#include "stdinc.h"
#include "newhash.h"
#include "extfunc.h"
#include "extvab.h"

#define preARCBLOCKSIZE 100000

static void loadArcs(char *graphfile);
static void loadContig(char *graphfile);

void loadUpdatedVertex(char *graphfile)
{
  char name[256], line[256];
  FILE *fp;
  Kmer word, bal_word;
  int num_kmer, i;
  char ch;

  sprintf(name, "%s.updated.vertex", graphfile);
  fp = ckopen(name, "r");

  while(fgets(line, sizeof(line), fp) != NULL)
    {
      if(line[0] == 'V')
        {
          sscanf(line + 6, "%d %c %d", &num_kmer, &ch, &overlaplen);
          printf("there're %d kmers in vertex file\n", num_kmer);
          //printf("total %d kmer in all contigs.\n",num_kmer);
          break;
        }
    }

  vt_array = (VERTEX *)ckalloc((2 * num_kmer) * sizeof(VERTEX));

  for(i = 0; i < num_kmer; i++)
    {
      fscanf(fp, "%llx ", &word);
      vt_array[i].kmer = word;
    }

  fclose(fp);

  for(i = 0; i < num_kmer; i++)
    {
      bal_word = reverseComplement(vt_array[i].kmer, overlaplen);
      vt_array[i + num_kmer].kmer = bal_word;
    }

  num_vt = num_kmer;
}
int cmp_int(const void *a, const void *b)
{
  int *A, *B;
  A = (int *)a;
  B = (int *)b;

  if(*A > *B)
    return 1;
  else if(*A == *B)
    return 0;
  else
    return -1;
}
int uniqueLenSearch(unsigned int *len_array, unsigned int *flag_array, int num, unsigned int target)
{
  int mid, low, high;
  low = 1;
  high = num;

  while(low <= high)
    {
      mid = (low + high) / 2;

      if(len_array[mid] == target)
        break;
      else if(target > len_array[mid])
        low = mid + 1;
      else
        high = mid - 1;
    }

  if(low > high)
    return -1;

  //locate the first same length unflaged
  return flag_array[mid]++;

}

int lengthSearch(unsigned int *len_array, unsigned int *flag_array, int num, unsigned int target)
{
  int mid, low, high, i;
  low = 1;
  high = num;

  while(low <= high)
    {
      mid = (low + high) / 2;

      if(len_array[mid] == target)
        break;
      else if(target > len_array[mid])
        low = mid + 1;
      else
        high = mid - 1;
    }

  if(low > high)
    return -1;

  //locate the first same length unflaged
  if(!flag_array[mid])
    {
      for(i = mid - 1; i > 0; i--)
        {
          if(len_array[i] != len_array[mid] || flag_array[i])
            break;
        }

      flag_array[i + 1] = 1;
      return i + 1;
    }
  else
    {
      for(i = mid + 1; i <= num; i++)
        {
          if(!flag_array[i])
            break;
        }

      flag_array[i] = 1;
      return i;
    }

}

void quick_sort_int(unsigned int *length_array, int low, int high)
{
  int i, j;
  Kmer pivot;

  if (low < high)
    {
      pivot = length_array[low];
      i = low;
      j = high;

      while(i < j)
        {
          while (i < j && length_array[j] >= pivot)
            j--;

          if(i < j)
            length_array[i++] = length_array[j];

          while (i < j && length_array[i] <= pivot)
            i++;

          if(i < j)
            length_array[j--] = length_array[i];
        }

      length_array[i] = pivot;

      quick_sort_int(length_array, low, i - 1);
      quick_sort_int(length_array, i + 1, high);
    }
}

void loadUpdatedEdges(char *graphfile)
{
  char c, name[256], line[1024];
  int bal_ed, cvg;
  FILE *fp, *out_fp;
  unsigned long long from_kmer, to_kmer;
  unsigned int num_ctgge, length, index = 0, num_kmer;
  unsigned int i = 0, j;
  unsigned int newIndex;
  unsigned int *length_array, *flag_array, diff_len;
  char *outfile = graphfile;
  long long cvgSum = 0;
  long long counter = 0;

  //get overlaplen from *.preGraphBasic
  /*sprintf(name, "%s.preGraphBasic", graphfile);
  fp = ckopen(name, "r");

  while(fgets(line,sizeof(line),fp)!=NULL){
  	if(line[0] == 'V'){
  		sscanf(line+6, "%d %c %d",&num_kmer,&c,&overlaplen);
  		//printf("K = %d\n",overlaplen);
  		break;
  	}
  }*/
  if(ctg_short == 0)
    ctg_short = overlaplen + 2;

  //fclose(fp);

  sprintf(name, "%s.updated.edge", graphfile);
  fp = ckopen(name, "r");
  sprintf(name, "%s.newContigIndex", outfile);
  out_fp = ckopen(name, "w");

  while(fgets(line, sizeof(line), fp) != NULL)
    {
      if(line[0] == 'E')
        {
          sscanf(line + 5, "%d", &num_ctgge);
          //printf("there're %d edge in edge file\n",num_ctgge);
          //printf("total %d contigs\n",num_ctgge);
          break;
        }
    }

  index_array = (unsigned int *)ckalloc((num_ctgge + 1) * sizeof(unsigned int));
  length_array = (unsigned int *)ckalloc((num_ctgge + 1) * sizeof(unsigned int));
  flag_array = (unsigned int *)ckalloc((num_ctgge + 1) * sizeof(unsigned int));

  while(fgets(line, sizeof(line), fp) != NULL)
    {
      if(line[0] == '>')
        {
          sscanf(line + 7, "%d", &length);
          index_array[++index] = length;
          length_array[++i] = length;
        }
    }

  num_ctg = index;
  orig2new = 1;
  //quick_sort_int(length_array,1,num_ctg);
  qsort(&(length_array[1]), num_ctg, sizeof(length_array[0]), cmp_int);
  //extract unique length
  diff_len = 0;

  for(i = 1; i <= num_ctg; i++)
    {
      for(j = i + 1; j <= num_ctg; j++)
        if(length_array[j] != length_array[i])
          break;

      length_array[++diff_len] = length_array[i];
      flag_array[diff_len] = i;
      i = j - 1;
    }

  /*
  for(i=1;i<=num_ctg;i++)
  	flag_array[i] = 0;
  */
  contig_array = (CONTIG *)ckalloc((num_ctg + 1) * sizeof(CONTIG));

  //load edges
  index = 0;
  rewind(fp);

  while(fgets(line, sizeof(line), fp) != NULL)
    {
      if(line[0] == '>')
        {
          //			if(overlaplen<=31)
          //				sscanf(line,">length %u,%llx,%llx,%d,%d",&length,&from_kmer,&to_kmer,&bal_ed,&cvg);
          //			else
          sscanf(line, ">length %u,%d,%d", &length, &bal_ed, &cvg);
          newIndex = uniqueLenSearch(length_array, flag_array, diff_len, length);
          index_array[++index] = newIndex;

          contig_array[newIndex].length = length;
          contig_array[newIndex].bal_edge = bal_ed + 1;
          contig_array[newIndex].downwardConnect = NULL;
          contig_array[newIndex].mask = 0;
          contig_array[newIndex].flag = 0;
          contig_array[newIndex].arcs = NULL;
          contig_array[newIndex].seq = NULL;
          contig_array[newIndex].multi = 0;
          contig_array[newIndex].inSubGraph = 0;
          contig_array[newIndex].cvg = cvg / 10;

          if(cvg)
            {
              counter += length;
              cvgSum += cvg * length;
            }

          fprintf(out_fp, "%d %d %d\n", index, newIndex, contig_array[newIndex].bal_edge);
        }
    }

  if(counter)
    //cvgAvg = cvgSum/counter > 2 ? cvgSum/counter : 3;
    cvgAvg = cvgSum / counter / 10 > 2 ? cvgSum / counter / 10 : 3;

  //mark repeats
  int bal_i;
  /*if(maskRep){
  	counter = 0;
  	for(i=1;i<=num_ctg;i++){
  		bal_i = getTwinCtg(i);
  		if((contig_array[i].cvg+contig_array[bal_i].cvg)>4*cvgAvg){
  			contig_array[i].mask = 1;
  			contig_array[bal_i].mask = 1;
  			counter += 2;
  		}
  		if(isSmallerThanTwin(i))
  			i++;
  	}
  	printf("average contig coverage : %d. Number of contig(s) masked because of high coverage: %llx\n",
  					cvgAvg,counter);
  }*/

  counter = 0;

  for(i = 1; i <= num_ctg; i++)
    {
      if(contig_array[i].mask)
        continue;

      bal_i = getTwinCtg(i);

      if(contig_array[i].length < ctg_short)
        {
          contig_array[i].mask = 1;
          contig_array[bal_i].mask = 1;
          counter += 2;
        }

      if(isSmallerThanTwin(i))
        i++;
    }

  //printf("Mask contigs shorter than %d, %lld contig masked\n",
  //					ctg_short,counter);
  printf("[%s]Number of contig(s) masked because of shortie: %lld\n", __FUNCTION__, counter);
  //loadArcs(graphfile);
  //tipsCount();
  loadContig(graphfile);
  //printf("done loading updated edges\n");
  fflush(stdout);
  free((void *)length_array);
  free((void *)flag_array);
  fclose(fp);
  fclose(out_fp);
}

/*static void add1Arc(unsigned int from_ed,unsigned int to_ed, unsigned int weight)
{
	preARC *parc;
	unsigned int from_c = index_array[from_ed];
	unsigned int to_c = index_array[to_ed];

	parc = allocatePreArc(to_c);
	parc->multiplicity = weight;
	parc->next = contig_array[from_c].arcs;
	contig_array[from_c].arcs = parc;
}*/

/*void loadArcs(char *graphfile)
{
	FILE *fp;
	char name[256],line[1024];
	unsigned int target,weight;
	unsigned int from_ed;
	char *seg;

	sprintf(name,"%s.Arc",graphfile);
	fp = ckopen(name,"r");

	createPreArcMemManager();
	arcCounter = 0;
	while(fgets(line,sizeof(line),fp)!=NULL){
		seg = strtok(line," ");
		from_ed = atoi(seg);
		//printf("%d\n",from_ed);
		while((seg=strtok(NULL," "))!=NULL){
			target = atoi(seg);
			seg = strtok(NULL," ");
			weight = atoi(seg);
			add1Arc(from_ed,target,weight);

		}
	}
	printf("%lld arcs loaded\n",arcCounter);
	fclose(fp);
}*/

void loadContig(char *graphfile)
{
  //fprintf(stderr,"[%s]entering this function\n",__FUNCTION__);
  char c, name[256], line[1024], *tightSeq = NULL;
  FILE *fp;
  int n = 0, length, index = -1, edgeno;
  unsigned int i;
  unsigned int newIndex;

  sprintf(name, "%s.contig", graphfile);
  fp = ckopen(name, "r");

  while(fgets(line, sizeof(line), fp) != NULL)
    {
      if(line[0] == '>')
        {
          if(index >= 0)
            {
              newIndex = index_array[edgeno];
              contig_array[newIndex].seq = tightSeq;
            }

          n = 0;
          index++;
          sscanf(line + 1, "%d %s %d", &edgeno, name, &length);
          //printf("contig %d, length %d\n",edgeno,length);
          tightSeq = (char *)ckalloc((length / 4 + 1) * sizeof(char));
          //fprintf(stderr,"[%s]loaded %d.\n",__FUNCTION__,edgeno);
        }
      else
        {
          int tmp_len = strlen(line);

          for(i = 0; i < tmp_len; i++)
            {
              if(line[i] >= 'a' && line[i] <= 'z')
                {
                  c = base2int(line[i] - 'a' + 'A');
                  writeChar2tightString(c, tightSeq, n++);
                }
              else if(line[i] >= 'A' && line[i] <= 'Z')
                {
                  c = base2int(line[i]);
                  writeChar2tightString(c, tightSeq, n++);
                }
            }
        }

    }

  if(index >= 0)
    {
      newIndex = index_array[edgeno];
      contig_array[newIndex].seq = tightSeq;
    }

  printf("[%s]input %d contigs\n", __FUNCTION__, index + 1);
  fclose(fp);

  //printf("the %dth contig with index 107\n",index);
}
void freeContig_array()
{
  if(!contig_array)
    return;

  unsigned int i;

  for(i = 1; i <= num_ctg; i++)
    {
      if(contig_array[i].seq)
        free((void *)contig_array[i].seq);

      if(contig_array[i].closeReads)
        freeStack(contig_array[i].closeReads);
    }

  free((void *)contig_array);
  contig_array = NULL;
}
/*
void loadCvg(char *graphfile)
{
	char name[256],line[1024];
	FILE *fp;
	int cvg;
	unsigned int newIndex,edgeno,bal_ctg;

	sprintf(name,"%s.contigCVG",graphfile);
	fp = fopen(name,"r");
	if(!fp){
		printf("contig coverage file %s is not found!\n",name);
		return;
	}

	while(fgets(line,sizeof(line),fp)!=NULL){
		if(line[0]=='>'){
			sscanf(line+1,"%d %d",&edgeno,&cvg);
			newIndex = index_array[edgeno];
			cvg = cvg <= 255 ? cvg:255;
			contig_array[newIndex].multi = cvg;
			bal_ctg = getTwinCtg(newIndex);
			contig_array[bal_ctg].multi= cvg;
		}
	}
	fclose(fp);
}
*/