X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=f0516e985d52673126d0463dab27489062b18131;hb=738f79179e4135a7225fc5c36e1ac4118aff0efb;hp=a2e3d6164cc300647913ea18b8657e901dbeb745;hpb=940d18951d460f9f3f0be6472327e68d09e480fe;p=jalview.git

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index a2e3d61..f0516e9 100755
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+++ b/help/help/html/releases.html
@@ -57,38 +57,198 @@ 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>11/08/2020</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-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>
+        </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>
+        </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-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.
+            Workaround is to try to save the file again, and if that
+            fails, delete the original file and save in place.
+          </li>
+          <li>
+            <!-- JAL-3702 -->Drag and drop of alignment file onto
+            alignment window not working correctly when in a HiDPI
+            scaled mode in Linux
+          </li>
+          <li>
+            <!-- JAL-3701 -->Stale build data in jalview standalone jar
+            builds (only affects 2.11.1.1 branch)
+          </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>27/03/2020</em></strong></td>
+          <em>22/04/2020</em></strong></td>
       <td align="left" valign="top">
         <ul>
           <li>
-          <!-- JAL-3187 -->Option to show 'virtual' codon features on protein (or vice versa)
+            <!-- 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
+            exported and re-imported as GFF3 files
           </li>
           <li>
-          <!-- JAL-3304 -->Option to export virtual features if shown
+            <!-- JAL-3376 -->Capture VCF &quot;fixed column&quot; values
+            POS, ID, QUAL, FILTER as Feature Attributes
           </li>
           <li>
-          <!-- JAL-3302 -->Option to transfer virtual features to Chimera
+            <!-- JAL-3375 -->More robust VCF numeric data field
+            validation while parsing
           </li>
           <li>
-          <!-- JAL-3121 -->Feature attributes from VCF files can be exported and re-imported as GFF3 files
+            <!-- JAL-3533 -->Feature Settings dialog keeps same screen
+            position if reopened
           </li>
           <li>
-            <!-- JAL-3376 -->Capture VCF &quot;fixed column&quot; values POS,
-            ID, QUAL, FILTER as Feature Attributes
+            <!-- JAL-3535 -->Feature Settings dialog title includes name
+            of associated view
           </li>
           <li>
-            <!-- JAL-3375 -->More robust VCF numeric data field validation while parsing
+            <!-- JAL-3538 -->Font anti-aliasing in alignment views
+            enabled by default
           </li>
           <li>
-            <!-- JAL-3533 -->Feature Settings dialog keeps same screen position if reopened 
-           </li>
+            <!-- JAL-3468 -->Very long feature descriptions truncated in
+            tooltips and menus
+          </li>
           <li>
-            <!-- JAL-3538 -->Font anti-aliasing in alignment views enabled by default
-           </li>
+            <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
+            with no feature types visible
+          </li>
           <li>
-            <!-- JAL-3468 -->Very long feature descriptions truncated in tooltips and menus
-           </li>
+          <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
+          </li>
         </ul><em>Jalview Installer</em>
 	    <ul>
           <li>
@@ -110,6 +270,9 @@ li:before {
           <li>
             <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
           </li>
+          <li>
+            <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds            
+          </li> 
         </ul> <em>Build System</em>
         <ul>
           <li>
@@ -120,14 +283,47 @@ li:before {
             report
           </li>
         </ul>
+        <em>Groovy Scripts</em>
+            <ul>
+          <li>
+            <!--  JAL-3547 -->exportconsensus.groovy prints a FASTA file
+            to stdout containing the consensus sequence for each
+            alignment in a Jalview session
+          </li>
+          <li>
+            <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
+            genomic sequence_variant annotation from CDS as
+            missense_variant or synonymous_variant on protein products.
+          </li>
+        </ul>
       </td>
       <td align="left" valign="top">
         <ul>
           <li>
-            <!-- JAL-3412 -->ID margins for CDS and Protein views not equal when split frame is first opened
+            <!-- JAL-3581 -->Hidden sequence markers still visible when
+            'Show hidden markers' option is not ticked
           </li>
           <li>
-            <!-- JAL-3296 -->Sequence position numbers in status bar not correct after editing a sequence's start position
+            <!-- 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>
+          <li>
+            <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
+            buttons in Feature Settings dialog are clicked when no
+            features are visible
+          </li>
+          <li>
+            <!-- JAL-3412 -->ID margins for CDS and Protein views not
+            equal when split frame is first opened
+          </li>
+          <li>
+            <!-- JAL-3296 -->Sequence position numbers in status bar not
+            correct after editing a sequence's start position
           </li>
           <li>
             <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
@@ -155,34 +351,45 @@ li:before {
             IllegalArgumentException in some circumstances
           </li>
           <li>
-            <!-- JAL-3534 -->Multiple feature settings dialogs can be opened for a view
+            <!-- JAL-3534 -->Multiple feature settings dialogs can be
+            opened for a view
           </li>
           <li>
-            <!-- JAL-2764 -->Feature Settings dialog is orphaned if alignment window is closed
+            <!-- JAL-2764 -->Feature Settings dialog is orphaned if
+            alignment window is closed
           </li>
           <li>
             <!-- JAL-3406 -->Credits missing some authors in Jalview
             help documentation for 2.11.0 release
           </li>
+          <li>
+            <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
+            includes Pfam ID as sequence's accession rather than its
+            Uniprot Accession
+          </li>
         </ul> <em>Java 11 Compatibility issues</em>
         <ul>
           <li>
-            <!-- JAL-2987 -->OSX - Can't view some search results in PDB/Uniprot search panel
+            <!-- JAL-2987 -->OSX - Can't view some search results in
+            PDB/Uniprot search panel
           </li>
-	</ul> <em>Installer</em>
+        </ul> <em>Installer</em>
         <ul>
-          <li><!-- JAL-3447 -->Jalview should not create file associations for 3D structure files (.pdb, .mmcif. .cif)
+          <li>
+            <!-- JAL-3447 -->Jalview should not create file associations
+            for 3D structure files (.pdb, .mmcif. .cif)
           </li>
         </ul> <em>Repository and Source Release</em>
         <ul>
           <li>
-            <!-- JAL-3474 -->removed obsolete .cvsignore files from repository
+            <!-- JAL-3474 -->removed obsolete .cvsignore files from
+            repository
           </li>
           <li>
-            <!-- JAL-3541 -->Clover report generation running out of memory
+            <!-- JAL-3541 -->Clover report generation running out of
+            memory
           </li>
-        </ul>
-        <em>New Known Issues</em>
+        </ul> <em>New Known Issues</em>
         <ul>
           <li>
             <!-- JAL-3523 -->OSX - Current working directory not
@@ -195,7 +402,12 @@ li:before {
             enabled
           </li>
           <li>
-            <!-- JAL-3542 -->Jalview Installation type always reports 'Source' in console output
+            <!-- JAL-3542 -->Jalview Installation type always reports
+            'Source' in console output
+          </li>
+          <li>
+            <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
+            bamboo server but run fine locally.
           </li>
         </ul>
       </td>