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Merge branch 'develop' into Release_2_9_Branch
[jalview.git] / help / html / menus / alignmentMenu.html
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index b1f7a06..7102fd7 100755 (executable)
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -1,31 +1,34 @@
 <html>
 <!--
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
 <head>
 <title>Alignment Window Menus</title>
 </head>
 
 <body>
 <head>
 <title>Alignment Window Menus</title>
 </head>
 
 <body>
-       <p>
-               <strong>Alignment Window Menus</strong>
-       </p>
-       <ul>
+  <!-- NOTE: THIS PAGE COLLECTS TOGETHER THE INDIVIDUAL ALIGNMENT WINDOW MENU PAGES - DON"T EDIT INDIVIDUAL ENTRIES HERE!  -->
+  <p>
+    <strong>Alignment Window Menus</strong>
+  </p>
+  <ul>
                <li><strong>File</strong>
                        <ul>
                                <li><strong>Fetch Sequence</strong><br> <em>Shows a
                <li><strong>File</strong>
                        <ul>
                                <li><strong>Fetch Sequence</strong><br> <em>Shows a
@@ -60,47 +63,50 @@
                                                Select the format of the text by selecting one of the following
                                                menu items.</em>
                                        <ul>
                                                Select the format of the text by selecting one of the following
                                                menu items.</em>
                                        <ul>
-                                               <li><strong>FASTA</strong> <em></em>
-                                               </li>
-                                               <li><strong>MSF</strong>
-                                               </li>
-                                               <li><strong>CLUSTAL</strong>
-                                               </li>
-                                               <li><strong>BLC</strong>
-                                               </li>
-                                               <li><strong>PIR</strong>
-                                               </li>
-                                               <li><strong>PFAM</strong>
-                                               </li>
+                                               <li><strong>FASTA</strong> </li>
+                                               <li><strong>MSF</strong></li>
+                                               <li><strong>CLUSTAL</strong></li>
+                                               <li><strong>BLC</strong></li>
+                                               <li><strong>PIR</strong></li>
+                                               <li><strong>PFAM</strong></li>
+                                               <li><strong>PileUp</strong></li>
+                                               <li><strong>AMSA</strong></li>
+                                               <li><strong>STH</strong></li>
+                                               <li><strong>Phylip</strong></li>
+                                               <li><strong>JSON</strong></li>
                                        </ul></li>
                                        </ul></li>
-                               <li><strong>Print (Control P)<br> </strong><em>Jalview
-                                               will print the alignment using the current fonts and colours of
-                                               your alignment. If the alignment has annotations visible, these
-                                               will be printed below the alignment. If the alignment is wrapped
-                                               the number of residues per line of your alignment will depend on
-                                               the paper width or your alignment window width, whichever is the
-                                               smaller. </em>
-                               </li>
-                               <li><strong>Export Image</strong> <em><br> Creates an
-                                               alignment graphic with the current view's annotation, alignment
-                                               background colours and group colours. If the alignment is <a
-                                               href="../features/wrap.html">wrapped</a>, the output will also be
-                                               wrapped and will have the same visible residue width as the open
-                                               alignment. </em>
-                                       <ul>
-                                               <li><strong>HTML<br> </strong><em>Create a <a
-                                                               href="../io/export.html">web page</a> from your alignment.</em>
-                                               </li>
-                                               <li><strong>EPS<br> </strong><em>Create an <a
-                                                               href="../io/export.html">Encapsulated Postscript</a> file from
-                                                               your alignment.</em>
-                                               </li>
-                                               <li><strong>PNG<br> </strong><em>Create a <a
-                                                               href="../io/export.html">Portable Network Graphics</a> file from
-                                                               your alignment.</em>
-                                               </li>
-                                       </ul></li>
-                               <li><strong>Export Features</strong><em><br> All
+<li><strong>Page Setup ...</strong><br>
+       <em>Open the printing system's Page Setup dialog box, to
+       control page size, layout and orientation.</em></li>
+       <li><strong>Print (Control P)<br>
+       </strong><em>Jalview will print the alignment using the current fonts and
+       colours of your alignment. If the alignment has annotations visible,
+       these will be printed below the alignment. If the alignment is wrapped
+       the number of residues per line of your alignment will depend on the
+       paper width or your alignment window width, whichever is the smaller. </em></li>
+       <li><strong>Export Image</strong> <em><br>
+       Creates an alignment graphic with the current view's annotation,
+       alignment background colours and group colours. If the alignment is <a
+               href="../features/wrap.html">wrapped</a>, the output will also be
+       wrapped and will have the same visible residue width as the open
+       alignment. </em>
+       <ul>
+               <li><strong>HTML<br>
+               </strong><em>Create a <a href="../io/export.html">web page</a> from your
+               alignment.</em></li>
+               <li><strong>EPS<br>
+               </strong><em>Create an <a href="../io/export.html">Encapsulated
+               Postscript</a> file from your alignment.</em></li>
+               <li><strong>PNG<br>
+               </strong><em>Create a <a href="../io/export.html">Portable Network
+               Graphics</a> file from your alignment.</em></li>
+               <li><strong>SVG<br>
+               </strong><em>Create a <a href="../io/export.html">Scalable Vector Graphics</a> file from your alignment for embedding in web pages.</em></li>
+               <li><strong>BioJS<br>
+               </strong><em>Create a <a href="../io/export.html">BioJS MSA Viewer HTML </a> file from your alignment.</em></li>
+       </ul>
+       </li>
+        <li><strong>Export Features</strong><em><br> All
                                                features visible on the alignment can be saved to file or
                                                displayed in a textbox in either Jalview or GFF format</em>
                                </li>
                                                features visible on the alignment can be saved to file or
                                                displayed in a textbox in either Jalview or GFF format</em>
                                </li>
@@ -110,7 +116,7 @@
                                </li>
                                <li><strong>Load Associated Tree<br> </strong><em>Jalview
                                                can <a href="../calculations/treeviewer.html">view trees</a>
                                </li>
                                <li><strong>Load Associated Tree<br> </strong><em>Jalview
                                                can <a href="../calculations/treeviewer.html">view trees</a>
-                                               stored in the Newick file format, and associate them with the
+                                                stored in the Newick file format, and associate them with the
                                                alignment. Note: the ids of the tree file and your alignment MUST
                                                be the same.</em></li>
                                <li><strong>Load Features / Annotations<br> </strong><em>Load
                                                alignment. Note: the ids of the tree file and your alignment MUST
                                                be the same.</em></li>
                                <li><strong>Load Features / Annotations<br> </strong><em>Load
@@ -120,7 +126,7 @@
                                                        annotations</a>.</em></li>
                                <li><strong>Close (Control W)</strong><br> <em>Close
                                                the alignment window. Make sure you have saved your alignment
                                                        annotations</a>.</em></li>
                                <li><strong>Close (Control W)</strong><br> <em>Close
                                                the alignment window. Make sure you have saved your alignment
-                                               before you close - either as a Jalview project or by using the <strong>Save
+                                               before you close - either from the Desktop's <strong>Save Project</strong> File menu option, or by using the <strong>Save
                                                        As</strong> menu.</em>
                                </li>
                        </ul></li>
                                                        As</strong> menu.</em>
                                </li>
                        </ul></li>
@@ -201,9 +207,9 @@
                                                the last redundancy deletion.</em>
                                </li>
                                <li><strong>Pad Gaps<br> </strong><em>When selected,
                                                the last redundancy deletion.</em>
                                </li>
                                <li><strong>Pad Gaps<br> </strong><em>When selected,
-                                               the alignment will be kept at minimal width (so there no empty
+                                               the alignment will be kept at minimal width (so there are no empty
                                                columns before or after the first or last aligned residue) and all
                                                columns before or after the first or last aligned residue) and all
-                                               sequences will be padded with gap characters to the before and
+                                               sequences will be padded with gap characters before and
                                                after their terminating residues.<br> This switch is useful
                                                when making a tree using unaligned sequences and when working with
                                                alignment analysis programs which require 'properly aligned
                                                after their terminating residues.<br> This switch is useful
                                                when making a tree using unaligned sequences and when working with
                                                alignment analysis programs which require 'properly aligned
@@ -214,42 +220,42 @@
                        </ul></li>
                <li><strong>Select</strong>
                        <ul>
                        </ul></li>
                <li><strong>Select</strong>
                        <ul>
-                               <li><strong><a href="../features/search.html">Find...
-                                                       (Control F)</a> </strong><em><br> Opens the Find dialog box to
-                                               search for residues, sequence name or residue position within the
-                                               alignment and create new sequence features from the queries. </em>
-                               </li>
-                               <li><strong>Select All (Control A)<br> </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></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 marked columns will
-                                               be deselected. </em><em> <br> Use &lt;ESCAPE&gt; to deselect
-                                               all.</em></li>
-                               <li><strong>Invert Sequence Selection (Control I)<br>
-                               </strong><em>Any sequence ids currently not selected will replace the
-                                               current selection. </em>
-                               </li>
-                               <li><strong>Invert Column Selection (Control Alt I)<br>
-                               </strong><em>Any columns currently not selected will replace the current
-                                               column selection. </em>
-                               </li>
-                                 <li><strong>Create Group (Control G)<br></strong>
-  <em>Create a group containing the currently selected sequences.</em></li>
+  <li><a href="../features/search.html"><strong>Find... (Control F)</strong></a><br>
+    <em>Opens the Find dialog box to search for residues, sequence name or residue 
+    position within the alignment and create new sequence features from the queries. 
+    </em>
+  <li><strong>Select All (Control A)</strong><strong><br>
+    </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>
+       <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 marked columns
+       will be deselected. </em><em> <br>
+       Use &lt;ESCAPE&gt; to deselect all.</em></li>
+       <li><strong>Invert Sequence Selection (Control I)<br>
+       </strong><em>Any sequence ids currently not selected will replace the
+       current selection. </em></li>
+       <li><strong>Invert Column Selection (Control Alt I)<br>
+       </strong><em>Any columns currently not selected will replace the current
+       column selection. </em></li>
+       <li><strong>Create Group (Control G)<br></strong>
+       <em>Create a group containing the currently selected sequences.</em></li>
   <li><strong>Remove Group (Shift Control G)<br></strong>
   <li><strong>Remove Group (Shift Control G)<br></strong>
-  <em>Ungroup the currently selected sequence group. (Create/Remove group new in Jalview 2.8.1)</em></li>
-                       <li><strong>Make Groups for selection<br /> </strong> <em>The currently
-                                               selected groups of the alignment will be subdivided according to
-                                               the contents of the currently selected region. <br />Use this to
-                                               subdivide an alignment based on the different combinations of
-                                               residues observed at specific positions. (new in jalview 2.5)</em>
-                               </li>
-       <li><strong>Undefine Groups (Control U)<br> </strong><em>The
-            alignment will be reset with no defined groups.<br> <strong>WARNING</strong>:
-            This cannot be undone.</em>
-        </li>
+  <em>Ungroup the currently selected sequence group.</em></li>
+               <li><strong>Make Groups for selection<br /></strong> <em>The
+                               currently selected groups of the alignment will be subdivided
+                               according to the contents of the currently selected region. <br />Use
+                               this to subdivide an alignment based on the different combinations
+                               of residues at marked columns.
+               </em></li>
+               <li><strong>Undefine Groups (Control U)<br>
+  </strong><em>The alignment will be reset with no defined groups.<br>
+  <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>
                </ul></li>
                <li><strong>View</strong>
                        <ul>
                </ul></li>
                <li><strong>View</strong>
                        <ul>
@@ -277,38 +283,10 @@
                                                selected, the view will automatically scroll to display the
                                                highlighted sequence position corresponding to the position under
                                                the mouse pointer in a linked alignment or structure view.</em></li>
                                                selected, the view will automatically scroll to display the
                                                highlighted sequence position corresponding to the position under
                                                the mouse pointer in a linked alignment or structure view.</em></li>
-                               <li><strong>Show Annotations<br> </strong><em>If this
-                                               is selected the &quot;Annotation Panel&quot; will be displayed
-                                               below the alignment. The default setting is to display the
-                                               conservation calculation, quality calculation and consensus values
-                                               as bar charts. </em>
-                               </li>
-                               <li><strong>Autocalculated Annotation<br> </strong><em>Settings
-                                       for the display of autocalculated annotation.</em>
-                                       <ul>
-                                               <li><strong>Apply to all groups<br> </strong><em> When
-                                                       ticked, any modification to the current settings will be applied
-                                                       to all autocalculated annotation.</em></li>
-                                               <li><strong>Show Consensus Histogram<br> </strong><em>
-                                                       Enable or disable the display of the histogram above the
-                                                       consensus sequence.</em></li>
-                                               <li><strong>Show Consensus Logo<br> </strong><em> Enable
-                                                       or disable the display of the Consensus Logo above the consensus
-                                                       sequence.</em></li>
-                                               <li><strong>Normalise Consensus Logo<br>
-                                               </strong><em>When enabled, scales all logo stacks to the same height,
-                                                               making it easier to compare symbol diversity in highly variable
-                                                               regions.</em></li>
-                                               <li><strong>Group Conservation<br> </strong><em> When
-                                                       ticked, display a conservation row for all groups (only available
-                                                       for protein alignments).</em></li>
-                                               <li><strong>Apply to all groups<br> </strong><em> When
-                                                       ticked, display a consensus row for all groups.</em></li>
-                                       </ul></li>
                                <li><strong>Show Sequence Features</strong><br> <em>Show
                                                or hide sequence features on this alignment.</em>
                                </li>
                                <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">Seqence
+                               <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
                                                        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
@@ -331,6 +309,61 @@
                                                using the mouse. </em>
                                </li>
                        </ul></li>
                                                using the mouse. </em>
                                </li>
                        </ul></li>
+               <li><strong>Annotations</strong><em> (Since Jalview 2.8.2)</em>
+                       <ul>
+                         <li><strong>Show Annotations<br> </strong><em>If this
+                                               is selected the &quot;Annotation Panel&quot; will be displayed
+                                               below the alignment. The default setting is to display the
+                                               conservation calculation, quality calculation and consensus values
+                                               as bar charts. </em>
+                         </li>
+                         <li><strong>Show Alignment Related</strong><em><br>
+                           Show all annotations that are for the alignment as a whole (for example, Consensus, 
+                           or secondary structure prediction from alignment).</em></li>
+                         <li><strong>Hide Alignment Related</strong><em><br>
+                           Hide all annotations that are for the alignment as a whole.</em></li>
+                         <li><strong>Show Sequence Related</strong><em><br>
+                           Show all annotations that are for individual sequences.</em></li>
+                         <li><strong>Hide Sequence Related</strong><em><br>
+                           Hide all annotations that are for individual sequences.</em></li>
+                         <li><em>You can also selectively show or hide annotations from the <a href="./popupMenu.html">Popup</a> 
+                           or <a href="../features/annotation.html">Annotation</a> menus.</em></li>
+                         <li><strong>Sort by Sequence</strong><em><br>Sort sequence-specific annotations by sequence order in the alignment
+                         (and within that, by label).</em></li>
+                         <li><strong>Sort by Label</strong><em><br>Sort sequence-specific annotations by label
+                         (and within that, by sequence order). If neither sort order is selected, no sorting is applied,
+                         allowing you to make a manual ordering of the annotations.</em></li>
+                         <li><strong>Autocalculated Annotation<br> </strong><em>Settings
+                                       for the display of autocalculated annotation.</em>
+                                       <ul>
+                                           <li><strong>Show first<br></strong><em>
+                                             Show autocalculated annotations above sequence-specific annotations.
+                                             Note this also applies to other annotations for the alignment, for example secondary
+                                             structure prediction from alignment.</em></li>
+                                           <li><strong>Show last<br></strong><em>
+                                             Show autocalculated / alignment annotations below sequence-specific annotations.</em></li>
+                                               <li><strong>Apply to all groups<br> </strong><em> When
+                                                       ticked, any modification to the current settings will be applied
+                                                       to all autocalculated annotation.</em></li>
+                                               <li><strong>Show Consensus Histogram<br> </strong><em>
+                                                       Enable or disable the display of the histogram above the
+                                                       consensus sequence.</em></li>
+                                               <li><strong>Show Consensus Logo<br> </strong><em> Enable
+                                                       or disable the display of the Consensus Logo above the consensus
+                                                       sequence.</em></li>
+                                               <li><strong>Normalise Consensus Logo<br>
+                                               </strong><em>When enabled, scales all logo stacks to the same height,
+                                                               making it easier to compare symbol diversity in highly variable
+                                                               regions.</em></li>
+                                               <li><strong>Group Conservation<br> </strong><em> When
+                                                       ticked, display a conservation row for all groups (only available
+                                                       for protein alignments).</em></li>
+                                               <li><strong>Group Consensus<br> </strong><em> When
+                                                       ticked, display a consensus row for all groups.</em></li>
+                                       </ul>
+                               </li>
+                       </ul>
+               </li>
                <li><strong>Alignment Window Format Menu</strong>
                        <ul>
                                <li><strong>Font...<br> </strong><em>Opens the
                <li><strong>Alignment Window Format Menu</strong>
                        <ul>
                                <li><strong>Font...<br> </strong><em>Opens the
@@ -473,19 +506,25 @@
                                                </li>
                                        </ul>
                                </li>
                                                </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>Average Distance Using % Identity</strong></li>
-                                               <li><strong>Neighbour Joining Using % Identity</strong></li>
-                                               <li><strong>Average Distance Using Blosum62</strong></li>
-                                               <li><strong>Neighbour Joining Using Blosum62<br>
-                                               </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>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>.</em><br>
                                <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>