support.cc

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//  These are the member functions for the support classes.

/*
** $Log$
*/

#include "eval.h"

#ifdef sgi
    #include <stdio.h>
    #include "support.h"
    #include "stateLibrary.h"
    #include "structs.h"
#else
    extern "C"
    {
	#include <stdio.h>
	#include "support.h"
	#include "stateLibrary.h"
	#include "structs.h"
    }
#endif

extern FILE *logFile;

extern class Eval evaluate;

Population::Population(Population &original)
: lhb(original.lhb), size(original.size)
{
   register int i;

#ifdef DEBUG
   (void)fprintf(logFile, "support.cc/Population::Population(Population &original)\n");
#endif /* DEBUG */

   heap = new Individual[size];
   for (i=0; i<size; i++) {
      heap[i] = original.heap[i];
      heap[i].age = 0L; // gmm, 1998-07-14
   }
}

/*  Heap Functions:  In this case, the heap condition means the maximal 
    element wrt fitness (i.e. the best) is at the top of the heap.  lhb 
    is the index of the last element to be inserted into the heap.  Some 
    the standard functions on the heap can be accomplished in the following 
    manner:
       Root = size - 1  (Note: that the root is fixed)
       LeftChild(I) = 2I - size
       RightChild(I) = 2I - size - 1
       Parent(I) = (I + size + 1)/2
    It is important to notice that the heap condition is maintained from
    lhb to size-1 *in reverse order*.
*/

void Population::swap(Individual &individual1, Individual &individual2)
{
   Individual temp;

#ifdef DEBUG
   (void)fprintf(logFile, "support.cc/void Population::swap(Individual &individual1, Individual &individual2)\n");
#endif /* DEBUG */


   temp = individual1;
   individual1 = individual2;
   individual2 = temp;
}

/*  This routine assumes that the heap condition is satisfied
    between lhb and size-1 and that the new individual is in
    position lhb-1.
*/
void Population::SiftUp(void)
{
   int i, parent;

#ifdef DEBUG
   (void)fprintf(logFile, "support.cc/void Population::SiftUp(void)\n");
#endif /* DEBUG */


   i = lhb-1;
   while (((parent=(i+size+1)/2)<size)&&(heap[parent].value(Normal_Eval)>heap[i].value(Normal_Eval))) {
      swap(heap[parent], heap[i]);
      i = parent;
   }
   lhb--;
}

/*  This routine assumes that the heap condition is satisfied
    between lhb & size-2 initially, and that the individual at size-1
    needs to be accomodated.*/
void Population::SiftDown(void)
{
   int i, child;

#ifdef DEBUG
   (void)fprintf(logFile, "support.cc/void Population::SiftDown(void)\n");
#endif /* DEBUG */


   i = size-1;
   while ((child=2*i-size)>=lhb) {
      if (child-1>=lhb) {
         if (heap[child-1].value(Normal_Eval)<heap[child].value(Normal_Eval)) {
            child--;
         }
      }
      /*  Now child holds the index of the best child of i  */
      if (heap[i].value(Normal_Eval)<heap[child].value(Normal_Eval)) {
         break;
      } else {
         swap(heap[child], heap[i]);
         i = child;
      }
   }
}

void Population::msort(int m)
{
   register int i;

#ifdef DEBUG
   (void)fprintf(logFile, "support.cc/void Population::msort(int m=%d)\n",m);
#endif /* DEBUG */


   //  First make a heap of the whole array, i.e lhb = 0 & uhb = size
   lhb = size-1;
   while (lhb>0) {
      SiftUp();
   }

   //  Now place the m best members at the beginning of the array
   for (i=0; i<m; i++) {
      swap(heap[i], heap[size-1]);
      lhb++;
      SiftDown();
   }
   
   //  Assert: heap[0..m-1] sorted
}

//void Population::print(ostream &output, int num)
//{
   //register int i;

//#ifdef DEBUG
   //(void)fprintf(logFile, "support.cc/void Population::print(ostream &output, int num=%d)\n",num);
//#endif /* DEBUG */


   //(void)fprintf(logFile, "The top %d individuals in the population:/n", num);
   //for (i=0; i<num; i++) {
      //(void)fprintf(logFile,"%lf\n", heap[i].value(Normal_Eval));
   //}
//}

void Population::print(FILE *output, int num) {
   register int i;

#ifdef DEBUG
   (void)fprintf(logFile, "support.cc/void Population::print(FILE *output, int num=%d)\n",num);
#endif /* DEBUG */

   (void)fprintf( output, "The top %d individuals in the population:\n\n", num);
   for (i=0; i<num; i++) {
      (void)fprintf( output, "(%d):\t %8.2f\n", i+1, heap[i].value(Normal_Eval));
   }
}

void Population::printPopulationAsStates(FILE *output, int num, int ntor) {
   register int i;
#ifdef DEBUG2
   register int j;
#endif /* DEBUG2 */
   double thisValue;

#ifdef DEBUG
   (void)fprintf(logFile, "support.cc/void Population::printPopulationAsStates(FILE *output, int num=%d, int ntor=%d)\n",num,ntor);
#endif /* DEBUG */

   (void)fprintf( output, "The top %d individuals in the population:\n\n", num);
   for (i=0; i<num; i++) {
      thisValue = heap[i].value(Normal_Eval);
      (void)fprintf( output, "(%d):\nEnergy= %8.2le\n", i+1, thisValue);
      heap[i].printIndividualsState(output, ntor);

#ifdef DEBUG2
      if (!finite(thisValue) || ISNAN(thisValue)) {//debug
	  // Convert state to coords and print it out...//debug
	  cnv_state_to_coords(heap[i].state(ntor), heap[i].mol->vt,  heap[i].mol->tlist,  ntor, heap[i].mol->crdpdb,  heap[i].mol->crd,  heap[i].mol->natom);//debug
	  for (j=0; j<heap[i].mol->natom; j++) {//debug
	    (void)fprintf( logFile, "ATOM  %5d  C   RES     1    %8.3f%8.3f%8.3f %+8.2f %+6.2f\n", i+1, heap[i].mol->crd[i][X], heap[i].mol->crd[i][Y], heap[i].mol->crd[i][Z], 0., 0.); //debug
	  }/*j*///debug
      }// thisValue is either infinite or not-a-number.//debug
#endif /* DEBUG2 */

   }// i
}


Genotype::Genotype(unsigned int init_number_of_vectors, Representation **
init_rep_vector)
: number_of_vectors(init_number_of_vectors), rep_vector(init_rep_vector),
  modified(0)
{
   register int i, j, k;

#ifdef DEBUG
   (void)fprintf(logFile, "support.cc/Genotype::Genotype(unsigned int init_number_of_vectors=%d, Representation **init_rep_vector)\n",init_number_of_vectors);
#endif /* DEBUG */


   number_of_genes = 0;
   for (i=0; i<number_of_vectors; i++) {
      number_of_genes += rep_vector[i]->number_of_points();
   }
 
   i=0;
   lookup = new Lookup[number_of_genes];
   for (j=0; j<number_of_vectors; j++) {
      for (k=0; k<rep_vector[j]->number_of_points(); k++) {
         lookup[i].vector = j;
         lookup[i].index = k;
         i++;
      }
   }
}

Genotype::Genotype(const Genotype &original)
{
   register int i;

#ifdef DEBUG
   (void)fprintf(logFile, "support.cc/Genotype::Genotype(Genotype &original)\n");
#endif /* DEBUG */


   number_of_genes = original.number_of_genes;
   number_of_vectors = original.number_of_vectors;
   modified = original.modified;
   if (original.rep_vector!=NULL) {
      rep_vector = new Representation*[number_of_vectors];
      lookup = new Lookup[number_of_genes];
   } else {
      rep_vector = NULL;
      lookup = NULL;
   }

   for (i=0; i<number_of_vectors; i++) {
      rep_vector[i] = original.rep_vector[i]->clone();
   }

   for (i=0; i<number_of_genes; i++) {
      lookup[i] = original.lookup[i];
   }
}

Genotype::~Genotype(void)
{
   register int i;

#ifdef DEBUG
   (void)fprintf(logFile, "support.cc/Genotype::~Genotype(void)\n");
#endif /* DEBUG */


   if (rep_vector!=NULL) {
      for (i=0; i<number_of_vectors; i++) {
         delete rep_vector[i];
      }
      delete [] rep_vector;
      delete [] lookup;
   }
}

Genotype &Genotype::operator=(const Genotype &original)
{
   register int i;

#ifdef DEBUG
   (void)fprintf(logFile, "support.cc/Genotype &Genotype::operator=(const Genotype &original)\n");
#endif /* DEBUG */


   if (rep_vector!=NULL) {
      for (i=0; i<number_of_vectors; i++) {
         delete rep_vector[i];
      }
      delete [] rep_vector;
      delete [] lookup;
   }

   number_of_vectors = original.number_of_vectors;
   number_of_genes = original.number_of_genes;
//   modified = original.modified;
   modified = 1;

   if (original.rep_vector!=NULL) {
      rep_vector = new Representation *[number_of_vectors];
      lookup = new Lookup[number_of_genes];
   } else {
      rep_vector = NULL;
      lookup = NULL;
   }

   for (i=0; i<number_of_vectors; i++) {
      rep_vector[i] = original.rep_vector[i]->clone();
   }

   for (i=0; i<number_of_genes; i++) {
      lookup[i] = original.lookup[i];
   }

   return(*this);
}

void Genotype::write(Element value, int gene_number)
{

#ifdef DEBUG
   (void)fprintf(logFile, "support.cc/void Genotype::write(Element value, int gene_number=%d)\n",gene_number);
#endif /* DEBUG */

   modified = 1;
   rep_vector[lookup[gene_number].vector]->write(value, lookup[gene_number].index);
}

void Genotype::write(unsigned char value, int gene_number)
{