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JAL-2418 JAL-1632 JAL-2416 calculations dialog documentation page and release notes
authorJim Procter <jprocter@issues.jalview.org>
Fri, 4 Aug 2017 12:40:20 +0000 (13:40 +0100)
committerJim Procter <jprocter@issues.jalview.org>
Fri, 4 Aug 2017 12:40:41 +0000 (13:40 +0100)
help/help.jhm patch | blob | history
help/helpTOC.xml patch | blob | history
help/html/calculations/calculatedialog.png [new file with mode: 0644] patch | blob
help/html/calculations/calculations.html [new file with mode: 0644] patch | blob
help/html/calculations/pca.html patch | blob | history
help/html/calculations/tree.html patch | blob | history
help/html/menus/alignmentMenu.html patch | blob | history
help/html/menus/alwcalculate.html patch | blob | history
help/html/releases.html patch | blob | history

diff --git a/help/help.jhm b/help/help.jhm
index 363f549..cb0c4c4 100755 (executable)
--- 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.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"/>
    
    
    <mapID target="nucleicAcids" url="html/na/index.html"/>
    
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index a8aadf5..f3311a7 100755 (executable)
--- 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="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"/>
                                <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="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" />
                        <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 (file)
index 0000000..fdc0c0d
Binary files /dev/null and b/help/html/calculations/calculatedialog.png differ
diff --git a/help/html/calculations/calculations.html b/help/html/calculations/calculations.html
new file mode 100644 (file)
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 (executable)
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -26,16 +26,20 @@
   <p>
     <strong>Principal Component Analysis</strong>
   </p>
   <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>
   <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>
   </p>
 
   <p>
diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html
index 59736ca..95904b6 100755 (executable)
--- 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
   </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
       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 (executable)
--- 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.
         </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
         <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
             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
               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,
             </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
             </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
             <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>
 
                 symbols will be rendered as a '.', highlighting
                 mutations in highly conserved alignments. </em></li>
 
-          </ul></li>
       </ul></li>
 
   </ul>
       </ul></li>
 
   </ul>
@@ -541,44 +540,26 @@
               viewer window.
           </em><br></li>
         </ul></li>
               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>
       </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
           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
                 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.
           </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 (executable)
--- a/help/html/menus/alwcalculate.html
+++ b/help/html/menus/alwcalculate.html
@@ -53,37 +53,19 @@
             window.
         </em><br></li>
       </ul></li>
             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>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
     <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 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -96,6 +96,10 @@ li:before {
               </ul>
             </li>
             <li>
               </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>
               <!-- JAL-2360,JAL-2371, -->More robust colours and shader
               model for alignments and groups
             </li>