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Mussagl Manual: Docs 1.0 updates (part two)
[mussa.git]
/
doc
/
manual
/
mussagl_manual.rst
diff --git
a/doc/manual/mussagl_manual.rst
b/doc/manual/mussagl_manual.rst
index ed4642d9dccc273d2d3df9ea9d1f7b1bad2e0477..df5426f561d53b5469b21289cb9916d09c99e0cd 100644
(file)
--- a/
doc/manual/mussagl_manual.rst
+++ b/
doc/manual/mussagl_manual.rst
@@
-39,17
+39,16
@@
Documentation for Mussagl v1.0
Status
======
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
--------------------------
Features to be Implemented
--------------------------
@@
-80,7
+79,7
@@
Short History of Mussa
Mussa Python/PMW Prototype
~~~~~~~~~~~~~~~~~~~~~~~~~~
Mussa Python/PMW Prototype
~~~~~~~~~~~~~~~~~~~~~~~~~~
-First Python/PMW based protoype.
+First Python/PMW based proto
t
ype.
Mussa C++/FLTK
~~~~~~~~~~~~~~
Mussa C++/FLTK
~~~~~~~~~~~~~~
@@
-128,11
+127,11
@@
Install
Mac OS X
~~~~~~~~
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
~~~~~~~~~~
Windows XP
~~~~~~~~~~
@@
-704,6
+703,10
@@
You should see the alignment at the base-pair level as shown below.
Sub-analysis
------------
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
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