Copyright (C) 1995, 1996, Medical Research Council, Laboratory of Molecular Biology.

• Preface
• Tk_utils Library
• Tcl Scripting of Gap4
• Database I/O in C
• Annotation Functions in C
• Contig Registration Scheme
• Writing Packages

Preface

This manual is a guide to programming with the newer Tcl/Tk based Staden Package programs. It covers both using the programs in a scripting environment and writing modules to extend the functionality of them. The main content current covers the Tcl interfaces, with very little of the C functions currently documented. The reader should also be familier with the Tcl language.

Conventions Used in This Manual

Italic is used for:

• variable names
• command line values
• structure fields

Fixed width bold is used for:

• Code examples
• Command line arguments
• Typed in commands
• Program output

The general format of the syntax for the more complex Tcl commands is to list the command name in bold followed by one or more command line arguments in bold with command line values in italic. The command line values have a brief description of the use of the value followed by the type and a default value. The Tcl convention of surrounding optional values in question marks is used. For instance the edit_contig command has the following syntax.

edit_contig
 -io            io_handle:integer
 -contig        identifier:string
?-reading       identifier:string()?
?-pos           position:integer(1)?

-io and -pos both take integer values. -pos is optional, and has a default value of 1. -contig and -reading both require string values. -reading is optional, and has a default value of a blank string.