Updated manual

* Updated threshold setting based on latest build of Mussagl
* Continued outline development
* Added FIXME: where ever work needs to be done.

diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index 1a5fb6a40737cdb9cacf18002c03388b8e4ee28b..1f348e365687f8cadb4142ac00bf695eebc5d8e8 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: March 23rd, 2006
+Last updated: May 15th, 2006
 
-Updated to Mussagl build: 141
+Updated to Mussagl build: 141 (Update to 193 in progress)
 
 
 .. contents::
@@ -212,36 +212,67 @@ click open.
    :align: center
 
 
+Main Window
+-----------
+
+Overview
+~~~~~~~~
+.. Screenshot with numbers showing features.
+
+Dynamic Threshold
+~~~~~~~~~~~~~~~~~
+
+Zoom
+~~~~
+
+Sequence Info
+~~~~~~~~~~~~~
+
+Scroll Bar
+~~~~~~~~~~
+.. Moving sequence
+
+
+Annotations / Motifs
+--------------------
+
+Annotations
+~~~~~~~~~~~
+
+Motifs
+~~~~~~
+
+Load Motifs from File
+*********************
+
+Motif Dialog
+************
+
+
 Detailed Info
 -------------
 
 Threshold
 ~~~~~~~~~
 
-The threshold of an analysis is in minimum number of base pair
-matches must be meet to in order to be kept as a match. Note that you
-can vary the threshold from within Mussagl. For example, if you
-choose a `window size`_ of **30** and a **threshold** of **20** the mussa
-nway transitive algorithm will store all matches that are 20 out of 30
-bp matches or better and pass it on to Mussagl. Mussagl will
-then allow you to dynamically choose a threshold from 10 to 30 base
-pairs. A threshold of 30 bps would only show 30 out of 30 bp
-matches. A threshold of 20 bps would show all matches of 20 out of 30
-bps or better. Choosing a threshold below 20 in this case won't have
-an effect [*]_ because the mussa algorithm didn't report and matches below
-this threshold.
-
-.. [*] In the future, Mussagl will automatically detect the minimum
-   threshold which was used when defining an analysis and not allow
-   you to select a threshold below the minimum. See `ticket #52
-   <http://woldlab.caltech.edu/cgi-bin/mussa/ticket/52>`_ for more
-   info.
+The threshold of an analysis is in minimum number of base pair matches
+must be meet to in order to be kept as a match. Note that you can vary
+the threshold from within Mussagl. For example, if you choose a
+`window size`_ of **30** and a **threshold** of **20** the mussa nway
+transitive algorithm will store all matches that are 20 out of 30 bp
+matches or better and pass it on to Mussagl. Mussagl will then allow
+you to dynamically choose a threshold from 20 to 30 base pairs. A
+threshold of 30 bps would only show 30 out of 30 bp matches. A
+threshold of 20 bps would show all matches of 20 out of 30 bps or
+better. If you would like to see results for matches lower than 20 out
+of 30, you will need to rerun the analysis with a lower threshold.
 
 Window Size
 ~~~~~~~~~~~
 
-The typical sizes people tend to choose are between 20 and 30. Feel
-free to analysis with this setting depending on your needs.
+The typical sizes people tend to choose are between 20 and 30. You
+will likely need to experiment with this setting depending on your
+needs and input sequence.
 
 
 Sequences
@@ -252,6 +283,9 @@ format. Mussa may take a long time to run (>10 minutes) if the total
 bp length near 280Kb. Once mussa has run once, you can reload
 previously run analyses.
 
+FIXME: We have learned more about how much sequence and how many to
+put in mussagl, this information should be documented here.
+
 
 Mussa File Formats
 ------------------
@@ -354,6 +388,9 @@ Motif File Format
 Format:
 
   <motif> <red> <green> <blue>
+  
+Example:
+
   GGCC 0.0 1 1