Gene Selkov, Jr. > Finnigan > Finnigan::ScanEvent

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Module Version: 0.0206   Source  

NAME ^

Finnigan::ScanEvent -- a decoder for ScanEvent, a detailed scan descriptor

SYNOPSIS ^

  use Finnigan;
  my $e = Finnigan::ScanEvent->decode(\*INPUT);
  say $e->size;
  say $e->dump;
  say join(" ", $e->preamble->list(decode => 'yes'));
  say $e->preamble->analyzer(decode => 'yes');
  $e->fraction_collector->dump;
  $e->reaction->dump if $e->preamble->ms_power > 1 # Reaction will not be present in MS1

DESCRIPTION ^

This is a variable-layout (but otherwise static) structure, contaning several key details about the scan. Most of those details are concentrated in its head element, ScanEventPreamble.

The layout depends on the number of precursor ions and is governed by the attribute named 'np'. The value np = 0 corresponds to an MS1 scan.

All variants contain a structure named FractionCollector, which is just a pair of double-precision numbers indicating the M/z range of the scan.

In addition to some unknowns that occur in all variants, the MS1 variant (np = 0) contains a copy of all conversion coefficients that determine the transformation of the spectra from the frequency domain to M/z (the other copy of the same coefficients is stored in the corresponding ScanParameterSet -- a somewhat overlapping structure in a parallel stream).

METHODS

decode($stream, $version)

The constructor method

purge_unused_data

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)

np

Get the number of precursor ions

preamble

Get the Finnigan::ScanEventPreamble object

fraction_collector

Get the Finnigan::FractionCollector object

precursors

Get the list full list of precursor descriptors Finnican::Reaction objects

reaction($n)

Get the precursor number n (a Finnigan::Reaction object). In the absence of the number argument, it returns the first precursor.

nparam

Get the number of conversion coefficients

unknown_double

Get the value of the unknown first coefficient (0 in all known cases)

I

Get the value of the coefficient I (0 in all known cases, Orbitrap data only)

A

Get the value of the coefficient A (0 in all known cases)

B

Get the value of the coefficient B (LTQ-FT, Orbitrap)

C

Get the value of the coefficient C (LTQ-FT, Orbitrap)

D

Get the value of the coefficient D (Orbitrap only)

E

Get the value of the coefficient E (Orbitrap only)

converter

Returns the pointer to the function for the forward conversion f → M/z

inverse_converter

Returns the pointer to the function for the inverse conversion M/z → f

stringify

Make a short text representation of the object

SEE ALSO ^

Finnigan::ScanEventPreamble

Finnigan::FractionCollector

Finnigan::Reaction

uf-trailer

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.

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