Mussagl Manual: Docs 1.0 (part 3)

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

diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index ed4642d9dccc273d2d3df9ea9d1f7b1bad2e0477..b980016da46a4b646aca913e529b67fde049c9c7 100644 (file)
--- a/doc/manual/mussagl_manual.rst
+++ b/doc/manual/mussagl_manual.rst
@@ -39,17 +39,16 @@ Documentation for Mussagl v1.0
 Status
 ======
 
-Major New Features
-------------------
-
- * Build 381
-   * Analysis "Save As" feature
-
-Change Log
-----------
+..
 
-.. INSERT CHANGE LOG HERE
-.. END INSERT CHANGE LOG
+  Major New Features
+  .. ------------------
+  
+  Change Log
+  .. ----------
+  
+  .. INSERT CHANGE LOG HERE
+  .. END INSERT CHANGE LOG
 
 Features to be Implemented
 --------------------------
@@ -80,7 +79,7 @@ Short History of Mussa
 Mussa Python/PMW Prototype
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-First Python/PMW based protoype.
+First Python/PMW based prototype.
 
 Mussa C++/FLTK
 ~~~~~~~~~~~~~~
@@ -128,11 +127,11 @@ Install
 
 Mac OS X
 ~~~~~~~~
-Once you have downloaded the .dmg file, double click on it and follow
-the install instructions. 
-
-FIXME: Mention how to launch the program.
 
+ * Download .dmg file.
+ * Double click on .dmg file.
+ * Drag Mussa icon to your /Applications folder.
+ * Double Click on Mussa icon to open program.
 
 Windows XP
 ~~~~~~~~~~
@@ -269,13 +268,15 @@ open.
 
 If you would like to see an example, you can load the
 **mck3test.mupa** file in the examples directory that comes with
-Mussagl.
+Mussagl or read the `Step 5 - Create Analysis` section from the
+`Obtaining Input Data - Continued`_ section.
 
 .. image:: images/load_mupa_dialog.png
    :alt: Load Mussa Parameters Dialog
    :align: center
 
 
+
 Load an analysis
 ~~~~~~~~~~~~~~~~
 
@@ -378,6 +379,9 @@ between the sequences (i.e. not reverse complement matches)
 The amount of sequence conservation shown will depend on how much your
 sequences are related and the `dynamic threshold`_ you are using.
 
+To **deselect**, click and drag over any white area and then release
+the mouse button.
+
 
 Blue conservation tracks
 ~~~~~~~~~~~~~~~~~~~~~~~~
@@ -395,6 +399,8 @@ to the sequence attached to the top of the blue line.
 The amount of sequence conservation shown will depend on how much your
 sequences are related and the `dynamic threshold`_ you are using.
 
+To **deselect**, click and drag over any white area and then release
+the mouse button.
 
 Zoom Factor
 ~~~~~~~~~~~
@@ -704,6 +710,10 @@ You should see the alignment at the base-pair level as shown below.
 Sub-analysis
 ------------
 
+Sub-analysis was created to allow you to analyze a sub-region using
+different parameters. This may allow you to find matches which may not
+have shown up with your initial settings.
+
 To run a sub-analysis **highlight** a section of sequence and *right
 click* on it and select **Add to subanalysis**. To the same for the
 sequences shown in orange in the screenshot below. Note that you **are