X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=089873937ec1ea6d14dd73b09eb1630a600c2422;hb=8f149d9613754f066b0aced1b4fdcd7169fa7e05;hp=5b6180d084faa935e8dbaf10b05ea428020844f5;hpb=68e1026a95c29b90a9ef4d65984c0c0ba191c0e9;p=jalview.git

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 5b6180d..0898739 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -57,6 +57,270 @@ li:before {
     </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>
+        </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-&gt;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">