From: Brandon King <kingb@caltech.edu>
Date: Thu, 6 Jul 2006 21:28:06 +0000 (+0000)
Subject: Manual: Motif update
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=commitdiff_plain;h=f30a7f64b61411746cb3d2e1f0a9443f2c8b9e1b

Manual: Motif update

 * Updated screenshots and text to reflect changes to the motif dialog box.
---

diff --git a/doc/manual/images/motif_dialog_enter_motif.png b/doc/manual/images/motif_dialog_enter_motif.png
index c5a98c9..8c2b1d9 100644
Binary files a/doc/manual/images/motif_dialog_enter_motif.png and b/doc/manual/images/motif_dialog_enter_motif.png differ
diff --git a/doc/manual/images/motif_dialog_start.png b/doc/manual/images/motif_dialog_start.png
index 110ca88..ef88d6e 100644
Binary files a/doc/manual/images/motif_dialog_start.png and b/doc/manual/images/motif_dialog_start.png differ
diff --git a/doc/manual/images/view_edit_motifs.png b/doc/manual/images/view_edit_motifs.png
index f6c8ce3..c8140ee 100644
Binary files a/doc/manual/images/view_edit_motifs.png and b/doc/manual/images/view_edit_motifs.png differ
diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index 273e65a..778e9ab 100644
--- a/doc/manual/mussagl_manual.rst
+++ b/doc/manual/mussagl_manual.rst
@@ -7,7 +7,7 @@ Brandon W. King
 
 Last updated: July 7th, 2006
 
-Updated to Mussagl build: 200 (Update to 286 in progress)
+Updated to Mussagl build: 287
 
 
 .. contents::
@@ -730,8 +730,16 @@ 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 +750,17 @@ 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