JAL-3111 JAL-3003 documentation note

[jalview.git] / help / help / html / releases.html

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 8cebf4f..8ef92b9 100755 (executable)
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -162,8 +162,8 @@ li:before {
                                                                when in wrapped mode
                                                        </li>
                                                        <li>
-                                                               <!-- JAL-3073 -->Can select columns by dragging left/right in
-                                                               annotations
+                                                               <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
+                                                               annotation
                                                        </li>
                                                        <li>
                                                                <!-- JAL-2814 -->Help button on Uniprot and PDB search panels
@@ -177,9 +177,11 @@ li:before {
                                                                popup menu
                                                        </li>
                                                        <li>
-                                                               <!-- JAL-3021 -->Sequence Details report opens positioned to top
-                                                               of report
-                                                       </li>
+                                                       <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
+                                                       <li>
+                                                       <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
+                                                       
+                                                        
                                                </ul></li>
                                        <li><strong>Java 11 Support</strong>
                                                <ul>
@@ -199,9 +201,19 @@ li:before {
             <!-- JAL-3035 -->DAS sequence retrieval and annotation
             capabilities removed from the Jalview Desktop
           </li>
+          <li>
+            <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
+            unmarshalling has been replaced by JAXB for Jalview projects
+            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> <em>Documentation</em>
+                               <ul>
+                                       <li>
+                                               <!-- JAL-3003 -->Added remarks about transparent rendering effects
+                                               not supported in EPS figure export
+                                       </li>
+                               </ul> <em>Development and Release Processes</em>
         <ul>
                                        <li>
                                                <!-- JAL-3196,JAL-3007 -->Jalview Native Application and
@@ -222,18 +234,14 @@ li:before {
                                                gradle-eclipse
                                        </li>
           <li>
-          Atlassian Bamboo continuous integration server for
+          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 (new updatable NCList
-            implementation) used for Sequence Feature collections</li>
-          <li>
-            <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
-            unmarshalling has been replaced by JAXB for Jalview projects
-            and XML based data retrieval clients</li>
+            <!-- JAL-3140 -->IntervalStoreJ (NCList
+            implementation that alows updates) used for Sequence Feature collections</li>          
         </ul>
       </td>
     <td align="left" valign="top">
@@ -277,7 +285,11 @@ li:before {
           <li>
             <!-- JAL-3178 -->Nonpositional features lose feature group
             on export as Jalview features file</li>
-          <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>
@@ -326,6 +338,8 @@ li:before {
           <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>
@@ -338,16 +352,22 @@ li:before {
             <!-- 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><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>
+            <!-- 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>
+                               </ul>
       </td>
     </tr>
     <tr>
@@ -555,7 +575,12 @@ li:before {
               <!-- JAL-2593 -->Improved performance when rendering lots
               of features (particularly when transparency is disabled)
             </li>
-          </ul>
+                                               <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>
       <td><div align="left">