From 2fa290ee6aec131266678becf395f968d0039989 Mon Sep 17 00:00:00 2001
From: Brandon King <kingb@caltech.edu>
Date: Mon, 16 Nov 2009 12:15:55 -0800
Subject: [PATCH] Qt Assistant document format changed from previous versions. 
 * The .adp file is now obsolete.  * Added new .qhp and .qhcp versions.

Use qcollectiongenerator mussagl_manual.qhcp to generate the help collection file.

To use the collection file with the assistant, use:
assistant -collectionFile mussagl_manual.qhc
---
 doc/manual/about.txt           |   5 +
 doc/manual/images/mussa.png    | Bin 0 -> 887 bytes
 doc/manual/mussagl_manual.adp  |   3 -
 doc/manual/mussagl_manual.qhcp |  31 ++++++
 doc/manual/mussagl_manual.qhp  | 191 +++++++++++++++++++++++++++++++++
 5 files changed, 227 insertions(+), 3 deletions(-)
 create mode 100644 doc/manual/about.txt
 create mode 100644 doc/manual/images/mussa.png
 create mode 100644 doc/manual/mussagl_manual.qhcp
 create mode 100644 doc/manual/mussagl_manual.qhp

diff --git a/doc/manual/about.txt b/doc/manual/about.txt
new file mode 100644
index 0000000..248e258
--- /dev/null
+++ b/doc/manual/about.txt
@@ -0,0 +1,5 @@
+MussaGL v1.1.0
+
+Authors:
+ Diane Trout, Tristan De Buysscher, Brandon King
+ 
\ No newline at end of file
diff --git a/doc/manual/images/mussa.png b/doc/manual/images/mussa.png
new file mode 100644
index 0000000000000000000000000000000000000000..02008b41fb6ec11a4708e8a99f83235b296854de
GIT binary patch
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literal 0
HcmV?d00001

diff --git a/doc/manual/mussagl_manual.adp b/doc/manual/mussagl_manual.adp
index bce529f..8fd2b55 100644
--- a/doc/manual/mussagl_manual.adp
+++ b/doc/manual/mussagl_manual.adp
@@ -131,9 +131,6 @@
 			 </section>
 			 <section ref="./mussagl_manual.html#python-interpreter" title="Python Interpreter"/>
 		</section>
-
-		   
-
             </section>
 
 	    
diff --git a/doc/manual/mussagl_manual.qhcp b/doc/manual/mussagl_manual.qhcp
new file mode 100644
index 0000000..72ed9b0
--- /dev/null
+++ b/doc/manual/mussagl_manual.qhcp
@@ -0,0 +1,31 @@
+<?xml version="1.0" encoding="utf-8" ?>
+ <QHelpCollectionProject version="1.0">
+     <assistant>
+         <title>MussaGL Manual</title>
+         <startPage>qthelp://edu.caltech.woldlab.mussagl.1_0_0/doc/mussagl_manual.html</startPage>
+         <currentFilter>myfilter</currentFilter>
+         <applicationIcon>images/mussa.png</applicationIcon>
+         <enableFilterFunctionality>false</enableFilterFunctionality>
+         <enableDocumentationManager>false</enableDocumentationManager>
+         <enableAddressBar visible="true">true</enableAddressBar>
+         <cacheDirectory>mycompany/myapplication</cacheDirectory>
+         <aboutMenuText>
+             <text>About MussaGL</text>
+         </aboutMenuText>
+         <aboutDialog>
+             <file>about.txt</file>
+             <icon>images/mussa.png</icon>
+         </aboutDialog>
+     </assistant>
+     <docFiles>
+         <generate>
+             <file>
+                 <input>mussagl_manual.qhp</input>
+                 <output>mussagl_manual.qch</output>
+             </file>
+         </generate>
+         <register>
+             <file>mussagl_manual.qch</file>
+         </register>
+     </docFiles>
+ </QHelpCollectionProject>
\ No newline at end of file
diff --git a/doc/manual/mussagl_manual.qhp b/doc/manual/mussagl_manual.qhp
new file mode 100644
index 0000000..d9dda51
--- /dev/null
+++ b/doc/manual/mussagl_manual.qhp
@@ -0,0 +1,191 @@
+<?xml version="1.0" encoding="UTF-8"?>
+ <QtHelpProject version="1.0">
+     <namespace>edu.caltech.woldlab.mussagl.1_0_0</namespace>
+     <virtualFolder>doc</virtualFolder>
+     <customFilter name="MussaGL 1.0">
+         <filterAttribute>mussagl</filterAttribute>
+         <filterAttribute>1.0</filterAttribute>
+     </customFilter>
+     <filterSection>
+         <filterAttribute>mussagl</filterAttribute>
+         <filterAttribute>1.0</filterAttribute>
+         <toc>
+            <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?">
+                    <section ref="./mussagl_manual.html#what-is-mussagl">About</section>
+                </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 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#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#deleting-a-motif" title="Deleting a Motif" />
+		    </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">
+		  <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 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>
+         </toc>
+         <keywords>
+             <keyword name="foo" id="MyApplication::foo" ref="doc.html#foo"/>
+             <keyword name="bar" ref="doc.html#bar"/>
+             <keyword id="MyApplication::foobar" ref="doc.html#foobar"/>
+         </keywords>
+         <files>
+             <file>mussagl_manual.html</file>
+             <file>images/annotation.png</file>
+            <file>images/arrow_template.xcf</file>
+            <file>images/color_chooser.png</file>
+            <file>images/conservation_tracks.png</file>
+            <file>images/copy_sequence.png</file>
+            <file>images/define_analysis.png</file>
+            <file>images/define_analysis_step1.png</file>
+            <file>images/define_analysis_step1a.png</file>
+            <file>images/define_analysis_step2.png</file>
+            <file>images/demo.png</file>
+            <file>images/dynamic_threshold.png</file>
+            <file>images/load_analysis_menu.png</file>
+            <file>images/load_mck_example.png</file>
+            <file>images/load_motif.png</file>
+            <file>images/load_mupa_dialog.png</file>
+            <file>images/load_mupa_menu.png</file>
+            <file>images/motif.png</file>
+            <file>images/motif_dialog_bar_after.png</file>
+            <file>images/motif_dialog_bar_before.png</file>
+            <file>images/motif_dialog_enter_motif.png</file>
+            <file>images/motif_dialog_start.png</file>
+            <file>images/motif_toggle.png</file>
+	    <file>images/mussa.png</file>
+            <file>images/mussa_alignment.png</file>
+            <file>images/new_mussa_window.png</file>
+            <file>images/new_mussa_window_menu.png</file>
+            <file>images/opened.png</file>
+            <file>images/save_analysis.png</file>
+            <file>images/save_analysis_as.png</file>
+            <file>images/save_motifs.png</file>
+            <file>images/save_to_image_dialog.png</file>
+            <file>images/save_to_image_menu.png</file>
+            <file>images/scroll_bar.png</file>
+            <file>images/select_sequence.png</file>
+            <file>images/sequence_bar.png</file>
+            <file>images/seq_info_bar.png</file>
+            <file>images/smn1_dir_structure.png</file>
+            <file>images/smn1_human_annot.png</file>
+            <file>images/smn1_human_annot_plus_human.png</file>
+            <file>images/smn1_human_protein.png</file>
+            <file>images/subanalysis_dialog.png</file>
+            <file>images/subanalysis_done.png</file>
+            <file>images/subanalysis_select_seqs.png</file>
+            <file>images/threshold_change.gif</file>
+            <file>images/ucsc_gb_smn1_description_page.png</file>
+            <file>images/ucsc_gb_smn1_human.png</file>
+            <file>images/ucsc_gb_smn1_human_blat.png</file>
+            <file>images/ucsc_gb_smn1_human_blat_hits.png</file>
+            <file>images/ucsc_gb_smn1_human_blat_paste.png</file>
+            <file>images/ucsc_gb_smn1_human_blat_to_browser.png</file>
+            <file>images/ucsc_gb_smn1_human_click_smn1.png</file>
+            <file>images/ucsc_gb_smn1_human_dna.png</file>
+            <file>images/ucsc_gb_smn1_human_dna_option.png</file>
+            <file>images/ucsc_gb_smn1_human_get_dna.png</file>
+            <file>images/ucsc_gb_smn1_human_get_genomic_sequence.png</file>
+            <file>images/ucsc_gb_smn1_human_get_genomic_sequence_diff.png</file>
+            <file>images/ucsc_gb_smn1_human_get_genomic_sequence_submit.png</file>
+            <file>images/ucsc_gb_smn1_human_sequence.png</file>
+            <file>images/ucsc_gene_sorter.png</file>
+            <file>images/ucsc_genome_browser_home.png</file>
+            <file>images/ucsc_gs_found.png</file>
+            <file>images/ucsc_gs_genome_position.png</file>
+            <file>images/ucsc_gs_smn1.png</file>
+            <file>images/ucsc_gs_sort_name_sim.png</file>
+            <file>images/ucsc_menu_bar_gene_sorter.png</file>
+            <file>images/view_edit_motifs.png</file>
+            <file>images/view_mussa_alignment.png</file>
+            <file>images/washed_out.png</file>
+            <file>images/window_overview.png</file>
+            <file>images/window_overview.xcf</file>
+            <file>images/zoom_factor.png</file>
+         </files>
+     </filterSection>
+ </QtHelpProject>
+ 
\ No newline at end of file
-- 
2.30.2