# include "Seq.h"


void ReadSelection(TokenizeData * d, int select[])
{
  int i = 0;
  InitLexer(d);
  while (TokenizeLine(d)) {
    if (OnBetwStrgs(d,"_BEG_SELECT_","_END_SELECT_")) {
      if (i>MAX_SEQ_SELECTION) STDERR("ERROR: i>MAX_SEQ_SELECTION");
      select[i] = d->D[1] ;
      i++ ;
    }
  }
  select[i] = 0;
}

bool ReadSelectionOneLine
  (TokenizeData * d, int select[],char * key,int SeqStartPos)
{
  InitLexer(d);
  while (TokenizeLine(d)) {
    if (Begins2With1P(key,d->T[0])) {
      int i=1, j=0;
      char * p = &(d->T[0][SeqStartPos]) ;
      while (*p != '#') {
	if (*p == '*' || *p == 'x' || *p == '$') {
	  select[j]=i;
	  j++;
	}
	i++; p++;
      }
      select[j] = 0;
      return true;
    }
  }
  return false;
}

void ReadSelectionWNames(TokenizeData * d, int select[], char * CannonicalNames[])
{
  int i = 0;
  InitLexer(d);
  while (TokenizeLine(d)) {
    if (OnBetwStrgs(d,"_BEG_SELECT_","_END_SELECT_")) {
      if (i>MAX_SEQ_SELECTION) STDERR("ERROR: i>MAX_SEQ_SELECTION");
      select[i] = d->D[1] ;
      CannonicalNames[i] = SaveString(d->T[2]);
      i++ ;
    }
  }
  select[i] = 0;
}


bool InSelectionP(int i, int *select)
{
  if (select == NULL || *select == 0) 
    return false;
  else if (i == *select)
    return true;
  else 
    return InSelectionP(i,++select);
}


int * InvertSelection(int *select, int *out, int SeqSz)
{
  int i,j,k=0;
  for (j=1; j<= SeqSz; j++) {
    if (!InSelectionP(j,select)) {
      out[k] = j;
      k++ ;
    }
  }
  out[k]=0;
  return out ;
}

void RemoveSel3FromSel2To(int *NewSel,int *CoreSel,int *select)
{
  int * SP ;
  while (*CoreSel) {
    int match = 0;
    for (SP = select; *SP ; SP++)
      if (*SP == *CoreSel) {
	match = 1;
	break ;
      }
    if (!match) {
      *NewSel = *CoreSel ;
      NewSel++ ;
    }
    CoreSel++ ;
  }  
}  


int IntMemberOf(int query, int * SetOfInt)
{
  if (*SetOfInt == 0)
    return NOT_A_MEMBER ;
  else if (*SetOfInt == query)
    return 0 ;
  else {
    int i = IntMemberOf(query, SetOfInt + 1) ;
    if (i == NOT_A_MEMBER) 
      return NOT_A_MEMBER ;
    else 
      return (i + 1) ;
  }
}

void PrintSetOfInt(int * SetOfInt)
{
  int i;
  for (i=0; SetOfInt[i] != 0 ; i++)
    printf("%d ",SetOfInt[i]);
  printf("\n");
}


int SizeSetOfInt(int * SetOfInt)
{
  if (SetOfInt == NULL || *SetOfInt == 0) 
    return 0 ;
  else {
    int i;
    for (i=0; SetOfInt[i] !=0 ; i++)  ;
    return i;
  }
}

int * ReadSetOfInt(TokenizeData * d)
{
  int *retval, i;
  if (!TokenizeLine(d))
    STDERR("You are at the end of the number line.");
  retval = ivector(0,d->NF+1);
  for (i=0; i<d->NF; i++) 
    retval[i] = d->D[i+1];
  retval[d->NF] = 0;
  return retval ;
}

int * NotIntersect(int * s1, int *s2)
{
  int i, j=0;
  int size = SizeSetOfInt(s1) + SizeSetOfInt(s2);
  int * s3 = ivector(0,size);
  for (i=0; s1[i] != 0; i++)
    if (IntMemberOf(s1[i],s2) == NOT_A_MEMBER) {
      s3[j++] = s1[i] ;
    }
  for (i=0; s2[i] != 0; i++)
    if (IntMemberOf(s2[i],s1) == NOT_A_MEMBER) {
      s3[j++] = s2[i] ;
    }
  s3[j] = 0;
  return s3;
}