--- /dev/null
+/* -*- 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);
+
+
+
+
git://source.jalview.org / jabaws.git / blobdiff