From: Brandon King Date: Tue, 17 Oct 2006 18:59:56 +0000 (+0000) Subject: Mussa Manual: updated motif dialog section. X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=commitdiff_plain;h=1ede1dbcc1e97b4ed9669a5ea9372119f9725cb5 Mussa Manual: updated motif dialog section. * Updated text/screenshots in the motif dialog section. (ticket #191) --- diff --git a/doc/manual/images/color_chooser.png b/doc/manual/images/color_chooser.png index 450cbb8..878bb59 100644 Binary files a/doc/manual/images/color_chooser.png and b/doc/manual/images/color_chooser.png differ diff --git a/doc/manual/images/motif_dialog_bar_after.png b/doc/manual/images/motif_dialog_bar_after.png index 9cf9e18..1a4723d 100644 Binary files a/doc/manual/images/motif_dialog_bar_after.png and b/doc/manual/images/motif_dialog_bar_after.png differ diff --git a/doc/manual/images/motif_dialog_bar_before.png b/doc/manual/images/motif_dialog_bar_before.png index 4a55c86..ed53f58 100644 Binary files a/doc/manual/images/motif_dialog_bar_before.png and b/doc/manual/images/motif_dialog_bar_before.png differ diff --git a/doc/manual/images/motif_dialog_enter_motif.png b/doc/manual/images/motif_dialog_enter_motif.png index 8c2b1d9..0fd0403 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 ef88d6e..ebd2e5c 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/mussagl_manual.rst b/doc/manual/mussagl_manual.rst index c02d631..23f08b9 100644 --- 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 +`_ by +`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 ---------------------