+
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
+ <em>18/01/2022</em></strong></td>
+ <td></td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
+ updated by Jalview or other applications (Windows, other non
+ Unix/BSD OSs)
+ </li>
+ </ul> <em>Security</em>
+ <ul>
+ <li>
+ <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
+ certificates.
+ </li>
+ </ul>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
+ <em>6/01/2022</em></strong></td>
+
+ <td align="left" valign="top"><em>Security</em>
+ <ul>
+ <li>
+ <!-- JAL-3934 -->Version bump library dependency: Log4j
+ 2.16.0 to 2.17.0.
+ </li>
+ </ul></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
+ <em>20/12/2021</em></strong></td>
+
+ <td align="left" valign="top"><em>Security</em>
+ <ul>
+ <li>
+ <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
+ (was log4j 1.2.x).
+ </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>
+ </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>