/* -*- 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: hhhmm.h 165 2010-12-22 16:24:48Z fabian $ */ // hhhmm.h class HMM { public: HMM(int maxseqdis=MAXSEQDIS, int maxres=/*MAXRES*/par.maxResLen); ~HMM(); HMM& operator=(HMM&); int n_display; // number of sequences stored for display of alignment (INCLUDING >ss_ and >cf_ sequences) int n_seqs; // number of sequences read in (INCLUDING >ss_ and >cf_ sequences) char** sname; // names of stored sequences char** seq; // residues of stored sequences (first at pos 1!) int ncons; // index of consensus sequence int nfirst; // index of first sequence (query sequence of HMM) int nss_dssp; // index of seq[] with secondary structure by dssp int nsa_dssp; // index of seq[] with solvent accessibility by dssp int nss_pred; // index of seq[] with predicted secondary structure int nss_conf; // index of seq[] with confidence values for secondary structure prediction int L; // length of HMM = number of match states; set in declaration of HMM object int N_in; // number of sequences in alignment int N_filtered; // number of sequences after filtering float* Neff_M; // Neff_M[i] = diversity of subalignment of seqs that have residue in col i float* Neff_I; // Neff_I[i] = diversity of subalignment of seqs that have insert in col i float* Neff_D; // Neff_D[i] = diversity of subalignment of seqs that have delete in col i float Neff_HMM; // average number of Neff over total length of HMM char* longname; // Full name of first sequence of original alignment (NAME field) char name[NAMELEN]; // HMM name = first word in longname in lower case char file[NAMELEN]; // Basename (with path, without extension) of alignment file that was used to construct the HMM char fam[NAMELEN]; // family ID (derived from name) (FAM field) char sfam[NAMELEN]; // superfamily ID (derived from name) char fold[NAMELEN]; // fold ID (derived from name) char cl[NAMELEN]; // class ID (derived from name) float lamda, mu; // coefficients for aa score distribution of HMM using parameters in 'Parameters par' bool has_pseudocounts; // set to true if HMM contains pseudocounts // Make a flat copy of q void FlatCopyTo(HMM& t); // Read an HMM from a HHsearch .hhm file and return 0 at end of file int Read(FILE* dbf, char* path=NULL); // Read an HMM from a HMMer .hmm file; return 0 at end of file int ReadHMMer(FILE* dbf, char* filestr=NULL); // Read an HMM from a HMMer3 .hmm file; return 0 at end of file int ReadHMMer3(FILE* dbf, char* filestr=NULL); // Add transition pseudocounts to HMM void AddTransitionPseudocounts(float gapd=par.gapd, float gape=par.gape, float gapf=par.gapf, float gapg=par.gapg, float gaph=par.gaph, float gapi=par.gapi, float gapb=par.gapb); // Use secondary structure-dependent gap penalties on top of the HMM transition penalties void UseSecStrucDependentGapPenalties(); // Generate an amino acid frequency matrix g[][] with full pseudocount admixture (tau=1) void PreparePseudocounts(); // Add amino acid pseudocounts to HMM: t.p[i][a] = (1-tau)*f[i][a] + tau*g[i][a] void AddAminoAcidPseudocounts(char pcm=par.pcm, float pca=par.pca, float pcb=par.pcb, float pcc=par.pcc); // Add no amino acid pseudocounts to HMM: copy t.p[i][a] = f[i][a] void NoAminoAcidPseudocounts() {for(int i=1; i<=L; i++) for(int a=0; a<20; a++) p[i][a]=f[i][a];}; // Factor Null model into HMM t void IncludeNullModelInHMM(HMM& q, HMM& t); // Write HMM to output file void WriteToFile(char* outfile); // Insert calibration line 'EVD lamda mu hashvalue' into HMM file void InsertCalibration(char* infile); // Write HMM to output file in HMMER format void WriteToFileHMMER(char* outfile); // Transform log to lin transition probs void Log2LinTransitionProbs(float beta=1.0); // Set query columns in His-tags etc to Null model distribution void NeutralizeTags(); // Calculate effective number of sequences using profiles INCLUDING pseudocounts float CalcNeff(); // Calculate consensus of HMM (needed to merge HMMs later) void CalculateConsensus(); // Store linear transition probabilities void StoreLinearTransitionProbs(); // Initialize f[i][a] with query HMM void MergeQueryHMM(HMM& q, float wk[]); // Normalize probabilities in total merged super-HMM void NormalizeHMMandTransitionsLin2Log(); // Rescale rate matrices P[a][b], R[a][b] according to HMM av. aa composition in pav[a] void RescaleMatrix(); #ifdef CLUSTALO void ClobberGlobal(void); char cQT; /* query or template */ #endif private: float** f; // f[i][a] = prob of finding amino acid a in column i WITHOUT pseudocounts float** g; // f[i][a] = prob of finding amino acid a in column i WITH pseudocounts float** p; // p[i][a] = prob of finding amino acid a in column i WITH OPTIMUM pseudocounts float** tr; // log2 of transition probabilities M2M M2I M2D I2M I2I D2M D2D M2M_GAPOPEN GAPOPEN GAPEXTD /* float** tr_lin; // transition probs in log space */ char trans_lin; // transition probs are given in log or lin space? (0: p_tr 1: log(p_tr) char* ss_dssp; // secondary structure determined by dssp 0:- 1:H 2:E 3:C 4:S 5:T 6:G 7:B char* sa_dssp; // solvent accessibility state determined by dssp 0:- 1:A (absolutely buried) 2:B 3:C 4:D 5:E (exposed) char* ss_pred; // predicted secondary structure 0:- 1:H 2:E 3:C char* ss_conf; // confidence value of prediction 0:- 1:0 ... 10:9 char* Xcons; // consensus sequence in internal representation (A=0 R=1 N=2 D=3 ...) float pav[NAA]; // pav[a] = average freq of amino acids in HMM (including subst matrix pseudocounts) float pnul[NAA]; // null model probabilities used in comparison (only set in template/db HMMs) int* l; // l[i] = pos. of j'th match state in aligment /* char trans_lin; // transition probs are given in log or lin space? (0: p_tr 1: log(p_tr) */ // Utility for Read() int Warning(FILE* dbf, char line[], char name[]) { if (v) cerr<<"\nWARNING: could not read line\n\'"<