Mussa Manual: updated motif dialog section.

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

diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index c02d631afc4420ec7d93aa67a68d6e18fa371760..23f08b97e642ca5105e797bd5aef36ed95110261 100644 (file)
--- a/doc/manual/mussagl_manual.rst
+++ b/doc/manual/mussagl_manual.rst
@@ -843,14 +843,6 @@ To save a motif list, select **File > Save Motifs** menu option.
 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 **Edit > Edit
 Motifs** menu item as shown below.
@@ -859,38 +851,44 @@ Motifs** menu item as shown below.
    :alt: "View > Edit Motifs" Menu
    :align: center
 
-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. 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.
+You will see a dialog box appear with a "apply" button in the bottom
+right and one rows for defining motifs and the color that will be
+displayed on the sequence. When you start adding your first motif, an
+additional row will be added. The check box in the first column
+defines whether the motif is displayed or not. The second column is
+the motif display color. The third column is for the name of your
+motif and finally, the fourth column is motif itself.
 
 .. image:: images/motif_dialog_start.png
    :alt: Motif Dialog
    :align: center
 
 Now let's make a motif **'AT[C or G]CT'**. Using the `IUPAC Nucleotide
-Code`_, type in **'ATSCT'** into the first box and 'My Motif' for the
-name in the second box as shown below.
+Code`_, type in **'ATSCT'** into the motif field and **'My Motif'** for
+the name in the name field as shown below. 
+
+Notice how a second row appeared when you started to add the first
+motif. Every time you add a new motif, a new row will appear allowing
+you to add as many motifs as you need.
 
 .. image:: images/motif_dialog_enter_motif.png
    :alt: Enter Motif
    :align: center
 
 Now choose a color for your motif by clicking on the colored area to
-the left of the motif. In the image above, you would click on the blue
-square, but by default the squares will be white. Remember to choose a
-color that will show up well with a black bar as the background.
+the left of the name field. Remember to choose a color that will show
+up well with a black bar as the background. A good tool for picking a
+color is the `Colour Contrast Analyser
+<http://juicystudio.com/services/colourcontrast.php>`_ by
+`juicystudio.com <http://juicystudio.com/>`_.
 
 .. image:: images/color_chooser.png
    :alt: Color Chooser
    :align: center
 
-Once you have selected the color for your motif, click on the 'set
-motifs' button. Notice that if Mussa finds matches to your motif will
-now show up in the main Mussagl window.
+Once you have selected the color for your motif, click on the
+**'apply'** button. Notice that if Mussa finds matches to your motif
+will now show up in the main Mussa window.
 
 Before Motif:
 
@@ -904,6 +902,10 @@ After Motif:
    :alt: Sequence bar after motif
    :align: center
 
+To save your motifs with your analysis, see the `save analysis`_
+section. To save your motifs to a file, see the `save motifs to file`_
+section.
+
 
 View Mussa Alignments
 ---------------------