--- /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: 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\'"<<line<<"\'\nin HMM "<<name<<" in "<<file<<"\n";
+ while (fgetline(line,LINELEN,dbf) && !(line[0]=='/' && line[1]=='/'));
+ if (line) return 2; //return status: skip HMM
+ return 0; //return status: end of database file
+ }
+
+ friend class Hit;
+ friend class Alignment;
+ friend class HMMshadow;
+};
+
+class HMMshadow {
+
+ public:
+ float *Neff_M;
+ float *Neff_I;
+ float *Neff_D;
+ float **f;
+ float **g;
+ float **p;
+ float **tr;
+ float pav[20];
+
+ void copyHMMtoShadow(const HMM &hmm) {
+ Neff_M = hmm.Neff_M;
+ Neff_I = hmm.Neff_I;
+ Neff_D = hmm.Neff_D;
+ f = hmm.f;
+ g = hmm.g;
+ p = hmm.p;
+ tr = hmm.tr;
+ memcpy(pav, hmm.pav, 20*sizeof(float));
+ }
+
+ void copyShadowToHMM(const HMM &hmm, const hmm_light rShadow) {
+
+ int i, j;
+
+ for (i = 0; i < rShadow.L+1; i++){
+ hmm.Neff_M[i] = rShadow.Neff_M[i];
+ hmm.Neff_I[i] = rShadow.Neff_I[i];
+ hmm.Neff_D[i] = rShadow.Neff_D[i];
+ for (j = 0; j < 20; j++){
+ hmm.f[i][j] = rShadow.f[i][j];
+ hmm.g[i][j] = rShadow.g[i][j];
+ hmm.p[i][j] = rShadow.p[i][j];
+ }
+ for (j = 0; j < 7; j++){
+ hmm.tr[i][j] = rShadow.tr[i][j];
+ }
+ memcpy((void *)hmm.pav, rShadow.pav, 20*sizeof(float));
+ }
+ } /* this is the end of copyShadowToHMM() */
+
+} /* class HMMshadow */;
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