From: Brandon King <kingb@caltech.edu>
Date: Tue, 23 May 2006 22:18:14 +0000 (+0000)
Subject: Manual: View mussa alignment section + minor fixes
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=commitdiff_plain;h=c06313f69d94b00220a3360eb4d3c95ee3b232a0

Manual: View mussa alignment section + minor fixes
---

diff --git a/doc/manual/images/mussa_alignment.png b/doc/manual/images/mussa_alignment.png
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diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index 475b8ce..938eb07 100644
--- a/doc/manual/mussagl_manual.rst
+++ b/doc/manual/mussagl_manual.rst
@@ -5,7 +5,7 @@ Mussagl Manual
 Brandon W. King
 ---------------
 
-Last updated: May 18th, 2006
+Last updated: May 23th, 2006
 
 Updated to Mussagl build: 141 (Update to 200 in progress)
 
@@ -159,7 +159,7 @@ Now click on the 'Browse' button next to the sequence input box and
 then select /examples/seq/human_mck_pro.fa file. Do the same in the
 next two sequence input boxes selecting mouse_mck_pro.fa and
 rabbit_mck_pro.fa as shown below. Note that you can create annotation
-files using the mussa `Annotation File Format` to add annotations to
+files using the mussa `Annotation File Format`_ to add annotations to
 your sequence.
 
 .. image:: images/define_analysis_step2.png
@@ -473,6 +473,54 @@ After Motif:
    :align: center
 
 
+View Mussa Alignements
+----------------------
+
+Mussagl allows you to zoom in on Mussa alignments by selecting the set
+of alignment(s) of interest. To do this, move the mouse near the
+alignment you are interested in viewing and then **PRESS** and
+**HOLD** the **LEFT mouse button** and **drag the mouse** to the other
+side of the conservation track so that you see a bounding box
+overlaping the alienment(s) of interest and then **let go** of the
+*left mouse button*.
+
+In the example below, I started by left clicking on the area marked by
+a red dot (upper left corner of bounding box) and draging the mouse to
+the area marked by a blue dot (lower right corner of the bounding box)
+and letting go of the left mouse button.
+
+.. image:: images/select_sequence.png
+   :alt: Select Sequence
+   :align: center
+
+All of the lines which were not selected should be washed out as shown
+below:
+
+.. image:: images/washed_out.png
+   :alt: Tracks washed out
+   :align: center
+
+With a selection made, goto the **View** menu and select **View mussa alignment**.
+
+.. image:: images/view_mussa_alignment.png
+   :alt: View mussa alignment
+   :align: center
+
+You should see the alignment at the base-pair level as shown below.
+
+.. image:: images/mussa_alignment.png
+   :alt: Mussa alignment
+   :align: center
+
+
+
+
+Saving to an Image
+---------------------------------
+
+FIXME: Need to write this section
+
+
 Detailed Information
 --------------------