Mussa Manual: save on close & save motif default behavior

 * Wrote the "Save on close" section. (ticket:189)
 * Documented default motif list extension, when not provided by user. (ticket:190)
 * Removed old "features to implement".

diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index 23f08b97e642ca5105e797bd5aef36ed95110261..015296b427afe890d4b3a1f7f3d84fcc6d417398 100644 (file)
--- a/doc/manual/mussagl_manual.rst
+++ b/doc/manual/mussagl_manual.rst
@@ -5,14 +5,14 @@ Mussagl Manual
 Brandon W. King
 ---------------
 
-Last updated: Oct 17th, 2006
+Last updated: Oct 18th, 2006
 
 Updated to Mussagl build: (In process to 424)
 
 
 .. Things to add
        * New features / change log
-       * Comment out anything isn't implemented yet.
+       * (DONE) Comment out anything isn't implemented yet.
        * (DONE) List of features that will be implemented in the future.
        * Look into the homology mapping of UCSC.
         * Add toggle to genomes.
@@ -54,11 +54,6 @@ 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
 
@@ -760,7 +755,12 @@ Saving
 Save on Close
 ~~~~~~~~~~~~~
 
-FIXME: Write this.
+When ever you create a new analysis or make a change such as
+adding/editing a motif or changing a species name, an asterisk (*)
+will appear in the title of the window showing that there are changes
+that have not been saved. If you close a Mussa window without saving
+changes, Mussa will ask you if you would like to save the changes that
+have been made.
 
 Save Analysis
 ~~~~~~~~~~~~~
@@ -833,7 +833,9 @@ Motifs from the `Motif Dialog`_ can be saved to file for use with
 other analyses. If you just want your motifs to be saved with your
 analysis, see the `save analysis`_ section for details.
 
-To save a motif list, select **File > Save Motifs** menu option.
+To save a motif list, select **File > Save Motifs** menu option. By
+default, Mussa will append .mtl if you do not provide a file extension
+(valid file extensions: .mtl & .txt).
 
 .. image:: images/save_motifs.png
    :alt: Save Motifs