</tr>
<tr>
<td width="60" align="center" nowrap><strong><a
- id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
- <em>17/09/2020</em></strong></td>
- <td align="left" valign="top">
- <ul>
- <li>
- <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
- residue in cursor mode
- </li>
- <li>
- <!-- JAL-3695 -->Support import of VCF 4.3 by updating
- HTSJDK from 2.12 to 2.23
- </li>
- <li>
- <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
- optimisations and improvements suggested by Bob Hanson and
- improved compatibility with JalviewJS
- </li>
- <li>
- <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
- alignments from Pfam and Rfam
- </li>
- <li>
- <!-- JAL-2656 -->Recognise GZipped content for URLs and File
- import (no longer based on .gz extension)
- </li>
- <li>
- <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
- </li>
- <li>
- <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
- ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
- EMBL flat file
- </li>
- <li>
- <!-- JAL-3667 -->Improved warning messages, debug logging
- and fixed Retry action when Jalview encounters errors when
- saving or making backup files.
- </li>
- <li>
- <!-- JAL-3676 -->Enhanced Jalview Java Console:
- <ul>
- <li>Jalview's logging level can be configured</li>
- <li>Copy to Clipboard Buttion</li>
- </ul>
- </li>
- <li>
- <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
- when running on Linux (Requires Java 11+)
- </li>
- </ul> <em>Launching Jalview</em>
- <ul>
- <li>
- <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
- through a system property
- </li>
- <li>
- <!-- JAL-3477 -->Improved built-in documentation and command
- line help for configuring Jalview's memory
- </li>
- </ul>
- </td>
- <td align="left" valign="top">
- <ul>
- <li>
- <!-- 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
- </li>
- <li>
- <!-- JAL-3493 -->Escape does not clear highlights on the
- alignment (Since Jalview 2.10.3)
- </li>
- <li>
- <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
- doesn't slide selected sequences, just sequence under cursor
- </li>
- <li>
- <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
- sequence under the cursor
- </li>
- <li>
- <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
- multiple EMBL gene products shown for a single contig
- </li>
- <li>
- <!-- JAL-3696 -->Errors encountered when processing variants
- from VCF files yield "Error processing VCF: Format specifier
- '%s'" on the console
- </li>
- <li>
- <!-- 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
- </li>
- <li>
- <!-- JAL-3673 -->Sequence ID for reference sequence is
- clipped when Right align Sequence IDs enabled
- </li>
- <li>
- <!-- JAL-2983 -->Slider with negative range values not
- rendered correctly in VAqua4 (Since 2.10.4)
- </li>
- <li>
- <!-- JAL-3685 -->Single quotes not displayed correctly in
- internationalised text for some messages and log output
- </li>
- <li>
- <!-- JAL-3490 -->Find doesn't report matches that span
- hidden gapped columns
- </li>
- <li>
- <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
- panels, Alignment viewport and annotation renderer.
- </li>
- <li>
- <!-- JAL-3561 -->Jalview ignores file format parameter
- specifying output format when exporting an alignment via the
- command line
- </li>
- <li>
- <!-- 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.)
- </li>
- </ul> <em>Launching Jalview</em>
- <ul>
- <li>
- <!-- JAL-3718 -->Jalview application fails when launched the
- first time for a version that has different jars to the
- previous launched version.
- </li>
- </ul> <em>Developing Jalview</em>
- <ul>
- <li>
- <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
- data, causing cloverReport gradle task to fail with an
- OutOfMemory error.
- </li>
- <li>
- <!-- JAL-3280 -->Migrated the Jalview Version Checker to
- monitor the release channel
- </li>
- </ul> <em>New Known defects</em>
- <ul>
- <li>
- <!-- 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)
- </li>
- <li>
- <!-- 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)
- </li>
- <li>
- <!-- 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
- </li>
- <li>
- <!-- JAL-3701 -->Stale build data in jalview standalone jar
- builds (only affects 2.11.1.1 branch)
- </li>
- <li>
- <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
- when alignment view restored from project (since Jalview 2.11.0)
- </li>
- </ul>
- </td>
- </tr>
- <tr>
- <td width="60" align="center" nowrap><strong><a
id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
<em>22/04/2020</em></strong></td>
<td align="left" valign="top">
git://source.jalview.org / jalview.git / blobdiff