/*
 * Output_pregraph.c
 * 
 * Copyright (c) 2011-2013 BGI-Shenzhen <soap at genomics dot org dot cn>. 
 *
 * This file is part of SOAPdenovo-Trans.
 *
 * SOAPdenovo-Trans 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-Trans 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-Trans.  If not, see <http://www.gnu.org/licenses/>.
 *
 */
#include <stdinc.h>
#include "newhash.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");
	printf ("%d vertex outputed\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");
		}
	}
	gzprintf (fp, "\n");
}