JAL-3224 JAL-3225 Some fixes in install4j template and build.gradle, and a correction...

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

diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html
index 14bb9ee..3529cae 100755 (executable)
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -60,15 +60,15 @@
     <em>Calculating PCAs for aligned sequences</em><br />Jalview can
     perform PCA analysis on both proteins and nucleotide sequence
     alignments. In both cases, components are generated by an
     <em>Calculating PCAs for aligned sequences</em><br />Jalview can
     perform PCA analysis on both proteins and nucleotide sequence
     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 with one of the available score
-    matrices, such as <a href="scorematrices.html#blosum62">BLOSUM62</a>,
+    eigenvector decomposition of the matrix formed from pairwise similarity
+    scores between each pair of sequences. The similarity score model is 
+    selected on the <a href="calculations.html">calculations dialog</a>, and
+    may use 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
     <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.
+      nucleotide substitution matrix</a>, or by sequence percentage identity,
+      or sequence feature similarity. 

   </p>
   <img src="pcaviewer.gif">
   <p>
   </p>
   <img src="pcaviewer.gif">
   <p>

@@ -78,8 +78,10 @@
     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
     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>
+    sequence, and grey if the sequence is part of the currently selected
+    group. The viewer also employs depth cueing, so points appear darker
+    the farther away they are, and become brighter as they are rotated
+    towards the front of the view.</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
   <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

@@ -142,16 +144,14 @@ left-clicking and dragging the mouse over the display. -->
     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:
     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
   <pre>
     jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true

+    jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3

     </pre>
     </pre>

-  Additionally, for PCAs performed with older versions of Jalview and
-  the Blosum62 matrix, it is also necessary to import the legacy
-  BLOSUM62 score matrix (which is asymmetric for mutations between C to
-  R) which can be downloaded at
-  http://www.jalview.org/examples/legacyBlosum62.scm
+  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>
   </p>

-

 </body>
 </html>
 </body>
 </html>