void RNAForestSZ::buildForest(unsigned int &pos, unsigned int &node) {
unsigned int node2;
switch (viennaStr_[pos]) {
case '.':
// set label
if (baseStr_.length())
lb_[node]=alpha2RNA_Alpha(baseStr_[pos]);
else
lb_[node]=ALPHA_BASE;
lml_[node]=node;
break;
case '(':
// left paring base
if (baseStr_.length())
lb_[node]=alpha2RNA_Alpha(baseStr_[pos]);
else
lb_[node]=ALPHA_BASE;
lml_[node]=node;
// build subforest right to (
node2=node;
node++;
pos++;
buildForest(pos,node);
// right bracket
assert(viennaStr_[pos]==')');
// right pairing base
if (baseStr_.length())
lb_[node]=alpha2RNA_Alpha(baseStr_[pos]);
else
lb_[node]=ALPHA_BASE;
lml_[node]=node;
node++;
lb_[node]=ALPHA_BASEPAIR;
lml_[node]=node2;
break;
case ')':
return;
break;
}
pos++;
node++;
if (pos<viennaStr_.length())
buildForest(pos,node);
}
void RNAProfileAlignment::makeLabel(RNA_Alphabet_Profile &p,char c)
{
int i;
// initialize profile entries to zero
for(i=0;i<RNA_ALPHABET_SIZE;i++)
p.p[i]=0.0;
i=alpha2RNA_Alpha(c);
p.p[i]=1.0;
// if it is acgu it is also a base
if(i<=ALPHA_PRO_BASE_U)
p.p[ALPHA_PRO_BASE]=1.0;
// set column string
p.columnStr=c;
}