Mussa Manual: Saving section

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

diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index 949a424f4dea77729101fa9992d57a9aa6a43085..c02d631afc4420ec7d93aa67a68d6e18fa371760 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
@@ -749,6 +754,43 @@ The scroll bar allows you to scroll through the sequence which is
 useful when you have zoomed in using the `zoom factor`_.
 
 
+Saving
+------
+
+Save on Close
+~~~~~~~~~~~~~
+
+FIXME: Write this.
+
+Save Analysis
+~~~~~~~~~~~~~
+
+After making changes, such as updating species names or adding/editing
+motifs, you can save these changes by selecting the **File > Save
+analysis** menu option or pressing **CTRL + S** (PC) or
+**Apple/Command Key + S** (on Mac).
+
+.. image:: images/save_analysis.png
+   :alt: Save analysis
+   :align: center
+
+Save Analysis As
+~~~~~~~~~~~~~~~~
+
+To save a copy of your analysis to a new location, select the **File >
+Save analysis as** menu option and choose a new location and name for
+your analysis.
+
+.. image:: images/save_analysis_as.png
+   :alt: Save analysis
+   :align: center
+
+Save Motif List
+~~~~~~~~~~~~~~~
+
+See `Save Motifs to File`_ in the `Motifs`_ section.
+
+
 Annotations / Motifs
 --------------------
 
@@ -787,7 +829,15 @@ To load a motif file, select **Load Motif List** item from the
 Save Motifs to File
 *******************
 
-Note: Currently not implemented
+Motifs from the `Motif Dialog`_ can be saved to file for use with
+other analyses. If you just want your motifs to be saved with your
+analysis, see the `save analysis`_ section for details.
+
+To save a motif list, select **File > Save Motifs** menu option.
+
+.. image:: images/save_motifs.png
+   :alt: Save Motifs
+   :align: center
 
 
 Motif Dialog