JAL-1503 documentation and release notes

[jalview.git] / help / html / calculations / pca.html

diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html
index 49019a7..ba9dc30 100755 (executable)
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -32,7 +32,8 @@ 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>
 
 of memory. A future release of Jalview will be able to avoid this by
 executing the calculation via a web service.</p>
 

-<p><strong>About PCA</strong>Principal components analysis is a technique for examining the
+<p><strong>About PCA</strong></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
 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

@@ -52,26 +53,26 @@ of variation in the data set.</p>
                        href="scorematrices.html#simplenucleotide">simple single
                        nucleotide substitution matrix</a>. The options available for
                calculation are given in the
                        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
+               <strong><em>Change Parameters</em></strong> menu.</p>
+       <p>
+       <em>PCA Calculation modes</em><br/>
+               The default Jalview calculation mode
+               (indicated when <em><strong>Jalview PCA Calculation</strong></em> is
+               ticked in the <strong><em>Change Parameters</em></strong> menu) is to
+               perform a 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 a matrix 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>)
                        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.
+               and implemented at the SeqSpace server at the EBI. This method
+               preconditions the matrix by multiplying it with its transpose, and can be employed in the PCA viewer by unchecking the <strong><em>Jalview
+                               PCA Calculation</em></strong> option in the <strong><em>Change
+                               Parameters</em></strong> menu.

        </p>
        </p>

-<img src="pcaviewer.gif">
+       <img src="pcaviewer.gif">

        <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
        <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