+
<html>
<!--
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
</p>
<table border="1">
<tr>
- <th nowrap><em>Release</em></th>
+ <th nowrap><a id="Jalview.$$Version-Rel$$"><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>24/02/2022</em></strong></td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3616 JAL-3551 JAL-2322 -->Support for viewing 3D
+ structures with ChimeraX and Pymol in addition to Jmol and
+ Chimera.
+ </li>
+ <li>
+ <!-- JAL-3503 -->New Preferences tab for adjusting Jalview's
+ memory settings at launch
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ <li>
+ <!-- JAL-3863 -->Support for Canonical Uniprot IDs
+ </li>
+ <li>
+ <!-- JAL-3204 -->Updated Jalview bindings for Uniprot XML
+ schema
+ </li>
+ </ul> <em>JalviewJS</em>
+ <ul>
+ <li>
+ <!-- 3624 -->PDB structures mapped to Uniprot Sequences with
+ SIFTS
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL-3163 -->Missing message bundle keys are only
+ reported once per key (avoids excessive log output in js
+ console)
+ </li>
+ <li>
+ <!-- JAL-3168 -->Feature type is included in the title of
+ the Feature Settings' Colour Chooser dialog
+ </li>
+ <li></li>
+ </ul> <em>Development</em>
+ <ul>
+ <li>First integrated JalviewJS and Jalview release</li>
+ <li>Updated building instructions</li>
+ <li>
+ <!-- JAL-3679 -->Improved JalviewJS/Jalview build process
+ for system package provided eclipse installs on linux
+ </li>
+ <li>Install4j 9.0.x used for installer packaging</li>
+ <li>Notarized MacOS installer for compatibility with Big
+ Sur and Monterey</li>
+ <li>
+ <!-- JAL-3805 -->Uninstaller application for old
+ (InstallAnywhere based) Jalview installations removed from
+ the DMG
+ </li>
+ <li>
+ <!-- JAL-3930 -->Improved use of installers for unattended
+ installation with a customizedId of "JALVIEW" in install4j's
+ Jalview Launcher
+ </li>
+
+ </ul>
+
+ </td>
+ <td>
+ <ul>
+ <li>
+ <!-- JAL-3674 -->Slow structure commands can block Jalview
+ execution
+ </li>
+ <li>
+ <!-- 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>
+ </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">
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-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>
git://source.jalview.org / jalview.git / blobdiff