/*
 * loadPath.c
 *
 * Copyright (c) 2008-2016 Ruibang Luo <aquaskyline.com>.
 *
 * This file is part of SOAPdenovo.
 *
 * SOAPdenovo is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * SOAPdenovo is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with SOAPdenovo.  If not, see <http://www.gnu.org/licenses/>.
 *
 */

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

/*************************************************
Function:
    add1marker2edge
Description:
    Records the id of read which crosses the edge.
Input:
    1. edgeno:      the edge index
    2. readid:      the read id
Output:
    None.
Return:
    None.
*************************************************/
static void add1marker2edge ( unsigned int edgeno, long long readid )
{
  if ( edge_array[edgeno].multi == 255 )
    {
      return;
    }

  unsigned int bal_ed = getTwinEdge ( edgeno );
  unsigned char counter = edge_array[edgeno].multi++;
  edge_array[edgeno].markers[counter] = readid;
  counter = edge_array[bal_ed].multi++;
  edge_array[bal_ed].markers[counter] = -readid;
}

/*************************************************
Function:
    loadPath
Description:
    1. Loads the path info.
    2. Records the ids of reads crossing edges.
Input:
    1. graphfile:       the input prefix
Output:
    None.
Return:
    None.
*************************************************/
boolean loadPath ( char *graphfile )
{
  FILE *fp;
  char name[256], line[1024];
  unsigned int i, bal_ed, num1, edgeno, num2;
  long long markCounter = 0, readid = 0;
  char *seg;
  sprintf ( name, "%s.markOnEdge", graphfile );
  fp = fopen ( name, "r" );

  if ( !fp )
    {
      return 0;
    }

  for ( i = 1; i <= num_ed; i++ )
    {
      edge_array[i].multi = 0;
    }

  for ( i = 1; i <= num_ed; i++ )
    {
      fscanf ( fp, "%d", &num1 );

      if ( EdSmallerThanTwin ( i ) )
        {
          fscanf ( fp, "%d", &num2 );
          bal_ed = getTwinEdge ( i );

          if ( num1 + num2 >= 255 )
            {
              edge_array[i].multi = 255;
              edge_array[bal_ed].multi = 255;
            }
          else
            {
              edge_array[i].multi = num1 + num2;
              edge_array[bal_ed].multi = num1 + num2;
              markCounter += 2 * ( num1 + num2 );
            }

          i++;
        }
      else
        {
          if ( 2 * num1 >= 255 )
            {
              edge_array[i].multi = 255;
            }
          else
            {
              edge_array[i].multi = 2 * num1;
              markCounter += 2 * num1;
            }
        }
    }

  fclose ( fp );
  fprintf ( stderr, "%lld markers overall.\n", markCounter );
  markersArray = ( long long * ) ckalloc ( markCounter * sizeof ( long long ) );
  markCounter = 0;

  for ( i = 1; i <= num_ed; i++ )
    {
      if ( edge_array[i].multi == 255 )
        {
          continue;
        }

      edge_array[i].markers = markersArray + markCounter;
      markCounter += edge_array[i].multi;
      edge_array[i].multi = 0;
    }

  sprintf ( name, "%s.path", graphfile );
  fp = fopen ( name, "r" );

  if ( !fp )
    {
      return 0;
    }

  while ( fgets ( line, sizeof ( line ), fp ) != NULL )
    {
      //printf("%s",line);
      readid++;
      seg = strtok ( line, " " );

      while ( seg )
        {
          edgeno = atoi ( seg );
          //printf("%s, %d\n",seg,edgeno);
          add1marker2edge ( edgeno, readid );
          seg = strtok ( NULL, " " );
        }
    }

  fclose ( fp );
  markCounter = 0;

  for ( i = 1; i <= num_ed; i++ )
    {
      if ( edge_array[i].multi == 255 )
        {
          continue;
        }

      markCounter += edge_array[i].multi;
    }

  fprintf ( stderr, "%lld marks loaded.\n", markCounter );
  return 1;
}

static int  comp ( const void *a , const void *b )
{
  long long m , n ;
  m = * ( long long * ) a > 0 ? * ( long long * ) a : -* ( long long * ) a;
  n = * ( long long * ) b > 0 ? * ( long long * ) b : -* ( long long * ) b;

  //      return (int)(m-n);
  if ( m > n )
    {
      return 1;
    }
  else if ( m < n )
    {
      return -1;
    }
  else
    {
      return 0;
    }
}

/*************************************************
Function:
    loadPathBin
Description:
    1. Loads the path info.
    2. Records the ids of reads crossing edges.
Input:
    1. graphfile:       the input prefix
Output:
    None.
Return:
    0 if it's fail to load the path.
*************************************************/

boolean loadPathBin ( char *graphfile )
{
  FILE *fp;
  char name[256];
  unsigned int i, bal_ed, num1, num2;
  long long markCounter = 0, readid = 0;
  unsigned char seg, ch;
  unsigned int *freadBuf;
  sprintf ( name, "%s.markOnEdge", graphfile );
  fp = fopen ( name, "r" );

  if ( !fp )
    {
      return 0;
    }

  for ( i = 1; i <= num_ed; i++ )
    {
      edge_array[i].multi = 0;
      edge_array[i].markers = NULL;
    }

  for ( i = 1; i <= num_ed; i++ )
    {
      fscanf ( fp, "%d", &num1 );

      if ( EdSmallerThanTwin ( i ) )
        {
          fscanf ( fp, "%d", &num2 );
          bal_ed = getTwinEdge ( i );

          if ( num1 + num2 >= 255 )
            {
              edge_array[i].multi = 255;
              edge_array[bal_ed].multi = 255;
            }
          else
            {
              edge_array[i].multi = num1 + num2;
              edge_array[bal_ed].multi = num1 + num2;
              markCounter += 2 * ( num1 + num2 );
            }

          i++;
        }
      else
        {
          if ( 2 * num1 >= 255 )
            {
              edge_array[i].multi = 255;
            }
          else
            {
              edge_array[i].multi = 2 * num1;
              markCounter += 2 * num1;
            }
        }
    }

  fclose ( fp );
  fprintf ( stderr, "%lld markers overall.\n", markCounter );
  markersArray = ( long long * ) ckalloc ( markCounter * sizeof ( long long ) );
  markCounter = 0;

  for ( i = 1; i <= num_ed; i++ )
    {
      if ( edge_array[i].multi == 255 )
        {
          continue;
        }

      edge_array[i].markers = markersArray + markCounter;
      markCounter += edge_array[i].multi;
      edge_array[i].multi = 0;
    }

  sprintf ( name, "%s.path", graphfile );
  fp = fopen ( name, "rb" );

  if ( !fp )
    {
      return 0;
    }

  freadBuf = ( unsigned int * ) ckalloc ( ( maxReadLen - overlaplen + 1 ) * sizeof ( unsigned int ) );

  while ( fread ( &ch, sizeof ( char ), 1, fp ) == 1 )
    {
      //printf("%s",line);
      if ( fread ( freadBuf, sizeof ( unsigned int ), ch, fp ) != ch )
        {
          break;
        }

      readid++;

      for ( seg = 0; seg < ch; seg++ )
        {
          add1marker2edge ( freadBuf[seg], readid );
        }
    }

  fclose ( fp );
  markCounter = 0;

  for ( i = 1; i <= num_ed; i++ )
    {
      if ( edge_array[i].multi == 255 )
        {
          continue;
        }

      markCounter += edge_array[i].multi;
    }

  for ( i = 0; i <= num_ed; i++ )
    {
      if ( edge_array[i].multi >= 2 && edge_array[i].multi != 255 )
        {
          qsort ( edge_array[i].markers, ( int ) edge_array[i].multi, sizeof ( long long ), comp );
        }
    }

  fprintf ( stderr, "%lld markers loaded.\n", markCounter );
  free ( ( void * ) freadBuf );
  return 1;
}