From: jprocter <Jim Procter>
Date: Tue, 22 Aug 2006 13:47:47 +0000 (+0000)
Subject: documentation - adding new Input data menu entries.
X-Git-Tag: Release_2_1~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8316c5a64282537b69e36040814d2b0a81e7a438;p=jalview.git

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
--- 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
   <strong>left mouse button</strong> pressed. The view can also be
   zoomed in and out with the up and down <strong>arrow
-  keys</strong>.</p>
+  keys</strong>. Labels will be shown for each sequence
+  if the entry in the View menu is checked, and the plot background
+  colour changed from the View&#8594;Background Colour.. dialog
+  box. The File menu allows the view to be saved (File&#8594;Save
+  submenu) as an EPS or PNG image or printed, and the original
+  alignment data and matrix resulting from its PCA analysis to be
+  retrieved.
+</p>
+ </p>
 <p>A tool tip gives the sequence ID corresponding to a point in the
   space, and clicking a point toggles the selection of the
   corresponding sequence in the alignment window. Rectangular region
@@ -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
   below the 3d display.
 </p>
+<p>
 
 </body>
 </html>
diff --git a/help/html/calculations/treeviewer.html b/help/html/calculations/treeviewer.html
index 77ed5eb..bc46771 100755
--- 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