From 03c2e1e928a8c2a4ea16d9b87cc851364c2a9a7b Mon Sep 17 00:00:00 2001
From: Brandon King <kingb@caltech.edu>
Date: Fri, 26 May 2006 21:45:33 +0000
Subject: [PATCH] Mussagl Manual QAssistant Profile

---
 doc/manual/mussagl_manual.adp | 97 +++++++++++++++++++++++++++++++++++
 1 file changed, 97 insertions(+)
 create mode 100644 doc/manual/mussagl_manual.adp

diff --git a/doc/manual/mussagl_manual.adp b/doc/manual/mussagl_manual.adp
new file mode 100644
index 0000000..2fb3b7b
--- /dev/null
+++ b/doc/manual/mussagl_manual.adp
@@ -0,0 +1,97 @@
+<!DOCTYPE DCF>
+<assistantconfig version="3.2.0">
+	
+	<profile>
+	  <property name="name">mussaglmanual</property>
+	  <property name="title">Mussagl Manual</property>
+	  <property name="applicationicon">images/handbook.png</property>
+	  <property name="startpage">mussagl_manual.html</property>
+	  <property name="aboutmenutext">About Mussagl Manual</property>
+	  <property name="abouturl">about.txt</property>
+	  <property name="assistantdocs">.</property>
+	</profile>
+
+        <DCF ref="mussagl_manual.html" icon="handbook.png" imagedir="../img/"
+	              title="Mussagl Manual">
+
+            <section ref="./mussagl_manual.html#contents" title="Contents" />
+
+            <section ref="./mussagl_manual.html#introduction" title="Introduction">
+                <section ref="./mussagl_manual.html#what-is-mussagl" title="What is Mussagl?">
+                    <keyword ref="./chap1/section1.html#foo">foo</keyword>
+                    <keyword ref="./chap1/section1.html#bla">bla</keyword>
+                    <section ref="./mussagl_manual.html#mussa-python-pmw-prototype" title="Mussa Python/PMW Prototype"/>
+                    <section ref="./mussagl_manual.html#mussa-c-fltk" title="Mussa C++/FLTK"/>
+                    <section ref="./mussagl_manual.html#mussa-c-qt-opengl" title="Mussagl C++/Qt/OpenGL"/>
+                </section>
+	    </section>
+            
+	    <section ref="./mussagl_manual.html#getting-mussagl" title="Getting Mussagl">
+                <section ref="./mussagl_manual.html#license" title="License"/>
+                <section ref="./mussagl_manual.html#platforms" title="Platforms"/>
+                <section ref="./mussagl_manual.html#download" title="Download"/>
+
+		<section ref="./mussagl_manual.html#install" title="Install">
+		  <section ref="./mussagl_manual.html#mac-os-x" title="Mac OS X"/>
+		  <section ref="./mussagl_manual.html#windows-xp" title="Windows XP"/>
+		  <section ref="./mussagl_manual.html#linux" title="Linux"/>
+		  <section ref="./mussagl_manual.html#build-from-source" title="Build from Source"/>
+                </section>
+
+            </section>
+
+	    <section ref="./mussagl_manual.html#using-mussagl" title="Using Mussagl">
+	    
+	        <section ref="./mussagl_manual.html#launch-mussagl" title="Launch Mussagl"/>
+                
+		<section ref="./mussagl_manual.html#create-load-analysis" title="Create/Load Analysis">
+		  <section ref="./mussagl_manual.html#create-a-new-analysis" title="Create a new analysis"/>
+		  <section ref="./mussagl_manual.html#load-a-mussa-parameter-file" title="Load a mussa parameter file"/>
+		  <section ref="./mussagl_manual.html#load-an-analysis" title="Load an analysis"/>
+                </section>
+
+		<section ref="./mussagl_manual.html#main-window" title="Main Window">
+		  <section ref="./mussagl_manual.html#overview" title="Overview"/>
+		  <section ref="./mussagl_manual.html#dna-sequence-black-bars" title="DNA Sequence (black bars)"/>
+		  <section ref="./mussagl_manual.html#annotation" title="Annotation"/>
+		  <section ref="./mussagl_manual.html#motif" title="Motif"/>
+		  <section ref="./mussagl_manual.html#conservation-tracks" title="Conservation Tracks"/>
+		  <section ref="./mussagl_manual.html#motif-toggle" title="Motif Toggle"/>
+		  <section ref="./mussagl_manual.html#zoom-factor" title="Zoom Factor"/>
+		  <section ref="./mussagl_manual.html#dynamic-threshold" title="Dynamic Threshold"/>
+		  <section ref="./mussagl_manual.html#sequence-information-bar" title="Sequence Information Bar"/>
+		  <section ref="./mussagl_manual.html#sequence-scroll-bar" title="Sequence Scroll Bar"/>
+                </section>
+
+		<section ref="./mussagl_manual.html#annotations-motifs" title="Annotations / Motifs">
+		  <section ref="./mussagl_manual.html#annotations" title="Annotations"/>
+		  <section ref="./mussagl_manual.html#motifs" title="Motifs">
+		    <section ref="./mussagl_manual.html#load-motifs-from-file" title="Load motifs from File"/>
+		    <section ref="./mussagl_manual.html#save-motifs-to-file" title="Save Motifs to File"/>
+		    <section ref="./mussagl_manual.html#motif-dialog" title="Motif Dialog"/>
+                  </section> 
+		  
+                </section>
+
+		<section ref="./mussagl_manual.html#view-mussa-alignments" title="View Mussa Alignments"/>
+		<section ref="./mussagl_manual.html#saving-to-an-image" title="Saving to an Image"/>
+
+		<section ref="./mussagl_manual.html#detailed-information" title="Detailed Information">
+		  <section ref="./mussagl_manual.html#threshold" title="Threshold"/>
+		  <section ref="./mussagl_manual.html#window-size" title="Window Size"/>
+		  <section ref="./mussagl_manual.html#sequences" title="Sequences"/>
+                </section>
+
+		<section ref="./mussagl_manual.html#mussa-file-formats" title="Mussa File Formats">
+		  <section ref="./mussagl_manual.html#parameter-file-format" title="Parameter File Format"/>
+		  <section ref="./mussagl_manual.html#annotation-file-format" title="Annotation File Format"/>
+		  <section ref="./mussagl_manual.html#motif-file-format" title="Motif File Format"/>
+		  <section ref="./mussagl_manual.html#iupac-necleotide-code" title="IUPAC Nucleotide Code"/>
+                </section>
+
+            </section>
+
+            
+            
+        </DCF>
+</assistantconfig>
\ No newline at end of file
-- 
2.30.2