text: /*
   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
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  	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. 
  
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  	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 
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  "Freely Available" means that no fee is charged for the item itself, 
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  	that recipients of the item may redistribute it under the same
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  2. You may apply bug fixes, portability fixes and other modifications 
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  c.	rename any non-standard executables so the names do not conflict 
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  d.	make other distribution arrangements with the Copyright Holder. 
  
  4. You may distribute the programs of this Package in object code or 
  executable form, provided that you do at least ONE of the following: 
  
  a.	distribute a Standard Version of the executables and library files, 
  	together with instructions (in the manual page or equivalent) on 
  	where to get the Standard Version. 
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  c.	give non-standard executables non-standard names, and clearly 
  	document the differences in manual pages (or equivalent), together 
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  d.	make other distribution arrangements with the Copyright Holder. 
  
  5. You may charge a reasonable copying fee for any distribution of 
  this Package. You may charge any fee you choose for support of 
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  However, you may distribute this Package in aggregate with other 
  (possibly commercial) programs as part of a larger (possibly 
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  this shall be construed as a mere form of aggregation, provided that 
  the complete Standard Version of the interpreter is so embedded. 
  
  6. The scripts and library files supplied as input to or produced as 
  output from the programs of this Package do not automatically fall 
  under the copyright of this Package, but belong to whomever generated 
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  Package via the so-called "undump" or "unexec" methods of producing 
  a binary executable image, then distribution of such an image shall 
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  fall under the restrictions of Paragraphs 3 and 4, provided that you 
  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 
  subroutines and variables of the language defined by this Package 
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  of input as in Paragraph 6, provided these subroutines do not change 
  the language in any way that would cause it to fail the regression 
  tests for the language. 
  
  8. Aggregation of this Package with a commercial distribution is always 
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  WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF 
  MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. 
  
  The End 
  */
  
  #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
  #include <set>
  
  #include "mscorestate.h"
  #include "mscorepam.h"
  #include "mplugin.h"
  #include "msequtilities.h"
  
  class XmlParameter;
  
  class mspectrumindex
  {
  public:
  	mspectrumindex() { }
  	virtual ~mspectrumindex() { }
  	
  	double m_dM; // the M+H + error for an mspectrum
  	size_t 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_dM < rhs.m_dM; 
  	}
  	bool operator<=(const mspectrumindex &rhs) const
  	{	
  		return m_dM <= rhs.m_dM; 
  	}
  	bool operator>=(const mspectrumindex &rhs) const
  	{	
  		return m_dM >= rhs.m_dM; 
  	}
  /*
   * 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_dM > rhs.m_dM; 
  	}
  /*
   * 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_dM == m_dM); 
  	}
  /*
   * simple copy operation, using the = operator
   */
  	mspectrumindex& operator=(const mspectrumindex &rhs)
  	{
  		m_dM = rhs.m_dM;
  		m_tA = rhs.m_tA;
  		return *this;
  	}
  };
  
  /*
   * 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() { }
  	
  	double m_dU; // the M+H + error for an mspectrum
  	double m_dL; // the M+H - error for an mspectrum
  	size_t 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 double &rhs)
  	{	
  		return m_dL < rhs; 
  	}
  /*
   * override the greater than operator, so that an mspectrumdetails can be easily compared to a
   * float M+H value
   */
  	bool operator>(const double &rhs)
  	{	
  		return m_dU > rhs; 
  	}
  /*
   * override the equivalence operator, so that an mspectrumdetails can be easily compared to a
   * float M+H value
   */
  	bool operator ==(const double &rhs)
  	{	
  		return (rhs >= m_dL && rhs <= m_dU); 
  	}
  /*
   * simple copy operation, using the = operator
   */
  	mspectrumdetails& operator=(const mspectrumdetails &rhs)
  	{
  		m_dU = rhs.m_dU;
  		m_dL = rhs.m_dL;
  		m_tA = rhs.m_tA;
  		return *this;
  	}
  };
  
  class PermuteState
  {
  public:
  	PermuteState() { m_pSeq = new char[256]; m_pPerm = new char[256]; m_lSize = 255;}
  	~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;
  };
  
  class MIType
  {
  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 mspec
  {
  public:
  	mspec() { m_fMH = 0.0; m_fZ = 1.0; m_uiType = 0;}
  	virtual ~mspec() { }
  	
  	double m_fMH; // the M+H value of an mspectrum
  	float m_fZ; // the charge value of an mspectrum
  	unsigned int m_uiType; // the type of fragmentation
  /*
   * simple copy operation, using the = operator
   */
  	mspec& operator=(const mspec &rhs)
  	{
  		m_fZ = rhs.m_fZ;
  		m_fMH = rhs.m_fMH;
  		m_uiType = rhs.m_uiType;
  		return *this;
  	}
  	mspec& operator=(const mspectrum &rhs)
  	{
  		m_fZ = rhs.m_fZ;
  		m_fMH = (float)rhs.m_dMH;
  		m_uiType = rhs.m_uiType;
  		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
  {
  public:
  	mscore(void);
  	virtual ~mscore(void);
  public:
  	double m_dErr; // error for the fragment ions
  	size_t m_tScored;
  	double m_dHomoError;
  	float m_fHyper; // current hyper score
  	double m_dParentErrMinus; // error for the parent ion M+H (not m/z)
  	double m_dParentErrPlus; // error for the parent ion M+H (not m/z)
  	double m_dMaxMass;
  	double m_dMinMass;
  	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
        unsigned long mconvert(double _m, const double _z); // 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
  	  unsigned long m_lCount;
  /*    End puggable scoring API. */
        virtual float ion_check(const unsigned long _v,const size_t _d) = 0; // finds a specific ion
  
  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);
  	double get_mh()	{
  		return m_dSeqMH;
  	};
  	bool load_next(void);
  	bool load_state(void);
  	bool load_seq(const unsigned long _t,const long _c);
  	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);
  	bool set_allowed_saps(string &_s);
  	double set_parent_error(const double _f,const bool _b);
  	double set_homo_error(const double _f);
  	double set_fragment_error(const double _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();
  	bool set_phospho_bias(const bool _b);
  	__inline__ bool check_terminii(void) {
  		return !m_seqUtil.m_piCtMod[m_pSeq[m_lSeqLength - 1]];
  	};
  	__inline__ bool set_complexity(const double _d) {
  		if (_d < 1.0) {
  			m_dComplexity = 1.0;
  		}
  		if (_d > 10.0) {
  			m_dComplexity = 10.0;
  		}
  		else
  		{
  			m_dComplexity = _d;
  		}
  		m_lComplexity = (unsigned long)pow(2.0, m_dComplexity);
  		return true;
  	};
  
  public:
  	enum	{
  		T_Y =	0x01,
  		T_B =	0x02,
  		T_X =	0x04,
  		T_A =	0x08,
  		T_C =	0x10,
  		T_Z =	0x20,
  	} 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,
  	} 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:
  	char *m_pSeq; // the current sequence
  	double m_dWE;
  	bool m_bPhosphoBias;
  	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_lMaxSeqLength; // current sequence length
  	unsigned long m_lMinSeqLength; // current sequence length
  	unsigned long m_lSize; // maximum sequence length - this can be adjusted on the fly
  	unsigned long m_lComplexity;
  	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
  	double m_dWidth; // current half-width of the entry for a single fragment ion in the m_vsmapMI map
  	                // this value is used by blur
  	double m_dComplexity;
  	float *m_pfSeq; // residue masses corresponding to the current sequence in daltons
  	int *m_piAA;
  	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:
  	bool add_A(const unsigned long _t,const long _c);
  	bool add_B(const unsigned long _t,const long _c);
  	bool add_C(const unsigned long _t,const long _c);
  	bool add_Y(const unsigned long _t,const long _c);
  	bool add_X(const unsigned long _t,const long _c);
  	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
  