Mussa Manual: Link to example data in UCSC genome browser section.

[mussa.git] / doc / manual / mussagl_manual.rst

diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index 5f1f9971f3a17ff9918712f12ca2badc7f18483a..5bd26d4188d989d768124240557fa34e925ed3ea 100644 (file)
--- a/doc/manual/mussagl_manual.rst
+++ b/doc/manual/mussagl_manual.rst
@@ -5,9 +5,9 @@ Mussagl Manual
 Brandon W. King
 ---------------
 
-Last updated: Sept 20th, 2006
+Last updated: Oct 16th, 2006
 
-Updated to Mussagl build: 287 (In process to 381)
+Updated to Mussagl build: 287? (In process to 424)
 
 
 .. Things to add
@@ -185,6 +185,10 @@ There are many methods of retrieving DNA sequence, but for this
 example we will retrieve SMN1 through the UCSC genome browser located
 at http://genome.ucsc.edu/.
 
+We have made the SMN1 data available at
+http://woldlab.caltech.edu/cgi-bin/mussa/wiki/ExampleData if you
+prefer to skip this section.
+
 .. image:: images/ucsc_genome_browser_home.png
    :alt: UCSC Genome Browser
    :align: center
@@ -762,6 +766,11 @@ It is possible to load motifs from a file which was saved from a
 previous run or by defining your own motif file. See the `Motif File
 Format`_ section for details.
 
+NOTE: Valid motif list file extensions are:
+  
+  * .mtl
+  * .txt
+
 To load a motif file, select **Load Motif List** item from the
 **File** menu and select a motif list file.
 
@@ -926,7 +935,36 @@ as shown in the screen shot below, and do one of the following:
 Saving to an Image
 ---------------------------------
 
-FIXME: Need to write this section
+ * Updated to build 419.
+
+To save your current mussa view to an image, select **File > Save to
+image...** as shown below.
+
+.. image:: images/save_to_image_menu.png
+   :alt: File > Save to image...
+   :align: center
+
+You can define the width and the height of the image to save. By
+default it will use the same size of your current view. Since the
+Mussa view is implemented using vectors, if you choose a larger size
+then your current view, Mussa will redraw at the higher resolution
+when saving. In other words, you get higher quality images when saving
+at a higher resolution.
+
+If you check the "Lock aspect ratio" check box, which I have circled
+in red, then when you change one value, say width, the other, height,
+will update automatically to keep the same aspect ratio.
+
+.. image:: images/save_to_image_dialog.png
+   :alt: Save to image dialog
+   :align: center
+
+Click save and choose a location and filename for your file.
+
+The valid image formats are:
+
+  * .png (default if no extension specified.)
+  * .jpg
 
 
 Detailed Information