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view clustalomega/clustal-omega-1.0.2/src/hhalign/hhalign.cpp @ 1:bc707542e5de
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| author | clustalomega |
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| date | Thu, 21 Jul 2011 13:35:08 -0400 |
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/* -*- 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 */