--- /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: hhhitlist.h 243 2011-05-31 13:49:19Z fabian $
+ */
+
+// hhhitlist.h
+
+//////////////////////////////////////////////////////////////////////////////
+// HitList is a list of hits of type Hit
+// which can be operated upon by several anaylsis methods
+//////////////////////////////////////////////////////////////////////////////
+class HitList : public List<Hit>
+{
+private:
+ double score[MAXPROF]; // HHsearch score of each HMM for ML fit
+ double weight[MAXPROF]; // weight of each HMM = 1/(size_fam[tfam]*size_sfam[hit.sfam]) for ML fit
+ int Nprof; // Number of HMMs for ML fit
+
+public:
+ int fams; // number of families found found in hitlist
+ int sfams; // number of superfamilies found in hitlist
+ int N_searched; // number of sequences searched from HMM database
+ Hash<float>* blast_logPvals;/* Hash containing names and log(P-values)
+ read from BLAST file (needed for HHblast) */
+
+ HitList() {blast_logPvals=NULL;}
+ ~HitList() {if (blast_logPvals) delete blast_logPvals;}
+
+ // Print summary listing of hits
+ void PrintHitList(HMM& q, char* outfile);
+
+#ifdef CLUSTALO
+ void ClobberGlobal(void);
+#endif
+
+ // Print alignments of query sequences against hit sequences
+ int PrintAlignments(
+#ifdef CLUSTALO
+ char **ppcFirstProf, char **ppcSecndProf,
+#endif
+ HMM& q, char* outfile, char outformat=0);
+
+ // Return a figure of merit for distinction of the score with positive from the scores with negatives
+ void Optimize(HMM& q, char* buffer);
+
+ // Print score distribution into file score_dist
+ void PrintScoreFile(HMM& q);
+
+ // Log likelihood for fitting the EVD to the score distribution
+ double RankOrderFitCorr(double* v);
+ // Static wrapper-function for calling the nonstatic member function RankOrderFitCorr()
+ static double RankOrderFitCorr_static(void* pt2hitlist, double* v);
+
+ // Log likelihood for fitting the EVD to the score distribution
+ double LogLikelihoodCorr(double* v);
+ // Static wrapper-function for calling the nonstatic member function LogLikelihoodCorr()
+ static double LogLikelihoodCorr_static(void* pt2hitlist, double* v);
+
+ // Log likelihood for fitting the EVD to the score distribution
+ double LogLikelihoodEVD(double* v);
+ // Static wrapper-function for calling the nonstatic member function LogLikelihoodEVD()
+ static double LogLikelihoodEVD_static(void* pt2hitlist, double* v);
+
+
+ // Subroutine to FindMin: new point given by highest point ihigh, fac and replaces ihigh if it is lower
+ double TryPoint(int ndim, double* p, double* y, double* psum, int ihigh, double fac, double (*Func)(void* pt2hitlist, double* v));
+
+ // Find minimum with simplex method of Nelder and Mead (1965)
+ float FindMin(int ndim, double* p, double* y, double tol, int& nfunc, double (*Func)(void* pt2hitlist, double* v));
+
+ // Do a maximum likelihood fit of the scores with an EV distribution with parameters lamda and mu
+ void MaxLikelihoodEVD(HMM& q, int nbest);
+
+ // Calculate correlation and score offset for HHblast composite E-values
+ void CalculateHHblastCorrelation(HMM& q);
+
+ // Calculate HHblast composite E-values
+ void CalculateHHblastEvalues(HMM& q);
+
+ // Calculate Pvalues as a function of query and template lengths and diversities
+ void CalculatePvalues(HMM& q);
+
+ // Set P-values, E-values and scores according to q.lamda and q.mu (if calibration from database scan is impossible)
+ void GetPvalsFromCalibration(HMM& q);
+
+ // HHblast: read PSI-BLAST E-values to determine correlation
+ void ReadBlastFile(HMM& q);
+
+ // Print first 20 hits of hitlist
+ void Debug()
+ {
+ Hit hit;
+ int i=0;
+ Reset();
+ printf("TARGET FAMILY LEN COL LOG-PVA S-AASS PROBAB SCORE_SORT\n");
+ while (++i<=20 && !End())
+ {
+ hit = ReadNext();
+ printf("%-10.10s %-10.10s %3i %3i %s %7.2f %6.2f %6.2f\n",hit.name,hit.fam,hit.L,hit.matched_cols,sprintg(-1.443*hit.logPval,7),-hit.score_aass,hit.Probab,hit.score_sort);
+ }
+ }
+
+ // Calculate P-values and Probabilities from transitive scoring over whole database
+ void TransitiveScoring();
+ void TransitiveScoring2();
+ void TransitiveScoring3();
+ void TransitiveScoring4();
+
+ // Score2Z transforms the -log(P-value) score into a Z-score for 0 < S
+ double Score2Z(double S);
+
+ // Z2Score transforms the Z-score into a -log(P-value) value
+ double Z2Score(double Z);
+
+ // Matrix manipulation
+ void PrintMatrix(float** V, int N);
+ void PrintMatrix(double** V, int N);
+ float NormalizationFactor(double** Csub,float* w, int M);
+ void Normalize(float* Ztq, char** fold, Hash<int>& excluded);
+ void InvertMatrix(double** B, double** A, int N);
+ void TransposeMatrix(double** V, int N);
+ void SVD(double **A, int n, double w[], double **V);
+
+};
+
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