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 79f0c33ccb9c1a23e73d4a32f2b938347ad8b7fd..5bd26d4188d989d768124240557fa34e925ed3ea 100644 (file)
--- a/doc/manual/mussagl_manual.rst
+++ b/doc/manual/mussagl_manual.rst
@@ -5,15 +5,15 @@ Mussagl Manual
 Brandon W. King
 ---------------
 
-Last updated: Sept 20th, 2006
+Last updated: Oct 16th, 2006
 
-Updated to Mussagl build: 287
+Updated to Mussagl build: 287? (In process to 424)
 
 
 .. Things to add
        * New features / change log
        * Comment out anything isn't implemented yet.
-       * List of features that will be implemented in the future.
+       * (DONE) List of features that will be implemented in the future.
        * Look into the homology mapping of UCSC.
         * Add toggle to genomes.
         * Document why one fast record per region.
@@ -36,6 +36,32 @@ Updated to Mussagl build: 287
 
 .. contents::
 
+Status
+======
+
+Major New Features
+------------------
+
+ * Build 381
+   * Analysis "Save As" feature
+
+Change Log
+----------
+
+.. INSERT CHANGE LOG HERE
+.. END INSERT CHANGE LOG
+
+Features to be Implemented
+--------------------------
+
+ * Motif editor supporting more than 10 motifs 
+   (Status: http://woldlab.caltech.edu/cgi-bin/mussa/ticket/122)
+ * Save motifs from Mussagl
+   (Status: http://woldlab.caltech.edu/cgi-bin/mussa/ticket/133)
+
+For an up-to-date list of features to be implemented visit:
+http://woldlab.caltech.edu/cgi-bin/mussa/roadmap
+
 Introduction
 ============
 
@@ -56,7 +82,6 @@ viewer.
 Short History of Mussa
 ----------------------
 
-
 Mussa Python/PMW Prototype
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -160,6 +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
@@ -737,6 +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.
 
@@ -901,7 +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