Finnigan::Decoder - a generic binary structure decoder


  use Finnigan;

  my $fields = [
    short_int => 'v',
    long_int => 'V',
    ascii_string => 'C60',
    wide_string => 'U0C18',
    audit_tag => 'object=Finnigan::AuditTag',
    time => 'windows_time',

  my $data = Finnigan::Decoder->read(\*STREAM, $fields);


This class is not inteded to be used directly; it is a parent class for all Finnigan decoders. The fields to decode are passed to the decoder's read() method in a list reference, where every even item specifies the key the item will be known as in the resulting hash, and every odd item specifies the unpack template.

Perl unpack templates are used to decode most fields. For some fields, non-perl templates are used, such as:

  • object: instructs the current decoder to call another Finnigan decoder at that location.

  • windows_time: instructs Finingan::Decoder to call its own Windows timestamp routine.

  • varstr: decoded as a Windows Pascal string in a special case in the Finnigan::Decoder::read() method.


read($class, $stream, $fields, $any_arg)

Returns a new decoder blessed into class $class and initialized with the values read from $stream and decoded according to a list of templates specified in $fields.

The fourth argument, $any_arg is not used by the Decoder class, but may be used by derived classes to pass parse context to their component decoders. For example, this can be useful to parse structures whose layout is governed by the data they contain; in that case if the layout indicator is read by the top-level decoder, it can be passed to lower-level decoders whose work depends on it. Also, this argument is used by the user program to pass the Finnigan file version to version-sensitive decoders.

Here is an example of the template list for a simple decoder:

  my $fields = [
    "mz"        => ['f<', 'Float32'],
    "abundance" => ['f<', 'Float32'],
decode($stream, $fields, $any_arg)

This method must be called on a blessed, instantiated Decoder. The read() method calls it internally, but it can also be used by the user code in those cases where not all data can be decoded with a plain list of templates. In some cases, it may be necessary to decode one part of an object, analyse it, make decisions about the rest (calculate sizes, layouts, etc.), and then grow the object under construction by decoding more data from the stream.

iterate_scalar($stream, $count, $name, $desc)

This method is similar to the decode metod, in that it does not instantiate a Decoder, but rather adds data to an existing one. Its purpose is to decode simple arrays whose elements have neither structure, nor behaviour, and can be described by a simple list. The list will consist of $count elements read into the current Decoder's attribute given in $name, according to the template specified in $desc. For example, to read a list of 4-byte integers, the template description must be of the form:

  $desc = ['V', 'UInt32']
iterate_object($stream, $count, $name, $class, $any_arg)

Similarly to iterate_scalar(), this method can be used to read a list of structures into the current decoder's attribute specified in the $name argument, but in this case, the list elements can be complex structures to be decoded with their own decoder specified in $class. The optional argument $any_arg can be used to parse context information to that decoder.


Delete the location, size and type data for all structure elements. Calling this method will free some memory when no introspection is needeed (the necessary measure in production-grade code)



Get the seek address of the decoded object


Get object size


Get the object's data hash (equivalent to $obj->{data}). Every data hash element contains the decoded value as well as location and type data.


Get an item by name (equivalent to $obj->{data}->{$key})


Extract the simple value hash (no location data, only the element names and values)


Dump the object's contents in three different styles, using absolute or relative addresses. The attribute $param->{style} can be set to wiki or html, or it can be absent or have any other value, it which case the dump will have a simple tabular format. The attribute $param->{relative}is a Boolean, requesting relative addresses when it is set to a truthy value.


Use this command to list all available Finnigan decoders:

 perl -MFinnigan -e 'Finnigan::list_modules'


Gene Selkov, <>


Copyright (C) 2010 by Gene Selkov

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.10.0 or, at your option, any later version of Perl 5 you may have available.