Contents

• Contents
• Getting Started
  • A Simple Example
    • The Main DD Window
    • Loading a File
    • Making a Restriction Map
    • The Importance of Constraints
    • Experimental Error
    • Asserting Constraints
    • Saving to a File
  • Data Entry
    • Graphical Data Entry
    • Typing in Values
  • Doing More With DD
• Reference
  • Six Main Windows
    • Buttons
      • Popup Menus.
        • Dialog Boxes.
          • How Do I Give This Command?
  • The Top Window
    • Help
    • Configure
      • Display in Monochrome/Color.
      • Set Default Data Directory.
        • Accept Directory <current directory>.
        • Subdirectories of Current Directory.
        • Move Up Directory Tree.
        • Macintosh Dialog Box.
      • Show Details of Map Building.
    • Exit
  • The Digest Data Window
    • Digests
      • Method 1: Graphical Interface.
        • Name of Lane.
          • Add New Fragments via Mouse.
          • Add New Fragments via Keyboard.
          • Change Enzyme.
          • Change Size-Estimate Error Ranges.
      • Method 2: Type in Values.
        • Define New Data Set Dialog Box.
          • Global Error Range.
      • Loaded Files and Double Digests.
      • Other Files in Data Directory.
      • Subdirectories of Data Directory.
      • Move Up Directory Tree.
    • Save
      • Save Data in a New File.
        • Save Data In New File Dialog Box.
      • Append Data to an Existing File.
        • Contents of Current Data Directory < directory name >.
        • Move up Directory tree.
        • Macintosh File Dialog Box.
      • Replace Data in an Existing File.
    • Error
      • Change Size-Estimate Error Ranges.
      • Change Basis of Size Comparisons.
        • Same Gel.
        • Separate Gels.
      • Unseen Fragments: Size Ceiling.
        • Size Ceiling Menu (0 bp to 4000 bp).
      • Unseen Fragments: Number Allowed Per Match.
        • Number of Unseen Fragments menu: (0, 1, 2).
    • Other
      • Choose Lane Standard.
      • Drop Lane Standard.
      • Hide/Show Lane Standard.
      • Critique Current Data.
      • Hide/Show Settings.
      • Rename Digest.
      • Set DNA Type.
    • Digest: <Title>
    • Gel Lane Title
      • Add New Fragments via Mouse.
      • Add New Fragments via Keyboard.
      • Change Size-Estimate Error Ranges.
      • Change Enzyme (or Lane Standard).
    • Band on Gel
      • About Fragment <enzyme, size>.
      • Assert Constraint.
      • Identical.
      • Not Identical.
      • Bigger Than.
      • Smaller Than.
      • Contains (Part Of).
      • Not Contains (Not Part of).
      • Change Size-Estimate Error Ranges.
      • Change Size Data.
      • Remove Fragment.
  • The Constraints Window
    • Constraints
      • Drop.
      • Negate (Un-Negate).
    • Add
      • Identical.
      • Not Identical.
      • Bigger Than.
      • Smaller Than.
      • Contains (Part Of).
      • Not Contains (Not Part of).
    • Drop
    • Negate
  • Maps
    • Make Maps
      • NOTE, WARNING or ERROR concerning your data.
      • WARNING: This looks like a hard problem.
    • Configure
      • Change Map Display Format.
        • Text and Linear Only.
        • Text and Circular Only.
        • Text, Linear, and Circular.
      • Change Map File Output Style.
      • Anchor a Double Digest Fragment in Left/12-O'Clock Position.
    • Save
      • Change Map File Output Style.
      • Save All Maps to File.
      • Save Current Map to File.
  • Match Details
• Installation and Internals
  • Macintosh
    • Installation
    • Troubleshooting
  • Unix and X11
    • Installation
    • Troubleshooting
  • All Versions
    • Error Recovery
    • Memory Management
    • Saving Large Map Files
  • Further Information and Suggestions
• About this document ...