1 // This file is part of the Mussa source distribution.
2 // http://mussa.caltech.edu/
3 // Contact author: Tristan De Buysscher, tristan@caltech.edu
5 // This program and all associated source code files are Copyright (C) 2005
6 // the California Institute of Technology, Pasadena, CA, 91125 USA. It is
7 // under the GNU Public License; please see the included LICENSE.txt
8 // file for more information, or contact Tristan directly.
12 #include "sequence.hh"
18 int main(int argc, char **argv)
22 string seqA_file, seqB_file, output_file;
24 int window, threshold;
25 int seqA_len, seqB_len;
27 time_t t1, t2, begin, end;
28 double setuptime, comp1time, comp2time, sorttime, savetime, totaltime;
32 cout << "fee fie foe fum" << endl;
37 window = atoi(* ++argv);
38 threshold = atoi(* ++argv);
39 output_file = * ++argv;
43 seqA.load_fasta(seqA_file, 1, 0, 0);
44 seqA_len = seqA.len();
45 //cout << setw(60) << seqA.hdr() << "\n";
47 seqB.load_fasta(seqB_file, 1, 0, 0);
48 seqB_len = seqB.len();
49 //cout << seqB.hdr() << "\n";
52 cout << "Length: Seq A = " << seqA_len;
53 cout << "; Seq B = " << seqB_len << "\n";
55 analysis.setup(ana_type, window, threshold, seqA_len, seqB_len);
58 setuptime = difftime(t2, t1);
61 analysis.seqcomp(seqA.seq(), seqB.seq(), false);
63 comp1time = difftime(t2, t1);
66 analysis.seqcomp(seqA.seq(), seqB.rev_comp(), true);
68 comp2time = difftime(t2, t1);
73 sorttime = difftime(t2, t1);
76 analysis.file_save(output_file);
78 savetime = difftime(t2, t1);
81 totaltime = difftime(end, begin);
83 cout << "setup\tcomp\trc_comp\tsave\ttotal\n";
84 cout << setuptime << "\t";
85 cout << comp1time << "\t";
86 cout << comp2time << "\t";
87 //cout << sorttime << "\t";
88 cout << savetime << "\t";
89 cout << totaltime << "\n";