Manual: Main Window section added

diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index 1f348e365687f8cadb4142ac00bf695eebc5d8e8..ebf16d36a4be94c6beb344f215dca9e2d2d4c754 100644 (file)
--- a/doc/manual/mussagl_manual.rst
+++ b/doc/manual/mussagl_manual.rst
@@ -5,9 +5,9 @@ Mussagl Manual
 By Brandon W. King
 ------------------
 
-Last updated: May 15th, 2006
+Last updated: May 18th, 2006
 
-Updated to Mussagl build: 141 (Update to 193 in progress)
+Updated to Mussagl build: 141 (Update to 200 in progress)
 
 
 .. contents::
@@ -219,18 +219,163 @@ Overview
 ~~~~~~~~
 .. Screenshot with numbers showing features.
 
+.. image:: images/window_overview.png
+   :alt: Mussa Window
+   :align: center
+
+Legend:
+
+ 1. `DNA Sequence (Black bars)`_
+ 
+ 2. Annotation_
+
+ 3. Motif_
+
+ 4. `Conservation tracks`_
+
+ 5. `Motif Toggle`_
+
+ 6. `Zoom Factor`_ (Base pairs per pixel)
+
+ 7. `Dynamic Threshold`_
+
+ 8. `Sequence Information Bar`_
+
+ 9. `Sequence Scroll Bar`_
+
+
+DNA Sequence (black bars)
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. image:: images/sequence_bar.png
+   :alt: Sequence Bar
+   :align: center
+
+Each of the black bars represents one of the loaded sequences, in this
+case the sequence around the gene 'MCK' in human, mouse, and rabit.
+
+FIXME: Should I mention the repeats here?
+
+
+Annotation
+~~~~~~~~~~
+
+.. figure:: images/annotation.png
+   :alt: Annotation
+   :align: center
+   
+   Annotation shown in green on sequence bar.
+
+
+Annotations can be included on any of the sequences using the `Load a
+mussa parameter file`_ method of loading your sequences. You can
+define annotations by location or using an exact subsequence and you
+may also choose any color for display of the annoation; see the
+`Annotation File Format`_ section for details.
+
+Note: Currently there is no way to add annotations using the GUI (only
+via the .mupa file). We plan to add this feature in the future, but it
+likely will not make it into the first release.
+
+
+Motif
+~~~~~
+
+.. figure:: images/motif.png
+   :alt: Motif
+   :align: center
+
+   Motif shown in light blue on sequence bar.
+
+The only real difference between an annotation and motif in mussagl is
+that you can define motifs from within the GUI. See the `Motifs`_
+section for more information.
+
+
+Conservation tracks
+~~~~~~~~~~~~~~~~~~~
+
+.. figure:: images/conservation_tracks.png
+   :alt: Conservation Tracks
+   :align: center
+   
+   Conservations tracks shown as red lines between sequence bars.
+
+The red lines between the sequence bars represent conservation between
+the sequences. The amount of sequence conservation shown will depend
+on the relatedness of your sequences and the `dynamic threshold` you
+are using. Sequences with lots of repeats will cause major slow downs
+in calculating the matches.
+
+
+Motif Toggle
+~~~~~~~~~~~~
+
+.. image:: images/motif_toggle.png
+   :alt: Motif Toggle
+   :align: center
+
+Toggles motifs on and off. This will not turn on and off annotations.
+
+Note: As of the current build (#200), this feature hasn't been
+implemented.
+
+
+Zoom Factor
+~~~~~~~~~~~
+
+.. image:: images/zoom_factor.png
+   :alt: Zoom Factor
+   :align: center
+
+The zoom factor represents the number of base pairs represented per
+pixel. When you zoom in far enough the sequence will switch from
+seeing a black bar, representing the sequence, to the actual sequence
+(well, ASCII representation of sequence).
+
+
 Dynamic Threshold
 ~~~~~~~~~~~~~~~~~
 
-Zoom
-~~~~
+.. image:: images/dynamic_threshold.png
+   :alt: Dynamic Threshold
+   :align: center
 
-Sequence Info
-~~~~~~~~~~~~~
+You can dynamically change the threshold for how strong of match you
+consider the conservation to be with one of two options:
 
-Scroll Bar
-~~~~~~~~~~
-.. Moving sequence
+ 1. Number of base pair matchs out of window size.
+ 
+ 2. Percent base pair conservation.
+
+See the Threshold_ section for more infromation.
+
+
+Sequence Information Bar
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. image:: images/seq_info_bar.png
+   :alt: Sequence Information Bar
+   :align: center
+
+The sequence infomation bars can be found to the left and right sides
+of mussagl. Next to each sequence you will find the following
+information:
+
+ 1. Species (If it has been defined)
+ 2. Total Size of Sequence
+ 3. Current base pair position
+
+
+Sequence Scroll Bar
+~~~~~~~~~~~~~~~~~~~
+
+.. image:: images/scroll_bar.png
+   :alt: Sequence Scroll Bar
+   :align: center
+
+The scroll bar allows you to scroll through the sequence which is
+useful when you have zoomed in using the `zoom factor`_.
 
 
 Annotations / Motifs
@@ -380,7 +525,7 @@ Example:
   1751 2000 Glorp Glorptype
 
 
-.. _motif:
+.. _motif_file_format:
 
 Motif File Format
 ~~~~~~~~~~~~~~~~~
@@ -401,4 +546,5 @@ Example:
 .. _wiki: http://mussa.caltech.edu
 .. _build: http://woldlab.caltech.edu/cgi-bin/mussa/wiki/MussaglBuild
 .. _fasta: http://en.wikipedia.org/wiki/FASTA_format
+.. _wpDnaMotif: http://en.wikipedia.org/wiki/DNA_motif