1 /* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
3 /*********************************************************************
4 * Clustal Omega - Multiple sequence alignment
6 * Copyright (C) 2010 University College Dublin
8 * Clustal-Omega is free software; you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License as
10 * published by the Free Software Foundation; either version 2 of the
11 * License, or (at your option) any later version.
13 * This file is part of Clustal-Omega.
15 ********************************************************************/
18 * RCS $Id: hhhit.h 243 2011-05-31 13:49:19Z fabian $
23 //////////////////////////////////////////////////////////////////////////////
24 /* Describes an alignment of two profiles.
25 Used as list element in Hits : List<Hit> */
26 //////////////////////////////////////////////////////////////////////////////
30 char* longname; // Name of HMM
31 char* name; // One-word name of HMM
32 char* file; // Basename (with path, without extension) of alignment file that was used to construct the HMM
33 // (path from db-file is prepended to FILE record in HMM file!)
34 char fam[IDLEN]; // family ID (derived from name) (FAM field)
35 char sfam[IDLEN]; // superfamily ID (derived from name)
36 char fold[IDLEN]; // fold ID (derived from name)
37 char cl[IDLEN]; // class ID (derived from name)
38 int index; // index of HMM in order of reading in (first=0)
39 char* dbfile; // full database file name from which HMM was read
40 long ftellpos; // start position of HMM in database file
42 float score; // Score of alignment (i.e. of Viterbi path)
43 float score_sort; // score to sort hits in output list (negative means first/best!)
44 float score_aass; // first: just hit.score, then hit.logPval-SSSCORE2NATLOG*hit.score_ss;(negative means best!)
45 float score_ss; // Part of score due to secondary structure
46 float Pval; // P-value for whole protein based on score distribution of query
47 float Pvalt; // P-value for whole protein based on score distribution of template
48 float logPval; // natural logarithm of Pval
49 float logPvalt; // natural logarithm of Pvalt
50 float Eval; // E-value for whole protein
51 float Probab; // probability in % for a positive (depends only on score)
52 float weight; // weight of hit for P-value calculation (= 1/#HMMs-in-family/#families-in-superfamily)
53 double Pforward; // scaled total forward probability : Pforward * Product_{i=1}^{Lq+1}(scale[i])
55 /* float score_comp; // compositional similarity score */
56 /* float logPcomp; // natural logarithm of Pvalue for compositional similarity score */
57 /* float Prep; // P-value for single-repeat hit */
58 /* float Erep; // E-value for single-repeat hit */
59 /* float logPrep; // natural logarithm of P-value for single-repeat hit */
60 float E1val; // E-value for whole protein from transitive scoring
61 float logP1val; // natural logarithm of P1val, the transitive P-value
63 int L; // Number of match states in template
64 int irep; // Index of single-repeat hit (1: highest scoring repeat hit)
65 int nrep; // Number of single-repeat hits with one template
67 int n_display; // number of sequences stored for display of alignment
68 char** sname; // names of stored sequences
69 char** seq; // residues of stored sequences (first at pos 1)
70 int nss_dssp; // index of dssp secondary structure sequence in seq[]
71 int nsa_dssp; // index of of dssp solvent accessibility in seq[]
72 int nss_pred; // index of dssp secondary structure sequence in seq[]
73 int nss_conf; // index of dssp secondary structure sequence in seq[]
74 int nfirst; // index of query sequence in seq[]
75 int ncons; // index of consensus sequence
77 int nsteps; // index for last step in Viterbi path; (first=1)
78 int* i; // i[step] = query match state at step of Viterbi path
79 int* j; // j[step] = template match state at step of Viterbi path
80 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)
81 float* S; // S[step] = match-match score contribution at alignment step
82 float* S_ss; // S_ss[step] = secondary structure score contribution
83 float* P_posterior; // P_posterior[step] = posterior prob for MM states (otherwise zero)
84 char* Xcons; // consensus sequence for aligned states in internal representation (A=0 R=1 N=2 D=3 ...)
85 int i1; // First aligned residue in query
86 int i2; // Last aligned residue in query
87 int j1; // First aligned residue in template
88 int j2; // Last aligned residue in template
89 int matched_cols; // number of matched columns in alignment against query
90 int ssm1; // SS scoring AFTER alignment? 0:no 1:yes; t->dssp q->psipred 2:yes; q->dssp t->psipred
91 int ssm2; // SS scoring DURING alignment? 0:no 1:yes; t->dssp q->psipred 2:yes; q->dssp t->psipred
92 char self; // 0: align two different HMMs 1: align HMM with itself
93 int min_overlap; // Minimum overlap between query and template
94 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)
95 float Neff_HMM; // Diversity of underlying alignment
97 // Constructor (only set pointers to NULL)
101 // Free all allocated memory (to delete list of hits)
104 // Allocate/delete memory for dynamic programming matrix
105 void AllocateBacktraceMatrix(int Nq, int Nt);
106 void DeleteBacktraceMatrix(int Nq);
107 void AllocateForwardMatrix(int Nq, int Nt);
108 void DeleteForwardMatrix(int Nq);
109 void AllocateBackwardMatrix(int Nq, int Nt);
110 void DeleteBackwardMatrix(int Nq);
112 // Compare an HMM with overlapping subalignments
113 void Viterbi(HMM& q, HMM& t, float** Sstruc=NULL);
115 // Compare two HMMs with each other in lin space
116 int Forward(HMM& q, HMM& t, float** Pstruc=NULL);
118 // Compare two HMMs with each other in lin space
119 int Backward(HMM& q, HMM& t);
121 // Find maximum accuracy alignment (after running Forward and Backward algorithms)
122 void MACAlignment(HMM& q, HMM& t);
124 // Trace back alignment of two profiles based on matrices bXX[][]
125 void Backtrace(HMM& q, HMM& t);
127 // Trace back alignment of two profiles based on matrices bXX[][]
128 void StochasticBacktrace(HMM& q, HMM& t, char maximize=0);
130 // Trace back MAC alignment of two profiles based on matrix bMM[][]
131 void BacktraceMAC(HMM& q, HMM& t);
133 // Calculate secondary structure score between columns i and j of two HMMs (query and template)
134 inline float ScoreSS(HMM& q, HMM& t, int i, int j, int ssm);
136 // Calculate secondary structure score between columns i and j of two HMMs (query and template)
137 inline float ScoreSS(HMM& q, HMM& t, int i, int j);
139 // Calculate total score (including secondary structure score and compositional bias correction
140 inline float ScoreTot(HMM& q, HMM& t, int i, int j);
142 // Calculate score (excluding secondary structure score and compositional bias correction
143 inline float ScoreAA(HMM& q, HMM& t, int i, int j);
145 // Comparison (used to sort list of hits)
146 int operator<(const Hit& hit2) {return score_sort<hit2.score_sort;}
148 // Merge HMM with next aligned HMM
149 void MergeHMM(HMM& Q, HMM& t, float wk[]);
152 void ClobberGlobal(void);
156 double** B_MM; // Backward matrices
159 char state; // 0: Start/STOP state 1: MM state 2: GD state (-D) 3: IM state 4: DG state (D-) 5 MI state
160 char** bMM; // (backtracing) bMM[i][j] = STOP:start of alignment MM:prev was MM GD:prev was GD etc
161 char** bGD; // (backtracing) bMM[i][j] = STOP:start of alignment MM:prev was MM SAME:prev was GD
162 char** bDG; // (backtracing)
163 char** bIM; // (backtracing)
164 char** bMI; // (backtracing)
165 char** cell_off; // cell_off[i][j]=1 means this cell will get score -infinity
167 double** F_MM; // Forward matrices
168 double** F_GD; // F_XY[i][j] * Prod_1^i(scale[i])
169 double** F_DG; // = Sum_x1..xl{ P(HMMs aligned up to Xi||Yj co-emmitted x1..xl ) / (Prod_k=1^l f(x_k)) }
170 double** F_IM; // end gaps are not penalized!
174 double** B_GD; // B_XY[i][j] * Prod_i+1^(L+1) (scale[i])
175 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)) }
176 double** B_IM; // end gaps are not penalized!
179 void InitializeBacktrace(HMM& q, HMM& t);
180 void InitializeForAlignment(HMM& q, HMM& t);
184 double Pvalue(double x, double a[]);
185 double Pvalue(float x, float lamda, float mu);
186 double logPvalue(float x, float lamda, float mu);
187 double logPvalue(float x, double a[]);
188 double Probab(Hit& hit);