X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Fcalculations%2Fpca.html;h=0104078be6e66707cb67fe623f80be11858d150f;hb=cbd3af30e8479bf3dbf8b269da3772fa952f17d2;hp=d1841a15bf369cefbbd3c471ab528a5f00b31081;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git

diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html
index d1841a1..0104078 100755
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -26,16 +26,23 @@
   <p>
     <strong>Principal Component Analysis</strong>
   </p>
+  <p>
+    A principal component analysis can be performed via the <a
+      href="calculations.html">calculations dialog</a> which is accessed
+    by selecting <strong>Calculate&#8594;Calculate Tree or
+      PCA...</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>
-    <em>Caveats</em><br />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.
+    <em>Caveats</em><br />The calculation can be computationally
+    expensive, and may fail for very large sets of sequences - usually
+    because the JVM has run out of memory. However, the PCA
+    implementation in Jalview 2.10.2 employs more memory efficient
+    matrix storage structures, allowing larger PCAs to be performed.
   </p>
 
   <p>
@@ -58,27 +65,9 @@
     pair of sequences - 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.
-  </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>) 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
+      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.
   </p>
   <img src="pcaviewer.gif">
@@ -141,5 +130,26 @@ left-clicking and dragging the mouse over the display. -->
       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>
+  </p>
+  <p>
+    <strong>Reproducing PCA calculations performed with older
+      Jalview releases</strong> Jalview 2.10.2 included a revised PCA
+    implementation which treated Gaps and non-standard residues in the
+    same way as 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>)
+    and implemented at the SeqSpace server at the EBI. To reproduce
+    calculations performed with earlier Jalview releases it is necessary
+    to execute the following Groovy script:
+  <pre>
+    jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
+    jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
+    </pre>
+  This script enables the legacy PCA mode where gaps were treated as
+  'X', and to modify the BLOSUM62 matrix so it is asymmetric for
+  mutations between C to R (this was a typo in the original Jalview
+  BLOSUM62 matrix which was fixed in 2.10.2).
+  </p>
 </body>
 </html>
