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* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
</p>
<table border="1">
<tr>
- <th nowrap><a id="Jalview.$$Version-Rel$$"><em>Release</em></th>
+ <th nowrap><em>Release</em></th>
<th><em>New Features</em></th>
<th><em>Issues Resolved</em></th>
</tr>
<tr>
<td width="60" align="center" nowrap><strong><a
- id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
- <em>29/09/2021</em></strong></td>
- <td align="left" valign="top">
- <ul>
- <li><!-- --></li>
- </ul>
- <em>Development</em>
- <ul>
- <li>Updated building instructions</li>
- </ul></td>
- <td>
- <ul>
- <li>
- <!-- JAL-3840 -->Occupancy calculation is incorrect for
- alignment columns with over -1+2^32 gaps (breaking filtering
- and display)
- </li>
- <li>
- <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
- scale factors being set with buggy window-managers (linux
- only)
- </li>
- <li>
- <!-- JAL-3915 -->Removed RNAview checkbox and logic from Structure Preferences
- </li>
- </ul> <em>Development</em>
- <ul>
- <li>Fixed non-fatal gradle errors during build</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.2.11.1.4">.4</a><br />
- <em>09/03/2021</em></strong></td>
- <td align="left" valign="top"><em>Improved control of
- Jalview's use of network services via jalview_properties</em>
- <ul>
- <li>
- <!-- JAL-3814 -->New .jalview_properties token controlling
- launch of the news browser (like -nonews argument)
- </li>
- <li>
- <!-- JAL-3813 -->New .jalview_properties token controlling
- download of linkout URLs from
- www.jalview.org/services/identifiers
- </li>
- <li>
- <!-- JAL-3812 -->New .jalview_properties token controlling
- download of BIOJSHTML templates
- </li>
- <li>
- <!-- JAL-3811 -->New 'Discover Web Services' option to
- trigger a one off JABAWS discovery if autodiscovery was
- disabled
- </li>
- </ul></td>
- <td align="left" valign="top">
- <ul>
- <li>
- <!-- JAL-3818 -->Intermittent deadlock opening structure in
- Jmol
- </li>
- </ul> <em>New Known defects</em>
- <ul>
- <li>
- <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
- always restored from project (since 2.10.3)
- </li>
- <li>
- <!-- JAL-3806 -->Selections from tree built from CDS aren't
- propagated to Protein alignment (since 2.11.1.3)
- </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.2.11.1.3">.3</a><br />
- <em>29/10/2020</em></strong></td>
- <td align="left" valign="top">
- <ul>
-
- </ul>
- </td>
- <td align="left" valign="top">
- <ul>
- <li>
- <!-- JAL-3765 -->Find doesn't always highlight all matching
- positions in a sequence (bug introduced in 2.11.1.2)
- </li>
- <li>
- <!-- JAL-3760 -->Alignments containing one or more protein
- sequences can be classed as nucleotide
- </li>
- <li>
- <!-- JAL-3748 -->CDS alignment doesn't match original CDS
- sequences after alignment of protein products (known defect
- first reported for 2.11.1.0)
- </li>
- <li>
- <!-- JAL-3725 -->No tooltip or popup menu for genomic
- features outwith CDS shown overlaid on protein
- </li>
- <li>
- <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
- correctly mapped by Jalview (e.g. affects viral CDS with
- ribosomal slippage, since 2.9.0)
- </li>
- <li>
- <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
- CDS features
- </li>
- <li>
- <!-- JAL-3700 -->Selections in CDS sequence panel don't
- always select corresponding protein sequences
- </li>
- <li>
- <!-- JAL-3759 --> <em>Make groups from selection</em> for a
- column selection doesn't always ignore hidden columns
- </li>
- </ul> <em>Installer</em>
- <ul>
- <li>
- <!-- JAL-3611 -->Space character in Jalview install path on
- Windows prevents install4j launching getdown
- </li>
- </ul> <em>Development</em>
- <ul>
- <li>
- <!-- JAL-3248 -->Fixed typos and specified compatible gradle
- version numbers in doc/building.md
- </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.2.11.1.2">.2</a><br />
- <em>25/09/2020</em></strong></td>
- <td align="left" valign="top">
- <ul>
- </ul>
- </td>
- <td align="left" valign="top">
- <ul>
- <li>
- <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
- "Encountered problems opening
- https://www.jalview.org/examples/exampleFile_2_7.jvp"
- </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.2.11.1.1">.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>
- <li>
- <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
- via command line
- </li>
- <li>
- <!-- JAL-3741 -->References to http://www.jalview.org in
- program and documentation
- </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>
- <li>
- <!-- JAL-3749 -->Duplicate CDS sequences are generated when
- protein products for certain ENA records are repeatedly
- shown via Calculate->Show Cross Refs
- </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