Merge branch 'patch/JAL-2197_jpredforjnets' into develop

[jalview.git] / help / html / menus / alignmentMenu.html

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index c8b2270..51ad601 100755 (executable)
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -278,6 +278,12 @@
               Columns by Annotation</a></strong> <br /> <em>Select or Hide
             columns in the alignment according to secondary structure,
             labels and values shown in alignment annotation rows. </em></li>
               Columns by Annotation</a></strong> <br /> <em>Select or Hide
             columns in the alignment according to secondary structure,
             labels and values shown in alignment annotation rows. </em></li>

+        <li><strong>Select Highlighted Columns</strong> <br /> <em>Selects
+        the columns currently highlighted as a result of a find, mouse
+        over, or selection event from a linked structure viewer or other
+        application. Modifiers will work on some platforms: ALT will add
+        all but the highlighted set to the column selection, and CTRL
+        (or META) will toggle the selection. </em></li>

       </ul></li>
     <li><strong>View</strong>
       <ul>
       </ul></li>
     <li><strong>View</strong>
       <ul>

@@ -632,22 +638,22 @@
         <ul>
           <li><strong>JPred Secondary Structure Prediction</strong><br>
             <em>Secondary structure prediction by network
         <ul>
           <li><strong>JPred Secondary Structure Prediction</strong><br>
             <em>Secondary structure prediction by network

-              consensus. See the <a href="../webServices/jnet.html">Jpred3</a>
+              consensus. See the <a href="../webServices/jnet.html">Jpred</a>

               client entry for more information. The behaviour of this
               calculation depends on the current selection:
               <ul>
                 <li>If nothing is selected, and the displayed
               client entry for more information. The behaviour of this
               calculation depends on the current selection:
               <ul>
                 <li>If nothing is selected, and the displayed

-                  sequences appear to be aligned, then a JNet prediction
+                  sequences appear to be aligned, then a JPred prediction

                   will be run for the first sequence in the alignment,
                   using the current alignment. Otherwise the first
                   sequence will be submitted for prediction.</li>
                 <li>If just one sequence (or a region on one
                   sequence) has been selected, it will be submitted to
                   will be run for the first sequence in the alignment,
                   using the current alignment. Otherwise the first
                   sequence will be submitted for prediction.</li>
                 <li>If just one sequence (or a region on one
                   sequence) has been selected, it will be submitted to

-                  the automatic JNet prediction server for homolog
+                  the automatic JPred prediction server for homolog

                   detection and prediction.</li>
                 <li>If a set of sequences are selected, and they
                   appear to be aligned, then the alignment will be used
                   detection and prediction.</li>
                 <li>If a set of sequences are selected, and they
                   appear to be aligned, then the alignment will be used

-                  for a Jnet prediction on the <strong>first</strong>
+                  for a JPred prediction on the <strong>first</strong>

                   sequence in the set (that is, the one that appears
                   first in the alignment window).
                 </li>
                   sequence in the set (that is, the one that appears
                   first in the alignment window).
                 </li>