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
 ------------------
 
 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::
 
 
 .. contents::


@@ -212,36 +212,67 @@ click open.
    :align: center
 
 
    :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
 ~~~~~~~~~
 
 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
 ~~~~~~~~~~~
 
 
 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
 
 
 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.
 
 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
 ------------------
 
 Mussa File Formats
 ------------------


@@ -354,6 +388,9 @@ Motif File Format
 Format:
 
   <motif> <red> <green> <blue>
 Format:
 
   <motif> <red> <green> <blue>

+  
+Example:
+

   GGCC 0.0 1 1
 
 
   GGCC 0.0 1 1