documentation - adding new Input data menu entries.

diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html
index 2e5c16b..32ab81d 100755 (executable)
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -38,7 +38,15 @@ href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=
   <p>The 3d view can be rotated by dragging the mouse with the\r
   <strong>left mouse button</strong> pressed. The view can also be\r
   zoomed in and out with the up and down <strong>arrow\r
-  keys</strong>.</p>\r
+  keys</strong>. Labels will be shown for each sequence\r
+  if the entry in the View menu is checked, and the plot background\r
+  colour changed from the View&#8594;Background Colour.. dialog\r
+  box. The File menu allows the view to be saved (File&#8594;Save\r
+  submenu) as an EPS or PNG image or printed, and the original\r
+  alignment data and matrix resulting from its PCA analysis to be\r
+  retrieved.\r
+</p>\r
+ </p>\r
 <p>A tool tip gives the sequence ID corresponding to a point in the\r
   space, and clicking a point toggles the selection of the\r
   corresponding sequence in the alignment window. Rectangular region\r
@@ -50,6 +58,7 @@ href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=
   dimension for the x, y, or z axis through each ones menu located\r
   below the 3d display.\r
 </p>\r
+<p>\r
 \r
 </body>\r
 </html>\r

diff --git a/help/html/calculations/treeviewer.html b/help/html/calculations/treeviewer.html
index 77ed5eb..bc46771 100755 (executable)
--- a/help/html/calculations/treeviewer.html
+++ b/help/html/calculations/treeviewer.html
@@ -38,8 +38,9 @@ with the <a href="../colourSchemes/conservation.html">conservation
 based colour scheme</a>.</p>
 <p><strong>File Menu</strong></p>
 <p>This menu allows the displayed tree to be saved as a Newick tree
-file (Save-&gt;Newick File), printed or exported as an image (PNG) or
-Postscript file.
+file (Save&#8594;Newick File), printed or exported as an image (PNG) or
+Postscript file. Finally, data used to calculate the tree can be
+retrieved with the 'Input Data...' entry.
 </p>
 <p><strong>View Menu</strong></p>
 <p>When the tree viewer is opened, it displays all the annotation