X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fcalculations%2Fpca.html;h=b042dd81cda1cee711138860a21cdb109432f4b9;hb=cafa2071799c16922a85b8637e33e6331e054f35;hp=acf9665da82547a12c0aba89aed4044a6eedd50a;hpb=bb105fcca41253815982584f4c8f6fae1f8e10a3;p=jalview.git

diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html
index acf9665..b042dd8 100755
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -1,4 +1,21 @@
 <html>
+<!--
+ * 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.
+ * 
+ * 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/>.
+-->
 <head>
 <title>Principal Component Analysis</title>
 </head>
@@ -23,9 +40,12 @@ of variation in the data set.</p>
 
 <p>In this case, the components are generated by an eigenvector
 decomposition of the matrix formed from the sum of BLOSUM scores at each
-aligned position between each pair of sequences. The basic method is
-described in the paper by G. Casari, C. Sander and A. Valencia.
-Structural Biology volume 2, no. 2, February 1995 (<a
+aligned position between each pair of sequences. The matrix is not
+symmetric - elements in the upper diagonal give the sum of scores for
+mutating in one direction, and the lower diagonal is the sum of scores
+for mutating in the other. This is a refinement of the method described
+in the paper by G. Casari, C. Sander and A. Valencia. Structural Biology
+volume 2, no. 2, February 1995 (<a
 	href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7749921">pubmed</a>)
 and implemented at the SeqSpace server at the EBI.</p>
 
@@ -43,7 +63,9 @@ 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>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
@@ -57,5 +79,6 @@ 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>
 <p>
+<p>
 </body>
 </html>
