--- /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: hhalign.cpp 250 2011-06-17 13:06:20Z fabian $
+ */
+
+/* hhalign.C:
+ * Align a multiple alignment to an alignment or HMM
+ * Print out aligned input sequences in a3m format
+ * Compile: g++ hhalign.C -o hhalign -I/usr/include/ -L/usr/lib -lpng -lz -O3 -fno-strict-aliasing
+ * Compile with efence: g++ hhalign.C -o hhalign -I/usr/include/ -lefence -L/usr/lib -lpng -lz -O -g
+ *
+ * Error codes: 0: ok 1: file format error 2: file access error
+ * 3: memory error 4: internal numeric error
+ * 5: command line error
+ */
+#undef PNG /* include options for making png files?
+ (will need the png library) */
+#define MAIN
+#include <iostream> // cin, cout, cerr
+#include <fstream> // ofstream, ifstream
+#include <string.h> // strcmp, strstr
+#include <stdio.h> // printf
+#include <stdlib.h> // exit
+#include <math.h> // sqrt, pow
+#include <limits.h> // INT_MIN
+#include <float.h> // FLT_MIN
+#include <time.h> // clock
+#include <ctype.h> // islower, isdigit etc
+
+using std::cout;
+using std::cerr;
+using std::endl;
+using std::ios;
+using std::ifstream;
+using std::ofstream;
+
+int iAux_GLOBAL;
+
+#include "general.h"
+#include "util-C.h" /* imax, fmax, iround, iceil, ifloor, strint, strscn,
+ strcut, substr, uprstr, uprchr, Basename etc. */
+#include "list-C.h" // list data structure
+#include "hash-C.h" // hash data structure
+
+#include "hhdecl-C.h" // Constants, global variables, struct Parameters
+#include "hhutil-C.h" /* MatchChr, InsertChr, aa2i, i2aa, log2,
+ fast_log2, WriteToScreen, */
+#include "hhmatrices-C.h" // BLOSUM50, GONNET, HSDM
+#include "hhhmm.h" // class HMM
+#include "hhhit.h" // class Hit
+#include "hhalignment.h" // class Alignment
+#include "hhhalfalignment.h" // class HalfAlignment
+#include "hhfullalignment.h" // class FullAlignment
+#include "hhhitlist.h" // class Hit
+#include "hhhmm-C.h" // class HMM
+#include "hhalignment-C.h" // class Alignment
+#include "hhhit-C.h" // class Hit
+#include "hhhalfalignment-C.h" // class HalfAlignment
+#include "hhfullalignment-C.h" // class FullAlignment
+#include "hhhitlist-C.h" // class HitList
+#include "hhfunc-C.h" // some functions common to hh programs
+
+#ifdef PNG
+#include "pngwriter.h" //PNGWriter (http://pngwriter.sourceforge.net/)
+#include "pngwriter.cc" //PNGWriter (http://pngwriter.sourceforge.net/)
+#endif
+
+////////////////////////////////////////////////////////////////////////
+// Global variables
+////////////////////////////////////////////////////////////////////////
+HMM *q; // Create query HMM with maximum of MAXRES match states
+HMM *t; /* Create template HMM with maximum of MAXRES
+ match states */
+Alignment *qali; /* (query alignment might be needed outside of hhfunc.C
+ for -a option) */
+Hit hit; // Ceate new hit object pointed at by hit
+HitList hitlist; /* list of hits with one Hit object for each
+ pairwise comparison done */
+char aliindices[256]; /* hash containing indices of all alignments
+ which to show in dot plot */
+char* dmapfile=NULL; /* where to write the coordinates for the HTML map file
+ (to click the alignments) */
+char* alitabfile=NULL; // where to write pairs of aligned residues
+char* strucfile=NULL; // where to read structure scores
+char* pngfile=NULL; // pointer to pngfile
+char* tcfile=NULL; // TCoffee output file name
+float probmin_tc=0.05; /* 5% minimum posterior probability for printing
+ pairs of residues for TCoffee */
+
+int dotW=10; // average score of dot plot over window [i-W..i+W]
+float dotthr=0.5; // score threshold for dot plot
+int dotscale=600; // size scale of dotplot
+char dotali=0; // show no alignments in dotplot
+float dotsat=0.3; // saturation of grid and alignments in dot plot
+float pself=0.001; // maximum p-value of 2nd and following self-alignments
+int Nstochali=0; // # of stochastically traced alignments in dot plot
+float** Pstruc=NULL; /* structure matrix which can be multiplied to prob
+ ratios from aa column comparisons in Forward() */
+float** Sstruc=NULL; /* structure matrix which can be added to log odds
+ from aa column comparisons in Forward() */
+
+
+
+
+
+////////////////////////////////////////////////////////////////////////////
+// Help functions
+////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief general help function, not accessible in Clustal-Omega
+ */
+#if 0
+void
+help()
+{
+ printf("\n");
+ printf("HHalign %s\n",VERSION_AND_DATE);
+ printf("Align a query alignment/HMM to a template alignment/HMM by HMM-HMM alignment\n");
+ printf("If only one alignment/HMM is given it is compared to itself and the best\n");
+ printf("off-diagonal alignment plus all further non-overlapping alignments above \n");
+ printf("significance threshold are shown.\n");
+ printf("%s",REFERENCE);
+ printf("%s",COPYRIGHT);
+ printf("\n");
+ printf("Usage: %s -i query [-t template] [options] \n",program_name);
+ printf(" -i <file> input query alignment (fasta/a2m/a3m) or HMM file (.hhm)\n");
+ printf(" -t <file> input template alignment (fasta/a2m/a3m) or HMM file (.hhm)\n");
+#ifdef PNG
+ printf(" -png <file> write dotplot into PNG-file (default=none) \n");
+#endif
+ printf("\n");
+ printf("Output options: \n");
+ printf(" -o <file> write output alignment to file\n");
+ printf(" -ofas <file> write alignments in FASTA, A2M (-oa2m) or A3M (-oa3m) format \n");
+ printf(" -a <file> write query alignment in a3m format to file (default=none)\n");
+ printf(" -aa <file> append query alignment in a3m format to file (default=none)\n");
+ printf(" -atab <file> write alignment as a table (with posteriors) to file (default=none)\n");
+ printf(" -v <int> verbose mode: 0:no screen output 1:only warings 2: verbose\n");
+ printf(" -seq [1,inf[ max. number of query/template sequences displayed (def=%i) \n",par.nseqdis);
+ printf(" -nocons don't show consensus sequence in alignments (default=show) \n");
+ printf(" -nopred don't show predicted 2ndary structure in alignments (default=show) \n");
+ printf(" -nodssp don't show DSSP 2ndary structure in alignments (default=show) \n");
+ printf(" -aliw int number of columns per line in alignment list (def=%i)\n",par.aliwidth);
+ printf(" -P <float> for self-comparison: max p-value of alignments (def=%.2g\n",pself);
+ printf(" -p <float> minimum probability in summary and alignment list (def=%G) \n",par.p);
+ printf(" -E <float> maximum E-value in summary and alignment list (def=%G) \n",par.E);
+ printf(" -Z <int> maximum number of lines in summary hit list (def=%i) \n",par.Z);
+ printf(" -z <int> minimum number of lines in summary hit list (def=%i) \n",par.z);
+ printf(" -B <int> maximum number of alignments in alignment list (def=%i) \n",par.B);
+ printf(" -b <int> minimum number of alignments in alignment list (def=%i) \n",par.b);
+ printf(" -rank int specify rank of alignment to write with -a or -aa option (default=1)\n");
+ printf("\n");
+#ifdef PNG
+ printf("Dotplot options:\n");
+ printf(" -dwin <int> average score in dotplot over window [i-W..i+W] (def=%i) \n",dotW);
+ printf(" -dthr <float> score threshold for dotplot (default=%.2f) \n",dotthr);
+ printf(" -dsca <int> if value <= 20: size of dot plot unit box in pixels \n");
+ printf(" if value > 20: maximum dot plot size in pixels (default=%i) \n",dotscale);
+ printf(" -dali <list> show alignments with indices in <list> in dot plot \n");
+ printf(" <list> = <index1> ... <indexN> or <list> = all \n");
+ printf("\n");
+#endif
+ printf("Filter input alignment (options can be combined): \n");
+ printf(" -id [0,100] maximum pairwise sequence identity (%%) (def=%i) \n",par.max_seqid);
+ printf(" -diff [0,inf[ filter most diverse set of sequences, keeping at least this \n");
+ printf(" many sequences in each block of >50 columns (def=%i)\n",par.Ndiff);
+ printf(" -cov [0,100] minimum coverage with query (%%) (def=%i) \n",par.coverage);
+ printf(" -qid [0,100] minimum sequence identity with query (%%) (def=%i) \n",par.qid);
+ printf(" -qsc [0,100] minimum score per column with query (def=%.1f)\n",par.qsc);
+// printf(" -csc [0,100] minimum score per column with core alignment (def=%-.2f)\n",par.coresc);
+// printf(" -qscc [0,100] minimum score per column of core sequence with query (def=%-.2f)\n",par.qsc_core);
+ printf("\n");
+ printf("Input alignment format: \n");
+ printf(" -M a2m use A2M/A3M (default): upper case = Match; lower case = Insert;\n");
+ printf(" '-' = Delete; '.' = gaps aligned to inserts (may be omitted) \n");
+ printf(" -M first use FASTA: columns with residue in 1st sequence are match states\n");
+ printf(" -M [0,100] use FASTA: columns with fewer than X%% gaps are match states \n");
+ printf("\n");
+ printf("HMM-HMM alignment options: \n");
+ printf(" -glob/-loc global or local alignment mode (def=local) \n");
+ printf(" -alt <int> show up to this number of alternative alignments (def=%i) \n",par.altali);
+ printf(" -vit use Viterbi algorithm for alignment instead of MAC algorithm \n");
+ printf(" -mac use Maximum Accuracy (MAC) alignment (default) \n");
+ printf(" -mact [0,1[ posterior probability threshold for MAC alignment (def=%.3f) \n",par.mact);
+ printf(" A threshold value of 0.0 yields global alignments.\n");
+ printf(" -sto <int> use global stochastic sampling algorithm to sample this many alignments\n");
+ printf(" -excl <range> exclude query positions from the alignment, e.g. '1-33,97-168'\n");
+ printf(" -shift [-1,1] score offset (def=%-.3f) \n",par.shift);
+ printf(" -corr [0,1] weight of term for pair correlations (def=%.2f) \n",par.corr);
+ printf(" -ssm 0-4 0:no ss scoring [default=%i] \n",par.ssm);
+ printf(" 1:ss scoring after alignment \n");
+ printf(" 2:ss scoring during alignment \n");
+ printf(" -ssw [0,1] weight of ss score (def=%-.2f) \n",par.ssw);
+ printf("\n");
+ printf(" -def read default options from ./.hhdefaults or <home>/.hhdefault. \n");
+ printf("\n");
+ printf("Example: %s -i T0187.a3m -t d1hz4a_.hhm -png T0187pdb.png \n",program_name);
+ cout<<endl;
+// printf("More help: \n");
+// printf(" -h out output options \n");
+// printf(" -h hmm options for building HMM from multiple alignment \n");
+// printf(" -h gap options for setting gap penalties \n");
+// printf(" -h ali options for HMM-HMM alignment \n");
+// printf(" -h all all options \n");
+}
+#endif
+
+/**
+ * @brief helpt for output, not accessible in Clustal-Omega
+ */
+#if 0
+void
+help_out()
+{
+ printf("\n");
+ printf("Output options: \n");
+ printf(" -v verbose mode (default: show only warnings) \n");
+ printf(" -v 0 suppress all screen output \n");
+ printf(" -nocons don't show consensus sequence in alignments (default=show) \n");
+ printf(" -nopred don't show predicted 2ndary structure in alignments (default=show) \n");
+ printf(" -nodssp don't show DSSP SS 2ndary structure in alignments (default=show) \n");
+ printf(" -seq [1,inf[ max. number of query/template sequences displayed (def=%i) \n",par.nseqdis);
+ printf(" -aliw [40,..[ number of columns per line in alignment list (def=%i)\n",par.aliwidth);
+ printf(" -P <float> for self-comparison: max p-value of alignments (def=%.2g\n",pself);
+ printf(" -p <float> minimum probability in summary and alignment list (def=%G) \n",par.p);
+ printf(" -E <float> maximum E-value in summary and alignment list (def=%G) \n",par.E);
+ printf(" -Z <int> maximum number of lines in summary hit list (def=%i) \n",par.Z);
+ printf(" -z <int> minimum number of lines in summary hit list (def=%i) \n",par.z);
+ printf(" -B <int> maximum number of alignments in alignment list (def=%i) \n",par.B);
+ printf(" -b <int> minimum number of alignments in alignment list (def=%i) \n",par.b);
+ printf(" -rank int specify rank of alignment to write with -a or -aa option (def=1)\n");
+ printf(" -tc <file> write a TCoffee library file for the pairwise comparison \n");
+ printf(" -tct [0,100] min. probobability of residue pairs for TCoffee (def=%i%%)\n",iround(100*probmin_tc));
+ printf("\n");
+#ifdef PNG
+ printf("Dotplot options:\n");
+ printf(" -dwin int average score in dotplot over window [i-W..i+W] (def=%i) \n",dotW);
+ printf(" -dthr float score threshold for dotplot (default=%.2f) \n",dotthr);
+ printf(" -dsca int size of dot plot box in pixels (default=%i) \n",dotscale);
+ printf(" -dali <list> show alignments with indices in <list> in dot plot\n");
+ printf(" <list> = <index1> ... <indexN> or <list> = all \n");
+ printf(" -dmap <file> print list of coordinates in png plot \n");
+#endif
+}
+#endif
+
+/**
+ * @brief help hit HMM options, not accessible in Clustal-Omega
+ */
+#if 0
+void
+help_hmm()
+{
+ printf("\n");
+ printf("Options to filter input alignment (options can be combined): \n");
+ printf(" -id [0,100] maximum pairwise sequence identity (%%) (def=%i) \n",par.max_seqid);
+ printf(" -diff [0,inf[ filter most diverse set of sequences, keeping at least this \n");
+ printf(" many sequences in each block of >50 columns (def=%i)\n",par.Ndiff);
+ printf(" -cov [0,100] minimum coverage with query (%%) (def=%i) \n",par.coverage);
+ printf(" -qid [0,100] minimum sequence identity with query (%%) (def=%i) \n",par.qid);
+ printf(" -qsc [0,100] minimum score per column with query (def=%.1f)\n",par.qsc);
+// printf(" -csc [0,100] minimum score per column with core alignment (def=%-.2f)\n",par.coresc);
+// printf(" -qscc [0,100] minimum score per column of core sequence with query (def=%-.2f)\n",par.qsc_core);
+ printf(" \n");
+ printf("HMM-building options: \n");
+ printf(" -M a2m use A2M/A3M (default): upper case = Match; lower case = Insert;\n");
+ printf(" '-' = Delete; '.' = gaps aligned to inserts (may be omitted) \n");
+ printf(" -M first use FASTA: columns with residue in 1st sequence are match states\n");
+ printf(" -M [0,100] use FASTA: columns with fewer than X%% gaps are match states \n");
+ printf(" -tags do NOT neutralize His-, C-myc-, FLAG-tags, and \n");
+ printf(" trypsin recognition sequence to background distribution \n");
+ printf(" \n");
+ printf("Pseudocount options: \n");
+ printf(" -Gonnet use the Gonnet substitution matrix (default) \n");
+ printf(" -Blosum50 use the Blosum50 substitution matrix \n");
+ printf(" -Blosum62 use the Blosum62 substitution matrix \n");
+ printf(" -HSDM use the structure-derived HSDM substitution matrix \n");
+ printf(" -pcm 0-3 Pseudocount mode (default=%-i) \n",par.pcm);
+ printf(" tau = substitution matrix pseudocount admixture \n");
+ printf(" 0: no pseudo counts: tau = 0 \n");
+ printf(" 1: constant tau = a \n");
+ printf(" 2: divergence-dependent: tau = a/(1 + ((Neff-1)/b)^c) \n");
+ printf(" Neff=( (Neff_q^d+Neff_t^d)/2 )^(1/d) \n");
+ printf(" Neff_q = av number of different AAs per column in query \n");
+ printf(" 3: column-specific: tau = \'2\' * (Neff(i)/Neff)^(w*Neff/20)\n");
+ printf(" -pca [0,1] set a (overall admixture) (def=%-.1f) \n",par.pca);
+ printf(" -pcb [1,inf[ set b (threshold for Neff) (def=%-.1f) \n",par.pcb);
+ printf(" -pcc [0,3] set c (extinction exponent for tau(Neff)) (def=%-.1f) \n",par.pcc);
+ printf(" -pcw [0,3] set w (weight of pos-specificity for pcs) (def=%-.1f) \n",par.pcw);
+}
+#endif
+
+/**
+ * @brief help with gap handling, not accessible in Clustal-Omega
+ */
+#if 0
+void
+help_gap()
+{
+ printf("\n");
+ printf("Gap cost options: \n");
+ printf(" -gapb [0,inf[ transition pseudocount admixture (def=%-.2f) \n",par.gapb);
+ printf(" -gapd [0,inf[ Transition pseudocount admixture for opening gap (default=%-.2f)\n",par.gapd);
+ printf(" -gape [0,1.5] Transition pseudocount admixture for extending gap (def=%-.1f)\n",par.gape);
+ printf(" -gapf ]0,inf] factor for increasing/reducing the gap open penalty for deletes (def=%-.2f)\n",par.gapf);
+ printf(" -gapg ]0,inf] factor for increasing/reducing the gap open penalty for deletes (def=%-.2f)\n",par.gapg);
+ printf(" -gaph ]0,inf] factor for increasing/reducing the gap extension penalty for deletes(def=%-.2f)\n",par.gaph);
+ printf(" -gapi ]0,inf] factor for increasing/reducing the gap extension penalty for inserts(def=%-.2f)\n",par.gapi);
+ printf(" -egq [0,inf[ penalty (bits) for end gaps aligned to query residues (def=%-.2f)\n",par.egq);
+ printf(" -egt [0,inf[ penalty (bits) for end gaps aligned to template residues (def=%-.2f)\n",par.egt);
+}
+#endif
+
+/**
+ * @brief help with alignment options, not accessible in Clustal-Omega
+ */
+#if 0
+void
+help_ali()
+{
+ printf("\n");
+ printf("Alignment options: \n");
+ printf(" -glob/-loc global or local alignment mode (def=global) \n");
+ printf(" -mac use Maximum Accuracy (MAC) alignment instead of Viterbi\n");
+ printf(" -mact [0,1] posterior prob threshold for MAC alignment (def=%.3f) \n",par.mact);
+ printf(" -sto <int> use global stochastic sampling algorithm to sample this many alignments\n");
+ printf(" -sc <int> amino acid score (tja: template HMM at column j) (def=%i)\n",par.columnscore);
+ printf(" 0 = log2 Sum(tja*qia/pa) (pa: aa background frequencies) \n");
+ printf(" 1 = log2 Sum(tja*qia/pqa) (pqa = 1/2*(pa+ta) ) \n");
+ printf(" 2 = log2 Sum(tja*qia/ta) (ta: av. aa freqs in template) \n");
+ printf(" 3 = log2 Sum(tja*qia/qa) (qa: av. aa freqs in query) \n");
+ printf(" -corr [0,1] weight of term for pair correlations (def=%.2f) \n",par.corr);
+ printf(" -shift [-1,1] score offset (def=%-.3f) \n",par.shift);
+ printf(" -r repeat identification: multiple hits not treated as independent\n");
+ printf(" -ssm 0-2 0:no ss scoring [default=%i] \n",par.ssm);
+ printf(" 1:ss scoring after alignment \n");
+ printf(" 2:ss scoring during alignment \n");
+ printf(" -ssw [0,1] weight of ss score compared to column score (def=%-.2f) \n",par.ssw);
+ printf(" -ssa [0,1] ss confusion matrix = (1-ssa)*I + ssa*psipred-confusion-matrix [def=%-.2f)\n",par.ssa);
+}
+#endif
+
+/**
+ * @brief general help menu, not accessible in Clustal-Omega
+ */
+#if 0
+void
+help_all()
+{
+ help();
+ help_out();
+ help_hmm();
+ help_gap();
+ help_ali();
+ printf("\n");
+ printf("Default options can be specified in './.hhdefaults' or '~/.hhdefaults'\n");
+}
+#endif
+
+/////////////////////////////////////////////////////////////////////////////
+//// Processing input options from command line and .hhdefaults file
+/////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief process arguments from commandline, not accessible from Clustal-Omega
+ */
+#if 0
+void
+ProcessArguments(int argc, char** argv)
+{
+ //Processing command line input
+ for (int i=1; i<argc; i++)
+ {
+ if (v>=4) cout<<i<<" "<<argv[i]<<endl; //PRINT
+ if (!strcmp(argv[i],"-i"))
+ {
+ if (++i>=argc || argv[i][0]=='-')
+ {help(); cerr<<endl<<"Error in "<<program_name<<": no query file following -i\n"; exit(4);}
+ else strcpy(par.infile,argv[i]);
+ }
+ else if (!strcmp(argv[i],"-t"))
+ {
+ if (++i>=argc || argv[i][0]=='-')
+ {help(); cerr<<endl<<"Error in "<<program_name<<": no template file following -d\n"; exit(4);}
+ else strcpy(par.tfile,argv[i]); /* FS, ProcessArguments */
+ }
+ else if (!strcmp(argv[i],"-o"))
+ {
+ if (++i>=argc)
+ {help(); cerr<<endl<<"Error in "<<program_name<<": no filename following -o\n"; exit(4);}
+ else strcpy(par.outfile,argv[i]);
+ }
+ else if (!strcmp(argv[i],"-ofas"))
+ {
+ par.outformat=1;
+ if (++i>=argc || argv[i][0]=='-')
+ {help() ; cerr<<endl<<"Error in "<<program_name<<": no output file following -o\n"; exit(4);}
+ else strcpy(par.pairwisealisfile,argv[i]);
+ }
+ else if (!strcmp(argv[i],"-oa2m"))
+ {
+ par.outformat=2;
+ if (++i>=argc || argv[i][0]=='-')
+ {help() ; cerr<<endl<<"Error in "<<program_name<<": no output file following -o\n"; exit(4);}
+ else strcpy(par.pairwisealisfile,argv[i]);
+ }
+ else if (!strcmp(argv[i],"-oa3m"))
+ {
+ par.outformat=3;
+ if (++i>=argc || argv[i][0]=='-')
+ {help() ; cerr<<endl<<"Error in "<<program_name<<": no output file following -o\n"; exit(4);}
+ else strcpy(par.pairwisealisfile,argv[i]);
+ }
+ else if (!strcmp(argv[i],"-rank") && (i<argc-1)) par.hitrank=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-Oa3m"))
+ {
+ par.append=0;
+ if (++i>=argc || argv[i][0]=='-')
+ {help() ; cerr<<endl<<"Error in "<<program_name<<": no output file following -Oa3m\n"; exit(4);}
+ else strcpy(par.alnfile,argv[i]);
+ }
+ else if (!strcmp(argv[i],"-Aa3m"))
+ {
+ par.append=1;
+ if (++i>=argc || argv[i][0]=='-')
+ {help() ; cerr<<endl<<"Error in "<<program_name<<": no output file following -Aa3m\n"; exit(4);}
+ else strcpy(par.alnfile,argv[i]);
+ }
+ else if (!strcmp(argv[i],"-Ohhm"))
+ {
+ par.append=0;
+ if (++i>=argc || argv[i][0]=='-')
+ {help() ; cerr<<endl<<"Error in "<<program_name<<": no output file following -Ohhm\n"; exit(4);}
+ else strcpy(par.hhmfile,argv[i]);
+ }
+ else if (!strcmp(argv[i],"-Ahhm"))
+ {
+ par.append=1;
+ if (++i>=argc || argv[i][0]=='-')
+ {help() ; cerr<<endl<<"Error in "<<program_name<<": no output file following -Ahhm\n"; exit(4);}
+ else strcpy(par.hhmfile,argv[i]);
+ }
+ else if (!strcmp(argv[i],"-Opsi"))
+ {
+ par.append=0;
+ if (++i>=argc || argv[i][0]=='-')
+ {help() ; cerr<<endl<<"Error in "<<program_name<<": no output file following -Opsi\n"; exit(4);}
+ else strcpy(par.psifile,argv[i]);
+ }
+ else if (!strcmp(argv[i],"-Apsi"))
+ {
+ par.append=1;
+ if (++i>=argc || argv[i][0]=='-')
+ {help() ; cerr<<endl<<"Error in "<<program_name<<": no output file following -Apsi\n"; exit(4);}
+ else strcpy(par.psifile,argv[i]);
+ }
+ else if (!strcmp(argv[i],"-png"))
+ {
+ if (++i>=argc)
+ {help(); cerr<<endl<<"Error in "<<program_name<<": no filename following -png\n"; exit(4);}
+ else
+ {
+ pngfile = new(char[strlen(argv[i])+1]);
+ strcpy(pngfile,argv[i]);
+ }
+ }
+ else if (!strcmp(argv[i],"-Struc"))
+ {
+ if (++i>=argc || argv[i][0]=='-')
+ {help(); cerr<<endl<<"Error in "<<program_name<<": no query file following -Struc\n"; exit(4);}
+ else
+ {
+ strucfile = new(char[strlen(argv[i])+1]);
+ strcpy(strucfile,argv[i]);
+ }
+ }
+ else if (!strcmp(argv[i],"-atab") || !strcmp(argv[i],"-Aliout"))
+ {
+ if (++i>=argc || argv[i][0]=='-')
+ {help(); cerr<<endl<<"Error in "<<program_name<<": no query file following -Struc\n"; exit(4);}
+ else
+ {
+ alitabfile = new(char[strlen(argv[i])+1]);
+ strcpy(alitabfile,argv[i]);
+ }
+ }
+ else if (!strcmp(argv[i],"-tc"))
+ {
+ if (++i>=argc || argv[i][0]=='-')
+ {help() ; cerr<<endl<<"Error in "<<program_name<<": no output file following -Opsi\n"; exit(4);}
+ else
+ {
+ tcfile = new(char[strlen(argv[i])+1]);
+ strcpy(tcfile,argv[i]);
+ }
+ }
+ else if (!strcmp(argv[i],"-h")|| !strcmp(argv[i],"--help"))
+ {
+ if (++i>=argc) {help(); exit(0);}
+ if (!strcmp(argv[i],"out")) {help_out(); exit(0);}
+ if (!strcmp(argv[i],"hmm")) {help_hmm(); exit(0);}
+ if (!strcmp(argv[i],"gap")) {help_gap(); exit(0);}
+ if (!strcmp(argv[i],"ali")) {help_ali(); exit(0);}
+ if (!strcmp(argv[i],"all")) {help_all(); exit(0);}
+ else {help(); exit(0);}
+ }
+ else if (!strcmp(argv[i],"-excl"))
+ {
+ if (++i>=argc) {help(); exit(4);}
+ par.exclstr = new(char[strlen(argv[i])+1]);
+ strcpy(par.exclstr,argv[i]);
+ }
+ else if (!strcmp(argv[i],"-v") && (i<argc-1) && argv[i+1][0]!='-' ) v=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-v")) v=2;
+ else if (!strcmp(argv[i],"-v0")) v=0;
+ else if (!strcmp(argv[i],"-v1")) v=1;
+ else if (!strcmp(argv[i],"-v2")) v=2;
+ else if (!strcmp(argv[i],"-v3")) v=3;
+ else if (!strcmp(argv[i],"-v4")) v=4;
+ else if (!strcmp(argv[i],"-v5")) v=5;
+ else if (!strcmp(argv[i],"-P") && (i<argc-1)) pself=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-p") && (i<argc-1)) par.p = atof(argv[++i]);
+ else if (!strcmp(argv[i],"-e") && (i<argc-1)) par.E = atof(argv[++i]);
+ else if (!strcmp(argv[i],"-E") && (i<argc-1)) par.E = atof(argv[++i]);
+ else if (!strcmp(argv[i],"-b") && (i<argc-1)) par.b = atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-B") && (i<argc-1)) par.B = atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-z") && (i<argc-1)) par.z = atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-Z") && (i<argc-1)) par.Z = atoi(argv[++i]);
+ else if (!strncmp(argv[i],"-nocons",7)) par.showcons=0;
+ else if (!strncmp(argv[i],"-nopred",7)) par.showpred=0;
+ else if (!strncmp(argv[i],"-nodssp",7)) par.showdssp=0;
+ else if (!strncmp(argv[i],"-mark",7)) par.mark=1;
+ else if (!strcmp(argv[i],"-seq") && (i<argc-1)) par.nseqdis=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-aliw") && (i<argc-1)) par.aliwidth=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-id") && (i<argc-1)) par.max_seqid=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-tct") && (i<argc-1)) probmin_tc=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-dwin") && (i<argc-1)) dotW=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-dsca") && (i<argc-1)) dotscale=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-dthr") && (i<argc-1)) dotthr=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-dali") && (i<argc-1))
+ {
+ dotali=1;
+ for (int index=0; index<256; index++) aliindices[index]=0;
+ while (i+1<argc && argv[i+1][0]!='-') // adds index to hash aliindices
+ {
+ i++;
+ if (strcmp(argv[i],"all")) aliindices[atoi(argv[i])]=1;
+ else dotali=2;
+ }
+ }
+ else if (!strcmp(argv[i],"-dmap"))
+ {
+ if (++i>=argc)
+ {help(); cerr<<endl<<"Error in "<<program_name<<": no filename following -o\n"; exit(4);}
+ else
+ {
+ dmapfile = new(char[strlen(argv[i])+1]);
+ strcpy(dmapfile,argv[i]);
+ }
+ }
+ else if (!strcmp(argv[i],"-dsat") && (i<argc-1)) dotsat=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-qid") && (i<argc-1)) par.qid=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-qsc") && (i<argc-1)) par.qsc=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-cov") && (i<argc-1)) par.coverage=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-diff") && (i<argc-1)) par.Ndiff=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-qscc") && (i<argc-1)) par.qsc_core=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-csc") && (i<argc-1)) par.coresc=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-Gonnet")) par.matrix=0;
+ else if (!strcmp(argv[i],"-HSDM")) par.matrix=1;
+ else if (!strcmp(argv[i],"-BLOSUM50")) par.matrix=2;
+ else if (!strcmp(argv[i],"-Blosum50")) par.matrix=2;
+ else if (!strcmp(argv[i],"-B50")) par.matrix=2;
+ else if (!strcmp(argv[i],"-BLOSUM62")) par.matrix=3;
+ else if (!strcmp(argv[i],"-Blosum62")) par.matrix=3;
+ else if (!strcmp(argv[i],"-B62")) par.matrix=3;
+ else if (!strcmp(argv[i],"-pcm") && (i<argc-1)) par.pcm=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-pca") && (i<argc-1)) par.pca=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-pcb") && (i<argc-1)) par.pcb=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-pcc") && (i<argc-1)) par.pcc=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-pcw") && (i<argc-1)) par.pcw=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-gapb") && (i<argc-1)) { par.gapb=atof(argv[++i]); if (par.gapb<=0.01) par.gapb=0.01;}
+ else if (!strcmp(argv[i],"-gapd") && (i<argc-1)) par.gapd=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-gape") && (i<argc-1)) par.gape=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-gapf") && (i<argc-1)) par.gapf=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-gapg") && (i<argc-1)) par.gapg=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-gaph") && (i<argc-1)) par.gaph=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-gapi") && (i<argc-1)) par.gapi=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-egq") && (i<argc-1)) par.egq=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-egt") && (i<argc-1)) par.egt=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-ssgap")) par.ssgap=1;
+ else if (!strcmp(argv[i],"-ssgapd") && (i<argc-1)) par.ssgapd=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-ssgape") && (i<argc-1)) par.ssgape=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-ssgapi") && (i<argc-1)) par.ssgapi=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-ssm") && (i<argc-1)) par.ssm=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-ssw") && (i<argc-1)) par.ssw=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-ssa") && (i<argc-1)) par.ssa=atof(argv[++i]);
+ else if (!strncmp(argv[i],"-glo",3)) {par.loc=0; if (par.mact>0.3 && par.mact<0.301) {par.mact=0;} }
+ else if (!strncmp(argv[i],"-loc",3)) par.loc=1;
+ else if (!strncmp(argv[i],"-alt",4) && (i<argc-1)) par.altali=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-map") || !strcmp(argv[i],"-MAP")) par.forward=2;
+ else if (!strcmp(argv[i],"-mac") || !strcmp(argv[i],"-MAC")) par.forward=2;
+ else if (!strcmp(argv[i],"-vit")) par.forward=0;
+ else if (!strcmp(argv[i],"-sto") && (i<argc-1)) {Nstochali=atoi(argv[++i]); par.forward=1;}
+ else if (!strcmp(argv[i],"-r")) par.repmode=1;
+ else if (!strcmp(argv[i],"-M") && (i<argc-1))
+ if (!strcmp(argv[++i],"a2m") || !strcmp(argv[i],"a3m")) par.M=1;
+ else if(!strcmp(argv[i],"first")) par.M=3;
+ else if (argv[i][0]>='0' && argv[i][0]<='9') {par.Mgaps=atoi(argv[i]); par.M=2;}
+ else cerr<<endl<<"WARNING: Ignoring unknown argument: -M "<<argv[i]<<"\n";
+ else if (!strcmp(argv[i],"-shift") && (i<argc-1)) par.shift=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-mact") && (i<argc-1)) {par.mact=atof(argv[++i]); par.forward=2;}
+ else if (!strcmp(argv[i],"-wstruc") && (i<argc-1)) par.wstruc=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-opt") && (i<argc-1)) par.opt=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-sc") && (i<argc-1)) par.columnscore=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-corr") && (i<argc-1)) par.corr=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-def")) par.readdefaultsfile=1;
+ else if (!strcmp(argv[i],"-ovlp") && (i<argc-1)) par.min_overlap=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-tags")) par.notags=0;
+ else if (!strcmp(argv[i],"-notags")) par.notags=1;
+ else cerr<<endl<<"WARNING: Ignoring unknown option "<<argv[i]<<" ...\n";
+ if (v>=4) cout<<i<<" "<<argv[i]<<endl; //PRINT
+ } // end of for-loop for command line input
+}
+#endif
+
+
+
+
+/////////////////////////////////////////////////////////////////////////////
+//// MAIN PROGRAM
+/////////////////////////////////////////////////////////////////////////////
+/**
+ *
+ * hhalign()
+ *
+ * @param[in,out] ppcFirstProf
+ * first profile to be aligned
+ * @param[in] iFirstCnt
+ * number of sequences in 1st profile
+ * @param[in,out] ppcSecndProf
+ * second profile to be aligned
+ * @param[in] iSecndCnt
+ * number of sequences in 2nd profile
+ * @param[out] dScore_p
+ * score of alignment
+ * @param[in] prHMM
+ * HMM info of external HMM (background)
+ * @param[in] pcPrealigned1
+ * (gapped) 1st sequence aligned to background HMM
+ * @param[in] pcRepresent1
+ * (gapped) sequence representing background HMM aligned to 1st sequence
+ * @param[in] pcPrealigned2
+ * (gapped) 2nd sequence aligned to background HMM
+ * @param[in] pcRepresent2
+ * (gapped) sequence representing background HMM aligned to 2nd sequence
+ * @param[in] rHhalignPara,
+ * various parameters passed down from commandline
+ * e.g., iMaxRamMB
+ *
+ * iFlag,zcAux,zcError are debugging arguments
+ *
+ * @return Non-zero on error
+ */
+extern "C" int
+hhalign(char **ppcFirstProf, int iFirstCnt, double *pdWeightsL,
+ char **ppcSecndProf, int iSecndCnt, double *pdWeightsR,
+ double *dScore_p, hmm_light *prHMM,
+ char *pcPrealigned1, char *pcRepresent1,
+ char *pcPrealigned2, char *pcRepresent2,
+ hhalign_para rHhalignPara,
+ int iFlag,
+ char zcAux[], char zcError[]) {
+
+
+#ifdef CLUSTALO
+ int iRetVal = RETURN_OK;
+ iAux_GLOBAL = iFlag;
+#ifndef CLUSTALO_NOFILE
+ int argc = 0;
+ char **argv = NULL;
+ argv = (char **)malloc(argc*sizeof(char *));
+ for (int i = 0; i < argc; i++){
+ argv[i] = (char *)malloc(100);
+ }
+ strcpy(argv[0], "./hhalign");
+ strcpy(argv[1], "-t");
+ strcpy(argv[2], "hhalign.C");
+ strcpy(argv[3], "-i");
+ strcpy(argv[4], "hhalign.C");
+ strcpy(argv[5], "-ofas");
+ strcpy(argv[6], "out");
+#endif
+#endif
+ /*char* argv_conf[MAXOPT];*/ /* Input arguments from .hhdefaults file
+ (first=1: argv_conf[0] is not used) */
+ /*int argc_conf;*/ // Number of arguments in argv_conf
+ /*char inext[IDLEN]="";*/ // Extension of query input file (hhm or a3m)
+ /*char text[IDLEN]="";*/ // Extension of template input file (hhm or a3m)
+ /*int** ali=NULL;*/ // ali[i][j]=1 if (i,j) is part of an alignment
+ /*int** alisto=NULL;*/ // ali[i][j]=1 if (i,j) is part of an alignment
+ int Nali; /* number of normally backtraced alignments
+ in dot plot */
+
+ SetDefaults();
+ strcpy(par.tfile,""); /* FS, Initialise Argument */
+ strcpy(par.alnfile,"");
+ par.p=0.0 ; /* minimum threshold for inclusion in hit list
+ and alignment listing */
+ par.E=1e6; /* maximum threshold for inclusion in hit list
+ and alignment listing */
+ par.b=1; // min number of alignments
+ par.B=100; // max number of alignments
+ par.z=1; // min number of lines in hit list
+ par.Z=100; // max number of lines in hit list
+ par.append=0; /* append alignment to output file
+ with -a option */
+ par.altali=1; /* find only ONE (possibly overlapping)
+ subalignment */
+ par.hitrank=0; /* rank of hit to be printed as a3m alignment
+ (default=0) */
+ par.outformat=3; // default output format for alignment is a3m
+ hit.self=0; // no self-alignment
+ par.forward=2; /* 0: Viterbi algorithm;
+ 1: Viterbi+stochastic sampling;
+ 2:Maximum Accuracy (MAC) algorithm */
+
+ // Make command line input globally available
+#ifndef CLUSTALO_NOFILE
+ par.argv=argv;
+ par.argc=argc;
+ RemovePathAndExtension(program_name,argv[0]);
+#endif
+
+#ifndef CLUSTALO_NOFILE
+ /* Enable changing verbose mode before defaults file
+ and command line are processed */
+ for (int i=1; i<argc; i++)
+ {
+ if (!strcmp(argv[i],"-def")) par.readdefaultsfile=1;
+ else if (argc>1 && !strcmp(argv[i],"-v0")) v=0;
+ else if (argc>1 && !strcmp(argv[i],"-v1")) v=1;
+ else if (argc>2 && !strcmp(argv[i],"-v")) v=atoi(argv[i+1]);
+ }
+
+ // Read .hhdefaults file?
+ if (par.readdefaultsfile)
+ {
+ // Process default otpions from .hhconfig file
+ ReadDefaultsFile(argc_conf,argv_conf);
+ ProcessArguments(argc_conf,argv_conf);
+ }
+#endif
+ /* Process command line options
+ (they override defaults from .hhdefaults file) */
+#ifndef CLUSTALO_NOFILE
+ ProcessArguments(argc,argv);
+#endif
+
+
+#ifdef CLUSTALO
+ int iAuxLen1 = strlen(ppcFirstProf[0]);
+ int iAuxLen2 = strlen(ppcSecndProf[0]);
+ if ( (0 == iAuxLen1) || (0 == iAuxLen2) ){ /* problem with empty profiles, FS, r249 -> r250 */
+ sprintf(zcError, "%s:%s:%d: strlen(prof1)=%d, strlen(prof2)=%d -- Nothing to align!\n",
+ __FUNCTION__, __FILE__, __LINE__, iAuxLen1, iAuxLen2);
+ iRetVal = RETURN_UNKNOWN;
+ /* Note: at this stage cannot do 'goto this_is_the_end;'
+ because would cross initialisation of several variables */
+ return iRetVal;
+ }
+ par.maxResLen = iAuxLen1 > iAuxLen2 ? iAuxLen1 : iAuxLen2;
+ const int ciGoodMeasureSeq = 10;
+ par.maxResLen += ciGoodMeasureSeq;
+ par.maxColCnt = iAuxLen1 + iAuxLen2 + ciGoodMeasureSeq;
+ //par.max_seqid=iFirstCnt+iSecndCnt+3; /* -id */
+ par.max_seqid=DEFAULT_FILTER; /* -id */
+ par.loc=0; par.mact=0; /* -glob */
+ par.nseqdis=iFirstCnt+iSecndCnt; /* -seq */
+ par.showcons=0; /* -nocons */
+ par.showdssp=0; /* -nodssp */
+ par.Mgaps=100; /* -M */
+ par.M=2; /* -M */
+ par.pdWg1=pdWeightsL; /* tree wg */
+ par.pdWg2=pdWeightsR; /* tree wg */
+ v = 0; /* -v0 */
+ /* NOTE: *qali declared globally but only created here,
+ pass in number of sequences to get rid of statically
+ defined MAXSEQ (FS)
+ */
+ Alignment qali(iFirstCnt+iSecndCnt);
+ HMM q(iFirstCnt+iSecndCnt);
+ HMM t(iFirstCnt+iSecndCnt);
+#endif
+
+
+#ifndef CLUSTALO_NOFILE
+ // Check command line input and default values
+ if (!*par.infile)
+ {help(); cerr<<endl<<"Error in "<<program_name<<": no query alignment file given (-i file)\n"; exit(4);}
+ if (par.forward==2 && par.loc==0)
+ {
+ if (par.mact<0.301 || par.mact>0.300)
+ if (v>=1) fprintf(stderr,"REMARK: in -mac -global mode -mact is forced to 0\n");
+ par.mact=0;
+ // par.loc=1; // global forward-backward algorithm seems to work fine! use it in place of local version.
+ }
+
+ // Get rootname (no directory path, no extension) and extension of infile
+ RemoveExtension(q.file,par.infile);
+ RemoveExtension(t.file,par.tfile); /* FS, NOFILE2 (commented out) */
+ Extension(inext,par.infile);
+ Extension(text,par.tfile); /*FS, NOFILE2 (commented out) */
+
+ // Check option compatibilities
+ if (par.nseqdis>MAXSEQDIS-3-par.showcons) par.nseqdis=MAXSEQDIS-3-par.showcons; //3 reserved for secondary structure
+ if (par.aliwidth<20) par.aliwidth=20;
+ if (par.pca<0.001) par.pca=0.001; // to avoid log(0)
+ if (par.b>par.B) par.B=par.b;
+ if (par.z>par.Z) par.Z=par.z;
+ if (par.hitrank>0) par.altali=0;
+
+ // Input parameters
+ if (v>=3)
+ {
+ cout<<"query file : "<<par.infile<<"\n";
+ cout<<"template file: "<<par.tfile<<"\n";/*FS, NOFILE2 (commented out) */
+ cout<<"Output file: "<<par.outfile<<"\n";
+ cout<<"Alignment file: "<<par.alnfile<<"\n";
+ }
+#endif /* NOFILE2 */
+
+
+ // Set (global variable) substitution matrix and derived matrices
+ SetSubstitutionMatrix();
+
+
+ // Set secondary structure substitution matrix
+ SetSecStrucSubstitutionMatrix();
+
+
+ /* moved Viterbi switch from after RnP() to here,
+ switch after RnP() ineffectual as RnP decides log/lin of transition,
+ however log/lin of transitions depends on MAC/Viterbi,
+ FS, r228 -> r229 */
+ int qL, tL;
+ if (iFirstCnt > 0) {
+ qL = strlen(ppcFirstProf[0]);
+ }
+ else {
+ qL = prHMM->L;
+ }
+ if (iSecndCnt > 0) {
+ tL = strlen(ppcSecndProf[0]);
+ }
+ else {
+ tL = prHMM->L;
+ }
+
+
+ // const float MEMSPACE_DYNPROG = 512*1024*1024;
+ /* determine amount of memory available for MAC on command-line; FS, r240 -> r241 */
+ const float MEMSPACE_DYNPROG = (double)1024*1024*rHhalignPara.iMacRamMB;
+ // longest allowable length of database HMM
+ int Lmaxmem=(int)((float)MEMSPACE_DYNPROG/qL/6/8);
+ if (par.forward==2 && tL+2>=Lmaxmem) {
+ if (v>=1)
+ cerr<<"WARNING: Not sufficient memory to realign with MAC algorithm. Using Viterbi algorithm."<<endl;
+ par.forward=0;
+
+ /* use different 'fudge' parameters for Viterbi, FS, r228 -> r229 */
+ par.pca = par.pcaV;
+ par.pcb = par.pcbV;
+ par.pcc = par.pccV;
+ par.pcw = par.pcwV;
+
+ par.gapb = par.gapbV;
+ par.gapd = par.gapdV;
+ par.gape = par.gapeV;
+ par.gapf = par.gapfV;
+ par.gapg = par.gapgV;
+ par.gaph = par.gaphV;
+ par.gapi = par.gapiV;
+
+ }
+
+
+ // Read input file (HMM, HHM, or alignment format), and add pseudocounts etc.
+ q.cQT = 'q';
+ if (OK != ReadAndPrepare(INTERN_ALN_2_HMM,
+ ppcFirstProf, iFirstCnt, prHMM,
+ pcPrealigned1, pcRepresent1, pdWeightsL,
+ (char*)(""), q, &qali)) {
+ sprintf(zcError, "%s:%s:%d: Problem Reading/Preparing q-profile (len=%d)\n",
+ __FUNCTION__, __FILE__, __LINE__, qL);
+ iRetVal = RETURN_FROM_RNP;
+ goto this_is_the_end;
+ }
+ // Set query columns in His-tags etc to Null model distribution
+ if (par.notags) q.NeutralizeTags();
+
+ // Do self-comparison?
+ if (0 /* !*par.tfile // FS, 2010-03-10 */)
+ {
+ // Deep-copy q into t
+ t = q;
+
+ // Find overlapping alternative alignments
+ hit.self=1;
+ }
+ // Read template alignment/HMM t and add pseudocounts
+ else
+ {
+ char infile[] = "";
+ /* Read input file (HMM, HHM, or alignment format),
+ and add pseudocounts etc. */
+ t.cQT = 't';
+ if (OK != ReadAndPrepare(INTERN_ALN_2_HMM,
+ ppcSecndProf, iSecndCnt, prHMM,
+ pcPrealigned2, pcRepresent2, pdWeightsR,
+ infile, t)) {
+ sprintf(zcError, "%s:%s:%d: Problem Reading/Preparing t-profile (len=%d)\n",
+ __FUNCTION__, __FILE__, __LINE__, tL);
+ iRetVal = RETURN_FROM_RNP;
+ goto this_is_the_end;
+ }
+ }
+
+ // Factor Null model into HMM t
+ t.IncludeNullModelInHMM(q,t);
+
+ /* switch at this stage is ineffectual as log/lin already decided in RnP().
+ FS, r228 -> r229 */
+ /*const float MEMSPACE_DYNPROG = 512*1024*1024;
+ // longest allowable length of database HMM
+ int Lmaxmem=(int)((float)MEMSPACE_DYNPROG/q.L/6/8);
+ if (par.forward==2 && t.L+2>=Lmaxmem)
+ {
+ if (v>=1)
+ cerr<<"WARNING: Not sufficient memory to realign with MAC algorithm. Using Viterbi algorithm."<<endl;
+ par.forward=0;
+ }*/
+
+ // Allocate memory for dynamic programming matrix
+ hit.AllocateBacktraceMatrix(q.L+2,t.L+2); // ...with a separate dynamic programming matrix (memory!!)
+ if (par.forward>=1 || Nstochali)
+ hit.AllocateForwardMatrix(q.L+2,t.L+2);
+ if (par.forward==2)
+ hit.AllocateBackwardMatrix(q.L+2,t.L+2);
+
+#ifndef CLUSTALO_NOFILE
+ // Read structure file for Forward() function?
+ if (strucfile && par.wstruc>0)
+ {
+ float PMIN=1E-20;
+ Pstruc = new(float*[q.L+2]);
+ for (int i=0; i<q.L+2; i++) Pstruc[i] = new(float[t.L+2]);
+ Sstruc = new(float*[q.L+2]);
+ for (int i=0; i<q.L+2; i++) Sstruc[i] = new(float[t.L+2]);
+ FILE* strucf=NULL;
+ if (strcmp(strucfile,"stdin"))
+ {
+ strucf = fopen(strucfile, "r");
+ if (!strucf) OpenFileError(strucfile);
+ }
+ else
+ {
+ strucf = stdin;
+ if (v>=2) printf("Reading structure matrix from standard input ... (for UNIX use ^D for 'end-of-file')\n");
+ }
+ for (int i=1; i<=q.L; i++)
+ {
+ for (int j=1; j<=t.L; j++)
+ {
+ float f;
+ if (fscanf(strucf,"%f",&f) <=0 )
+ {
+ fprintf(stderr,"Error: too few numbers in file %s while reading line %i, column %i\n",strucfile,i,j);
+ exit(1);
+ }
+ if (par.wstruc==1)
+ Pstruc[i][j]=fmax(f,PMIN);
+ else
+ Pstruc[i][j]=fmax(pow(f,par.wstruc),PMIN);
+// printf("%10.2E ",f);
+ Sstruc[i][j] = par.wstruc * log2(f);
+ }
+// printf("\n");
+ }
+ fclose(strucf);
+ } /* (strucfile && par.wstruc>0) */
+#endif
+
+ /* Do (self-)comparison, store results if score>SMIN,
+ and try next best alignment */
+ /* FIXME very ambigous and possibly faulty if-else */
+ if (v>=2) {
+ if (par.forward==2) {
+ printf("Using maximum accuracy (MAC) alignment algorithm ...\n");
+ }
+ else if (par.forward==0) {
+ printf("Using Viterbi algorithm ...\n");
+ }
+ else if (par.forward==1) {
+ printf("Using stochastic sampling algorithm ...\n");
+ }
+ else {
+ printf("\nWhat alignment algorithm are we using??\n");
+ }
+ }
+
+
+ for (hit.irep=1; hit.irep<=imax(par.hitrank,par.altali); hit.irep++)
+ {
+ if (par.forward==0)
+ {
+ // generate Viterbi alignment
+ hit.Viterbi(q,t,Sstruc);
+ hit.Backtrace(q,t);
+ }
+ else if (par.forward==1)
+ {
+ // generate a single stochastically sampled alignment
+ hit.Forward(q,t,Pstruc);
+ srand( time(NULL) ); // initialize random generator
+ hit.StochasticBacktrace(q,t);
+ hitlist.Push(hit); /* insert hit at beginning of list
+ (last repeats first!) */
+ (hit.irep)++;
+ break;
+ }
+ else if (par.forward==2)
+ {
+ // generate forward alignment
+ if (OK != hit.Forward(q,t,Pstruc)){
+ fprintf(stderr, "%s:%s:%d: cannot complete hit.Forward\n",
+ __FUNCTION__, __FILE__, __LINE__);
+ iRetVal = RETURN_FROM_MAC; /* spot double overflow in Forward(). FS, r241 -> r243 */
+ goto this_is_the_end;
+ }
+ if (OK != hit.Backward(q,t)){
+ fprintf(stderr, "%s:%s:%d: cannot complete hit.backward\n",
+ __FUNCTION__, __FILE__, __LINE__);
+ iRetVal = RETURN_FROM_MAC; /* spot double overflow in hit.Backward(). FS, r241 -> r243 */
+ goto this_is_the_end;
+ }
+ hit.MACAlignment(q,t);
+ if ((isnan(hit.score)) || (isnan(hit.Pforward))){
+ printf("nan after MAC\n");
+ }
+ hit.BacktraceMAC(q,t);
+ if ((isnan(hit.score)) || (isnan(hit.Pforward))){
+ printf("nan after backtrace\n");
+ }
+ } /* use MAC algorithm */
+ // printf ("%-12.12s %-12.12s irep=%-2i score=%6.2f hit.Pvalt=%.2g\n",hit.name,hit.fam,hit.irep,hit.score,hit.Pvalt);
+ *dScore_p = hit.score;
+
+ if (hit.irep<=par.hitrank || hit.score>SMIN || (hit.Pvalt<pself && hit.score>0 ))
+ hitlist.Push(hit); // insert hit at beginning of list (last repeats first!) and do next alignment
+ else
+ {
+ if (hit.irep==1) hitlist.Push(hit); // first hit will be inserted into hitlist anyway, even if not significant
+ hit = hitlist.ReadLast(); // last alignment was not significant => read last (significant) hit from list
+ break;
+ /* FIXME: memory leak during normal alignment: both push'es above are not freed:
+ * valgrind --leak-check=full --show-reachable=yes ./src/clustalo -i ~/void/protein.fa -o /dev/null -v
+ ==9506== 1,456 bytes in 1 blocks are still reachable in loss record 4 of 5
+ ==9506== at 0x4C2726C: operator new(unsigned long) (vg_replace_malloc.c:230)
+ ==9506== by 0x4618C5: List<Hit>::Push(Hit) (list-C.h:134)
+ ==9506== by 0x45E87A: hhalign (hhalign.cpp:914)
+ ==9506== by 0x413F8C: HhalignWrapper (hhalign_wrapper.c:405)
+ ==9506== by 0x41A7B5: MyMain (mymain.c:676)
+ ==9506== by 0x4031A6: main (main.cpp:37)
+ ==9506==
+ ==9506==
+ ==9506== 4,442 (4,368 direct, 74 indirect) bytes in 3 blocks are definitely lost in loss record 5 of 5
+ ==9506== at 0x4C2726C: operator new(unsigned long) (vg_replace_malloc.c:230)
+ ==9506== by 0x4618C5: List<Hit>::Push(Hit) (list-C.h:134)
+ ==9506== by 0x45E7C0: hhalign (hhalign.cpp:911)
+ ==9506== by 0x413F8C: HhalignWrapper (hhalign_wrapper.c:405)
+ ==9506== by 0x41A7B5: MyMain (mymain.c:676)
+ ==9506== by 0x4031A6: main (main.cpp:37)
+ */
+ }
+ } /* 1 <= hit.irep <= imax(par.hitrank,par.altali) */
+ Nali = hit.irep;
+
+
+#ifndef CLUSTALO_NOFILE
+ // Write posterior probability matrix as TCoffee library file
+ if (tcfile)
+ {
+ if (v>=2) printf("Writing TCoffee library file to %s\n",tcfile);
+ int i,j;
+ FILE* tcf=NULL;
+ if (strcmp(tcfile,"stdout")) tcf = fopen(tcfile, "w"); else tcf = stdout;
+ if (!tcf) OpenFileError(tcfile);
+ fprintf(tcf,"! TC_LIB_FORMAT_01\n");
+ fprintf(tcf,"%i\n",2); // two sequences in library file
+ fprintf(tcf,"%s %i %s\n",q.name,q.L,q.seq[q.nfirst]+1);
+ fprintf(tcf,"%s %i %s\n",hit.name,hit.L,hit.seq[hit.nfirst]+1);
+ fprintf(tcf,"#1 2\n");
+ for (i=1; i<=q.L; i++) // print all pairs (i,j) with probability above PROBTCMIN
+ for (j=1; j<=t.L; j++)
+ if (hit.B_MM[i][j]>probmin_tc)
+ fprintf(tcf,"%5i %5i %5i\n",i,j,iround(100.0*hit.B_MM[i][j]));
+ for (int step=hit.nsteps; step>=1; step--) // print all pairs on MAC alignment which were not yet printed
+ {
+ i=hit.i[step]; j=hit.j[step];
+ // printf("%5i %5i %5i %i\n",i,j,iround(100.0*hit.B_MM[i][j]),hit.states[step]);
+ if (hit.states[step]>=MM && hit.B_MM[i][j]<=probmin_tc)
+ fprintf(tcf,"%5i %5i %5i\n",i,j,iround(100.0*hit.B_MM[i][j]));
+ }
+
+
+ fprintf(tcf,"! SEQ_1_TO_N\n");
+ fclose(tcf);
+ // for (i=1; i<=q.L; i++)
+ // {
+ // double sum=0.0;
+ // for (j=1; j<=t.L; j++) sum+=hit.B_MM[i][j];
+ // printf("i=%-3i sum=%7.4f\n",i,sum);
+ // }
+ // printf("\n");
+ } /* if (tcfile) */
+
+ // Write last alignment into alitabfile
+ if (alitabfile)
+ {
+ FILE* alitabf=NULL;
+ if (strcmp(alitabfile,"stdout")) alitabf = fopen(alitabfile, "w"); else alitabf = stdout;
+ if (!alitabf) OpenFileError(alitabfile);
+ if (par.forward==2)
+ {
+ fprintf(alitabf," i j score SS probab\n");
+ for (int step=hit.nsteps; step>=1; step--)
+ if (hit.states[step]>=MM)
+ fprintf(alitabf,"%5i %5i %6.2f %6.2f %7.4f\n",hit.i[step],hit.j[step],hit.S[step],hit.S_ss[step],hit.P_posterior[step]);
+ }
+ else
+ {
+ fprintf(alitabf," i j score SS\n");
+ for (int step=hit.nsteps; step>=1; step--)
+ if (hit.states[step]>=MM)
+ fprintf(alitabf,"%5i %5i %6.2f %6.2f\n",hit.i[step],hit.j[step],hit.S[step],hit.S_ss[step]);
+ }
+ fclose(alitabf);
+ } /* if (alitabfile) */
+#endif
+
+ // Do Stochastic backtracing?
+ if (par.forward==1)
+ for (int i=1; i<Nstochali; i++)
+ {
+ hit.StochasticBacktrace(q,t);
+ hitlist.Push(hit); //insert hit at beginning of list (last repeats first!)
+ (hit.irep)++;
+ }
+ else // Set P-value, E-value and probability
+ {
+ if (q.mu) hitlist.GetPvalsFromCalibration(q);
+ else if (t.mu) hitlist.GetPvalsFromCalibration(t);
+ }
+
+ // Print FASTA or A2M alignments?
+#ifndef CLUSTALO_NOFILE
+ if (*par.pairwisealisfile)
+#endif
+ {
+ if (v>=2) {
+ cout<<"Printing alignments in " <<
+ (par.outformat==1? "FASTA" : par.outformat==2?"A2M" :"A3M") <<
+ " format to "<<par.pairwisealisfile<<"\n";
+ }
+ int iPrAliRtn = hitlist.PrintAlignments(
+#ifdef CLUSTALO
+ ppcFirstProf, ppcSecndProf,
+#endif
+ q, par.pairwisealisfile, par.outformat);
+ if (OK != iPrAliRtn){
+ fprintf(stderr, "%s:%s:%d: Could not print alignments\n",
+ __FUNCTION__, __FILE__, __LINE__);
+ iRetVal = RETURN_FROM_PRINT_ALI; /* this is where mis-alignment was originally spotted,
+ hope to trap it now earlier. FS, r241 -> r243 */
+ goto this_is_the_end;
+ }
+ } /* if (*par.pairwisealisfile) */
+
+#ifndef CLUSTALO_NOFILE
+ // Print hit list and alignments
+ if (*par.outfile)
+ {
+ hitlist.PrintHitList(q, par.outfile);
+ hitlist.PrintAlignments(
+#ifdef CLUSTALO
+ ppcFirstProf, ppcSecndProf,
+#endif
+ q, par.outfile);
+ if (v>=2) {
+ WriteToScreen(par.outfile,1000); //write only hit list to screen
+ }
+ }
+#endif
+
+
+ ///////////////////////////////////////////////////////////////////////
+#ifndef CLUSTALO_NOFILE
+ // Show results for hit with rank par.hitrank
+ if (par.hitrank==0) hit=hitlist.Read(1); else hit=hitlist.Read(par.hitrank);
+
+ // Generate output alignment or HMM file?
+ if (*par.alnfile || *par.psifile || *par.hhmfile)
+ {
+ if (par.append==0)
+ {
+ if (v>=2 && *par.alnfile) printf("Merging template to query alignment and writing resulting alignment in A3M format to %s...\n",par.alnfile);
+ if (v>=2 && *par.psifile) printf("Merging template to query alignment and writing resulting alignment in PSI format to %s...\n",par.psifile);
+ }
+ else
+ {
+ if (v>=2 && *par.alnfile) printf("Merging template to query alignment and appending template alignment in A3M format to %s...\n",par.alnfile);
+ if (v>=2 && *par.psifile) printf("Merging template to query alignment and appending template alignment in PSI format to %s...\n",par.psifile);
+ }
+
+ // Read query alignment into Qali
+ Alignment Qali; // output A3M generated by merging A3M alignments for significant hits to the query alignment
+ char qa3mfile[NAMELEN];
+ RemoveExtension(qa3mfile,par.infile); // directory??
+ strcat(qa3mfile,".a3m");
+ FILE* qa3mf=fopen(qa3mfile,"r");
+ if (!qa3mf) OpenFileError(qa3mfile);
+ Qali.Read(qa3mf,qa3mfile);
+ fclose(qa3mf);
+
+ // Align query with template in master-slave mode
+ Qali.MergeMasterSlave(hit,par.tfile); /*FS, NOFILE2 (commented out) */
+
+ // Write output A3M alignment?
+ if (*par.alnfile) {
+ Qali.WriteToFile(par.alnfile,"a3m");
+ }
+
+ if (*par.psifile)
+ {
+ /* Convert ASCII to int (0-20),throw out all insert states,
+ record their number in I[k][i] */
+ Qali.Compress("merged A3M file");
+
+ // Write output PSI-BLAST-formatted alignment?
+ Qali.WriteToFile(par.psifile,"psi");
+ }
+ } /* if (*par.alnfile || *par.psifile || *par.hhmfile) */
+#endif /* NOFILE2 */
+ //////////////////////////////////////////////////////////////////////////
+
+
+
+
+ // double log2Pvalue;
+ // if (par.ssm && (par.ssm1 || par.ssm2))
+ // {
+ // log2Pvalue=hit.logPval/0.693147181+0.45*(4.0*par.ssw/0.15-hit.score_ss);
+ // if (v>=2)
+ // printf("Aligned %s with %s:\nApproximate P-value INCLUDING SS SCORE = %7.2g\n",q.name,t.name,pow(2.0,log2Pvalue));
+ // } else {
+ // if (v>=2)
+ // printf("Aligned %s with %s:\nApproximate P-value (without SS score) = %7.2g\n",q.name,t.name,hit.Pval);
+ // }
+
+ if (v>=2)
+ {
+ if (par.hitrank==0)
+ printf("Aligned %s with %s: Score = %-7.2f P-value = %-7.2g\n",
+ q.name,t.name,hit.score,hit.Pval);
+ else
+ printf("Aligned %s with %s (rank %i): Score = %-7.2f P-value = %-7.2g\n",
+ q.name,t.name,par.hitrank,hit.score,hit.Pval);
+ }
+
+
+ this_is_the_end:
+
+ // Delete memory for dynamic programming matrix
+ hit.DeleteBacktraceMatrix(q.L+2);
+ if (par.forward>=1 || Nstochali)
+ hit.DeleteForwardMatrix(q.L+2);
+ if (par.forward==2)
+ hit.DeleteBackwardMatrix(q.L+2);
+ /* if (Pstruc) {
+ for (int i=0; i<q.L+2; i++) delete[](Pstruc[i]); delete[](Pstruc);}
+ */
+
+ // Delete content of hits in hitlist
+ hitlist.Reset();
+ while (!hitlist.End())
+ hitlist.ReadNext().Delete(); // Delete content of hit object
+
+ if (strucfile && par.wstruc>0)
+ {
+ for (int i=0; i<q.L+2; i++){
+ delete[] Pstruc[i]; Pstruc[i] = NULL;
+ }
+ delete[] Pstruc; Pstruc = NULL;
+ for (int i=0; i<q.L+2; i++){
+ delete[] Sstruc[i]; Sstruc[i] = NULL;
+ }
+ delete[] Sstruc; Sstruc = NULL;
+ delete[] strucfile; strucfile = NULL;
+ }
+
+ if (pngfile){
+ delete[] pngfile; pngfile = NULL;
+ }
+ if (alitabfile){
+ delete[] alitabfile; alitabfile = NULL;
+ }
+ if (tcfile){
+ delete[] tcfile; tcfile = NULL;
+ }
+ if (par.exclstr){
+ delete[] par.exclstr; par.exclstr = NULL;
+ }
+
+#ifndef CLUSTALO_NOFILE
+ // Print 'Done!'
+ FILE* outf=NULL;
+ if (!strcmp(par.outfile,"stdout")) printf("Done!\n");
+ else
+ {
+ if (*par.outfile)
+ {
+ outf=fopen(par.outfile,"a"); //open for append
+ fprintf(outf,"Done!\n");
+ fclose(outf);
+ }
+ if (v>=2) printf("Done\n");
+ }
+#endif
+
+ //qali.ClobberGlobal();
+ hit.ClobberGlobal();
+ if (iFirstCnt > 0){
+ q.ClobberGlobal();
+ }
+ if (iSecndCnt > 0){
+ t.ClobberGlobal();
+ }
+ hitlist.ClobberGlobal();
+
+ return iRetVal;
+
+} /* this is the end of hhalign() //end main */
+
+//////////////////////////////////////////////////////////////////////////////
+// END OF MAIN
+//////////////////////////////////////////////////////////////////////////////
+
+/*
+ * EOF hhalign.C
+ */
+
git://source.jalview.org / jabaws.git / blobdiff