X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=f3ab75dfbbc55786166c79c35ee50254ede337c9;hb=d5888333a51923fe86a35262e11be07c22e2798b;hp=37c8b19085863864830dd9532c35b7f28913e0be;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index 37c8b19..f3ab75d 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -33,7 +33,7 @@
       <ul>
         <li><strong>Fetch Sequence</strong><br> <em>Shows
             a dialog window in which you can retrieve known ids from
-            Uniprot, EMBL, EMBLCDS, PFAM, Rfam, or PDB database using
+            UniProt, EMBL, EMBLCDS, PFAM, Rfam, or PDB database using
             Web Services provided by the European Bioinformatics
             Institute. See <a href="../features/seqfetch.html">Sequence
               Fetcher</a>
@@ -133,10 +133,9 @@
         </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
@@ -196,7 +195,7 @@
             &quot;Deselect All&quot; to deselect all columns.</em></li>
         <li><strong>Remove Right (Control R)<br>
         </strong><em>If the alignment has marked columns, the alignment will
-            be trimmed to the left of the leftmost marked column. To
+            be trimmed to the right of the rightmost marked column. To
             mark a column, mouse click the scale bar above the
             alignment. Click again to unmark a column, or select
             &quot;Deselect All&quot; to deselect all columns.</em></li>
@@ -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
-            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
-            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
@@ -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
-            href="../features/preferences.html"
-          >preferences</a>.
+            href="../features/preferences.html">preferences</a>.
         </em></li>
       </ul></li>
     <li><strong>Select</strong>
@@ -248,7 +244,7 @@
         </strong><em>Selects all the sequences and residues in the
             alignment. <br> Use &lt;CTRL&gt; and A (&lt;APPLE&gt;
             and A on a MacOSX) to select all.
-        </em></em></li>
+        </em></li>
         <li><strong>Deselect All (Escape)<br>
         </strong><em>Removes the current selection box (red dashed box) from
             the alignment window. All selected sequences, residues and
@@ -278,11 +274,16 @@
             <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>
@@ -310,12 +311,10 @@
         <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
-              servers.</em></li>
+            href="../features/featuresettings.html">Sequence
+              Feature Settings...</a> </strong><br> <em>Opens the
+              Sequence Feature Settings dialog box to control the colour
+              and display of sequence features on the alignment.</em></li>
         <li><strong>Sequence ID Tooltip</strong><em>
             (application only) <br>This submenu's options allow the
             inclusion or exclusion of non-positional sequence features
@@ -403,22 +402,21 @@
             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>
-            <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
@@ -427,12 +425,12 @@
             </strong><em>If this box is selected then the sequence names
                 displayed in the sequence label area will be aligned
                 against the left-hand edge of the alignment display,
-                rather than the left-hand edge of the alignment window.
+                rather than the left-hand edge of the alignment window.</em>
             </li>
             <li><strong>Show Hidden Markers<br>
             </strong><em>When this box is selected, positions in the
                 alignment where rows and columns are hidden will be
-                marked by blue arrows. </li>
+                marked by blue arrows. </em></li>
             <li><strong>Boxes</strong><em><br> If this is
                 selected the background of a residue will be coloured
                 using the selected background colour. Useful if used in
@@ -461,7 +459,6 @@
                 symbols will be rendered as a '.', highlighting
                 mutations in highly conserved alignments. </em></li>
 
-          </ul></li>
       </ul></li>
 
   </ul>
@@ -474,11 +471,10 @@
           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
@@ -507,8 +503,8 @@
       <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.
@@ -542,44 +538,26 @@
               viewer window.
           </em><br></li>
         </ul></li>
-      <li><strong>Calculate Tree </strong> <br> <em>Functions
-          for calculating trees on the alignment or the currently
-          selected region. See <a href="../calculations/tree.html">calculating
-            trees</a>.
-      </em>
-        <ul>
-          <li><strong>Neighbour Joining Using PAM250 </strong></li>
-          <li><strong>Neighbour Joining Using Sequence
-              Feature Similarity</strong></li>
-          <li><strong>Neighbour Joining Using Blosum62 </strong></li>
-          <li><strong>Neighbour Joining Using % Identity</strong></li>
-          <li><strong>Average Distance Using PAM250 </strong></li>
-          <li><strong>Average Distance Using Sequence
-              Feature Similarity</strong></li>
-          <li><strong>Average Distance Using Blosum62</strong></li>
-          <li><strong>Average Distance Using % Identity</strong></li>
-        </ul> <strong>Note: Since Version 2.8.1, a number of
-          additional similarity measures for tree calculation are
-          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>.
+    <li><strong>Calculate Tree or PCA ...</strong><em> <br> Opens the 
+    <a href="../calculations/calculations.html">calculations dialog</a> for
+        for calculating <a href="../calculations/tree.html">trees</a> or
+         <a href="../calculations/pca.html">principle component analysis 
+         plots</a> on the alignment or the currently selected
+        region. 
       </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>.
-      </em> <br></li>
-      <li><strong>Extract Scores ... (optional)</strong><br> <em>This
-          option is only visible if Jalview detects one or more
-          white-space separated values in the description line of the
-          alignment sequences.<br> When selected, these numbers are
-          parsed into sequence associated annotation which can then be
-          used to sort the alignment via the Sort by&#8594;Score menu.
-      </em> <br></li>
-      <li><strong>Autocalculate Consensus</strong><br> <em>For
+    <li><strong>Pairwise Alignments</strong><br> <em>Applies
+        Smith and Waterman algorithm to selected sequences. See <a
+        href="../calculations/pairwise.html">pairwise
+          alignments</a>.
+    </em><br></li>
+    <li><strong>Extract Scores ... (optional)</strong><br> <em>This
+        option is only visible if Jalview detects one or more
+        white-space separated values in the description line of the
+        alignment sequences.<br> When selected, these numbers are
+        parsed into sequence associated annotation which can then be
+        used to sort the alignment via the Sort by&#8594;Score menu.
+    </em> <br></li>
+    <li><strong>Autocalculate Consensus</strong><br> <em>For
           large alignments it can be useful to deselect
           &quot;Autocalculate Consensus&quot; when editing. This
           prevents the sometimes lengthy calculations performed after
@@ -599,63 +577,60 @@
       is dynamic, and may contain user-defined web service entries in
       addition to any of the following ones:</em>
     <ul>
-      <li><strong>Fetch DB References</strong><br> <em>This
-          submenu contains options for accessing any of the database
-          services that Jalview is aware of (e.g. DAS sequence servers
-          and the WSDBFetch service provided by the EBI) to verify
-          sequence start/end positions and retrieve all database cross
-          references and PDB ids associated with all or just the
-          selected sequences in the alignment.
-          <ul>
-            <li>'Trim Retrieved Sequences' - when checked, Jalview
-              will discard any additional sequence data for accessions
-              associated with sequences in the alignment. <br> <strong>Note:
-                Disabling this could cause out of memory errors when
-                working with genomic sequence records !</strong><br> <strong>Added
-                in Jalview 2.8.1</strong>
-            </li>
-            <li>'Standard Databases' will check sequences against
-              the EBI databases plus any active DAS sequence sources<</li>
-          </ul> Other sub-menus allow you to pick a specific source to query
-          - sources are listed alphabetically according to their
-          nickname.
-      </em><br></li>
-    </ul>
+				<li><strong>Fetch DB References</strong><br> <em>This
+						submenu contains options for accessing any of the database
+						services that Jalview is aware of (e.g. those provided by
+						EMBL-EBI) to verify sequence start/end positions and retrieve all
+						database cross references and PDB ids associated with all or just
+						the selected sequences in the alignment.
+						<ul>
+							<li>'Trim Retrieved Sequences' - when checked, Jalview will
+								discard any additional sequence data for accessions associated
+								with sequences in the alignment. <br> <strong>Note:
+									Disabling this could cause out of memory errors when working
+									with genomic sequence records !</strong><br> <strong>Added
+									in Jalview 2.8.1</strong>
+							</li>
+							<li>'Standard Databases' will check sequences against the
+								EBI databases.</li>
+						</ul> Other sub-menus allow you to pick a specific source to query -
+						sources are listed alphabetically according to their nickname.
+				</em><br></li>
+			</ul>
     <p>Selecting items from the following submenus will start a
       remote service on compute facilities at the University of Dundee,
       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
-              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
-                  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
-                  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
-                  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>
@@ -667,8 +642,8 @@
           <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
-              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>
