multiseq.c

#include"mwt.h"

//#include<LEDA/graph.h>
//#include<LEDA/node_array.h>
//#include<LEDA/tuple.h>
#include<ctype.h>
#include<fstream.h>
#include<iostream.h>

int main(int argc, char* argv[]) {

  ifstream is(argv[1]);

  //  GRAPH<string, two_tuple<int, double> > H;
  //  H.read_gml(is);

  int sequences;
  int edges;
  is >> sequences >> edges;

  int length[sequences];
  char name[sequences][100];
  char stri[sequences][1000];

  for(int i=0; i<sequences; i++) {
    is >> length[i] >> name[i] >> stri[i];
    cout<<name[i]<<" "<<stri[i]<<endl;
  };

  int start_node[edges];
  int end_node[edges];
  int type[edges];
  double cost[edges];
  int sol[edges];

  for(int i=0; i<edges; i++) {
    is >> start_node[i] >> end_node[i] >> type[i] >> cost[i];
  }

  MWT(sequences, length, edges, start_node, end_node, type, cost, sol);

  int SI[sequences+1], si[sequences+1];
  SI[0]=0;
  for(int i=0; i<sequences; i++) {
    SI[i+1]=SI[i]+length[i];
    si[i]=SI[i];
  };
  si[sequences]=SI[sequences];

  int N[SI[sequences]][sequences];
  int S[SI[sequences]];
  int s=0;
  for(int i=0; i<SI[sequences]; i++) {
    if(i==SI[s+1]) s++;
    S[i]=s;
    for(int j=0; j<sequences; j++) N[i][j]=-1;
  };

  for(int i=0; i<edges; i++) {
    if((sol[i]==1) && (type[i]==-1)) {
      N[start_node[i]][S[end_node[i]]]=end_node[i];
      N[end_node[i]][S[start_node[i]]]=start_node[i];
    }
  }

  char os[sequences][1000];

  int PN[sequences];
  bool b, cont;
  int p=0;

  do {
    for(int i=0; i<sequences; i++) PN[i]=0;
    for(int i=0; i<sequences; i++) if(SI[i]<si[i+1]) {
      b=true;
      for(int j=0; j<sequences; j++) if(N[SI[i]][j]!=-1) {
        if (N[SI[i]][j]>SI[j])
          b=false;
      }
      if(b) PN[i]=1;
    }

    cont=false;
    for(int i=0; i<sequences; i++) if(PN[i]==1) {
      //cout<<p<<" phase write "<<i<<" "<<S[i]<<endl; 
      os[i][p]=(char) tolower(stri[i][SI[i]-si[i]]);
      SI[i]++;
      cont=true;
    } else os[i][p]='.';
     p++;
  } while(cont);

  for(int i=0; i<sequences; i++) os[i][p-1]='\0';

  for(int i=0; i<sequences; i++) cout<<os[i]<<endl;

  char* mfsname=argv[2];
  ofstream msf(mfsname);

  msf<<".PileUp\n\nMFS: 94 Type: P\n\n//\n";

  for(int i=0; i<sequences; i++) {
    msf<<"\n "<<name[i]<<" "<<os[i];
  }
  msf<<endl<<endl;

  return 0;
}

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