Mussa Manual: Todo comments

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

diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index 273e65a99899a71ff3e16259f5e29e6c6c58812d..19b9690359cee9c742a041dc49c57066b4ab5324 100644 (file)
--- a/doc/manual/mussagl_manual.rst
+++ b/doc/manual/mussagl_manual.rst
@@ -7,7 +7,31 @@ Brandon W. King
 
 Last updated: July 7th, 2006
 
-Updated to Mussagl build: 200 (Update to 286 in progress)
+Updated to Mussagl build: 287
+
+
+.. Things to add
+       * New features / change log
+       * Comment out anything isn't implemented yet.
+       * List of features that will be implemented in the future.
+       * Look into the homology mapping of UCSC.
+        * Add toggle to genomes.
+        * Document why one fast record per region.
+        * How to deal with the hazards of small utrs vis motif finder. (Add warning)
+       * Add warning about saving fasta file.
+       * Add a general principles section near the top
+               * Using comparison algorithm which will pickup all repeats
+               * Add info about repeatmasking
+               * Checking upstream and downstream genes for make sure you are in the right regions.
+       * Later on: look into Ensembl
+       * Look into method of homology instead of blating.
+       * Mention advantages of using mupa.
+       * Mention the difference between using arrows and scroll bar
+       * Document the color for motifs
+       * Update for Mac user left click
+
+* Wormbase/Flybase/mirBASE
+
 
 
 .. contents::
@@ -730,8 +754,16 @@ Note: Currently not implemented
 Motif Dialog
 ************
 
+**New Features:**
+ 
+Build 276
+ * Allow for toggling individual motifs on and off.
+
+Build 269
+ * Field added for naming motifs.
+
 Mussa has the ability to find lab motifs using the `IUPAC Nucleotide
-Code`_ for defining a motif. To define a motif, select **View > Edit
+Code`_ for defining a motif. To define a motif, select **Edit > Edit
 Motifs** menu item as shown below.
 
 .. image:: images/view_edit_motifs.png
@@ -742,14 +774,17 @@ You will see a dialog box appear with a "set motifs" button and 10
 rows for defining motifs and the color that will be displayed on the
 sequence. By default all 10 motifs start off as with white as the
 color. In the image below, I changed the color from white to blue to
-make it easier to see.
+make it easier to see. The first text box is for the motif and the
+second box is for the name of the motif. The check box defines whether
+the motif is displayed or not.
 
 .. image:: images/motif_dialog_start.png
    :alt: Motif Dialog
    :align: center
 
 Now lets make a motif **'AT[C or G]CT'**. Using the `IUPAC Nucleotide
-Code`_, type in **'ATSCT'** into the first box as shown below.
+Code`_, type in **'ATSCT'** into the first box and 'My Motif' for the
+name in the second box as shown below.
 
 .. image:: images/motif_dialog_enter_motif.png
    :alt: Enter Motif