From bddac385a4c7ebc6c8e1cff017a340a5e5266d60 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Sun, 8 Jul 2012 16:37:08 +0100
Subject: [PATCH] documentation for PCA calculation parameters and reset
 button.

---
 help/html/calculations/pca.html |   16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html
index b042dd8..695c45a 100755
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -65,20 +65,28 @@ 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. 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>
+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>
-- 
1.7.10.2