Beispiel #1
0
double IMM::scoreSingleBase(const Sequence &seq,const BOOM::String &str,
				    int index,Symbol s,char c)
{
  const char *p=str.c_str();
  switch(getStrand())
    {
    case PLUS_STRAND:
      {
	int maxOrder=(index>N ? N : index);
	for(int order=maxOrder ; order>=0 ; --order)
	  {
	    BOOM::StringMap<double> &model=*(*models)[order];
	    if(model.isDefined(p,index-order,order+1))
	      return model.lookup(p,index-order,order+1);
	  }
	throw BOOM::String("IMM::scoreSingleBase('+',")+
	  index+",strlen="+strlen(p)+",str="+
	  str.substring(index,maxOrder)+")";
      }

    case MINUS_STRAND:
      {
	/*
	  On the minus strand we have to take our contexts from the
	  right (but only because we trained the model that way)
	 */
	int seqLen=str.length();
	int maxOrder=seqLen-index-1;
	if(maxOrder>N) maxOrder=N;
	for(int order=maxOrder ; order>=0 ; --order)
	  {
	    BOOM::StringMap<double> &model=*(*models)[order];
	    if(model.isDefined(p,index,order+1)) 
	      return model.lookup(p,index,order+1);
	  }
	throw BOOM::Stacktrace(
          BOOM::String("IMM::scoreSingleBase('-',")+
	    index+",strlen="+strlen(p)+",str="+
	  str.substring(index,maxOrder)+")");
      }

    default: throw BOOM::String(__FILE__)+__LINE__;
    }
}
BOOM::String SignalPeptide::getSequence()
{
  BOOM::String sequence;
  int n=exons.size();
  for(int i=0 ; i<n ; ++i)
    sequence+=exons[i].getSequence();
  if(sequence[0]=='M') 
    sequence=sequence.substring(1,sequence.length()-1);
  return sequence;
}
void PeptideExon::loadSequence(const BOOM::String &substrate)
{
  sequence=substrate.substring(begin,end-begin);
}