#include <stdio.h>
#include <stdlib.h>

#include "intset.h"
#include "mmapfile.c"

#include "readpairs.c"
#include "writegraph.c"

#define MaxCliqSz (1<<13)

#define Symmetrize(op,m,n,i,j) { \
    op (BitMatrixRow ((m), (n), (i)), (j)); \
    if (!directed) op (BitMatrixRow ((m), (n), (j)), (i)); \
  }

void usage () {
  fprintf (stderr, "\
args: [-lnbpR] [-d] [-s #] {adj-list|signed-mtx|num-mtx} [<node-name-list>]\n\
output: bit matrix\n\
input format spec:\n\
 -l   list of pairs of names [separated by any of <tab><space>\"#$%&\'():;,]\n\
 -n   list of pairs of pairs of names, the first element of which is relevant\n\
 -b   a matrix of \'0\'s and \'1\'s [separated by <tab> or <space>]\n\
 -p   a matrix of negative and positive 1-digit numbers\n\
 -R   list of cliques in RNSC output format\n\
 -d   directed graph\n\
 -s # skip the first # lines\n\
in the cases of matrix format, the <node-name-list> file name is needed\n");
  exit (1);
}

main (int argc, char **argv) {
  BitMatrix graph;
  char *start, *c, *be, ch, *buf;
  struct stat st;
  FILE *f;
  int arg = 1, mode = 0, directed = 0, skip = 0, trace = 0, i, j, k, l, n;
  while (arg < argc && argv[arg][0] == '-') {
    switch (argv[arg++][1]) {
    case 'D': trace = 1; break;
    case 'd': directed = 1; break;
    case 'l': mode = 0; break;
    case 'n': mode = 1; break;
    case 'b': mode = 2; break;
    case 'p': mode = 3; break;
    case 'R': mode = 4; break;
    case 's':
      if (arg >= argc || sscanf (argv[arg++], "%d", &skip) != 1 || skip < 0)
	usage ();
      break;
    default: usage ();
    }
  }
  if (arg >= argc) usage ();
  c = start = mmapFile (f = openFile (argv[arg++]), &st);
  be = start + st.st_size;
  for (i = 0; i < skip && c < be; ++i)
    while (*c++ != '\n');
  switch (mode) {
  case 0:
  case 1: {
    while (c < be) {
      i = getNameIndex (&c, '-');
      if (mode) getNameIndex (&c, '-');
      j = getNameIndex (&c, '-');
      if (mode) getNameIndex (&c, '-');
      while (*c++ != '\n');
    }
    n = nNodes;
    if (trace) fprintf (stderr, "%d nodes seen\n", n);
    graph = NewEmptyBitMatrix (n, n);
    for (c = start, i = 0; i < skip && c < be; ++i)
      while (*c++ != '\n');
    int nEdges, nDups, nSelf;
    for (nEdges = nDups = nSelf = 0; c < be;) {
      i = getNameIndex (&c, '-');
      if (mode) getNameIndex (&c, '-');
      j = getNameIndex (&c, '-');
      if (mode) getNameIndex (&c, '-');
      if (i == j) ++nSelf;
      else if (Member (BitMatrixRow (graph, n, i), j)) ++nDups;
      else {
	Symmetrize (SetAdd, graph, n, i, j);
	++nEdges;
      }
      while (*c++ != '\n');
    }
    if (trace) fprintf (stderr, "%d edges, %d dups, %d self\n",
			nEdges, nDups, nSelf);
    break;
  }
  case 2:
  case 3: {
    FILE *fn;
    if (arg+1 >= argc) usage ();
    c = start = mmapFile (fn = openFile (argv[arg]), &st);
    be = start + st.st_size;
    while (c < be) getNameIndex (&c, '-');
    munmap (start, st.st_size);
    fclose (fn);
    n = nNodes;
    if (trace) fprintf (stderr, "read %d names\n", n);
    graph = NewEmptyBitMatrix (n, n);
    for (i = 0; c < be; ++i) {
      j = 0;
      ch = *c++;
      do {
	if (ch == '-') ++c;
	else if (mode == 3 || ch == '1')
	  SetAdd (BitMatrixRow (graph, n, i), j);
	++j;
	while ((ch = *c++) == '\t' || ch == ' ');
      } while (ch != '\n');
      if (j != n) {
	fprintf (stderr, "matrix row %d: %d entries instead of %d\n",
		 i, j, n);
	exit (1);
      }
    }
    if (i != n) {
      fprintf (stderr, "%d rows instead of %d\n", i, n);
      exit (1);
    }
    break;
  }
  case 4: {
    int nod[MaxCliqSz];
    l = 1;
    for (c = start; *c++ != 'C'; );
    while (c < be) {
      while (*c++ != 'z');
      c += 2;
      for (j = 0; (ch = *c++) != '.'; j = j * 10 + ch - '0');
      while (*c++ != '\n');
      ++l;
      for (; j--; *(c += 3) == ' ' ? ++c : NULL)
	getNameIndex (&c, '-');
      if (*c++ != '\n' || (c += 10, *c++ != '\n')) {
	fprintf (stderr, "missing nodes at line %d\n", l);
	exit (1);
      }
      ++l;
    }
    n = nNodes;
    if (trace) fprintf (stderr, "%d nodes seen\n", n);
    graph = NewEmptyBitMatrix (n, n);
    int nEdges = 0;
    for (c = start; *c++ != 'C'; );
    while (c < be) {
      while (*c++ != 'z');
      c += 2;
      for (j = 0; (ch = *c++) != '.'; j = j * 10 + ch - '0');
      while (*c++ != '\n');
      nEdges += (j*(j-1))>>1;
      for (k = 0; j--; *(c += 3) == ' ' ? ++c : NULL) {
	getNameIndex (&c, '-');
	nod[k] = i;
	for (l = 0; l < k; ++l) Symmetrize (SetAdd, graph, n, i, nod[l]);
	++k;
      }
      c += 12;
    }
    break;
  }
  }
  munmap (start, st.st_size);
  fclose (f);
  writeGraph (n, graph, (char **) revlist2arrayN (nameList, n));
}