The application definition is given at the top of the file:

application: seqret 
[
  documentation: "Reads and writes (returns) sequences"
  groups: "Edit"
]

The application name (seqret) is given after the application: token. A succinct description of the application function ("Reads and writes (returns) sequences") is given after the documentation: attribute and will be printed to screen when the program is run. It also appears when the program is run with the -help qualifier. This text is also searched by the wossname utility, which displays applications after searching for keywords.

The groups: attribute has the value of "Edit", indicating that seqret belongs to the group "Edit", i.e. applications for sequence editing. All EMBOSS and EMBASSY applications are put into groups of related functionality (Section 4.2.4.1, “Application Group Names File (groups.standard)”).

Other attributes (see Section 4.3, “Data Definition”) may be given in the application definition.

The ACD file is organised into sections for Input, Advanced and Output sections, which are enclosed within text tokens (section: input, endsection: input etc):

section: input 
[
  information: "Input section"
  type: "page"
]
.
.
.
endsection: input

Clearly, the Input and Output sections are used for application inputs and outputs respectively. Advanced is used for application options which are never prompted for at the command line. In practice there are other types of application parameters and corresponding sections that might appear in the ACD file (see Section 4.1, “Introduction to ACD File Development”).

These sections contain the ACD data definitions which define the application input and output data and other application parameters. Conceptually the data definitions can be thought of as two basic types, either basic input and output files or other types that control the application. For example, sequence and outseq are data definitions for input and output files:

seqall: sequence  
[
    parameter: "Y"
    type: "gapany"
    features: "$(feature)"
]
.
.
.
seqoutall: outseq  
[
    parameter: "Y"
    features: "$(feature)"
]

In contrast, boolean: feature is a control definition which, if set by the user, will cause seqret to read sequence feature information, if available, from the input file.

boolean: firstonly is another control definition which, if set, will cause only a single sequence to be read:

boolean: feature  
[
    information: "Use feature information"
]
.
.
.
boolean: firstonly  
[
    information: "Read one sequence and stop"
]

In practice, many different ACD datatypes (Section A.2, “Datatypes”) are available. Programming these data definitions is covered in greater detail in Section 5.5, “Programming with Objects”.

Each ACD definition has attributes which are name: value pairs. Attributes are of two basic types. Global attributes are available for all datatypes whereas datatype-specific attributes are available for individual or groups of related datatypes.

Consider the definitions for feature and sequence:

boolean: feature  
[
    information: "Use feature information"
]

seqall: sequence  
[
    parameter: "Y"
    type: "gapany"
    features: "$(feature)"
]

parameter: and information: are global attributes whereas type: and features: are datatype-specific.

parameter: "Y" defines a data definition to be a parameter as opposed to some kind of qualifier. A value for a parameter can be given on the command line with or without a flag (parameter name) as described above. All parameters are required by the application and a value will be prompted for if one is not given on the command line.

parameter: "Y" is not given for the boolean definitions which means, in the absence of standard: "Y" or additional: "Y" attributes, that they will default to being an advanced qualifier. An advanced qualifier is never prompted for. Had standard: "Y" or additional: "Y" been defined, then the data definitions would be standard or additional qualifiers. More information on the behaviour of qualifiers and parameters is available (Section 4.1, “Introduction to ACD File Development”).

information: gives a very succinct description of the data definition. The text is used in Web forms and other GUIs. It is also the text used to prompt the user for a value at the command line. You'll notice information: is not defined for the sequence inputs and outputs. A default prompt is provided by EMBOSS for these datatypes. All boolean: datatypes have the default value of False which means that a default needn't be defined explicitly in the ACD file.

The type: attribute is specific to the sequence datatypes. type: "gapany" indicates that the input sequence can be of any type and may contain gap characters. In practice many different sequence types are supported (Section A.7, “Sequence Types”).

The features: attribute is also sequence-specific. The attribute definition looks a little strange:

The $ syntax means "retrieve the value of ...", in this case "retrieve the value of the feature ACD definition", such that the features: attribute of outseq is set to that value. In other words, the input sequence will include features if the user turned the feature advanced qualifier on by giving it on the command line, e.g. seqret -feature. Whilst it is not strictly necessary to have features: "$(feature)" (the information is after all specified in boolean: feature) it makes the application source code a good deal cleaner.

In addition to global and datatype-specific attributes there are two other types of attribute that may appear in an ACD file. Calculated attributes receive a value once the ACD file has been processed and application input files have been read. Finally, there are datatype-specific command line qualifiers which are defined for single or groups of ACD datatypes and may be hard-coded as attributes within an ACD file. See: