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mspectrumcondition.h
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/*
Copyright (C) 2003 Ronald C Beavis, all rights reserved
X! tandem
This software is a component of the X! proteomics software
development project
Use of this software governed by the Artistic license, as reproduced here:
The Artistic License for all X! software, binaries and documentation
Preamble
The intent of this document is to state the conditions under which a
Package may be copied, such that the Copyright Holder maintains some
semblance of artistic control over the development of the package,
while giving the users of the package the right to use and distribute
the Package in a more-or-less customary fashion, plus the right to
make reasonable modifications.
Definitions
"Package" refers to the collection of files distributed by the Copyright
Holder, and derivatives of that collection of files created through
textual modification.
"Standard Version" refers to such a Package if it has not been modified,
or has been modified in accordance with the wishes of the Copyright
Holder as specified below.
"Copyright Holder" is whoever is named in the copyright or copyrights
for the package.
"You" is you, if you're thinking about copying or distributing this Package.
"Reasonable copying fee" is whatever you can justify on the basis of
media cost, duplication charges, time of people involved, and so on.
(You will not be required to justify it to the Copyright Holder, but
only to the computing community at large as a market that must bear
the fee.)
"Freely Available" means that no fee is charged for the item itself,
though there may be fees involved in handling the item. It also means
that recipients of the item may redistribute it under the same
conditions they received it.
1. You may make and give away verbatim copies of the source form of the
Standard Version of this Package without restriction, provided that
you duplicate all of the original copyright notices and associated
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2. You may apply bug fixes, portability fixes and other modifications
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following:
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Freely Available, such as by posting said modifications to Usenet
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do not represent such an executable image as a Standard Version of
this Package.
7. C subroutines (or comparably compiled subroutines in other languages)
supplied by you and linked into this Package in order to emulate
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when no overt attempt is made to make this Package's interfaces visible
to the end user of the commercial distribution. Such use shall not be
construed as a distribution of this Package.
9. The name of the Copyright Holder may not be used to endorse or promote
products derived from this software without specific prior written permission.
10. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
The End
*/
#ifndef MSPECTRUMCONDITION_H
#define MSPECTRUMCONDITION_H
// File version: 2003-07-01
// File version: 2005-01-01
/*
modified December 2010 by Insilicos LLC to support object serialization for
Hadoop and MPI use
*/
/*
* the mspectrumcondition object analyzes tandem mass spectra and alters them to
* be suitable for searching. it loads a set of parameters from an XmlParameters
* object and uses those values for the spectrum analysis. this object contains
* more "get" and "set" type methods than most of the other objects in this
* project: there was considerable experimentation necessary to refine the spectrum
* analysis methods and these additional methods were used for these experiments.
*
* mspectrumcondition performs a series of operations on a spectrum list to make
* compatible with the scoring methods. the spectrum can be normalized, adjacent
* peaks removed, parent ion masses excluded, low mass parents excluded, highly
* charged parents excluded, low mass fragments excluded, and low intensity
* fragment ions excluded.
*/
#include "xmlparameter.h"
#include "mspectrum.h"
class mscore;
class mspectrumcondition
{
public:
mspectrumcondition(void);
virtual ~mspectrumcondition(void);
bool m_bCondition; // enables the use of all conditioning methods
bool condition(mspectrum &_s, mscore &_score); // method to apply current conditioning to a spectrum
bool get_noise_suppression(void); // retrieves the value of the m_bUseNoiseSuppression member
bool load(XmlParameter &_x); // sets the values for member values using an XmlParameter object
bool set_max_peaks(const long _p); // sets the maximum number of peaks in a spectrum
bool set_dynamic_range(const float _p); // sets the maximum dynamic range of a spectrum
bool set_parent_exclusion(const float _l,const float _u); // sets an upper and lower bound for excluding neutral losses around a parent ion
bool set_lowest_mass(const float _m); // sets the lowest m/z value in a spectrum
bool set_max_charge(const long _m); // sets the maximum charge allowable for a spectrum
bool set_min_size(const long _m); // sets the minimum number of ions in a spectrum
bool set_min_mass(const float _m); // sets the minimum parent ion mass allowed
bool set_max_mass(const float _m); // sets the maximum parent ion mass allowed
bool use_dynamic_range(const bool _f); // enables using the dynamic range
bool use_charge_suppression(const bool _f); // enables the rejection of highly charged parents
bool use_condition(const bool _f); // enables the use of all spectrum conditioning (must be true)
bool use_lowest_mass(const bool _f); // enables the removal of very low m/z peaks from a spectrum
bool use_max_peaks(const bool _f); // enables removing low intensity peaks
bool use_min_size(const bool _f); // enables using the minimum number of peaks to exclude spectra
bool use_min_mass(const bool _f); // enables using a minimum parent ion mass to exclude spectra
bool use_noise_suppression(const bool _f); // enables the rejection of noise spectra
bool use_parent_exclusion(const bool _f); // enables the exclusion of neutrals near the parent ion mass
//protected: let serialization get at these bpratt 9/20/2010
bool m_bUseChargeSuppression; // enables the rejection of highly charge parent ions
bool m_bUseDynamicRange; // enables using the dynamic range
bool m_bUseLowestMass; // enables the removal of very low m/z peaks from a spectrum
bool m_bUseMaxPeaks; // enables removing low intensity peaks
bool m_bUseMinMass; // sets the minimum parent ion mass allowed
bool m_bUseMaxMass; // sets the maximum parent ion mass allowed
bool m_bUseMinSize; // enables using the minimum number of peaks to exclude spectra
bool m_bUseNoiseSuppression; // enables the detection of purely noise spectra
bool m_bUseParent; // enables the exclusion of spectra by the parent ion mass
bool m_bUseNeutralLoss;
bool m_bUsePhosphoDetection;
size_t m_tMaxPeaks; // the maximum number of peaks in a spectrum
float m_fDynamicRange; // the normalized intensity of the most intense peak in a spectrum
float m_fLowestMass; // the lowest m/z in a spectrum
long m_lMinSize; // the minimum number of peaks in a spectrum
float m_fMinMass; // the minimum parent ion mass in a spectrum
float m_fMaxMass; // the maximum parent ion mass in a spectrum
float m_fParentLower; // the low end of the mass window for excluding parent ion neutral losses
float m_fParentUpper; // the high end of the mass window for excluding parent ion neutral losses (just passed the last C13 isotope peak)
float m_fMaxZ; // the maximum parent ion charge allowed
float m_fNeutralLoss;
float m_fNeutralLossWidth;
float m_fFactor;
bool find_loss(mspectrum &_s,const float _d,const float _t);
bool check_neutral(mspectrum &_s); // determines if there are neutral loss peaks in a spectrum
bool clean_isotopes(mspectrum &_s); // removes isotope peaks
bool dynamic_range(mspectrum &_s); // normalizes the spectrum using the dynamic range
bool is_noise(mspectrum &_s); // determines if a spectrum is purely noise
bool remove_isotopes(mspectrum &_s); // removes peaks too close to be real isotope peaks
bool remove_neutral(mspectrum &_s); // removes neutral loss ions
bool remove_parent(mspectrum &_s); // removes parent ions & neutrals
bool remove_small(mspectrum &_s); // removes low intensity peaks
bool remove_low_masses(mspectrum &_s); // removes low m/z peaks
};
#endif