X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=cc30e05f9b25f621854246f3fab0cfe8584bd041;hb=c9769b2d6a5be219683270e630eb045b8cfe897e;hp=f506be3bdf57e7783546343e02459d26f6dda115;hpb=8a50c3eee6424eba07bc16daf2ff3823fa0f405f;p=jalview.git

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index f506be3..cc30e05 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -57,13 +57,38 @@ li:before {
     </tr>
     <tr>
       <td width="60" align="center" nowrap>
-          <strong><a name="Jalview.2.11">2.11</a><br />
-            <em>20/06/2019</em></strong>
+          <strong><a name="Jalview.2.11.0">2.11.0</a><br />
+            <em>02/07/2019</em></strong>
       </td>
       <td align="left" valign="top">
         <ul>
           <li>
+            <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
+            Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
+            source project) rather than InstallAnywhere
+          </li>
+          <li>
+            <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
+            settings, receive over the air updates and launch specific
+            versions via (<a href="https://github.com/threerings/getdown">Three
+              Rings' GetDown</a>)
+          </li>
+					<li>
+						<!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
+						formats supported by jalview (including .jvp project files)
+					</li>
+					<li>
+						<!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
+						arguments and switch between different getdown channels
+					</li>
+					<li>
+						<!-- JAL-3141 -->Backup files created when saving Jalview project
+						or alignment files
+					</li>
+
+					<li>
             <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
+            <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li> 
           <li>
             <!-- JAL-2620 -->Alternative genetic code tables for
             'Translate as cDNA'</li>
@@ -71,6 +96,10 @@ li:before {
             <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
 					<li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
 						<ul>
+						          <li>
+            <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
+            implementation that allows updates) used for Sequence Feature collections</li>
+          <li>
 							<li>
 								<!-- JAL-2808,JAL-2069 -->Sequence features can be filtered and
 								shaded according to any associated attributes (e.g. variant
@@ -78,6 +107,10 @@ li:before {
 								column 9 of GFF file)
 							</li>
 							<li>
+								<!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
+								recognise variant features
+							</li>
+							<li>
 								<!-- JAL-2897 -->Show synonymous codon variants on peptide
 								sequences
 							</li>
@@ -86,7 +119,7 @@ li:before {
 								details
 							</li>
 							<li>
-								<!-- JAL-3139,JAL-2816 -->More efficient sequence feature render
+								<!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
 								algorithm (Z-sort/transparency and filter aware)
 							</li>
 							<li>
@@ -96,23 +129,23 @@ li:before {
 						</ul>
 					</li>
 					<li>
-            <!-- JAL-3141 -->Backup files created when saving Jalview project
-            or alignment files
-          </li>
-          <li><strong>Principal Components Analysis Viewer</strong>
+						<!-- JAL-3205 -->Symmetric score matrices for faster
+						tree and PCA calculations
+					</li>
+					<li><strong>Principal Components Analysis Viewer</strong>
             <ul>
 							<li>
 								<!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
 								and Viewer state saved in Jalview Project
 							</li>
-							<li>'Change parameters' option removed from viewer's
+							<li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
 								drop-down menus</li>
 							<li>
 								<!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
 								incrementally
 							</li>
 							<li>
-								<!-- JAL-2965 -->PCA plot is depth cued
+								<!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
 							</li>
 						</ul>
 					</li>
@@ -122,7 +155,7 @@ li:before {
 					<li><strong>Speed and Efficiency</strong>
 					<ul>
 							<li>
-								<!-- JAL-3198 -->More efficient creation of selections and
+								<!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
 								multiple groups when working with large alignments
 							</li>
 							<li>
@@ -137,7 +170,7 @@ li:before {
 								view
 							</li>
 							<li>
-								<!-- JAL-2527 -->Alignment Overview now WYSIWIS (What you see is
+								<!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
 								what is shown)<br />Only visible region of alignment is shown by
 								default (can be changed in user preferences)
 							</li>
@@ -183,13 +216,10 @@ li:before {
 							
 							 
 						</ul></li>
-					<li><strong>Java 11 Support</strong>
+						<li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li> 
+					<li><strong>Java 11 Support (not yet on general release)</strong>
 						<ul>
 							<li>
-								<!-- JAL- -->Java 11 Native Desktop installer, standalone JAR
-								and getdown release channels
-							</li>
-							<li>
 								<!--  -->OSX GUI integrations for App menu's 'About' entry and
 								trapping CMD-Q
 							</li>
@@ -207,158 +237,267 @@ li:before {
             and XML based data retrieval clients</li>
           <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li> 
           <li><!--  -->Jalview Desktop no longer distributed via Java Web Start</li>
-        </ul>
-        <em>Development and Release Processes</em>
-        <ul>
-					<li>
-						<!-- JAL-3196,JAL-3007 -->Jalview Native Application and
-						Installers built with Install4j (licensed to the Jalview open
-						source project) rather than InstallAnywhere
-					</li>
+        </ul> <em>Documentation</em>
+				<ul>
 					<li>
-						<!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
-						settings, receive over the air updates and launch specific
-						versions via (<a href="https://github.com/threerings/getdown">Three
-							Rings' GetDown</a>)
+						<!-- JAL-3003 -->Added remarks about transparent rendering effects
+						not supported in EPS figure export
 					</li>
-					<li>
-						<!-- JAL-3196,JAL-3179 -->Build system migrated from Ant to Gradle
+					<li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
+				</ul> <em>Development and Release Processes</em>
+        <ul>
+        	<li>
+						<!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
 					</li>
+					<li><!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
 					<li>
 						<!-- JAL-3225 -->Eclipse project configuration managed with
 						gradle-eclipse
 					</li>
-          <li>
+          <li><!-- JAL-3174,JAL-2886,JAL-2729 -->
           Atlassian Bamboo continuous integration for
             unattended Test Suite execution</li>
           <li>
             <!-- JAL-2864 -->Memory test suite to detect leaks in common
             operations</li>
-          <li>
-            <!-- JAL-3140 -->IntervalStoreJ (NCList
-            implementation that alows updates) used for Sequence Feature collections</li>          
+          <li><!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor issues resolved.</li>
+          <li><!-- JAL-3248 -->Developer documentation migrated to markdown (with HTML rendering)</li>          
         </ul>
       </td>
-    <td align="left" valign="top">
-        <ul>
-          <li>
-            <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl</li>
-          <li>
-            <!-- JAL-3244 -->'View [Structure] Mappings' and structure superposition in Jmol fail on Windows</li>
-          <li>
-            <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with monospaced font</li>
-          <li>
-            <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
-            Jalview project involving multiple views</li>
-          <li>
-            <!-- JAL-3164 -->Overview for complementary view in a linked
-            CDS/Protein alignment is not updated when Hide Columns by
-            Annotation dialog hides columns</li>
-          <li>
-            <!-- JAL-3158 -->Selection highlighting in the complement of
-            a CDS/Protein alignment stops working after making a
-            selection in one view, then making another selection in the
-            other view</li>
-          <li>
-            <!-- JAL-3161 -->Annotations tooltip changes beyond visible columns</li>
-          <li>
-            <!-- JAL-3154 -->Table Columns could be re-ordered in
-            Feature Settings and Jalview Preferences panels</li>
-          <li>
-            <!-- JAL-2865 -->Jalview hangs when closing windows
-            or the overview updates with large alignments</li>
-          <li>
-            <!-- JAL-2750 -->Tree and PCA calculation fails for selected
-            region if columns were selected by dragging right-to-left
-            and the mouse moved to the left of the first column</li>
-            <li>
-            <!-- JAL-3218 -->Couldn't hide selected columns adjacent 
-            to a hidden column marker via scale popup menu</li>
-          <li>
-            <!-- JAL-2846 -->Error message for trying to load in invalid
-            URLs doesn't tell users the invalid URL</li>
+			<td align="left" valign="top">
+				<ul>
+					<li>
+						<!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
+					</li>
+					<li>
+						<!-- JAL-3244 -->'View [Structure] Mappings' and structure
+						superposition in Jmol fail on Windows
+					</li>
+					<li>
+						<!-- JAL-3286 -->Blank error dialog is displayed when discovering
+						structures for sequences with lots of PDB structures
+					</li>
+					<li>
+						<!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
+						monospaced font
+					</li>
+					<li>
+						<!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
+						project involving multiple views
+					</li>
+					<li>
+						<!-- JAL-3164 -->Overview for complementary view in a linked
+						CDS/Protein alignment is not updated when Hide Columns by
+						Annotation dialog hides columns
+					</li>
+					<li>
+						<!-- JAL-3158 -->Selection highlighting in the complement of a
+						CDS/Protein alignment stops working after making a selection in
+						one view, then making another selection in the other view
+					</li>
+					<li>
+						<!-- JAL-3161 -->Annotations tooltip changes beyond visible
+						columns
+					</li>
+					<li>
+						<!-- JAL-3154 -->Table Columns could be re-ordered in Feature
+						Settings and Jalview Preferences panels
+					</li>
+					<li>
+						<!-- JAL-2865 -->Jalview hangs when closing windows or the
+						overview updates with large alignments
+					</li>
+					<li>
+						<!-- JAL-2750 -->Tree and PCA calculation fails for selected
+						region if columns were selected by dragging right-to-left and the
+						mouse moved to the left of the first column
+					</li>
+					<li>
+						<!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
+						hidden column marker via scale popup menu
+					</li>
+					<li>
+						<!-- JAL-2846 -->Error message for trying to load in invalid URLs
+						doesn't tell users the invalid URL
+					</li>
+					<li>
+						<!-- JAL-3178 -->Nonpositional features lose feature group on
+						export as Jalview features file
+					</li>
+					<li>
+						<!-- JAL-2816 -->Tooltips displayed for features filtered by
+						score from view
+					</li>
+					<li>
+						<!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
+						show cross references or Fetch Database References are shown in
+						red in original view
+					</li>
           <li>
-            <!-- JAL-3178 -->Nonpositional features lose feature group
-            on export as Jalview features file</li>
+            <!-- JAL-2898 -->stop_gained variants not shown correctly on
+            peptide sequence
+          </li>
 					<li>
 						<!-- JAL-2060 -->'Graduated colour' option not offered for
 						manually created features (where if feature score is Float.NaN)
 					</li>
 					<li>
-            <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or 
-            printed when columns are hidden</li>
-          <li>
-            <!-- JAL-3082 -->Regular expression error for '(' in Select Columns by Annotation description</li>
-          <li>
-            <!-- JAL-3072 -->Scroll doesn't stop on mouse up after 
-            dragging out of Scale or Annotation Panel</li>
-          <li>
-            <!-- JAL-3075 -->Column selection incorrect after scrolling out of scale panel</li>
-          <li>
-            <!-- JAL-3074 -->Left/right drag in annotation can scroll alignment down</li>
-          <li>
-            <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in scale panel</li>
-          <li>
-            <!-- JAL-3002 -->Column display is out by one after Page Down, Page Up in wrapped mode</li>
-          <li>
-            <!-- JAL-2839 -->Finder doesn't skip hidden regions</li>
-          <li>
-            <!-- JAL-2932 -->Finder searches in minimised alignments</li>
-          <li>
-            <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected on
-            opening an alignment</li>
-          <li>
-            <!-- JAL-3180 -->'Colour by Annotation' not marked selected in Colour menu</li>
-          <li>
-            <!-- JAL-3201 -->Per-group Clustal colour scheme changes when 
-            different groups in the alignment are selected</li>
-          <li>
-            <!-- JAL-2717 -->Internationalised colour scheme names not shown correctly in menu</li>
-          <li>
-            <!-- JAL-3206 -->Colour by Annotation can go black at min/max threshold limit</li>
-          <li>
-            <!-- JAL-3125 -->Value input for graduated feature colour threshold gets 'unrounded'</li>
-          <li>
-            <!-- JAL-2982 -->PCA image export doesn't respect background colour</li>
-          <li>
-            <!-- JAL-2963 -->PCA points don't dim when rotated about y axis</li>
-          <li>
-            <!-- JAL-2959 -->PCA Print dialog continues after Cancel</li>
-          <li>
-            <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not Tree font</li>
-          <li>
-            <!-- JAL-2964 -->Associate Tree with All Views not restored from project file</li>
-          <li>
-            <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview shown in complementary view</li>
-          <li>
-            <!-- JAL-2898 -->stop_gained variants not shown correctly on peptide sequence</li>
-          <li>
-            <!-- JAL-3021 -->Sequence Details report opens positioned to top of report</li>
-          <li>
-            <!-- JAL-914 -->Help page can be opened twice</li>
-        </ul>
-        <em>Editing</em>
-        <ul>
-          <li>
-            <!-- JAL-2822 -->Start and End should be updated when
-            sequence data at beginning or end of alignment added/removed
-            via 'Edit' sequence</li>
-          <li>
-            <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
-            sequence features correctly when start of sequence is
-            removed (Known defect since 2.10)</li>
-        </ul>
-        <em>New Known Defects</em>
-        <ul>
-          <li>
-            <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project</li> 
-          <li>
-            <!-- JAL-3213 -->Alignment panel height can be too small after 'New View'</li> 
-          <li>
-            <!-- JAL-3240 -->Display is incorrect after removing gapped columns within hidden columns</li> 
-        </ul>
-      </td>
-    </tr>
+						<!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
+						when columns are hidden
+					</li>
+					<li>
+						<!-- JAL-3082 -->Regular expression error for '(' in Select
+						Columns by Annotation description
+					</li>
+					<li>
+						<!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
+						out of Scale or Annotation Panel
+					</li>
+					<li>
+						<!-- JAL-3075 -->Column selection incorrect after scrolling out of
+						scale panel
+					</li>
+					<li>
+						<!-- JAL-3074 -->Left/right drag in annotation can scroll
+						alignment down
+					</li>
+					<li>
+						<!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
+						scale panel
+					</li>
+					<li>
+						<!-- JAL-3002 -->Column display is out by one after Page Down,
+						Page Up in wrapped mode
+					</li>
+					<li>
+						<!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
+					</li>
+					<li>
+						<!-- JAL-2932 -->Finder searches in minimised alignments
+					</li>
+					<li>
+						<!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
+						on opening an alignment
+					</li>
+					<li>
+						<!-- JAL-3180 -->'Colour by Annotation' not marked selected in
+						Colour menu
+					</li>
+					<li>
+						<!-- JAL-3201 -->Per-group Clustal colour scheme changes when
+						different groups in the alignment are selected
+					</li>
+					<li>
+						<!-- JAL-2717 -->Internationalised colour scheme names not shown
+						correctly in menu
+					</li>
+					<li>
+						<!-- JAL-3206 -->Colour by Annotation can go black at min/max
+						threshold limit
+					</li>
+					<li>
+						<!-- JAL-3125 -->Value input for graduated feature colour
+						threshold gets 'unrounded'
+					</li>
+					<li>
+						<!-- JAL-2982 -->PCA image export doesn't respect background
+						colour
+					</li>
+					<li>
+						<!-- JAL-2963 -->PCA points don't dim when rotated about y axis
+					</li>
+					<li>
+						<!-- JAL-2959 -->PCA Print dialog continues after Cancel
+					</li>
+					<li>
+						<!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
+						Tree font
+					</li>
+					<li>
+						<!-- JAL-2964 -->Associate Tree with All Views not restored from
+						project file
+					</li>
+					<li>
+						<!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
+						shown in complementary view
+					</li>
+					<li>
+						<!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
+						without normalisation
+					</li>
+					<li>
+						<!-- JAL-3021 -->Sequence Details report opens positioned to top
+						of report
+					</li>
+					<li>
+						<!-- JAL-914 -->Help page can be opened twice
+					</li>
+				</ul> <em>Editing</em>
+				<ul>
+					<li>
+						<!-- JAL-2822 -->Start and End should be updated when sequence
+						data at beginning or end of alignment added/removed via 'Edit'
+						sequence
+					</li>
+					<li>
+						<!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
+						relocate sequence features correctly when start of sequence is
+						removed (Known defect since 2.10)
+					</li>
+					<li>
+						<!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
+						dialog corrupts dataset sequence
+					</li>
+					<li>
+						<!-- JAL-868 -->Structure colours not updated when associated tree
+						repartitions the alignment view (Regression in 2.10.5)
+					</li>
+				</ul>
+				<em>Datamodel</em>
+				<ul>
+					<li>
+						<!-- JAL-2986 -->Sequence.findIndex returns wrong value when
+						sequence's End is greater than its length
+					</li>
+				</ul> <em>New Known Defects</em>
+				<ul>
+					<li>
+						<!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
+						regions of protein alignment.
+					</li>
+					<li>
+						<!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
+						is restored from a Jalview 2.11 project
+					</li>
+					<li>
+						<!-- JAL-3213 -->Alignment panel height can be too small after
+						'New View'
+					</li>
+					<li>
+						<!-- JAL-3240 -->Display is incorrect after removing gapped
+						columns within hidden columns
+					</li>
+					<li>
+						<!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
+						window after dragging left to select columns to left of visible
+						region
+					</li>
+					<li>
+						<!-- JAL-2876 -->Features coloured according to their description
+						string and thresholded by score in earlier versions of Jalview are
+						not shown as thresholded features in 2.11. To workaround please
+						create a Score filter instead.
+					</li>
+					 <li><strong>Java 11 Specific defects</strong>
+            <ul>
+              <li>
+              <!-- JAL-3235 -->Jalview Properties file is not sorted alphabetically when saved</li>
+              
+            </ul></li>
+					
+				</ul>
+			</td>
+		</tr>
     <tr>
     <td width="60" nowrap>
       <div align="center">
@@ -531,6 +670,10 @@ li:before {
                 open URL in the browser can be dropped onto Jalview.</em>
             </li>
           </ul>
+          <em>New Known Defects</em>
+          <ul>
+            <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
+          </ul>
         </div></td>
     </tr>
     <tr>
@@ -564,6 +707,11 @@ li:before {
               <!-- JAL-2593 -->Improved performance when rendering lots
               of features (particularly when transparency is disabled)
             </li>
+            <li>
+              <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
+              exchange of Jalview features and Chimera attributes made
+              generally available
+            </li>
           </ul>
           </div>
       </td>
@@ -685,7 +833,11 @@ li:before {
               Sequences' enabled) or Ensembl isoforms (Workaround in
               2.10.4 is to fail back to N&amp;W mapping)
             </li>
-          </ul>
+						<li>
+							<!-- JAL-2990 -->Export Annotations from File Menu with CSV
+							option gives blank output
+						</li>
+					</ul>
         </div>
           </td>
     </tr>
@@ -1437,6 +1589,15 @@ li:before {
               <!-- JAL-2589 -->User defined gap colour not shown in
               overview when features overlaid on alignment
             </li>
+            <li>
+              <!-- JAL-2567 -->Feature settings for different views not
+              recovered correctly from Jalview project file
+            </li>
+            <li>
+              <!-- JAL-2256 -->Feature colours in overview when first opened
+              (automatically via preferences) are different to the main
+              alignment panel
+            </li>
           </ul>
           <em>Data import/export</em>
           <ul>