From d0129f1807458a2497636b633cb0cc17c27a86fd Mon Sep 17 00:00:00 2001
From: Brandon King <kingb@caltech.edu>
Date: Wed, 1 Nov 2006 17:39:10 +0000
Subject: [PATCH] Mussagl Manual: mussa_manual.adp updated for 1.0 docs  *
 Updated for 1.0 documentation.

---
 doc/manual/mussagl_manual.adp | 63 ++++++++++++++++++++++++++++++-----
 1 file changed, 55 insertions(+), 8 deletions(-)

diff --git a/doc/manual/mussagl_manual.adp b/doc/manual/mussagl_manual.adp
index 2fb3b7b..bce529f 100644
--- a/doc/manual/mussagl_manual.adp
+++ b/doc/manual/mussagl_manual.adp
@@ -16,14 +16,19 @@
 
             <section ref="./mussagl_manual.html#contents" title="Contents" />
 
+	    <section ref="./mussagl_manual.html#status" title="Status">
+		<section ref="./mussagl_manual.html#features-to-be-implemented" />
+            </section>
+
             <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"/>
+                    <keyword ref="./mussagl_manual.html#what-is-mussagl">About</keyword>
+                </section>
+                <section ref="./mussagl_manual.html#short-history-of-mussa" title="Short History of Mussa">
+		    <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>
             
 	    <section ref="./mussagl_manual.html#getting-mussagl" title="Getting Mussagl">
@@ -55,25 +60,40 @@
 		  <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#red-conservation-tracks" title="Red Conservation Tracks"/>
+		  <section ref="./mussagl_manual.html#blue-conservation-tracks" title="Blue Conservation Tracks"/>
 		  <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#saving" title="Saving">
+		  <section ref="./mussagl_manual.html#save-on-close" title="Save on close" />
+		  <section ref="./mussagl_manual.html#save-analysis" title="Save Analysis" />
+		  <section ref="./mussagl_manual.html#save-analysis-as" title="Save Analysis As" />
+		  <section ref="./mussagl_manual.html#save-motif-list" title="Save Motif List" />
+		</section>
+		
+		<section ref="./mussagl_manual.html#viewing-multiple-analyses" title="Viewing Multiple Analyses" />
+		
+
 		<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 ref="./mussagl_manual.html#motif-dialog" title="Motif Dialog">
+                        <section ref="./mussagl_manual.html#deleting-a-motif" title="Deleting a Motif" />
+		    </section>
                   </section> 
 		  
-                </section>
+                </section>		
 
 		<section ref="./mussagl_manual.html#view-mussa-alignments" title="View Mussa Alignments"/>
+		<section ref="./mussagl_manual.html#sub-analysis" title="Sub-analysis" />
+		<section ref="./mussagl_manual.html#copying-sequence-to-clipboard" title="Copying sequence to clipboard" />
+
 		<section ref="./mussagl_manual.html#saving-to-an-image" title="Saving to an Image"/>
 
 		<section ref="./mussagl_manual.html#detailed-information" title="Detailed Information">
@@ -89,8 +109,35 @@
 		  <section ref="./mussagl_manual.html#iupac-necleotide-code" title="IUPAC Nucleotide Code"/>
                 </section>
 
+		<section ref="./mussagl_manual.html#obtaining-input-data-continued" title="Obtaining Input Data - Continued">
+			<section ref="./mussagl_manual.html#ucsc-genome-browser-method" title="UCSC Genome Browser Method" >
+				<section ref="./mussagl_manual.html#step-1-find-smn1" title="Step 1 - Find SMN1"/>
+				<section ref="./mussagl_manual.html#step-2-download-cds-utr-sequence-for-annotations" title="Step 2 - Download CDS/UTR sequence for annotations"/>
+				<section ref="./mussagl_manual.html#step-3-download-gene-and-upstream-downstream-sequence" title="Step 3 - Download gene and upstream/downstream sequence"/>
+				<section ref="./mussagl_manual.html#step-4-same-similar-related-gene-other-species" title="Step 4 - Same/similar/related gene other species."/>
+				<section ref="./mussagl_manual.html#step-5-create-analysis" title="Step 5 - Create Analysis"/>
+			</section>
+		</section>
+
+
+		 <section ref="./mussagl_manual.html#understanding-mussa" title="Understanding Mussa"/>
+			 <section ref="./mussagl_manual.html#command-line" title="Command Line"/>
+			 <section ref="./mussagl_manual.html#performance" title="Performance">
+				 <section ref="./mussagl_manual.html#algorithm-behavior" title="Algorithm Behavior"/>
+				 <section ref="./mussagl_manual.html#repeats" title="Repeats"/>
+			 </section>
+			 <section ref="./mussagl_manual.html#details" title="Details">
+				 <section ref="./mussagl_manual.html#case-conservation-track-suddenly-stops" title="Case: Conservation track suddenly stops"/>
+			 </section>
+			 <section ref="./mussagl_manual.html#python-interpreter" title="Python Interpreter"/>
+		</section>
+
+		   
+
             </section>
 
+	    
+
             
             
         </DCF>
-- 
2.30.2