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 5739797..51ad601 100755 (executable)
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -133,10 +133,9 @@
         </em></li>
         <li><strong>Load Features / Annotations<br>
         </strong><em>Load files describing precalculated <a
         </em></li>
         <li><strong>Load Features / Annotations<br>
         </strong><em>Load files describing precalculated <a

-            href="../features/featuresFormat.html"
-          >sequence features</a> or <a
-            href="../features/annotationsFormat.html"
-          >alignment annotations</a>.
+            href="../features/featuresFormat.html">sequence
+              features</a> or <a href="../features/annotationsFormat.html">alignment
+              annotations</a>.

         </em></li>
         <li><strong>Close (Control W)</strong><br> <em>Close
             the alignment window. Make sure you have saved your
         </em></li>
         <li><strong>Close (Control W)</strong><br> <em>Close
             the alignment window. Make sure you have saved your

@@ -204,16 +203,14 @@
         </strong><em>All columns which only contain gap characters
             (&quot;-&quot;, &quot;.&quot;) will be deleted.<br> You
             may set the default gap character in <a
         </strong><em>All columns which only contain gap characters
             (&quot;-&quot;, &quot;.&quot;) will be deleted.<br> You
             may set the default gap character in <a

-            href="../features/preferences.html"
-          >preferences</a>.
+            href="../features/preferences.html">preferences</a>.

         </em></li>
         <li><strong>Remove All Gaps (Control Shift E)</strong><br>
           <em>Gap characters (&quot;-&quot;, &quot;.&quot;) will be
             deleted from the selected area of the alignment. If no
             selection is made, ALL the gaps in the alignment will be
             removed.<br> You may set the default gap character in <a
         </em></li>
         <li><strong>Remove All Gaps (Control Shift E)</strong><br>
           <em>Gap characters (&quot;-&quot;, &quot;.&quot;) will be
             deleted from the selected area of the alignment. If no
             selection is made, ALL the gaps in the alignment will be
             removed.<br> You may set the default gap character in <a

-            href="../features/preferences.html"
-          >preferences</a>.
+            href="../features/preferences.html">preferences</a>.

         </em></li>
         <li><strong>Remove Redundancy (Control D)<br>
         </strong><em>Selecting this option brings up a window asking you to
         </em></li>
         <li><strong>Remove Redundancy (Control D)<br>
         </strong><em>Selecting this option brings up a window asking you to

@@ -233,8 +230,7 @@
             with alignment analysis programs which require 'properly
             aligned sequences' to be all the same length.<br> You
             may set the default for <strong>Pad Gaps</strong> in the <a
             with alignment analysis programs which require 'properly
             aligned sequences' to be all the same length.<br> You
             may set the default for <strong>Pad Gaps</strong> in the <a

-            href="../features/preferences.html"
-          >preferences</a>.
+            href="../features/preferences.html">preferences</a>.

         </em></li>
       </ul></li>
     <li><strong>Select</strong>
         </em></li>
       </ul></li>
     <li><strong>Select</strong>

@@ -278,11 +274,16 @@
             <strong>WARNING</strong>: This cannot be undone.
         </em></li>
         <li><strong><a
             <strong>WARNING</strong>: This cannot be undone.
         </em></li>
         <li><strong><a

-            href="../features/columnFilterByAnnotation.html"
-          >Select/Hide 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>
+            href="../features/columnFilterByAnnotation.html">Select/Hide
+              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>

@@ -310,11 +311,11 @@
         <li><strong>Show Sequence Features</strong><br> <em>Show
             or hide sequence features on this alignment.</em></li>
         <li><strong><a
         <li><strong>Show Sequence Features</strong><br> <em>Show
             or hide sequence features on this alignment.</em></li>
         <li><strong><a

-            href="../features/featuresettings.html"
-          >Sequence Feature Settings...</a> </strong><em><br> <em>Opens
-              the Sequence Feature Settings dialog box to control the
-              colour and display of sequence features on the alignment,
-              and configure and retrieve features from DAS annotation
+            href="../features/featuresettings.html">Sequence
+              Feature Settings...</a> </strong><em><br> <em>Opens the
+              Sequence Feature Settings dialog box to control the colour
+              and display of sequence features on the alignment, and
+              configure and retrieve features from DAS annotation

               servers.</em></li>
         <li><strong>Sequence ID Tooltip</strong><em>
             (application only) <br>This submenu's options allow the
               servers.</em></li>
         <li><strong>Sequence ID Tooltip</strong><em>
             (application only) <br>This submenu's options allow the

@@ -403,22 +404,21 @@
             rendering. </em></li>
         <li><strong>Wrap<br>
         </strong><em>When ticked, the alignment display is &quot;<a
             rendering. </em></li>
         <li><strong>Wrap<br>
         </strong><em>When ticked, the alignment display is &quot;<a

-            href="../features/wrap.html"
-          >wrapped</a>&quot; to the width of the alignment window. This is
-            useful if your alignment has only a few sequences to view
-            its full width at once.
+            href="../features/wrap.html">wrapped</a>&quot; to
+            the width of the alignment window. This is useful if your
+            alignment has only a few sequences to view its full width at
+            once.

         </em><br> Additional options for display of sequence numbering
           and scales are also visible in wrapped layout mode:<br>
           <ul>
         </em><br> Additional options for display of sequence numbering
           and scales are also visible in wrapped layout mode:<br>
           <ul>

-            <li><strong>Scale Above</strong><br>
-            <em> Show the alignment column position scale.</em></li>
-            <li><strong>Scale Left</strong><br>
-            <em> Show the sequence position for the first aligned
-                residue in each row in the left column of the alignment.</em></li>
-            <li><strong>Scale Right</strong><br>
-            <em> Show the sequence position for the last aligned
-                residue in each row in the right-most column of the
-                alignment.</em></li>
+            <li><strong>Scale Above</strong><br> <em>
+                Show the alignment column position scale.</em></li>
+            <li><strong>Scale Left</strong><br> <em> Show
+                the sequence position for the first aligned residue in
+                each row in the left column of the alignment.</em></li>
+            <li><strong>Scale Right</strong><br> <em>
+                Show the sequence position for the last aligned residue
+                in each row in the right-most column of the alignment.</em></li>

             <li><strong>Show Sequence Limits<br>
             </strong><em>If this box is selected the sequence name will have
                 the start and end position of the sequence appended to
             <li><strong>Show Sequence Limits<br>
             </strong><em>If this box is selected the sequence name will have
                 the start and end position of the sequence appended to

@@ -474,11 +474,10 @@
           colour will be applied to all currently defined groups.<br>
       </em></li>
       <li><strong><a
           colour will be applied to all currently defined groups.<br>
       </em></li>
       <li><strong><a

-          href="../colourSchemes/textcolour.html"
-        >Colour Text...</a> </strong><em><br> Opens the Colour Text
-          dialog box to set a different text colour for light and dark
-          background, and the intensity threshold for transition between
-          them. </em></li>
+          href="../colourSchemes/textcolour.html">Colour
+            Text...</a> </strong><em><br> Opens the Colour Text dialog box
+          to set a different text colour for light and dark background,
+          and the intensity threshold for transition between them. </em></li>

       <li>Colour Scheme options: <strong>None, ClustalX,
           Blosum62 Score, Percentage Identity, Zappo, Taylor,
           Hydrophobicity, Helix Propensity, Strand Propensity, Turn
       <li>Colour Scheme options: <strong>None, ClustalX,
           Blosum62 Score, Percentage Identity, Zappo, Taylor,
           Hydrophobicity, Helix Propensity, Strand Propensity, Turn

@@ -507,8 +506,8 @@
       <li><strong>By Annotation</strong><br> <em>Colours
           the alignment on a per-column value from a specified
           annotation. See <a
       <li><strong>By Annotation</strong><br> <em>Colours
           the alignment on a per-column value from a specified
           annotation. See <a

-          href="../colourSchemes/annotationColouring.html"
-        >Annotation Colouring</a>.
+          href="../colourSchemes/annotationColouring.html">Annotation
+            Colouring</a>.

       </em><br></li>
       <li><strong>By RNA Helices</strong><br> <em>Colours
           the helices of an RNA alignment loaded from a Stockholm file.
       </em><br></li>
       <li><strong>By RNA Helices</strong><br> <em>Colours
           the helices of an RNA alignment loaded from a Stockholm file.

@@ -563,14 +562,14 @@
           provided in this menu.</strong></li>
       <li><strong>Pairwise Alignments</strong><br> <em>Applies
           Smith and Waterman algorithm to selected sequences. See <a
           provided in this menu.</strong></li>
       <li><strong>Pairwise Alignments</strong><br> <em>Applies
           Smith and Waterman algorithm to selected sequences. See <a

-          href="../calculations/pairwise.html"
-        >pairwise alignments</a>.
+          href="../calculations/pairwise.html">pairwise
+            alignments</a>.

       </em><br></li>
       <li><strong>Principal Component Analysis</strong><br> <em>Shows
           a spatial clustering of the sequences based on similarity
           scores calculated with the alignment. See <a
       </em><br></li>
       <li><strong>Principal Component Analysis</strong><br> <em>Shows
           a spatial clustering of the sequences based on similarity
           scores calculated with the alignment. See <a

-          href="../calculations/pca.html"
-        >Principal Component Analysis</a>.
+          href="../calculations/pca.html">Principal
+            Component Analysis</a>.

       </em> <br></li>
       <li><strong>Extract Scores ... (optional)</strong><br> <em>This
           option is only visible if Jalview detects one or more
       </em> <br></li>
       <li><strong>Extract Scores ... (optional)</strong><br> <em>This
           option is only visible if Jalview detects one or more

@@ -626,36 +625,35 @@
       or elsewhere. You need a continuous network connection in order to
       use these services through Jalview.</p>
     <ul>
       or elsewhere. You need a continuous network connection in order to
       use these services through Jalview.</p>
     <ul>

-      <li><strong>Alignment</strong><br />
-      <em> Align the currently selected sequences or all sequences
-          in the alignment, or re-align unaligned sequences to the
-          aligned sequences. Entries in this menu provide access to the
-          various alignment programs supported by <a
-          href="../webServices/JABAWS.html"
-        >JABAWS</a>. See the <a href="../webServices/msaclient.html">Multiple
-            Sequence Alignment webservice client</a> entry for more
-          information.
+      <li><strong>Alignment</strong><br /> <em> Align the
+          currently selected sequences or all sequences in the
+          alignment, or re-align unaligned sequences to the aligned
+          sequences. Entries in this menu provide access to the various
+          alignment programs supported by <a
+          href="../webServices/JABAWS.html">JABAWS</a>. See the
+          <a href="../webServices/msaclient.html">Multiple Sequence
+            Alignment webservice client</a> entry for more information.

       </em></li>
       <li><strong>Secondary Structure Prediction</strong>
         <ul>
           <li><strong>JPred Secondary Structure Prediction</strong><br>
             <em>Secondary structure prediction by network
       </em></li>
       <li><strong>Secondary Structure Prediction</strong>
         <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>

@@ -667,8 +665,8 @@
           <li><strong>Multi-Harmony</strong><br> <em>Performs
               functional residue analysis on a protein family alignment
               with sub-families defined on it. See the <a
           <li><strong>Multi-Harmony</strong><br> <em>Performs
               functional residue analysis on a protein family alignment
               with sub-families defined on it. See the <a

-              href="../webServices/shmr.html"
-            >Multi-Harmony service</a> entry for more information.
+              href="../webServices/shmr.html">Multi-Harmony
+                service</a> entry for more information.

           </em></li>
         </ul></li>
     </ul></li>
           </em></li>
         </ul></li>
     </ul></li>