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

static char tabs[2][1024];

static boolean splitColumn(char *line)
{
  int len = strlen(line);
  int i = 0, j;
  int tabs_n = 0;

  while(i < len)
    {
      if(line[i] >= 32 && line[i] <= 126 && line[i] != '=')
        {
          j = 0;

          while(i < len && line[i] >= 32 && line[i] <= 126 && line[i] != '=')
            {
              tabs[tabs_n][j++] = line[i];
              i++;
            }

          tabs[tabs_n][j] = '\0';
          tabs_n++;

          if(tabs_n == 2)
            return 1;
        }

      i++;
    }

  if(tabs_n == 2)
    return 1;
  else
    return 0;
}

static int cmp_lib(const void *a, const void *b)
{
  LIB_INFO *A, *B;
  A = (LIB_INFO *)a;
  B = (LIB_INFO *)b;

  if(A->avg_ins > B->avg_ins)
    return 1;
  else if(A->avg_ins == B->avg_ins)
    return 0;
  else
    return -1;
}

void scan_libInfo(char *libfile)
{
  FILE *fp;
  char line[1024], ch;
  int i, j, index;
  int libCounter;
  boolean flag;

  fp = ckopen(libfile, "r");
  num_libs = 0;

  while(fgets(line, 1024, fp))
    {
      ch = line[5];
      line[5] = '\0';

      if(strcmp(line, "[LIB]") == 0)
        num_libs++;

      if(!num_libs)
        {
          line[5] = ch;
          flag = splitColumn(line);

          if(!flag)
            continue;

          if(strcmp(tabs[0], "max_rd_len") == 0)
            maxReadLen = atoi(tabs[1]);
        }
    }

  //count file numbers of each type
  lib_array = (LIB_INFO *)ckalloc(num_libs * sizeof(LIB_INFO));

  for(i = 0; i < num_libs; i++)
    {
      lib_array[i].asm_flag = 3;
      lib_array[i].rd_len_cutoff = 0;
      lib_array[i].rank = 0;
      lib_array[i].pair_num_cut = 1;
      lib_array[i].map_len = 0;
      lib_array[i].num_s_a_file = 0;
      lib_array[i].num_s_q_file = 0;
      lib_array[i].num_p_file = 0;

      lib_array[i].num_a1_file = 0;
      lib_array[i].num_a2_file = 0;
      lib_array[i].num_q1_file = 0;
      lib_array[i].num_q2_file = 0;
    }

  libCounter = -1;
  rewind(fp);

  i = -1;

  while(fgets(line, 1024, fp))
    {
      ch = line[5];
      line[5] = '\0';

      if(strcmp(line, "[LIB]") == 0)
        {
          i++;
          continue;
        }

      line[5] = ch;
      flag = splitColumn(line);

      if(!flag)
        continue;

      if(strcmp(tabs[0], "f1") == 0)
        {
          lib_array[i].num_a1_file++;
        }
      else if(strcmp(tabs[0], "q1") == 0)
        {
          lib_array[i].num_q1_file++;
        }
      else if(strcmp(tabs[0], "f2") == 0)
        {
          lib_array[i].num_a2_file++;
        }
      else if(strcmp(tabs[0], "q2") == 0)
        {
          lib_array[i].num_q2_file++;
        }
      else if(strcmp(tabs[0], "f") == 0)
        {
          lib_array[i].num_s_a_file++;
        }
      else if(strcmp(tabs[0], "q") == 0)
        {
          lib_array[i].num_s_q_file++;
        }
      else if(strcmp(tabs[0], "p") == 0)
        {
          lib_array[i].num_p_file++;
        }
    }

  //allocate memory for filenames
  for(i = 0; i < num_libs; i++)
    {

      if(lib_array[i].num_s_a_file)
        {
          lib_array[i].s_a_fname = (char **)ckalloc(lib_array[i].num_s_a_file * sizeof(char *));

          for(j = 0; j < lib_array[i].num_s_a_file; j++)
            lib_array[i].s_a_fname[j] = (char *)ckalloc(1024 * sizeof(char));
        }

      if(lib_array[i].num_s_q_file)
        {
          lib_array[i].s_q_fname = (char **)ckalloc(lib_array[i].num_s_q_file * sizeof(char *));

          for(j = 0; j < lib_array[i].num_s_q_file; j++)
            lib_array[i].s_q_fname[j] = (char *)ckalloc(1024 * sizeof(char));
        }

      if(lib_array[i].num_p_file)
        {
          lib_array[i].p_fname = (char **)ckalloc(lib_array[i].num_p_file * sizeof(char *));

          for(j = 0; j < lib_array[i].num_p_file; j++)
            lib_array[i].p_fname[j] = (char *)ckalloc(1024 * sizeof(char));
        }

      if(lib_array[i].num_a1_file)
        {
          lib_array[i].a1_fname = (char **)ckalloc(lib_array[i].num_a1_file * sizeof(char *));

          for(j = 0; j < lib_array[i].num_a1_file; j++)
            lib_array[i].a1_fname[j] = (char *)ckalloc(1024 * sizeof(char));
        }

      if(lib_array[i].num_a2_file)
        {
          lib_array[i].a2_fname = (char **)ckalloc(lib_array[i].num_a2_file * sizeof(char *));

          for(j = 0; j < lib_array[i].num_a2_file; j++)
            lib_array[i].a2_fname[j] = (char *)ckalloc(1024 * sizeof(char));
        }

      if(lib_array[i].num_q1_file)
        {
          lib_array[i].q1_fname = (char **)ckalloc(lib_array[i].num_q1_file * sizeof(char *));

          for(j = 0; j < lib_array[i].num_q1_file; j++)
            lib_array[i].q1_fname[j] = (char *)ckalloc(1024 * sizeof(char));
        }

      if(lib_array[i].num_q2_file)
        {
          lib_array[i].q2_fname = (char **)ckalloc(lib_array[i].num_q2_file * sizeof(char *));

          for(j = 0; j < lib_array[i].num_q2_file; j++)
            lib_array[i].q2_fname[j] = (char *)ckalloc(1024 * sizeof(char));
        }
    }

  // get file names
  for(i = 0; i < num_libs; i++)
    {
      lib_array[i].curr_type = 1;
      lib_array[i].curr_index = 0;
      lib_array[i].fp1 = NULL;
      lib_array[i].fp2 = NULL;

      lib_array[i].num_s_a_file = 0;
      lib_array[i].num_s_q_file = 0;
      lib_array[i].num_p_file = 0;

      lib_array[i].num_a1_file = 0;
      lib_array[i].num_a2_file = 0;
      lib_array[i].num_q1_file = 0;
      lib_array[i].num_q2_file = 0;
    }

  libCounter = -1;
  rewind(fp);

  i = -1;

  while(fgets(line, 1024, fp))
    {
      ch = line[5];
      line[5] = '\0';

      if(strcmp(line, "[LIB]") == 0)
        {
          i++;
          continue;
        }

      line[5] = ch;
      flag = splitColumn(line);

      if(!flag)
        continue;

      if(strcmp(tabs[0], "f1") == 0)
        {
          index = lib_array[i].num_a1_file++;
          strcpy(lib_array[i].a1_fname[index], tabs[1]);
        }
      else if(strcmp(tabs[0], "q1") == 0)
        {
          index = lib_array[i].num_q1_file++;
          strcpy(lib_array[i].q1_fname[index], tabs[1]);
        }
      else if(strcmp(tabs[0], "f2") == 0)
        {
          index = lib_array[i].num_a2_file++;
          strcpy(lib_array[i].a2_fname[index], tabs[1]);
        }
      else if(strcmp(tabs[0], "q2") == 0)
        {
          index = lib_array[i].num_q2_file++;
          strcpy(lib_array[i].q2_fname[index], tabs[1]);
        }
      else if(strcmp(tabs[0], "f") == 0)
        {
          index = lib_array[i].num_s_a_file++;
          strcpy(lib_array[i].s_a_fname[index], tabs[1]);
        }
      else if(strcmp(tabs[0], "q") == 0)
        {
          index = lib_array[i].num_s_q_file++;
          strcpy(lib_array[i].s_q_fname[index], tabs[1]);
        }
      else if(strcmp(tabs[0], "p") == 0)
        {
          index = lib_array[i].num_p_file++;
          strcpy(lib_array[i].p_fname[index], tabs[1]);
        }
      else if(strcmp(tabs[0], "min_ins") == 0)
        lib_array[i].min_ins = atoi(tabs[1]);
      else if(strcmp(tabs[0], "max_ins") == 0)
        lib_array[i].max_ins = atoi(tabs[1]);
      else if(strcmp(tabs[0], "avg_ins") == 0)
        lib_array[i].avg_ins = atoi(tabs[1]);
      else if(strcmp(tabs[0], "rd_len_cutoff") == 0)
        lib_array[i].rd_len_cutoff = atoi(tabs[1]);
      else if(strcmp(tabs[0], "reverse_seq") == 0)
        lib_array[i].reverse = atoi(tabs[1]);
      else if(strcmp(tabs[0], "asm_flags") == 0)
        lib_array[i].asm_flag = atoi(tabs[1]);
      else if(strcmp(tabs[0], "rank") == 0)
        lib_array[i].rank = atoi(tabs[1]);
      else if(strcmp(tabs[0], "pair_num_cutoff") == 0)
        lib_array[i].pair_num_cut = atoi(tabs[1]);
      else if(strcmp(tabs[0], "rd_len_cutoff") == 0)
        lib_array[i].rd_len_cutoff = atoi(tabs[1]);
      else if(strcmp(tabs[0], "map_len") == 0)
        lib_array[i].map_len = atoi(tabs[1]);

    }

  fclose(fp);

  qsort(&lib_array[0], num_libs, sizeof(LIB_INFO), cmp_lib);
}

int getMaxLongReadLen(int num_libs)
{
  int i;
  int maxLong = 0;
  boolean Has = 0;

  for(i = 0; i < num_libs; i++)
    {
      if(lib_array[i].asm_flag != 4)
        continue;

      Has = 1;
      maxLong = maxLong < lib_array[i].rd_len_cutoff ? lib_array[i].rd_len_cutoff : maxLong;
    }

  if(!Has)
    return maxLong;
  else
    return maxLong > 0 ? maxLong : maxReadLen;
}

void free_libs()
{

  if(!lib_array)
    return;

  int i, j;

  for(i = 0; i < num_libs; i++)
    {
      //printf("[LIB] %d, avg_ins %d, reverse %d \n",i,lib_array[i].avg_ins,lib_array[i].reverse);
      if(lib_array[i].num_s_a_file)
        {
          //printf("%d single fasta files\n",lib_array[i].num_s_a_file);
          for(j = 0; j < lib_array[i].num_s_a_file; j++)
            free((void *)lib_array[i].s_a_fname[j]);

          free((void *)lib_array[i].s_a_fname);
        }

      if(lib_array[i].num_s_q_file)
        {
          //printf("%d single fastq files\n",lib_array[i].num_s_q_file);
          for(j = 0; j < lib_array[i].num_s_q_file; j++)
            free((void *)lib_array[i].s_q_fname[j]);

          free((void *)lib_array[i].s_q_fname);
        }

      if(lib_array[i].num_p_file)
        {
          //printf("%d paired fasta files\n",lib_array[i].num_p_file);
          for(j = 0; j < lib_array[i].num_p_file; j++)
            free((void *)lib_array[i].p_fname[j]);

          free((void *)lib_array[i].p_fname);
        }

      if(lib_array[i].num_a1_file)
        {
          //printf("%d read1 fasta files\n",lib_array[i].num_a1_file);
          for(j = 0; j < lib_array[i].num_a1_file; j++)
            free((void *)lib_array[i].a1_fname[j]);

          free((void *)lib_array[i].a1_fname);
        }

      if(lib_array[i].num_a2_file)
        {
          //printf("%d read2 fasta files\n",lib_array[i].num_a2_file);
          for(j = 0; j < lib_array[i].num_a2_file; j++)
            free((void *)lib_array[i].a2_fname[j]);

          free((void *)lib_array[i].a2_fname);
        }

      if(lib_array[i].num_q1_file)
        {
          //printf("%d read1 fastq files\n",lib_array[i].num_q1_file);
          for(j = 0; j < lib_array[i].num_q1_file; j++)
            free((void *)lib_array[i].q1_fname[j]);

          free((void *)lib_array[i].q1_fname);
        }

      if(lib_array[i].num_q2_file)
        {
          //printf("%d read2 fastq files\n",lib_array[i].num_q2_file);
          for(j = 0; j < lib_array[i].num_q2_file; j++)
            free((void *)lib_array[i].q2_fname[j]);

          free((void *)lib_array[i].q2_fname);
        }
    }

  num_libs = 0;
  free((void *)lib_array);
}

void alloc_pe_mem(int gradsCounter)
{
  if(gradsCounter)
    pes = (PE_INFO *)ckalloc(gradsCounter * sizeof(PE_INFO));
}

void free_pe_mem()
{
  if(pes)
    {
      free((void *)pes);
      pes = NULL;
    }
}