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Getting Started
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Double Digester Manual
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Double Digester Manual
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
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