/*
 * loadPath.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 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;
}

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);
	printf ("%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;
	}

	printf ("%lld marks loaded\n", markCounter);
	return 1;
}

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);
	printf ("%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;
	}

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