X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=685c3ee0f768d011c5ace3bb346da94228a389b4;hb=3f4d633d2c586d6da5cb47493d34267dcc6dab59;hp=60e31793f3ad03630e21fc2ab2d334f8d1537a54;hpb=cfcd397b19f70fb39d6d21437db8eb6ffcac3914;p=jalview.git

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 60e3179..685c3ee 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -57,14 +57,177 @@ li:before {
     </tr>
     <tr>
       <td width="60" align="center" nowrap><strong><a
+          id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
+          <em>8/09/2020</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-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>
+        </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-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>
+        </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, in feature reports and for export.
+            <!-- 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
@@ -98,6 +261,9 @@ li:before {
             <!-- 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>
@@ -153,6 +319,11 @@ li:before {
             'Show hidden markers' option is not ticked
           </li>
           <li>
+            <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
+            PNG output when 'Automatically set ID width' is set in
+            jalview preferences or properties file
+          </li>
+          <li>
             <!-- JAL-3571 -->Feature Editor dialog can be opened when
             'Show Sequence Features' option is not ticked
           </li>
@@ -253,9 +424,6 @@ li:before {
             <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
             bamboo server but run fine locally.
           </li>
-          <li>
-            <!-- JAL-3574 -->Filtering features by genomic location (POS) is broken by rounding
-          </li>
         </ul>
       </td>
     </tr>