Merge branch 'bug/JAL-998_wrap-sequence-tooltip' into Release_2_8_2_Branch

[jalview.git] / help / html / features / annotation.html

diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html
index 8e9bcdf..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>
@@ -46,16 +55,23 @@ menu, which is obtained by clicking anywhere on the annotation row labels
 area (below the sequence ID area).
 </p>
 <ul>
-  <li>Add New Row<br>
+  <li><strong>Add New Row</strong><br>
     <em>Adds a new, named annotation row (a dialog box will pop up for you to 
     enter the label for the new row). </em> </li>
-  <li>Hide Row<br>
+  <li><strong>Edit Label/Description</strong><br>
+    <em>This opens a dialog where you can change the name (displayed label), or the description
+    (as shown on the label tooltip) of the clicked annotation. </em> </li>
+  <li><strong>Hide This Row</strong><br>
     <em>Hides the annotation row whose label was clicked in order to bring up 
     the menu.</em> </li>
-  <li>Delete Row<br>
+  <li><strong>Hide All <em>&lt;label&gt;</em></strong><br>
+    <em>Hides all annotation rows whose label matches the one clicked. 
+    (This option is only shown for annotations that relate to individual sequences, 
+    not for whole alignment annotations. Since Jalview 2.8.2.)</em> </li>
+  <li><strong>Delete This Row</strong><br>
     <em>Deletes the annotation row whose label was clicked in order to bring up 
     the menu.</em> </li>
-  <li>Show All Hidden Rows<br>
+  <li><strong>Show All Hidden Rows</strong><br>
     <em>Shows all hidden annotation rows.</em> </li>
           <li><strong>Export Annotation</strong> <em>(Application only)</em><br>
        <em>Annotations can be saved to file or output to a text window in either the