JAL-1517 JAL-1587 JAL-674 secondary structure and annotation from prediction services...

diff --git a/help/help.jhm b/help/help.jhm
index c6cc626..b6b0063 100755 (executable)
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -39,6 +39,7 @@
    <mapID target="disorder" url="html/webServices/proteinDisorder.html"/>
    <mapID target="aacon" url="html/webServices/AACon.html"/>
    <mapID target="rnaalifold" url="html/webServices/RNAalifold.html"/>
+   <mapID target="seqannots" url="html/features/annotation.html#seqannots"/>
    <mapID target="seqfetch" url="html/features/seqfetch.html"/>
    <mapID target="dbreffetcher" url="html/webServices/dbreffetcher.html"/>
    <mapID target="seqmappings" url="html/features/seqmappings.html"/>
@@ -54,6 +55,7 @@
    <mapID target="pdbjmol" url="html/features/jmol.html"/>
    <mapID target="chimera" url="html/features/chimera.html"/>
    <mapID target="varna" url="html/features/varna.html"/>
+   <mapID target="xsspannotation" url="html/features/xsspannotation.html"/>
    <mapID target="preferences" url="html/features/preferences.html"/>     
    <mapID target="commandline" url="html/features/commandline.html"/>
    <mapID target="clarguments" url="html/features/clarguments.html"/>

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 6ae5c78..1d45e7a 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -97,6 +97,9 @@
                <tocitem text="Pairwise Alignments" target="pairwise"/>
                <tocitem text="Remove Redundancy" target="redundancy"/>
        </tocitem>
+       <tocitem text="Sequence Annotations" target="seqannots" expand="true">
+               <tocitem text="Annotation from Structure" target="xsspannotation" expand="false"/>
+       </tocitem>
        <tocitem text="Alignment Annotations" target ="alannotation" expand="false">
           <tocitem text="Conservation" target="calcs.alconserv"/>          
           <tocitem text="Quality" target="calcs.alquality"/>

diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html
index 49128c2..a036bd5 100755 (executable)
--- a/help/html/features/annotation.html
+++ b/help/html/features/annotation.html
@@ -39,6 +39,15 @@ and symbolic annotations can be added to an alignment via an <a
 href="annotationsFormat.html">Annotations File</a> dragged into the
 alignment window or loaded from the alignment's file menu.
 </p>
+<p><a name="seqannots"/><strong>Sequence Reference Annotation</strong>
+</p>
+<p>
+               Sequence reference annotation is created from 3D structure
+               data, and from the results of sequence based prediction of
+               <a href="../webServices/jnet.html">secondary structure</a> and <a
+                       href="../webServices/proteinDisorder.html">disordered region</a>
+               prediction methods. 
+</p>
 <p><strong>Interactive Alignment Annotation</strong></p>
 <p>
 Annotation rows are added using the <strong>Annotation Label</strong>

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 511b85f..63bb815 100755 (executable)
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -41,7 +41,7 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
       <li><strong>Hide Annotations...<br>
           </strong><em>Choose to hide either All or 
           a selected type of annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
-      <li><strong>Add Reference Annotations...<br>
+      <li><a name="addrefannot"><strong>Add Reference Annotations<br>
           </strong><em>Add to the alignment window any annotations on the selected sequences
           which have been read from reference sources or calculated (for example, 
           secondary structure derived from 3D structure). (Since Jalview 2.8.2)</em></li>
@@ -134,7 +134,7 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
         window will be displayed asking for a new sequence name and sequence description 
         to be entered. Press OK to accept your edit. To save sequence descriptions, 
         you must save in Fasta, PIR or Jalview File format.</em></li>
-      <li><em> </em></li>
+      <li><a href="sqaddrefannot"><strong>Add Reference Annotations<br></strong><em>When enabled, copies any available alignment annotation for this sequence to the current view.</em></li>
       <li><strong>Represent Group With (Sequence Id)</strong><br>
         <em>All sequences in the current selection group will be hidden, apart 
         from (Sequence Id). Any edits performed on the visible representative 

diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html
index 9a7acd9..5555c73 100755 (executable)
--- a/help/html/webServices/jnet.html
+++ b/help/html/webServices/jnet.html
@@ -110,10 +110,11 @@ The annotation bars below the alignment are as follows:
        invoked to rationalise significantly different primary predictions.</em></li>
 </ul>
 </p>
+<em>JNet annotation created in Jalview 2.8.2 and later versions can be displayed on other alignments via the <a href="">Add reference annotation</a></em>
 <em>As of Jalview 2.6, the Jnet service accessed accessed via the
 'Secondary structure prediction' submenu should be considered a legacy
 Jalview SOAP service, and will be replaced in the near future by a
-JABAWS Jnet service.</em>
+JABAWS Jnet service (now available in the Jalview 2.9 development version).</em>
 
 </body>
 </html>