X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fpca.html;h=695c45af0294c005df52df2eb58c5c4469aee073;hb=c218877a5572ea819f2a521e2205351d7b67bc93;hp=d9b4b45010475cf3b3192fc47c39dfa7a21a7518;hpb=c53aeee9a688f68d64106a968876e542f701fbc6;p=jalview.git

diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html
index d9b4b45..695c45a 100755
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -63,19 +63,30 @@ View menu is checked, and the plot background colour changed from the
 View&#8594;Background Colour.. dialog box. The File menu allows the view
 to be saved (<strong>File&#8594;Save</strong> submenu) as an EPS or PNG
 image or printed, and the original alignment data and matrix resulting
-from its PCA analysis to be retrieved.</p>
+from its PCA analysis to be retrieved. The coordinates for the whole PCA
+space, or just the current view may also be exported as CSV files for
+visualization in another program or further analysis.<p>
+<p>Options for coordinates export are:</p>
+<ul>
+<li>Output Values - complete dump of analysis (TxT* matrix computed from sum of scores for all pairs of aligned residues from from i->j and j->i, conditioned matrix to be diagonalised, tridiagonal form, major eigenvalues found)</li>
+<li>Output Points - The eigenvector matrix - rows correspond to sequences, columns correspond to each dimension in the PCA</li>
+<li>Transformed Points - The 3D coordinates for each sequence as shown in the PCA plot</li></ul>
+
 <p>A tool tip gives the sequence ID corresponding to a point in the
 space, and clicking a point toggles the selection of the corresponding
-sequence in the associated alignment window views. Rectangular region
+sequence in the associated alignment window views.<!-- Rectangular region
 based selection is also possible, by holding the 'S' key whilst
-left-clicking and dragging the mouse over the display. By default,
+left-clicking and dragging the mouse over the display. --> By default,
 points are only associated with the alignment view from which the PCA
 was calculated, but this may be changed via the <strong>View&#8594;Associate
 Nodes</strong> sub-menu.</p>
 <p>Initially, the display shows the first three components of the
 similarity space, but any eigenvector can be used by changing the
 selected dimension for the x, y, or z axis through each ones menu
-located below the 3d display.</p>
+located below the 3d display. The <em>Reset</em> button will reset axis and rotation settings to their defaults.</p>
+<p>
 <p>
+<em>The output of points and transformed point coordinates was added to the Jalview desktop in v2.7.</em>
+<em>The Reset button, and Nucleotide or Protein calculation settings were added in Jalview 2.8.</em>
 </body>
 </html>
