src/ClustalOmega/src/hhalign/hhhit.h
dafeef0b
 /* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
 
 /*********************************************************************
  * Clustal Omega - Multiple sequence alignment
  *
  * Copyright (C) 2010 University College Dublin
  *
  * Clustal-Omega is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License as
  * published by the Free Software Foundation; either version 2 of the
  * License, or (at your option) any later version.
  *
  * This file is part of Clustal-Omega.
  *
  ********************************************************************/
 
 /*
  * RCS $Id: hhhit.h 243 2011-05-31 13:49:19Z fabian $
  */
 
 // hhhit.h
 
 //////////////////////////////////////////////////////////////////////////////
 /* Describes an alignment of two profiles. 
    Used as list element in Hits : List<Hit> */
 //////////////////////////////////////////////////////////////////////////////
 class Hit
 {
  public:  
   char* longname;       // Name of HMM
   char* name;           // One-word name of HMM
   char* file;           // Basename (with path, without extension) of alignment file that was used to construct the HMM
                         // (path from db-file is prepended to FILE record in HMM file!)
   char fam[IDLEN];      // family ID (derived from name) (FAM field)
   char sfam[IDLEN];     // superfamily ID (derived from name) 
   char fold[IDLEN];     // fold ID (derived from name)
   char cl[IDLEN];       // class ID (derived from name)
   int index;            // index of HMM in order of reading in (first=0)
   char* dbfile;         // full database file name from which HMM was read
   long ftellpos;        // start position of HMM in database file
 
   float score;          // Score of alignment (i.e. of Viterbi path)
   float score_sort;     // score to sort hits in output list (negative means first/best!)
   float score_aass;     // first: just hit.score, then hit.logPval-SSSCORE2NATLOG*hit.score_ss;(negative means best!)
   float score_ss;       // Part of score due to secondary structure
   float Pval;           // P-value for whole protein based on score distribution of query
   float Pvalt;          // P-value for whole protein based on score distribution of template
   float logPval;        // natural logarithm of Pval
   float logPvalt;       // natural logarithm of Pvalt
   float Eval;           // E-value for whole protein
   float Probab;         // probability in % for a positive (depends only on score)
   float weight;         // weight of hit for P-value calculation (= 1/#HMMs-in-family/#families-in-superfamily)
   double Pforward;      // scaled total forward probability : Pforward * Product_{i=1}^{Lq+1}(scale[i])
   
 /*   float score_comp;     // compositional similarity score */
 /*   float logPcomp;       // natural logarithm of Pvalue for compositional similarity score */
 /*   float Prep;           // P-value for single-repeat hit */
 /*   float Erep;           // E-value for single-repeat hit */
 /*   float logPrep;        // natural logarithm of P-value for single-repeat hit */
   float E1val;          // E-value for whole protein from transitive scoring
   float logP1val;       // natural logarithm of P1val, the transitive P-value
 
   int L;                // Number of match states in template
   int irep;             // Index  of single-repeat hit (1: highest scoring repeat hit)
   int nrep;             // Number of single-repeat hits with one template
   
   int n_display;        // number of sequences stored for display of alignment 
   char** sname;         // names of stored sequences 
   char** seq;           // residues of stored sequences (first at pos 1)
   int nss_dssp;         // index of dssp secondary structure sequence in seq[]
   int nsa_dssp;         // index of of dssp solvent accessibility in seq[]
   int nss_pred;         // index of dssp secondary structure sequence in seq[]
   int nss_conf;         // index of dssp secondary structure sequence in seq[]
   int nfirst;           // index of query sequence in seq[]
   int ncons;            // index of consensus sequence
   
   int nsteps;           // index for last step in Viterbi path; (first=1)
   int* i;               // i[step] = query match state at step of Viterbi path
   int* j;               // j[step] = template match state at step of Viterbi path
   char* states;         // state at step of Viterbi path  0: Start  1: M(MM)  2: A(-D)  3: B(IM)  4: C(D-)  5 D(MI)
   float* S;             // S[step] = match-match score contribution at alignment step
   float* S_ss;          // S_ss[step] = secondary structure score contribution
   float* P_posterior;   // P_posterior[step] = posterior prob for MM states (otherwise zero)
   char* Xcons;          // consensus sequence for aligned states in internal representation (A=0 R=1 N=2 D=3 ...)
   int i1;               // First aligned residue in query
   int i2;               // Last aligned residue in query
   int j1;               // First aligned residue in template 
   int j2;               // Last aligned residue in template
   int matched_cols;     // number of matched columns in alignment against query
   int ssm1;             // SS scoring AFTER  alignment? 0:no  1:yes; t->dssp q->psipred  2:yes; q->dssp t->psipred
   int ssm2;             // SS scoring DURING alignment? 0:no  1:yes; t->dssp q->psipred  2:yes; q->dssp t->psipred
   char self;            // 0: align two different HMMs  1: align HMM with itself
   int min_overlap;      // Minimum overlap between query and template
   float sum_of_probs;   // sum of probabilities for Maximum ACcuracy alignment (if dssp states defined, only aligned pairs with defined dssp state contribute to sum)
   float Neff_HMM;       // Diversity of underlying alignment
 
   // Constructor (only set pointers to NULL)
   Hit();
   ~Hit(){};
   
   // Free all allocated memory (to delete list of hits)
   void Delete();
 
   // Allocate/delete memory for dynamic programming matrix
   void AllocateBacktraceMatrix(int Nq, int Nt);
   void DeleteBacktraceMatrix(int Nq);
   void AllocateForwardMatrix(int Nq, int Nt);
   void DeleteForwardMatrix(int Nq);
   void AllocateBackwardMatrix(int Nq, int Nt);
   void DeleteBackwardMatrix(int Nq);
   
   // Compare an HMM with overlapping subalignments
   void Viterbi(HMM& q, HMM& t, float** Sstruc=NULL);
 
   // Compare two HMMs with each other in lin space
   int Forward(HMM& q, HMM& t, float** Pstruc=NULL);
 
   // Compare two HMMs with each other in lin space
   int Backward(HMM& q, HMM& t);
 
    // Find maximum accuracy alignment (after running Forward and Backward algorithms)
   void MACAlignment(HMM& q, HMM& t);
 
   // Trace back alignment of two profiles based on matrices bXX[][]
   void Backtrace(HMM& q, HMM& t);
 
   // Trace back alignment of two profiles based on matrices bXX[][]
   void StochasticBacktrace(HMM& q, HMM& t, char maximize=0);
 
   // Trace back MAC alignment of two profiles based on matrix bMM[][]
   void BacktraceMAC(HMM& q, HMM& t);
 
   // Calculate secondary structure score between columns i and j of two HMMs (query and template)
   inline float ScoreSS(HMM& q, HMM& t, int i, int j, int ssm);
 
   // Calculate secondary structure score between columns i and j of two HMMs (query and template)
   inline float ScoreSS(HMM& q, HMM& t, int i, int j);
 
   // Calculate total score (including secondary structure score and compositional bias correction
   inline float ScoreTot(HMM& q, HMM& t, int i, int j);
 
   // Calculate score (excluding secondary structure score and compositional bias correction
   inline float ScoreAA(HMM& q, HMM& t, int i, int j);
 
   // Comparison (used to sort list of hits)
   int operator<(const Hit& hit2)  {return score_sort<hit2.score_sort;}
 
   // Merge HMM with next aligned HMM  
   void MergeHMM(HMM& Q, HMM& t, float wk[]);
 
 #ifdef CLUSTALO
   void ClobberGlobal(void);
 #endif  
 
 
   double** B_MM;        // Backward matrices
   
 private:
   char state;          // 0: Start/STOP state  1: MM state  2: GD state (-D)  3: IM state  4: DG state (D-)  5 MI state
   char** bMM;          // (backtracing) bMM[i][j] = STOP:start of alignment  MM:prev was MM  GD:prev was GD etc
   char** bGD;          // (backtracing) bMM[i][j] = STOP:start of alignment  MM:prev was MM  SAME:prev was GD
   char** bDG;          // (backtracing)
   char** bIM;          // (backtracing)
   char** bMI;          // (backtracing)
   char** cell_off;     // cell_off[i][j]=1 means this cell will get score -infinity
 
   double** F_MM;        // Forward matrices 
   double** F_GD;        // F_XY[i][j] * Prod_1^i(scale[i]) 
   double** F_DG;        //   = Sum_x1..xl{ P(HMMs aligned up to Xi||Yj co-emmitted x1..xl ) / (Prod_k=1^l f(x_k)) }   
   double** F_IM;        // end gaps are not penalized!
   double** F_MI;        // 
   double* scale;        // 
 
   double** B_GD;        // B_XY[i][j] * Prod_i+1^(L+1) (scale[i])
   double** B_DG;        //   = Sum_x2..xl{ P(HMMs aligned from Xi||Yj to end co-emmitted x2..xl ) / (Prod_k=2^l f(x_k)) }   
   double** B_IM;        // end gaps are not penalized!
   double** B_MI;        // 
 
   void InitializeBacktrace(HMM& q, HMM& t);
   void InitializeForAlignment(HMM& q, HMM& t);
 };
 
 
 double Pvalue(double x, double a[]);
 double Pvalue(float x, float lamda, float mu);
 double logPvalue(float x, float lamda, float mu);
 double logPvalue(float x, double a[]);
 double Probab(Hit& hit);