Mussa Manual: create/load analysis section updated

 * Updated text/screenshots in the "Create new analysis" section (ticket #169)
 * Updated text/screenshots in "Load a mussa parameter file" section. (ticket #181)
 * Updated text/screenshots in "Load an analysis" section. (ticket #185)

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diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index 949a424f4dea77729101fa9992d57a9aa6a43085..9d3d61ef9627ed73e325b07aa74f2a3d550e8393 100644 (file)
--- a/doc/manual/mussagl_manual.rst
+++ b/doc/manual/mussagl_manual.rst
@@ -5,9 +5,9 @@ Mussagl Manual
 Brandon W. King
 ---------------
 
-Last updated: Oct 16th, 2006
+Last updated: Oct 17th, 2006
 
-Updated to Mussagl build: 287? (In process to 424)
+Updated to Mussagl build: (In process to 424)
 
 
 .. Things to add
@@ -507,11 +507,12 @@ Instructions:
     'demo_w30_t20'. Mussa will create a folder with this name to store
     the analysis files in once it has been run.
 
- 2. Choose a `window size`_. For this demo **choose 30**.
-
- 3. Choose a threshold_... for this demo **choose 20**. See the
+ 2. Choose a threshold_... for this demo **choose 20**. See the
     Threshold_ section for more detailed information.
 
+ 3. Choose a `window size`_. For this demo **choose 30**.
+
+
  4. Choose the number of sequences_ you would like. For this demo
     **choose 3**.
 
@@ -519,12 +520,13 @@ Instructions:
    :alt: Steps 1-4
    :align: center
 
-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
-your sequence.
+First enter the species name of "Human" in the first "Species" text
+box. 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. Make sure to give them a species
+name as well. Note that you can create annotation files using the
+mussa `Annotation File Format`_ to add annotations to your sequence.
 
 .. image:: images/define_analysis_step2.png
    :alt: Choose sequences
@@ -537,10 +539,13 @@ something similar to the following screen shot.
    :alt: Mussagl Demo
    :align: center
 
-This analysis is now saved in a directory called **demo_w30_t20** in
-the current working directory. If you close and reopen Mussagl, you
-can reload the saved analysis. See `Load an analysis`_ section below
-for details.
+By default your analysis is NOT saved. If you try to close an analysis
+without saving, you will be prompted with a dialog box asking you if
+you would like to save your analysis. The `Saving`_ section for
+details on saving your analysis. When saving, choose directory and
+give the analysis the name **demo_w30_t20**. If you close and reopen
+Mussagl, you will then be able to load the saved analysis. See `Load
+an analysis`_ section below for details.
 
 
 Load a mussa parameter file
@@ -551,7 +556,7 @@ parameter file. See the `Parameter File Format`_ section for details
 on creating a .mupa file.
 
 Once you have a .mupa file created, load Mussagl and select the **File >
-Load Mussa Parameters** menu option. Select the .mupa file and click
+Create Analysis from File** menu option. Select the .mupa file and click
 open. 
 
 .. image:: images/load_mupa_menu.png
@@ -571,7 +576,7 @@ Load an analysis
 ~~~~~~~~~~~~~~~~
 
 To load a previously run analysis open Mussagl and select the **File >
-Load Analysis** menu option. Select an analysis **directory** and
+Open Existing Analysis** menu option. Select an analysis **directory** and
 click open.
 
 .. image:: images/load_analysis_menu.png