Chapter 9. A Complete Application

Table of Contents

9.1. The ACD File (seqret.acd)
9.1.1. Application Definition
9.1.2. ACD File Sections
9.1.3. Data Definitions
9.1.4. Attributes
9.2. The C Source Code (seqret.c)
9.2.1. Variable Declarations
9.2.2. ACD File and Command line Processing
9.2.3. Retrieving Values from the ACD File
9.2.4. Sequence Handling
9.2.5. Exiting Cleanly
9.3. Inbuilt Functionality
9.4. Documentation (seqret.html)
9.5. Quality Assurance Tests

seqret was the first EMBOSS application and got its name from the its function (it can be used to retrieve sequences from databases) and partly from how the application source belies the complexity of the underlying library code. In simple terms, the program reads in a sequence and writes it out again, but there are many options which make it rather powerful. Its command line interface will prompt for an input stream of one or more sequences of any type, and prompt for an output stream. seqret reads and writes any sequence format that EMBOSS supports and uses the powerful Uniform Sequence Address or USA (see the EMBOSS Users Guide) for specifying the location and format of the sequence data.

The C source code, ACD file, quality assurance tests and documentation for seqret are exposed below, to give you an appreciation of all the basic components of a fully functioning EMBOSS application.