mscore.h

// -*- mode: c++ -*-

/*
 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

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*/

#ifndef MSCORE_H
#define MSCORE_H
/*
	The pluggable scoring system was devised and implemented by Brendan Maclean. It allows
	developers to simply add new scoring systems to X! Tandem for any purpose. Unless you have
	some specific need, it is best to leave PLUGGABLE_SCORING defined.
*/
//#define PLUGGABLE_SCORING
// File version: 2004-02-01
// File version: 2004-03-01

/* 
   changes for MPI and Hadoop bpratt Insilicos LLC after:
   Modified 2007 Robert D Bjornson for X!!Tandem, Parallel MPI version.
*/

#include <set>

#include "mscorestate.h"
#include "mscorepam.h"
#include "mplugin.h"
#include "msequtilities.h"

class XmlParameter;

class mprocess; // make sure the load_next() declaration understands that mprocess is a class to avoid problems with casts, otherwise.  


class mspectrumindex
{
public:
	mspectrumindex() { }
	virtual ~mspectrumindex() { }
	
	float m_fM; // the M+H + error for an mspectrum
	unsigned long m_tA; // the index number for an mspectrum, in the m_vSpectra vector
/*
 * override the less than operator, so that an mspectrumdetails can be easily compared to a
 * float M+H value
 */
	bool operator<(const mspectrumindex &rhs) const
	{	
		return m_fM < rhs.m_fM; 
	}
	bool operator<=(const mspectrumindex &rhs) const
	{	
		return m_fM <= rhs.m_fM; 
	}
	bool operator>=(const mspectrumindex &rhs) const
	{	
		return m_fM >= rhs.m_fM; 
	}
/*
 * override the greater than operator, so that an mspectrumdetails can be easily compared to a
 * float M+H value
 */
	bool operator>(const mspectrumindex &rhs) const
	{	
		return m_fM > rhs.m_fM; 
	}
/*
 * override the equivalence operator, so that an mspectrumdetails can be easily compared to a
 * float M+H value
 */
	bool operator ==(const mspectrumindex &rhs) const
	{	
		return (rhs.m_fM == m_fM); 
	}
/*
 * simple copy operation, using the = operator
 */
	mspectrumindex& operator=(const mspectrumindex &rhs)
	{
		m_fM = rhs.m_fM;
		m_tA = rhs.m_tA;
		return *this;
	}
#ifdef HAVE_MULTINODE_TANDEM  // support for Hadoop and/or MPI?
  friend class boost::serialization::access;
  template<class Archive>
  void serialize(Archive &ar, const unsigned int version)
    {
		ar & m_fM;
		ar & m_tA;
    }
#endif
};

/*
 * mspectrumdetails is a specialty class used by mscore to check whether a particular mspectrum
 * has a parent ion M+H within error of a given peptide sequence (with modifications if appropriate)
 */
class mspectrumdetails
{
public:
	mspectrumdetails() { }
	virtual ~mspectrumdetails() { }
	
	float m_fU; // the M+H + error for an mspectrum
	float m_fL; // the M+H - error for an mspectrum
	long m_lA; // the index number for an mspectrum, in the m_vSpectra vector
#ifdef HAVE_MULTINODE_TANDEM  // support for Hadoop and/or MPI?
  friend class boost::serialization::access;
  template<class Archive>
  void serialize(Archive &ar, const unsigned int version)
    {
		ar & m_fU;
		ar & m_fL;
		ar & m_lA;
    }
#endif
  /*
 * override the less than operator, so that an mspectrumdetails can be easily compared to a
 * float M+H value
 */
	bool operator<(const float &rhs)
	{	
		return m_fL < rhs; 
	}
/*
 * override the greater than operator, so that an mspectrumdetails can be easily compared to a
 * float M+H value
 */
	bool operator>(const float &rhs)
	{	
		return m_fU > rhs; 
	}
/*
 * override the equivalence operator, so that an mspectrumdetails can be easily compared to a
 * float M+H value
 */
	bool operator ==(const float &rhs)
	{	
		return (rhs >= m_fL && rhs <= m_fU); 
	}
/*
 * simple copy operation, using the = operator
 */
	mspectrumdetails& operator=(const mspectrumdetails &rhs)
	{
		m_fU = rhs.m_fU;
		m_fL = rhs.m_fL;
		m_lA = rhs.m_lA;
		return *this;
	}
};

class PermuteState
{
public:
	PermuteState() { m_pSeq = new char[256]; m_pPerm = new char[256]; m_lSize = 255;
					 m_tPos = 0; m_tEnd = 0;*m_pSeq=0;*m_pPerm=0;m_bRev=false;} // bpratt 4-5-11
	~PermuteState() { delete[] m_pSeq; delete[] m_pPerm;}
	size_t m_tPos;
	size_t m_tEnd;
	char *m_pSeq;
	char *m_pPerm;
	unsigned long m_lSize;
	bool m_bRev;
#ifdef HAVE_MULTINODE_TANDEM  // support for Hadoop and/or MPI?
  friend class boost::serialization::access;
  template<class Archive>
  void serialize(Archive &ar, const unsigned int version)
    {
      ar & m_tPos;
      ar & m_tEnd;
      ar & m_lSize;
	  size_t n=0;
	  do {
        ar & m_pSeq[n];
	  } while (m_pSeq[n++]);
	  n=0;
	  do {
        ar & m_pPerm[n];
	  } while (m_pPerm[n++]);
      ar & m_bRev;
    }
#endif
};

class MIType
{
#ifdef HAVE_MULTINODE_TANDEM  // support for Hadoop and/or MPI?
  friend class boost::serialization::access;
  template<class Archive>
  void serialize(Archive &ar, const unsigned int version)
    {
		ar & m_lM;
		ar & m_fI;
		ar & m_lA;
    }
#endif
public:
	MIType() { }
	virtual ~MIType() { }
	
	unsigned long m_lM; // the M+H + error for an mspectrum
	float m_fI; // the M+H - error for an mspectrum
	long m_lA; // the index number for an mspectrum, in the m_vSpectra vector
/*
 * simple copy operation, using the = operator
 */
	MIType& operator=(const MIType &rhs)
	{
		m_fI = rhs.m_fI;
		m_lM = rhs.m_lM;
		return *this;
	}
};

typedef vector<MIType> vmiType;
class vectorvmiType : public vector<vmiType> {
#ifdef HAVE_MULTINODE_TANDEM  // autoserialize fails for vector of vectors
  friend class boost::serialization::access;
  template<class Archive>
  void serialize(Archive &ar, const unsigned int version)
    {
		size_t s = this->size();
		size_t initial_s = s;
		ar & s;
		if (s > initial_s) { // loading
			this->resize(s);
		}
		while (s--) {
			ar & (*this)[s];
		}
    }
#endif
};

class mspec
{
#ifdef HAVE_MULTINODE_TANDEM
  friend class boost::serialization::access;
  template<class Archive>
  void serialize(Archive &ar, const unsigned int version)
    {
		ar & m_fMH;
		ar & m_fZ;
    }
#endif
public:
	mspec() { m_fMH = 0.0; m_fZ = 1.0;}
	virtual ~mspec() { }
	
	double m_fMH; // the M+H value of an mspectrum
	float m_fZ; // the charge value of an mspectrum
/*
 * simple copy operation, using the = operator
 */
	mspec& operator=(const mspec &rhs)
	{
		m_fZ = rhs.m_fZ;
		m_fMH = rhs.m_fMH;
		return *this;
	}
	mspec& operator=(const mspectrum &rhs)
	{
		m_fZ = rhs.m_fZ;
		m_fMH = (float)rhs.m_dMH;
		return *this;
	}
};
/*
 * mscore is the class that contains most of the logic for comparing one sequence with
 * many tandem mass spectra. mprocess contains a comprehensive example of how to use an mscore
 * class. mscore has been optimized for speed, without any specific modifications to take
 * advantage of processor architectures.
 */
class mscore : public mplugin
{
#ifdef HAVE_MULTINODE_TANDEM
  friend class boost::serialization::access;
  template<class Archive>
  void serialize(Archive &ar, const unsigned int version)
    {
#define SERIALIZE(ar,var) {std::string varname(#var);ar & varname;ar & var;}
	SERIALIZE(ar, m_fErr); // error for the fragment ions
	SERIALIZE(ar, m_fHomoError);
	SERIALIZE(ar, m_fHyper); // current hyper score
	SERIALIZE(ar, m_fParentErrMinus); // error for the parent ion M+H (not m/z)
	SERIALIZE(ar, m_fParentErrPlus); // error for the parent ion M+H (not m/z)
	SERIALIZE(ar, m_fMaxMass);
	SERIALIZE(ar, m_fMinMass);
	SERIALIZE(ar, m_lMaxCharge); // current parent ion charge
	SERIALIZE(ar, m_lMaxPeaks); // if > 0, the m_lMaxPeaks most intense peaks will be used
	SERIALIZE(ar, m_dScale); // scale for use in hconvert
    SERIALIZE(ar, m_seqUtil); // class contains variables and constants for calculating sequence and
						     // fragment masses
	SERIALIZE(ar, m_seqUtilAvg); // class contains variables and constants for calculating fragment masses
								// based on average atomic masses
	// omitted SERIALIZE(ar, m_pSeqUtilFrag); // pointer to the msequtilities object to use for fragment ion masses
	// omitted SERIALIZE(ar, m_State); // class stores information about the potential modification state machine
	// omitted SERIALIZE(ar, m_Pam); // class stores information about point mutations state machine
 	// omitted SERIALIZE(ar, m_Sap); // class stores information about single amino acid polymorphisms state machine

	// omitted SERIALIZE(ar, m_Term); // class stores information about potential modification of the N- & C-terminii
	SERIALIZE(ar, m_plCount);// ion count information, indexed using the mscore_type_a enum
	SERIALIZE(ar, m_pfScore);// convolute score information, indexed using the mscore_type_a enum

	SERIALIZE(ar, m_lType); // current ion type - value from mscore_type
	SERIALIZE(ar, m_bUsePam); // true if the peptide will be checked for all possible point mutations
 	SERIALIZE(ar, m_bUseSaps); // true if the peptide will be checked for all known single amino acid polymorphisms
	SERIALIZE(ar, m_bIsC); // true if the current peptide contains the C-terminus of the protein
	SERIALIZE(ar, m_bIsN); // true if the current peptide contains the N-terminus of the protein
	SERIALIZE(ar, m_bIsotopeError); // true if the spectrum mass may be associated with the wrong isotopic peak
	SERIALIZE(ar, m_lMILength); // current length of the mi vector
	SERIALIZE(ar, m_lSeqLength); // current sequence length
	unsigned long former_lsize = m_lSize;
	SERIALIZE(ar, m_lSize); // maximum sequence length - this can be adjusted on the fly
	SERIALIZE(ar, m_lSpectra); // current length of the m_vSpec vector
	SERIALIZE(ar, m_lErrorType); // current ion mass accuracy information - value from mscore_error
	SERIALIZE(ar, m_fScore); // current convolution score
	SERIALIZE(ar, m_dSeqMH); // current sequence M+H - changed from m_fSeqMH to improve accuracy of parent ion mass calculations
	SERIALIZE(ar, m_fWidth); // current half-width of the entry for a single fragment ion in the m_vsmapMI map
	                // this value is used by blur
	if (former_lsize != m_lSize) { // looks like we're loading - initial value is incorrect
		delete[] m_pfSeq;
		delete[] m_plSeq;
		delete[] m_pSeq;
		m_pfSeq = new float[m_lSize];
		m_plSeq = new unsigned long[m_lSize];
		m_pSeq = new char[m_lSize];
	}
	for (size_t a=m_lSize;a--;) {
		ar & m_pSeq[a]; // the current sequence
		ar & m_pfSeq[a]; // residue masses corresponding to the current sequence in daltons
		ar & m_plSeq[a]; // residue masses corresponding to the current sequence, converted into integers
	}
	SERIALIZE(ar, m_lId); // id of the current spectrum
	SERIALIZE(ar, m_tSeqPos); // zero-based absolute position of the current peptide in the protein sequence
	SERIALIZE(ar, m_lDetails);
	SERIALIZE(ar, m_iCharge);
	SERIALIZE(ar, m_bMini);
	SERIALIZE(ar, m_vSpec); // vector of all spectra being considered
	                        // for all spectra being considered
	SERIALIZE(ar, m_vDetails); // vector of mspectrumdetails objects, for looking up parent ion M+H
	                                     // values of mass spectra
	//  huh, std::set doesn't work
	int s = (int)m_sIndex.size();
	ar & s;
	if (s != (int)m_sIndex.size()) { // loading
		while (s--) {
			mspectrumindex itmp;
			ar & itmp;
			m_sIndex.insert(itmp);
		}
	} else {
		set<mspectrumindex>::iterator it = m_sIndex.begin();
		while (it != m_sIndex.end()) {
			mspectrumindex itmp = *it++;
			ar & itmp;
		}
	}
	SERIALIZE(ar, m_psPermute);
    }
#endif
public:
	mscore(void);
	virtual ~mscore(void);
public:
	float m_fErr; // error for the fragment ions
	float m_fHomoError;
	float m_fHyper; // current hyper score
	float m_fParentErrMinus; // error for the parent ion M+H (not m/z)
	float m_fParentErrPlus; // error for the parent ion M+H (not m/z)
	float m_fMaxMass;
	float m_fMinMass;
	long m_lMaxCharge; // current parent ion charge
	unsigned long m_lMaxPeaks; // if > 0, the m_lMaxPeaks most intense peaks will be used
	double m_dScale; // scale for use in hconvert
	msequtilities m_seqUtil; // class contains variables and constants for calculating sequence and
						     // fragment masses
	msequtilities m_seqUtilAvg; // class contains variables and constants for calculating fragment masses
								// based on average atomic masses
	msequtilities* m_pSeqUtilFrag; // pointer to the msequtilities object to use for fragment ion masses
	mscorestate m_State; // class stores information about the potential modification state machine
	mscorepam m_Pam; // class stores information about point mutations state machine
	mscoresap m_Sap; // class stores information about single amino acid polymorphisms state machine
	mscoreterm m_Term; // class stores information about potential modification of the N- & C-terminii
	unsigned long m_plCount[16];// ion count information, indexed using the mscore_type_a enum
	float m_pfScore[16];// convolute score information, indexed using the mscore_type_a enum

	unsigned long m_lType; // current ion type - value from mscore_type

public:

/*
      The following section represents the pluggable scoring API devised and
      implemented by Brendan MacLean. It allows developers to simply add new
      scoring systems to X! Tandem for any purpose.  Please do not modify without
      considering carefully how changes might impact external scoring plug-ins.
*/
      virtual bool load_param(XmlParameter &_x); // allows score object to issue warnings,
                                                                  // or set variables based on xml
      virtual bool precondition(mspectrum &_s); // called before spectrum conditioning 
      virtual bool add_details(mspectrum &_s);
      virtual bool add_mi(mspectrum &_s);
      virtual void prescore(const size_t _i); // called before scoring
      virtual float score(const size_t _i);
/*
      If you have no need for scoring plug-ins other than mscore_tandem, making
      this function non-virtual can yield a 10% perf improvement.
*/
#ifdef PLUGGABLE_SCORING
      virtual unsigned long mconvert(double _m, const long _c); // convert mass to integer ion m/z for mi vector
#else
      unsigned long mconvert(double _m, const long _c); // convert mass to integer ion m/z for mi vector
#endif
      virtual double hfactor(long _l); // hyper scoring factor from number of ions matched
      virtual double sfactor(); // factor applied to final convolution score
      virtual float hconvert(float _h); // convert hyper score to histogram score
      virtual void report_score(char* _buff, float _h); // format hyper score for output
      virtual bool clear();
protected:
      virtual double dot(unsigned long *_v) = 0; // this is where the real scoring happens
/*    End puggable scoring API. */

public:
	unsigned long add_seq(const char *_s,const bool _n,const bool _c,const unsigned long _l,const int _f);
	bool sort_details();
	bool get_aa(vector<maa> &_m,const size_t _a,double &_d);
	virtual bool load_next(const mprocess *_parentProcess);  // made virtual and added arg in support of pluggable scoring bpratt
	bool load_state(void);
#ifdef PLUGGABLE_SCORING
// To mimic SEQUEST-like scoring, a scoring plugin has to modify the theoretical fragment ion series to 
// adjust intensities and add appropriate neutral losses, which is accomplished by overriding this method.
    virtual bool load_seq(const unsigned long _t,const long _c);
#else
	bool load_seq(const unsigned long _t,const long _c);
#endif
	double seq_mh(void); // changed from float to accomodate more accurate parent ion mass calculation (2005.02.01)
	unsigned long set_seq(const char *_s,const bool _n,const bool _c,const unsigned long _l,const int _f);
	bool set_isotope_error(const bool _b);
	unsigned long set_type(const unsigned long _t);
	unsigned long set_error(const unsigned long _t);
	bool set_pam(const bool _b);
	bool set_saps(const bool _b,string &_s);
	float set_parent_error(const float _f,const bool _b);
	float set_homo_error(const float _f);
	float set_fragment_error(const float _f);
	void set_fragment_masstype(masscalc::massType _t);
	bool test_parents(size_t &_t);
	bool set_pos(const size_t _t);
	bool set_mini(const bool _b);
	bool reset_permute();
	bool permute();
public:
	enum	{
		T_Y =	0x01,
		T_B =	0x02,
		T_X =	0x04,
		T_A =	0x08,
		T_C =	0x10,
		T_Z =	0x20,
		T_Y_18 = 0x100,
		T_X_18 = 0x200,
		T_A_18 = 0x400,
		T_B_18 = 0x800,
		T_C_18 = 0x1000,
		T_Y_17 = 0x10000,
		T_X_17 = 0x20000,
		T_A_17 = 0x40000,
		T_B_17 = 0x80000,
		T_C_17 = 0x100000,
	} mscore_type; // enum for referencing information about specific ion types.
	enum	{
		S_Y =	1,
		S_B =	2,
		S_X =	3,
		S_A =	4,
		S_C =	5,
		S_Z =	6,
		S_Y_18 = 7,
		S_X_18 = 8,
		S_A_18 = 9,
		S_B_18 = 10,
		S_Y_17 = 11,
		S_X_17 = 12,
		S_A_17 = 13,
		S_B_17 = 14,
		S_C_17 = 15,
	} mscore_type_a; // enum for referencing information about specific ion types.
	enum	{
		T_PARENT_DALTONS = 0x01,
		T_PARENT_PPM = 0x02,
		T_FRAGMENT_DALTONS = 0x04,
		T_FRAGMENT_PPM =	0x08,
	} mscore_error; // enum for referencing information about ion mass measurement accuracy.

protected:
	bool m_bUsePam; // true if the peptide will be checked for all possible point mutations
	bool m_bUseSaps; // true if the peptide will be checked for all known single amino acid polymorphisms
	bool m_bIsC; // true if the current peptide contains the C-terminus of the protein
	bool m_bIsN; // true if the current peptide contains the N-terminus of the protein
	bool m_bIsotopeError; // true if the spectrum mass may be associated with the wrong isotopic peak
	unsigned long m_lMILength; // current length of the mi vector
	unsigned long m_lSeqLength; // current sequence length
	unsigned long m_lSize; // maximum sequence length - this can be adjusted on the fly
	long m_lSpectra; // current length of the m_vSpec vector
	unsigned long m_lErrorType; // current ion mass accuracy information - value from mscore_error
	float m_fScore; // current convolution score
	double m_dSeqMH; // current sequence M+H - changed from m_fSeqMH to improve accuracy of parent ion mass calculations
	float m_fWidth; // current half-width of the entry for a single fragment ion in the m_vsmapMI map
	                // this value is used by blur
	float *m_pfSeq; // residue masses corresponding to the current sequence in daltons
	unsigned long *m_plSeq; // residue masses corresponding to the current sequence, converted into integers
	char *m_pSeq; // the current sequence
	size_t m_lId; // id of the current spectrum
	size_t m_tSeqPos; // zero-based absolute position of the current peptide in the protein sequence
	long m_lDetails;
	int m_iCharge;
  bool m_bMini;
protected:
	vector<mspec> m_vSpec; // vector of all spectra being considered
	                        // for all spectra being considered
	vector<mspectrumdetails> m_vDetails; // vector of mspectrumdetails objects, for looking up parent ion M+H
	                                     // values of mass spectra
	set<mspectrumindex> m_sIndex;
	PermuteState m_psPermute;

protected:
	virtual bool add_A(const unsigned long _t,const long _c);
	virtual bool add_B(const unsigned long _t,const long _c);
	virtual bool add_C(const unsigned long _t,const long _c);
	virtual bool add_Y(const unsigned long _t,const long _c);
	virtual bool add_X(const unsigned long _t,const long _c);
	virtual bool add_Z(const unsigned long _t,const long _c);
	bool check_parents(void);
	bool load_next_pam(void);
	bool load_next_sap(void);
	bool check_pam_mass();
	bool load_next_term(void);
	bool run_state_machine(void);
};

/*
 * mscoremanager contains static short-cuts for dealing with mscore
 * plug-ins.
 */
class mscoremanager
{
public:
	static const char* TYPE;

	static mscore* create_mscore(XmlParameter &_x);
	static void register_factory(const char* _spec, mpluginfactory* _f);
};

bool lessThanDetails(const mspectrumdetails &_l,const mspectrumdetails &_r);
bool lessThanMI(const mi &_l,const mi &_r);

#endif