doc/manual/mussagl_manual.adp

   1 <!DOCTYPE DCF>
   2 <assistantconfig version="3.2.0">
   3
   4         <profile>
   5           <property name="name">mussaglmanual</property>
   6           <property name="title">Mussagl Manual</property>
   7           <property name="applicationicon">images/handbook.png</property>
   8           <property name="startpage">mussagl_manual.html</property>
   9           <property name="aboutmenutext">About Mussagl Manual</property>
  10           <property name="abouturl">about.txt</property>
  11           <property name="assistantdocs">.</property>
  12         </profile>
  13
  14         <DCF ref="mussagl_manual.html" icon="handbook.png" imagedir="../img/"
  15                       title="Mussagl Manual">
  16
  17             <section ref="./mussagl_manual.html#contents" title="Contents" />
  18
  19             <section ref="./mussagl_manual.html#status" title="Status">
  20                 <section ref="./mussagl_manual.html#features-to-be-implemented" />
  21             </section>
  22
  23             <section ref="./mussagl_manual.html#introduction" title="Introduction">
  24                 <section ref="./mussagl_manual.html#what-is-mussagl" title="What is Mussagl?">
  25                     <keyword ref="./mussagl_manual.html#what-is-mussagl">About</keyword>
  26                 </section>
  27                 <section ref="./mussagl_manual.html#short-history-of-mussa" title="Short History of Mussa">
  28                     <section ref="./mussagl_manual.html#mussa-python-pmw-prototype" title="Mussa Python/PMW Prototype"/>
  29                     <section ref="./mussagl_manual.html#mussa-c-fltk" title="Mussa C++/FLTK"/>
  30                     <section ref="./mussagl_manual.html#mussa-c-qt-opengl" title="Mussagl C++/Qt/OpenGL"/>
  31                 </section>
  32             </section>
  33
  34             <section ref="./mussagl_manual.html#getting-mussagl" title="Getting Mussagl">
  35                 <section ref="./mussagl_manual.html#license" title="License"/>
  36                 <section ref="./mussagl_manual.html#platforms" title="Platforms"/>
  37                 <section ref="./mussagl_manual.html#download" title="Download"/>
  38
  39                 <section ref="./mussagl_manual.html#install" title="Install">
  40                   <section ref="./mussagl_manual.html#mac-os-x" title="Mac OS X"/>
  41                   <section ref="./mussagl_manual.html#windows-xp" title="Windows XP"/>
  42                   <section ref="./mussagl_manual.html#linux" title="Linux"/>
  43                   <section ref="./mussagl_manual.html#build-from-source" title="Build from Source"/>
  44                 </section>
  45
  46             </section>
  47
  48             <section ref="./mussagl_manual.html#using-mussagl" title="Using Mussagl">
  49
  50                 <section ref="./mussagl_manual.html#launch-mussagl" title="Launch Mussagl"/>
  51
  52                 <section ref="./mussagl_manual.html#create-load-analysis" title="Create/Load Analysis">
  53                   <section ref="./mussagl_manual.html#create-a-new-analysis" title="Create a new analysis"/>
  54                   <section ref="./mussagl_manual.html#load-a-mussa-parameter-file" title="Load a mussa parameter file"/>
  55                   <section ref="./mussagl_manual.html#load-an-analysis" title="Load an analysis"/>
  56                 </section>
  57
  58                 <section ref="./mussagl_manual.html#main-window" title="Main Window">
  59                   <section ref="./mussagl_manual.html#overview" title="Overview"/>
  60                   <section ref="./mussagl_manual.html#dna-sequence-black-bars" title="DNA Sequence (black bars)"/>
  61                   <section ref="./mussagl_manual.html#annotation" title="Annotation"/>
  62                   <section ref="./mussagl_manual.html#motif" title="Motif"/>
  63                   <section ref="./mussagl_manual.html#red-conservation-tracks" title="Red Conservation Tracks"/>
  64                   <section ref="./mussagl_manual.html#blue-conservation-tracks" title="Blue Conservation Tracks"/>
  65                   <section ref="./mussagl_manual.html#zoom-factor" title="Zoom Factor"/>
  66                   <section ref="./mussagl_manual.html#dynamic-threshold" title="Dynamic Threshold"/>
  67                   <section ref="./mussagl_manual.html#sequence-information-bar" title="Sequence Information Bar"/>
  68                   <section ref="./mussagl_manual.html#sequence-scroll-bar" title="Sequence Scroll Bar"/>
  69                 </section>
  70
  71                 <section ref="./mussagl_manual.html#saving" title="Saving">
  72                   <section ref="./mussagl_manual.html#save-on-close" title="Save on close" />
  73                   <section ref="./mussagl_manual.html#save-analysis" title="Save Analysis" />
  74                   <section ref="./mussagl_manual.html#save-analysis-as" title="Save Analysis As" />
  75                   <section ref="./mussagl_manual.html#save-motif-list" title="Save Motif List" />
  76                 </section>
  77
  78                 <section ref="./mussagl_manual.html#viewing-multiple-analyses" title="Viewing Multiple Analyses" />
  79
  80
  81                 <section ref="./mussagl_manual.html#annotations-motifs" title="Annotations / Motifs">
  82                   <section ref="./mussagl_manual.html#annotations" title="Annotations"/>
  83                   <section ref="./mussagl_manual.html#motifs" title="Motifs">
  84                     <section ref="./mussagl_manual.html#load-motifs-from-file" title="Load motifs from File"/>
  85                     <section ref="./mussagl_manual.html#save-motifs-to-file" title="Save Motifs to File"/>
  86                     <section ref="./mussagl_manual.html#motif-dialog" title="Motif Dialog">
  87                         <section ref="./mussagl_manual.html#deleting-a-motif" title="Deleting a Motif" />
  88                     </section>
  89                   </section>
  90
  91                 </section>
  92
  93                 <section ref="./mussagl_manual.html#view-mussa-alignments" title="View Mussa Alignments"/>
  94                 <section ref="./mussagl_manual.html#sub-analysis" title="Sub-analysis" />
  95                 <section ref="./mussagl_manual.html#copying-sequence-to-clipboard" title="Copying sequence to clipboard" />
  96
  97                 <section ref="./mussagl_manual.html#saving-to-an-image" title="Saving to an Image"/>
  98
  99                 <section ref="./mussagl_manual.html#detailed-information" title="Detailed Information">
 100                   <section ref="./mussagl_manual.html#threshold" title="Threshold"/>
 101                   <section ref="./mussagl_manual.html#window-size" title="Window Size"/>
 102                   <section ref="./mussagl_manual.html#sequences" title="Sequences"/>
 103                 </section>
 104
 105                 <section ref="./mussagl_manual.html#mussa-file-formats" title="Mussa File Formats">
 106                   <section ref="./mussagl_manual.html#parameter-file-format" title="Parameter File Format"/>
 107                   <section ref="./mussagl_manual.html#annotation-file-format" title="Annotation File Format"/>
 108                   <section ref="./mussagl_manual.html#motif-file-format" title="Motif File Format"/>
 109                   <section ref="./mussagl_manual.html#iupac-necleotide-code" title="IUPAC Nucleotide Code"/>
 110                 </section>
 111
 112                 <section ref="./mussagl_manual.html#obtaining-input-data-continued" title="Obtaining Input Data - Continued">
 113                         <section ref="./mussagl_manual.html#ucsc-genome-browser-method" title="UCSC Genome Browser Method" >
 114                                 <section ref="./mussagl_manual.html#step-1-find-smn1" title="Step 1 - Find SMN1"/>
 115                                 <section ref="./mussagl_manual.html#step-2-download-cds-utr-sequence-for-annotations" title="Step 2 - Download CDS/UTR sequence for annotations"/>
 116                                 <section ref="./mussagl_manual.html#step-3-download-gene-and-upstream-downstream-sequence" title="Step 3 - Download gene and upstream/downstream sequence"/>
 117                                 <section ref="./mussagl_manual.html#step-4-same-similar-related-gene-other-species" title="Step 4 - Same/similar/related gene other species."/>
 118                                 <section ref="./mussagl_manual.html#step-5-create-analysis" title="Step 5 - Create Analysis"/>
 119                         </section>
 120                 </section>
 121
 122
 123                  <section ref="./mussagl_manual.html#understanding-mussa" title="Understanding Mussa"/>
 124                          <section ref="./mussagl_manual.html#command-line" title="Command Line"/>
 125                          <section ref="./mussagl_manual.html#performance" title="Performance">
 126                                  <section ref="./mussagl_manual.html#algorithm-behavior" title="Algorithm Behavior"/>
 127                                  <section ref="./mussagl_manual.html#repeats" title="Repeats"/>
 128                          </section>
 129                          <section ref="./mussagl_manual.html#details" title="Details">
 130                                  <section ref="./mussagl_manual.html#case-conservation-track-suddenly-stops" title="Case: Conservation track suddenly stops"/>
 131                          </section>
 132                          <section ref="./mussagl_manual.html#python-interpreter" title="Python Interpreter"/>
 133                 </section>
 134             </section>
 135
 136
 137
 138
 139
 140         </DCF>
 141 </assistantconfig>