Mussa Manual: Deleting a Motif

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

diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index 23f08b97e642ca5105e797bd5aef36ed95110261..45df62b8074c762224e7b5d918f60637b17b40d3 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
 ~~~~~~~~~~~~~
@@ -791,6 +791,37 @@ Save Motif List
 See `Save Motifs to File`_ in the `Motifs`_ section.
 
 
+Viewing Multiple Analyses
+-------------------------
+
+Some times it is useful to view more than one analysis at a time. To
+do accomplish this, Mussa allows you to open a new Mussa window by
+selecting the **File > New Mussa Window** menu option.
+
+.. image:: images/new_mussa_window_menu.png
+   :alt: New Mussa Window Menu Option
+   :align: center
+
+A new Mussa window will pop up.
+
+.. figure:: images/new_mussa_window.png
+   :alt: New Mussa Window
+   :align: center
+
+   A new Mussa window on the right, in which I have loaded a second
+   experiment.
+
+Now you can create or load an existing analysis, in this new window,
+as described in the `Create/Load Analysis`_ section. 
+
+You can view as many analyses as you can fit on your screen or until
+you run out of available RAM. If you notice a rapid decrease in
+performance and hear lots of noise coming from your hard drive, you
+probably ran out of RAM and are now using virtual memory (i.e. much
+much slower). If this happens, you may need to avoid opening as many
+analyses at one time.
+
+
 Annotations / Motifs
 --------------------
 
@@ -833,7 +864,9 @@ 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
@@ -906,6 +939,11 @@ To save your motifs with your analysis, see the `save analysis`_
 section. To save your motifs to a file, see the `save motifs to file`_
 section.
 
+Deleting a Motif
+^^^^^^^^^^^^^^^^
+
+To delete a motif, remove all text from the name and sequence columns
+and close the motif editor.
 
 View Mussa Alignments
 ---------------------
@@ -989,6 +1027,7 @@ as shown in the screen shot below, and do one of the following:
    :alt: Copy sequence
    :align: center
 
+
 Saving to an Image
 ---------------------------------