/*
 * 31mer/output_pregraph.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>
static int outvCounter = 0;

//after this LINKFLAGFILTER in the Kmer is destroyed
static void output1vt ( kmer_t *node1, FILE *fp )
{
  if ( !node1 )
    {
      return;
    }

  if ( ! ( node1->linear ) && ! ( node1->deleted ) )
    {
      outvCounter++;
      print_kmer ( fp, node1->seq, ' ' );

      if ( outvCounter % 8 == 0 )
        {
          fprintf ( fp, "\n" );
        }
    }
}

void output_vertex ( char *outfile )
{
  char temp[256];
  FILE *fp;
  int i;
  kmer_t *node;
  KmerSet *set;
  sprintf ( temp, "%s.vertex", outfile );
  fp = ckopen ( temp, "w" );

  for ( i = 0; i < thrd_num; i++ )
    {
      set = KmerSets[i];
      set->iter_ptr = 0;

      while ( set->iter_ptr < set->size )
        {
          if ( !is_kmer_entity_null ( set->flags, set->iter_ptr ) )
            {
              node = set->array + set->iter_ptr;
              output1vt ( node, fp );
            }

          set->iter_ptr++;
        }
    }

  fprintf ( fp, "\n" );
  fprintf ( stderr, "%d vertex(es) output.\n", outvCounter );
  fclose ( fp );
  sprintf ( temp, "%s.preGraphBasic", outfile );
  fp = ckopen ( temp, "w" );
  fprintf ( fp, "VERTEX %d K %d\n", outvCounter, overlaplen );
  fprintf ( fp, "\nEDGEs %d\n", num_ed );
  fprintf ( fp, "\nMaxReadLen %d MinReadLen %d MaxNameLen %d\n", maxReadLen4all, minReadLen, maxNameLen );
  fclose ( fp );
}

void output_1edge ( preEDGE *edge, gzFile *fp )
{
  int i;
  gzprintf ( fp, ">length %d,", edge->length );
  print_kmer_gz ( fp, edge->from_node, ',' );
  print_kmer_gz ( fp, edge->to_node, ',' );
  gzprintf ( fp, "cvg %d, %d\n", edge->cvg, edge->bal_edge );

  for ( i = 0; i < edge->length; i++ )
    {
      gzprintf ( fp, "%c", int2base ( ( int ) edge->seq[i] ) );

      if ( ( i + 1 ) % 100 == 0 )
        {
          gzprintf ( fp, "\n" );
        }
    }

  if ( edge->length % 100 != 0 )
    {
      gzprintf ( fp, "\n" );
    }
}