/*
 * Connect.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"

#define CNBLOCKSIZE 100000

void createCntMemManager ()
{
	if (!cn_mem_manager)
	{
		cn_mem_manager = createMem_manager (CNBLOCKSIZE, sizeof (CONNECT));
	}
	else
	{
		printf ("cn_mem_manger was created\n");
	}
}

void destroyConnectMem ()
{
	freeMem_manager (cn_mem_manager);
	cn_mem_manager = NULL;
}

CONNECT *allocateCN (unsigned int contigId, int gap)
{
	CONNECT *newCN;

	newCN = (CONNECT *) getItem (cn_mem_manager);
	newCN->contigID = contigId;
	newCN->gapLen = gap;
	newCN->minGap = 0;
	newCN->maxGap = 0;
	newCN->bySmall = 0;
	newCN->weakPoint = 0;
	newCN->weight = 1;
	newCN->weightNotInherit = 0;
	newCN->mask = 0;
	newCN->used = 0;
	newCN->checking = 0;
	newCN->deleted = 0;
	newCN->prevInScaf = 0;
	newCN->inherit = 0;
	newCN->singleInScaf = 0;
	newCN->nextInScaf = NULL;
	return newCN;
}

void output_cntGVZ (char *outfile)
{
	char name[256];
	FILE *fp;
	unsigned int i;
	CONNECT *connect;
	boolean flag;

	sprintf (name, "%s.scaffold.gvz", outfile);
	fp = ckopen (name, "w");
	fprintf (fp, "digraph G{\n");
	fprintf (fp, "\tsize=\"512,512\";\n");

	for (i = num_ctg; i > 0; i--)
	{
		//if(contig_array[i].mask||!contig_array[i].downwardConnect)
		if (!contig_array[i].downwardConnect)
		{
			continue;
		}

		connect = contig_array[i].downwardConnect;

		while (connect)
		{
			//if(connect->mask||connect->deleted){
			if (connect->deleted)
			{
				connect = connect->next;
				continue;
			}

			if (connect->prevInScaf || connect->nextInScaf)
			{
				flag = 1;
			}
			else
			{
				flag = 0;
			}

			if (!connect->mask)
				fprintf (fp, "\tC%d_%d -> C%d_%d [label = \"%d(%d_%d)\"];\n", i, contig_array[i].length, connect->contigID, contig_array[connect->contigID].length,
					connect->gapLen, flag, connect->weight);
			else
				fprintf (fp, "\tC%d_%d -> C%d_%d [label = \"%d(%d_%d)\", color = red];\n", i, contig_array[i].length, connect->contigID, contig_array[connect->contigID].length,
					connect->gapLen, flag, connect->weight);

			connect = connect->next;
		}
	}

	fprintf (fp, "}\n");
	fclose (fp);
}

/***************** below this line all codes are about lookup table *****************/

void createCntLookupTable ()
{
	if (!cntLookupTable)
	{
		cntLookupTable = (CONNECT **) ckalloc ((3 * num_ctg + 1) * sizeof (CONNECT *));
	}
}

void deleteCntLookupTable ()
{
	if (cntLookupTable)
	{
		free ((void *) cntLookupTable);
		cntLookupTable = NULL;
	}
}

void putCnt2LookupTable (unsigned int from_c, CONNECT * cnt)
{
	if (!cnt || !cntLookupTable)
	{
		return;
	}

	unsigned int index = 2 * from_c + cnt->contigID;

	cnt->nextInLookupTable = cntLookupTable[index];
	cntLookupTable[index] = cnt;
}

static CONNECT *getCntInLookupTable (unsigned int from_c, unsigned int to_c)
{
	unsigned int index = 2 * from_c + to_c;
	CONNECT *ite_cnt = cntLookupTable[index];

	while (ite_cnt)
	{
		if (ite_cnt->contigID == to_c)
		{
			return ite_cnt;
		}

		ite_cnt = ite_cnt->nextInLookupTable;
	}

	return NULL;
}

CONNECT *getCntBetween (unsigned int from_c, unsigned int to_c)
{
	CONNECT *pcnt;

	if (cntLookupTable)
	{
		pcnt = getCntInLookupTable (from_c, to_c);
		return pcnt;
	}

	pcnt = contig_array[from_c].downwardConnect;

	while (pcnt)
	{
		if (pcnt->contigID == to_c)
		{
			return pcnt;
		}

		pcnt = pcnt->next;
	}

	return pcnt;
}

/*
void removeCntInLookupTable(unsigned int from_c,unsigned int to_c)
{
    unsigned int index = 2*from_c + to_c;
    CONNECT *ite_cnt = cntLookupTable[index];
    CONNECT *cnt;

    if(!ite_cnt){
        printf("removeCntInLookupTable: not found A\n");
        return;
    }
    if(ite_cnt->contigID==to_c){
        cntLookupTable[index] = ite_cnt->nextInLookupTable;
        return;
    }

    while(ite_cnt->nextInLookupTable&&ite_cnt->nextInLookupTable->contigID!=to_c)
        ite_cnt = ite_cnt->nextInLookupTable;

    if(ite_cnt->nextInLookupTable){
        cnt = ite_cnt->nextInLookupTable;
        ite_cnt->nextInLookupTable = cnt->nextInLookupTable;
        return;
    }
    printf("removeCntInLookupTable: not found B\n");
    return;
}
*/