JAL-3746 more what’s new and release notes

diff --git a/help/help/help.jhm b/help/help/help.jhm
index 4efcd8f..78eaa70 100755 (executable)
--- a/help/help/help.jhm
+++ b/help/help/help.jhm
@@ -150,6 +150,7 @@
    <mapID target="pdbfts" url="html/features/pdbsequencefetcher.html#pdbfts" />
    <mapID target="siftsmapping" url="html/features/siftsmapping.html" />
    <mapID target="pdbchooser" url="html/features/structurechooser.html" />
+   <mapID target="structuresvia3dbeacons" url="html/features/structurechooser.html#3dbeaconssearch" />   
    <mapID target="selectcolbyannot" url="html/features/columnFilterByAnnotation.html" />
    <mapID target="biojsmsa" url="html/features/biojsmsa.html" />
    

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index 9f1942c..cbef398 100755 (executable)
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -24,9 +24,10 @@
        <tocitem text="Jalview Documentation" target="home" expand="true">
                        <tocitem text="What's new" target="new" expand="true">
                                <tocitem text="Latest Release Notes" target="release"/>
-        <tocitem text="Virtual Features in CDS/Protein Views" target="splitframe.virtualfeats"/>
-                               <tocitem text="VCF Variant Attributes" target="importvcf.attribs"/>
-                               <tocitem text="Feature Filters and Attribute Colourschemes" target="features.featureschemes" />
+        <tocitem text="Support for ChimeraX" target="chimera"/>
+                               <tocitem text="Support for Pymol" target="pymol"/>
+                               <tocitem text="Structures via 3D Beacons" target="structuresvia3dbeacons" />
+                               <tocitem text="Startup Memory Settings" target="startupprefs" />
         <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
                </tocitem>
                
@@ -133,7 +134,7 @@
                        <tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
                        <tocitem text="PDB &amp; 3D-Beacons Structure Chooser" target="pdbchooser" />
                        <tocitem text="Jmol Viewer" target="pdbjmol" />
-                       <tocitem text="Chimera Viewer" target="chimera" />
+                       <tocitem text="Chimera/X Viewer" target="chimera" />
                        <tocitem text="Pymol Viewer" target="pymol" />                  
                </tocitem>
                <tocitem text="Viewing RNA structures" target="varna" expand="false"/>

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index a8d346b..3b74773 100755 (executable)
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -63,42 +63,182 @@ li:before {
       <td align="left" valign="top">
         <ul>
           <li>
+            <!-- JAL-3616 JAL-3551 JAL-2322 -->Support for viewing 3D
+            structures with ChimeraX and Pymol in addition to Jmol and
+            Chimera.
+          </li>
+          <li>
+            <!-- JAL-3503 -->New Preferences tab for adjusting Jalview's
+            memory settings at launch
+          </li>
+          <li>
+            <!-- JAL- -->
+          </li>
+          <li>
+            <!-- JAL- -->
+          </li>
+          <li>
+            <!-- JAL- -->
+          </li>
+          <li>
+            <!-- JAL- -->
+          </li>
+          <li>
             <!-- JAL- -->
           </li>
           <li>
+            <!-- JAL- -->
+          <li>
             <!-- JAL-3863 -->Support for Canonical Uniprot IDs
           </li>
+          <li>
+            <!-- JAL-3204 -->Updated Jalview bindings for Uniprot XML
+            schema
+          </li>
         </ul> <em>JalviewJS</em>
-        <ul><li><!-- 3624 -->PDB structures mapped to Uniprot Sequences with SIFTS</li>
-        <li></li> 
+        <ul>
+          <li>
+            <!-- 3624 -->PDB structures mapped to Uniprot Sequences with
+            SIFTS
+          </li>
+          <li>
+            <!-- JAL- -->
+          </li>
+          <li>
+            <!-- JAL- -->
+          </li>
+          <li>
+            <!-- JAL- -->
+          </li>
+          <li>
+            <!-- JAL-3163 -->Missing message bundle keys are only
+            reported once per key (avoids excessive log output in js
+            console)
+          </li>
+          <li>
+            <!-- JAL-3168 -->Feature type is included in the title of
+            the Feature Settings' Colour Chooser dialog
+          </li>
+          <li></li>
         </ul> <em>Development</em>
         <ul>
-          <li>Updated building instructions</li>
           <li>First integrated JalviewJS and Jalview release</li>
+          <li>Updated building instructions</li>
+          <li>
+            <!-- JAL-3679 -->Improved JalviewJS/Jalview build process
+            for system package provided eclipse installs on linux
+          </li>
+          <li>Install4j 9.0.x used for installer packaging</li>
+          <li>Notarized MacOS installer for compatibility with Big
+            Sur and Monterey</li>
+          <li>
+            <!-- JAL-3805 -->Uninstaller application for old
+            (InstallAnywhere based) Jalview installations removed from
+            the DMG
+          </li>
+          <li>
+            <!-- JAL-3930 -->Improved use of installers for unattended
+            installation with a customizedId of "JALVIEW" in install4j's
+            Jalview Launcher
+          </li>
+
         </ul>
 
       </td>
       <td>
         <ul>
+                  <li>
+            <!-- JAL-3674 -->Slow structure commands can block Jalview
+            execution
+          </li>
+        <li>
+            <!-- JAL-3904 -->Structure window's viewer-specific menu
+            disappears when only one structure is shown (and many
+            sequences:one chain mappings are present)
+          </li>
           <li>
-            <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not propagated between Linked CDS - Protein alignments and their trees (known defect from 2.11.1.3) 
+            <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
+            the first SEQUENCE_GROUP defined
+
+          </li>
+        
+          <li>
+            <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not
+            propagated between Linked CDS - Protein alignments and their
+            trees (known defect from 2.11.1.3)
           </li>
           <li>
             <!-- JAL-3761  -->Not all codon positions highlighted for
             overlapping exon splice sites (e.g due to RNA slippage)
           </li>
+                    <li>
+            <!-- JAL-3794 -->X was not being recognised as the unknown base
+            in DNA sequences
+          </li>
           <li>
             <!-- JAL-3915 -->Removed RNAview checkbox and logic from
             Structure Preferences
           </li>
-          <li><!--  JAL-3583 -->Tooltip behaviour improved (slightly)</li>
-          <li><!-- JAL-3162 -->Can edit a feature so that start &gt; end</li>
-          <li><!-- JAL-2848 -->Cancel from Amend Features doesn't reset a modified graduated colour</li>
+          <li>
+            <!--  JAL-3583 -->Tooltip behaviour improved (slightly)
+          </li>
+          <li>
+            <!-- JAL-3162 -->Can edit a feature so that start &gt; end
+          </li>
+          <li>
+            <!-- JAL-2848 -->Cancel from Amend Features doesn't reset a
+            modified graduated colour
+          </li>
+          <li>
+            <!-- JAL-3788 -->New View with automatic 'Show Overview'
+            preference enabled results in Null Pointer Exceptions when
+            clustal colouring is enabled
+          </li>
+          <li><!-- JAL-3275 -->Can open multiple Preferences panels</li>
+          <li>
+            <!-- JAL-3949 -->Standard out logging broken: messages only
+            routing to stderr and appear as a raw template
+          </li>
+        </ul> <em>JalviewJS</em>
+        <ul>
+          <li>
+            <!-- -->
+          </li>
+          <li>
+            <!-- -->
+          </li>
+          <li>
+            <!-- -->
+          </li>
+          <li>
+            <!-- -->
+          </li>
+          <li>
+            <!-- -->
+          </li>
+          <li>
+            <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
+            via Info.args when there are arguments on the URL
+          </li>
+          <li>
+            <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
+          </li>
+          <li>
+            <!-- JAL-3603 -->Annotation file fails to load from URL in
+            JalviewJS
+          </li>
         </ul> <em>Development</em>
         <ul>
-          <li>Gradle<ul><li>Fixed non-fatal gradle errors during build</li>
-          <li><!--  JAL-3745 -->Updated build.gradle for use with Gradle v.6.6+</li></ul></li>
-           
+          <li>Gradle
+            <ul>
+              <li>Fixed non-fatal gradle errors during build</li>
+              <li>
+                <!--  JAL-3745 -->Updated build.gradle for use with
+                Gradle v.6.6+
+              </li>
+            </ul>
+          </li>
+
         </ul>
       </td>
     </tr>

diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html
index 5ecf293..9ee2ab0 100755 (executable)
--- a/help/help/html/whatsNew.html
+++ b/help/help/html/whatsNew.html
@@ -38,7 +38,7 @@
   
   <ul>
     <li><strong>Linked viewing with <em>ChimeraX</em> and
-        <em>PyMol</em></strong><br />Simply configure your prefered viewer for 3D
+        <em>PyMol</em></strong><br />Simply configure your preferred viewer for 3D
       molecular data in <a href="features/preferences.html#structure">Jalview's
         structure preferences</a>, make sure that Jalview can locate the
       viewer's installation, and open a new view via the 3D Structure