NAME

Finnigan::Peaks -- a decoder for PeaksList, the list of peak centroids

SYNOPSIS

use Finnigan;
my $entry = Finnigan::ScanIndexEntry->decode(\*INPUT);
say $entry->offset; # returns an offset from the start of scan data stream 
say $entry->data_size;
$entry->dump;

DESCRIPTION

ScanIndexEntry is a static (fixed-size) structure containing the pointer to a scan, the scan's data size and some auxiliary information about the scan.

ScanIndexEntry elements seem to form a linked list. Each ScanIndexEntry contains the index of the next entry.

Although in all observed instances the scans were sequential and their indices could be ignored, it may not always be the case.

It is not clear whether scan index numbers start at 0 or at 1. If they start at 0, the list link index must point to the next item. If they start at 1, then "index" will become "previous" and "next" becomes "index" -- the list will be linked from tail to head. Although observations are lacking, I am inclined to interpret it as a forward-linked list, simply from common sense.

METHODS

decode($stream)

The constructor method

count

Get the number of peaks in the list

peaks

Get the list of Finnigan::Peak objects

peak

Same as peaks. I find the dereference expressions easier to read when the reference name is singular: $scan->peak->[0] (rather than $scan->peaks->[0]). However, I prefer the plural form when there is no dereferencing: $peaks = $scan->peaks;q

all

Get the reference to an array containing the pairs of abundance? values of each centroided peak. This method avoids the expense of calling the Finnigan::Peak accessors.

list

Print the entire peak list to STDOUT

SEE ALSO

Finnigan::RunHeader

AUTHOR

Gene Selkov, <selkovjr@gmail.com>

COPYRIGHT AND LICENSE

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.