From 80ac7d84002118186a11658f38abfa5c4fe3d8da Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 4 Aug 2017 13:40:20 +0100
Subject: [PATCH] JAL-2418 JAL-1632 JAL-2416 calculations dialog documentation
 page and release notes

---
 help/help.jhm                              |    1 +
 help/helpTOC.xml                           |    7 ++-
 help/html/calculations/calculatedialog.png |  Bin 0 -> 23917 bytes
 help/html/calculations/calculations.html   |   55 +++++++++++++++++++++++
 help/html/calculations/pca.html            |   12 +++--
 help/html/calculations/tree.html           |    4 +-
 help/html/menus/alignmentMenu.html         |   67 ++++++++++------------------
 help/html/menus/alwcalculate.html          |   34 ++++----------
 help/html/releases.html                    |    4 ++
 9 files changed, 107 insertions(+), 77 deletions(-)
 create mode 100644 help/html/calculations/calculatedialog.png
 create mode 100644 help/html/calculations/calculations.html

diff --git a/help/help.jhm b/help/help.jhm
index 363f549..cb0c4c4 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -109,6 +109,7 @@
    <mapID target="calcs.alconserv" url="html/calculations/conservation.html"/>
    <mapID target="calcs.alstrconsensus" url="html/calculations/structureconsensus.html"/>  
    <mapID target="calcs.consensus" url="html/calculations/consensus.html"/>   
+   <mapID target="calcs.dialog" url="html/calculations/calculations.html"/>
    
    <mapID target="nucleicAcids" url="html/na/index.html"/>
    
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index a8aadf5..f3311a7 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -24,6 +24,7 @@
 	<tocitem text="Jalview Documentation" target="home" expand="true">
 			<tocitem text="What's new" target="new" expand="true">
 				<tocitem text="Latest Release Notes" target="release"/>
+        <tocitem text="Calculations Dialog" target="calcs.dialog"/>
 				<tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
 				<tocitem text="Custom Colourschemes in Groovy" target="groovy.colours"/>
 				<tocitem text="Omit hidden regions in Overview" target="overview"/>
@@ -109,8 +110,10 @@
 		
 		<tocitem text="Calculations" expand="false">
 			<tocitem text="Sorting alignments" target="sorting" />
-			<tocitem text="Calculating trees" target="trees" />
-			<tocitem text="Principal Component Analysis" target="pca" />
+			<tocitem text="Trees and PCA" target="calcs.dialog" expand="false">
+  			  <tocitem text="Calculating trees" target="trees" />
+  			  <tocitem text="Principal Component Analysis" target="pca" />
+  			</tocitem>
 			<tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
 			<tocitem text="Pairwise Alignments" target="pairwise" />
 			<tocitem text="Remove Redundancy" target="redundancy" />
diff --git a/help/html/calculations/calculatedialog.png b/help/html/calculations/calculatedialog.png
new file mode 100644
index 0000000000000000000000000000000000000000..fdc0c0d0faf1513c796258910e0a99321837ae89
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diff --git a/help/html/calculations/calculations.html b/help/html/calculations/calculations.html
new file mode 100644
index 0000000..c194cd9
--- /dev/null
+++ b/help/html/calculations/calculations.html
@@ -0,0 +1,55 @@
+<html>
+<!--
+ * 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 
+ * 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.
+ * 
+ * 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.
+ -->
+<head>
+<title>The Alignment Calculations Dialog</title>
+</head>
+<body>
+  <p>
+    <strong>The Alignment Calculations Dialog</strong>
+  </p>
+  <img
+    alt="Alignment Calculations dialog box - opened via Calculations->Tree or PCA..."
+    src="calculatedialog.png" width="350" height="241">
+  <p>
+    The <strong>Calculations Dialog</strong> (shown above) is opened via
+    the <strong>Calculations&#8594;Calculate Tree or PCA...</strong>
+    menu entry.
+  </p>
+  <p>
+    It allows you to select the type of alignment analysis calculation (<a
+      href="pca.html">PCA</a> or <a href="tree.html">Tree</a>), and the
+    sequence similarity score model that will be used to perform the
+    analysis.
+  </p>
+  <p>
+    <strong>Adding additional score models</strong><br />Jalview can
+    import substitution matrices in both <a
+      href="http://www.genome.jp/aaindex/aaindex_help.html">AAindex</a>
+    and NCBI format (see e.g. <a
+      href="http://ftp.ncbi.nlm.nih.gov/blast/matrices/">ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/</a>).
+    In Jalview 2.10.2, the easiest way to import new models is to drag
+    the score model file onto any alignment window. See the <a
+      href="scorematrices.html">Substitution Matrices Documentation</a>
+    for more information.
+  </p>
+</body>
+</html>
diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html
index c38d9ac..7ffb160 100755
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -26,16 +26,20 @@
   <p>
     <strong>Principal Component Analysis</strong>
   </p>
+  <p>A principal component analysis can be performed via the 
+  <a href="calculations.html">calculations dialog</a> which is accessed by selecting <strong>Calculate&#8594;Calculate
+      Tree or PCA...</strong>.</p>
   <p>This calculation creates a spatial representation of the
     similarities within a selected group, or all of the sequences in an
     alignment. After the calculation finishes, a 3D viewer displays the
     set of sequences as points in 'similarity space', and similar
     sequences tend to lie near each other in the space.</p>
   <p>
-    <em>Caveats</em><br />The calculation is computationally expensive,
-    and may fail for very large sets of sequences - usually because the
-    JVM has run out of memory. A future release of Jalview will be able
-    to avoid this by executing the calculation via a web service.
+    <em>Caveats</em><br />The calculation can be computationally
+    expensive, and may fail for very large sets of sequences - usually
+    because the JVM has run out of memory. However, the PCA
+    implementation in Jalview 2.10.2 employs more memory efficient
+    matrix storage structures, allowing larger PCAs to be performed.
   </p>
 
   <p>
diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html
index 59736ca..95904b6 100755
--- a/help/html/calculations/tree.html
+++ b/help/html/calculations/tree.html
@@ -28,8 +28,8 @@
   </p>
   <p>
     Trees are calculated on either the complete alignment, or just the
-    currently selected group of sequences, using the functions in the <strong>Calculate&#8594;Calculate
-      tree</strong> submenu. Once calculated, trees are displayed in a new <a
+    currently selected group of sequences, via the <a href="calculations.html">calculations dialog</a> opened from the <strong>Calculate&#8594;Calculate
+      Tree or PCA...</strong> menu entry. Once calculated, trees are displayed in a new <a
       href="../calculations/treeviewer.html">tree viewing
       window</a>. There are four different calculations, using one of two
     distance measures and constructing the tree from one of two
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index 51ad601..00a2ec4 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -244,7 +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
@@ -312,7 +312,7 @@
             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
+              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, and
               configure and retrieve features from DAS annotation
@@ -427,12 +427,12 @@
             </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 +461,6 @@
                 symbols will be rendered as a '.', highlighting
                 mutations in highly conserved alignments. </em></li>
 
-          </ul></li>
       </ul></li>
 
   </ul>
@@ -541,44 +540,26 @@
               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
@@ -614,7 +595,7 @@
                 in Jalview 2.8.1</strong>
             </li>
             <li>'Standard Databases' will check sequences against
-              the EBI databases plus any active DAS sequence sources<</li>
+              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.
diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html
index 8032348..c7a1c87 100755
--- a/help/html/menus/alwcalculate.html
+++ b/help/html/menus/alwcalculate.html
@@ -53,37 +53,19 @@
             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<br>
-        </strong></li>
-        <li><strong>Neighbour Joining Using Sequence
-            Feature Similarity</strong></li>
-        <li><strong>Neighbour Joining Using Blosum62<br>
-        </strong></li>
-        <li><strong>Neighbour Joining Using % Identity</strong></li>
-        <li><strong>Average Distance Using PAM250<br>
-        </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></li>
+    <li><strong>Calculate Tree or PCA ...</strong> <br> <em>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>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>Principal Component Analysis</strong><br> <em>Shows
-        a spatial clustering of the sequences based on similarity scores
-        calculated over 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
diff --git a/help/html/releases.html b/help/html/releases.html
index 10d5781..ec4f4ec 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -96,6 +96,10 @@ li:before {
               </ul>
             </li>
             <li>
+              <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
+              a calculation dialog box
+            </li>
+            <li>
               <!-- JAL-2360,JAL-2371, -->More robust colours and shader
               model for alignments and groups
             </li>
-- 
1.7.10.2