/*
 * arc.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"

#define preARCBLOCKSIZE 100000

void createPreArcMemManager ()
{
  prearc_mem_manager = createMem_manager ( preARCBLOCKSIZE, sizeof ( preARC ) );
}

void prlDestroyPreArcMem ()
{
  if ( !preArc_mem_managers )
    {
      return;
    }

  int i;

  for ( i = 0; i < thrd_num; i++ )
    {
      freeMem_manager ( preArc_mem_managers[i] );
    }

  free ( ( void * ) preArc_mem_managers );
  preArc_mem_managers = NULL;
}

void destroyPreArcMem ()
{
  freeMem_manager ( prearc_mem_manager );
  prearc_mem_manager = NULL;
}

preARC *prlAllocatePreArc ( unsigned int edgeid, MEM_MANAGER *manager )
{
  preARC *newArc;
  newArc = ( preARC * ) getItem ( manager );
  newArc->to_ed = edgeid;
  newArc->multiplicity = 1;
  newArc->next = NULL;
  return newArc;
}

preARC *allocatePreArc ( unsigned int edgeid )
{
  arcCounter++;
  preARC *newArc;
  newArc = ( preARC * ) getItem ( prearc_mem_manager );
  newArc->to_ed = edgeid;
  newArc->multiplicity = 1;
  newArc->next = NULL;
  return newArc;
}

void output_arcGVZ ( char *outfile, boolean IsContig )
{
  ARC *pArc;
  preARC *pPreArc;
  char name[256];
  FILE *fp;
  unsigned int i;
  sprintf ( name, "%s.arc.gvz", outfile );
  fp = ckopen ( name, "w" );
  fprintf ( fp, "digraph G{\n" );
  fprintf ( fp, "\tsize=\"512,512\";\n" );

  for ( i = 1; i <= num_ed; i++ )
    {
      if ( IsContig )
        {
          pPreArc = contig_array[i].arcs;

          while ( pPreArc )
            {
              fprintf ( fp, "\tC%d -> C%d[label =\"%d\"];\n", i, pPreArc->to_ed, pPreArc->multiplicity );
              pPreArc = pPreArc->next;
            }
        }
      else
        {
          pArc = edge_array[i].arcs;

          while ( pArc )
            {
              fprintf ( fp, "\tC%d -> C%d[label =\"%d\"];\n", i, pArc->to_ed, pArc->multiplicity );
              pArc = pArc->next;
            }
        }
    }

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

/**************** below this line all codes are about ARC ****************/
#define ARCBLOCKSIZE 100000
void createArcMemo ()
{
  if ( !arc_mem_manager )
    {
      arc_mem_manager = createMem_manager ( ARCBLOCKSIZE, sizeof ( ARC ) );
    }
  else
    {
      fprintf ( stderr, "Warning from createArcMemo: arc_mem_manager is a active pointer.\n" );
    }
}

void destroyArcMem ()
{
  freeMem_manager ( arc_mem_manager );
  arc_mem_manager = NULL;
}

ARC *allocateArc ( unsigned int edgeid )
{
  arcCounter++;
  ARC *newArc;
  newArc = ( ARC * ) getItem ( arc_mem_manager );
  newArc->to_ed = edgeid;
  newArc->multiplicity = 1;
  newArc->prev = NULL;
  newArc->next = NULL;
  return newArc;
}

void dismissArc ( ARC *arc )
{
  returnItem ( arc_mem_manager, arc );
}

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

void createArcLookupTable ()
{
  if ( !arcLookupTable )
    {
      arcLookupTable = ( ARC ** ) ckalloc ( ( 3 * num_ed + 1 ) * sizeof ( ARC * ) );
    }
}

void deleteArcLookupTable ()
{
  if ( arcLookupTable )
    {
      free ( ( void * ) arcLookupTable );
      arcLookupTable = NULL;
    }
}

void putArc2LookupTable ( unsigned int from_ed, ARC *arc )
{
  if ( !arc || !arcLookupTable )
    {
      return;
    }

  unsigned int index = 2 * from_ed + arc->to_ed;
  arc->nextInLookupTable = arcLookupTable[index];
  arcLookupTable[index] = arc;
}

static ARC *getArcInLookupTable ( unsigned int from_ed, unsigned int to_ed )
{
  unsigned int index = 2 * from_ed + to_ed;
  ARC *ite_arc = arcLookupTable[index];

  while ( ite_arc )
    {
      if ( ite_arc->to_ed == to_ed )
        {
          return ite_arc;
        }

      ite_arc = ite_arc->nextInLookupTable;
    }

  return NULL;
}

void removeArcInLookupTable ( unsigned int from_ed, unsigned int to_ed )
{
  unsigned int index = 2 * from_ed + to_ed;
  ARC *ite_arc = arcLookupTable[index];
  ARC *arc;

  if ( !ite_arc )
    {
      fprintf ( stderr, "RemoveArcInLookupTable: not found A.\n" );
      return;
    }

  if ( ite_arc->to_ed == to_ed )
    {
      arcLookupTable[index] = ite_arc->nextInLookupTable;
      return;
    }

  while ( ite_arc->nextInLookupTable && ite_arc->nextInLookupTable->to_ed != to_ed )
    {
      ite_arc = ite_arc->nextInLookupTable;
    }

  if ( ite_arc->nextInLookupTable )
    {
      arc = ite_arc->nextInLookupTable;
      ite_arc->nextInLookupTable = arc->nextInLookupTable;
      return;
    }

  fprintf ( stderr, "RemoveArcInLookupTable: not found B.\n" );
  return;
}

void recordArcsInLookupTable ()
{
  unsigned int i;
  ARC *ite_arc;

  for ( i = 1; i <= num_ed; i++ )
    {
      ite_arc = edge_array[i].arcs;

      while ( ite_arc )
        {
          putArc2LookupTable ( i, ite_arc );
          ite_arc = ite_arc->next;
        }
    }
}

/*************************************************
Function:
    getArcBetween
Description:
    Gets the arc between the edge "from_ed" and the edge "to_ed", then return it.
Input:
    1. from_ed:     the origin edge
    2. to_ed:       the destination edge
Output:
    None.
Return:
    The arc between the edge "from_ed" and the edge "to_ed".
*************************************************/
ARC *getArcBetween ( unsigned int from_ed, unsigned int to_ed )
{
  ARC *parc;

  if ( arcLookupTable )
    {
      parc = getArcInLookupTable ( from_ed, to_ed );
      return parc;
    }

  parc = edge_array[from_ed].arcs;

  while ( parc )
    {
      if ( parc->to_ed == to_ed )
        {
          return parc;
        }

      parc = parc->next;
    }

  return parc;
}

/*************************************************
Function:
    validArcCount
Description:
    Compute the count of the valid arc, whose weight is larger than "cutoff", then return it.
Input:
    1. arc:         the head of the "preARC" linked list
    2. cutoff:      the minimum requirement for the weight of the valid arc
Output:
    None.
Return:
    The number of the valid arc.
*************************************************/
int validArcCount ( preARC *arc, int cutoff )
{
  int arc_num = 0;

  while ( arc )
    {
      if ( arc->multiplicity >= cutoff )
        {
          ++arc_num;
        }

      arc = arc->next;
    }

  return arc_num;
}

/*************************************************
Function:
    maxArcWeight
Description:
    Gets the maximum weight in all arcs, then return it.
Input:
    1. arc:     the head of the "preARC" linked list
Output:
    None.
Return:
    The maximum weight.
*************************************************/
unsigned int maxArcWeight ( preARC *arc )
{
  unsigned int max = 0;

  while ( arc )
    {
      if ( arc->multiplicity > max )
        {
          max = arc->multiplicity;
        }

      arc = arc->next;
    }

  return max;
}