jalview Desktop's look and feel through a system property +- Improved built-in documentation and command line help for configuring Jalview's memory + + +## Issues Resolved + +- 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 +- Escape does not clear highlights on the alignment (Since Jalview 2.10.3) +- Alt+Left or Right arrow in cursor mode doesn't slide selected sequences, just sequence under cursor +- Alt+Up/Down in cursor mode doesn't move sequence under the cursor +- Peptide-to-CDS tracking broken when multiple EMBL gene products shown for a single contig +- Errors encountered when processing variants from VCF files yield "Error processing VCF: Format specifier '%s'" on the console +- Count of features not shown can be wrong when there are both local and complementary features mapped to the position under the cursor +- Sequence ID for reference sequence is clipped when Right align Sequence IDs enabled +- Slider with negative range values not rendered correctly in VAqua4 (Since 2.10.4) +- Single quotes not displayed correctly in internationalised text for some messages and log output +- Find doesn't report matches that span hidden gapped columns +- Resolved memory leaks in Tree and PCA panels, Alignment viewport and annotation renderer. +- Jalview ignores file format parameter specifying output format when exporting an alignment via the command line +- 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.) +- Dragging a PDB file onto an alignment with sequence features displayed causes displayed features to be hidden. +- Cannot process alignments from HTTPS urls via command line +- References to http://www.jalview.org in program and documentation + + +### Launching Jalview +- Jalview application fails when launched the first time for a version that has different jars to the previous launched version. + + +### Developing Jalview +- Fixed issue with cleaning up old coverage data, causing cloverReport gradle task to fail with an OutOfMemory error. +- Migrated the Jalview Version Checker to monitor the release channel + + +### New Known defects +- 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) +- Co-located features exported and re-imported are ordered differently when shown on alignment and in tooltips. (Also affects v2.11.1.0) +- 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 +- Stale build data in jalview standalone jar builds (only affects 2.11.1.1 branch) +- Sequence ID colourscheme not re-applied when alignment view restored from project (since Jalview 2.11.0) +- Duplicate CDS sequences are generated when protein products for certain ENA records are repeatedly shown via Calculate->Show Cross Refs