+ <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 forĀ 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">
+ <ul>
+ <li>
+ <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
+ 'virtual' codon features shown on protein (or vice versa)
+ for display in alignments, on structure views (including
+ transfer to UCSF chimera), in feature reports and for
+ export.
+ </li>
+ <li>
+ <!-- JAL-3121 -->Feature attributes from VCF files can be
+ exported and re-imported as GFF3 files
+ </li>
+ <li>
+ <!-- JAL-3376 -->Capture VCF "fixed column" values
+ POS, ID, QUAL, FILTER as Feature Attributes
+ </li>
+ <li>
+ <!-- JAL-3375 -->More robust VCF numeric data field
+ validation while parsing
+ </li>
+ <li>
+ <!-- JAL-3533 -->Feature Settings dialog keeps same screen
+ position if reopened
+ </li>
+ <li>
+ <!-- JAL-3535 -->Feature Settings dialog title includes name
+ of associated view
+ </li>
+ <li>
+ <!-- JAL-3538 -->Font anti-aliasing in alignment views
+ enabled by default
+ </li>
+ <li>
+ <!-- JAL-3468 -->Very long feature descriptions truncated in
+ tooltips and menus
+ </li>
+ <li>
+ <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
+ with no feature types visible
+ </li>
+ <li>
+ <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
+ </li>
+ </ul><em>Jalview Installer</em>
+ <ul>
+ <li>
+ <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
+ in console (may be null when Jalview launched as executable jar or via conda)
+ </li>
+ <li>
+ <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
+ </li>
+ <li>
+ <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
+ </li>
+ <li>
+ <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
+ <li>
+ <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>