JAL-1503 document updated PCA interface

diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html
index 0d6e85e..49019a7 100755 (executable)
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -46,25 +46,30 @@ of variation in the data set.</p>
                alignments. In both cases, components are generated by an eigenvector
                decomposition of the matrix formed from the sum of substitution matrix
                scores at each aligned position between each pair of sequences -
-               computed either with <a href="scorematrices.html#blosum62">BLOSUM62</a> or the <a
-                       href="scorematrices.html#simplenucleotide">simple single nucleotide
-                       substitution matrix</a>. The options available for calculation are given
-               in the <strong><em>Change Parameters</em></strong> menu.<br />
-               Jalview allows two types of PCA calculation. The default <em><strong>Jalview
-                               PCA Calculation</strong></em> mode (indicated when that option is ticked in the <strong><em>Change
-                               Parameters</em></strong> menu) of the viewer performs PCA on a matrix where
-               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. For protein substitution models like BLOSUM62,
-               this gives an asymmetric matrix, and a different PCA to one produced
-               with the method described in the paper by G. Casari, C. Sander and A.
-               Valencia. Structural Biology volume 2, no. 2, February 1995 (<a
+               computed with one of the available score matrices, such as
+               <a href="scorematrices.html#blosum62">BLOSUM62</a>, <a
+                       href="scorematrices.html#pam250">PAM250</a>, or the <a
+                       href="scorematrices.html#simplenucleotide">simple single
+                       nucleotide substitution matrix</a>. The options available for
+               calculation are given in the
+               <strong><em>Change Parameters</em></strong> menu.<br /> Jalview allows
+               two types of PCA calculation. The default
+               <em><strong>Jalview PCA Calculation</strong></em> mode (indicated when
+               that option is ticked in the
+               <strong><em>Change Parameters</em></strong> menu) of the viewer
+               performs PCA on a matrix where 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. For protein substitution
+               models like BLOSUM62, this gives an asymmetric matrix, and a different
+               PCA to one produced with 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. The original method
                preconditions the matrix by multiplying it with its transpose, and
-               this mode is enabled by unchecking the <strong><em>Jalview
-                               PCA Calculation</em></strong> option in the <strong><em>Change
-                               Parameters</em></strong> menu.
+               this mode is enabled by unchecking the
+               <strong><em>Jalview PCA Calculation</em></strong> option in the
+               <strong><em>Change Parameters</em></strong> menu.
        </p>
 <img src="pcaviewer.gif">
        <p><strong>The PCA Viewer</strong></p>
@@ -106,5 +111,6 @@ located below the 3d display. The <strong><em>Reset</em></strong> button will re
 <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 Change Parameters menu were added in Jalview 2.8.</em>
+<em>Support for PAM250 based PCA was added in Jalview 2.8.1.</em>
 </body>
 </html>

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