<html>
-<head>
-<title>Principal Component Analysis</title>
-</head>
-<body>
-<p><strong>Principal Component Analysis</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>Note: 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.</p>
-<p>Principal components analysis is a technique for examining the
-structure of complex data sets. The components are a set of dimensions
-formed from the measured values in the data set, and the principle
-component is the one with the greatest magnitude, or length. The sets of
-measurements that differ the most should lie at either end of this
-principle axis, and the other axes correspond to less extreme patterns
-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
- 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>
-
-<p><strong>The PCA Viewer</strong></p>
-<p>This is an interactive display of the sequences positioned within
-the similarity space, as points in a rotateable 3D scatterplot. The
-colour of each sequence point is the same as the sequence group colours,
-white if no colour has been defined for the sequence, and green if the
-sequence is part of a the currently selected group.</p>
-<p>The 3d view can be rotated by dragging the mouse with the <strong>left
-mouse button</strong> pressed. The view can also be zoomed in and out with the up
-and down <strong>arrow keys</strong> (and the roll bar of the mouse if
-present). Labels will be shown for each sequence if the entry in the
-View menu is checked, and the plot background colour changed from the
-View→Background Colour.. dialog box. The File menu allows the view
-to be saved (<strong>File→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>
-<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
-based selection is also possible, by holding the 'S' key whilst
-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→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>
-<p>
-</body>
-</html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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/>.
+-->
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