+ <!-- JAL-3904 -->Structure window's viewer-specific menu
+ disappears when only one structure is shown (and many
+ sequences:one chain mappings are present)
+ </li>
+ <li>
+ <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
+ the first SEQUENCE_GROUP defined
+
+ </li>
+
+ <li>
+ <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not
+ propagated between Linked CDS - Protein alignments and their
+ trees (known defect from 2.11.1.3)
+ </li>
+ <li>
+ <!-- JAL-3761 -->Not all codon positions highlighted for
+ overlapping exon splice sites (e.g due to RNA slippage)
+ </li>
+ <li>
+ <!-- JAL-3794 -->X was not being recognised as the unknown base
+ in DNA sequences
+ </li>
+ <li>
+ <!-- JAL-3915 -->Removed RNAview checkbox and logic from
+ Structure Preferences
+ </li>
+ <li>
+ <!-- JAL-3583 -->Tooltip behaviour improved (slightly)
+ </li>
+ <li>
+ <!-- JAL-3162 -->Can edit a feature so that start > end
+ </li>
+ <li>
+ <!-- JAL-2848 -->Cancel from Amend Features doesn't reset a
+ modified graduated colour
+ </li>
+ <li>
+ <!-- JAL-3788 -->New View with automatic 'Show Overview'
+ preference enabled results in Null Pointer Exceptions when
+ clustal colouring is enabled
+ </li>
+ <li><!-- JAL-3275 -->Can open multiple Preferences panels</li>
+ <li>
+ <!-- JAL-3949 -->Standard out logging broken: messages only
+ routing to stderr and appear as a raw template
+ </li>
+ </ul> <em>JalviewJS</em>
+ <ul>
+ <li>
+ <!-- -->
+ </li>
+ <li>
+ <!-- -->
+ </li>
+ <li>
+ <!-- -->
+ </li>
+ <li>
+ <!-- -->
+ </li>
+ <li>
+ <!-- -->
+ </li>
+ <li>
+ <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
+ via Info.args when there are arguments on the URL
+ </li>
+ <li>
+ <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
+ </li>
+ <li>
+ <!-- JAL-3603 -->Annotation file fails to load from URL in
+ JalviewJS
+ </li>
+ </ul> <em>Development</em>
+ <ul>
+ <li>Gradle
+ <ul>
+ <li>Fixed non-fatal gradle errors during build</li>
+ <li>
+ <!-- JAL-3745 -->Updated build.gradle for use with
+ Gradle v.6.6+
+ </li>
+ </ul>
+ </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.2.11.1.7">.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>