101 lines
1.9 KiB
C++
101 lines
1.9 KiB
C++
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#include <iostream>
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#include <string>
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#include <sys/time.h>
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#include <mpi.h>
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#include <stdlib.h> /* exit() */
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#include <sys/types.h>
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#include <sys/stat.h>
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#include <fcntl.h>
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#include "Sequence.h"
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using namespace std;
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void usage()
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{
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cerr << "Usage: maximum-parsimony <sequence-file>" << endl;
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exit(42);
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}
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string getsequence(int fd)
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{
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string s;
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char chr;
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bool saw_name = false;
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for (;;)
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{
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int bytes_read = read(fd, &chr, 1);
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if (bytes_read < 1)
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{
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if (s == "")
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break;
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else
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{
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cerr << "Unexpected EOF in the middle of a line!" << endl;
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exit(2);
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}
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}
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else if (chr == '\n')
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{
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break;
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}
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else if (chr == ' ' || chr == '\t')
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{
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saw_name = true;
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}
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else
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{
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if (saw_name)
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s += chr;
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}
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}
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return s;
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}
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int main(int argc, char * argv[])
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{
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int my_rank;
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int world_size; /* the number of processes */
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char * filename = NULL;
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MPI_Init(&argc, &argv);
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MPI_Comm_rank(MPI_COMM_WORLD, &my_rank);
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MPI_Comm_size(MPI_COMM_WORLD, &world_size);
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for (int i = 0; i < argc; i++)
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{
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filename = argv[i];
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}
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if (filename == NULL)
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usage();
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int fd = open(filename, O_RDONLY);
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if (fd < 0)
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{
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cerr << "Couldn't open '" << filename << "'!" << endl;
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exit(1);
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}
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vector<Sequence *> sequences;
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for (;;)
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{
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string seqstr = getsequence(fd);
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if (seqstr == "")
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break;
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Sequence * seq = new Sequence(seqstr.c_str());
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sequences.push_back(seq);
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}
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close(fd);
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cout << "Found " << sequences.size() << " sequences:" << endl;
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for (int i = 0, sz = sequences.size(); i < sz; i++)
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{
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cout << *sequences[i] << endl;
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}
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MPI_Finalize();
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return 0;
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}
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