if (m->control_pressed) { return -1; }
int c = readNodeChar(f);
-
+ string k;
+k = c;
+ cout << "at beginning = " << k <<endl;
if(c == '('){
- int lc = readNewickInt(f, n, T);
- if (lc == -1) { return -1; } //reports an error in reading
+
+ //to account for multifurcating trees generated by fasttree, we are forcing them to be bifurcating
+ //read all children
+ vector<int> childrenNodes;
+ while(f.peek() != ')'){
+ int child = readNewickInt(f, n, T);
+ if (child == -1) { return -1; } //reports an error in reading
+
+ childrenNodes.push_back(child);
+
+ //after a child you either have , or ), check for both
+ if(f.peek()==')'){ break; }
+ else if (f.peek()==',') { readSpecialChar(f,',',"comma"); }
+ else { string k;
+ k = f.peek();
+ cout << "in here k = " << k << '\t' << f.tellg() <<endl;
+ }
+ }
+ cout << childrenNodes.size() << endl;
+ if (childrenNodes.size() < 2) { m->mothurOut("Error in tree, please correct."); m->mothurOutEndLine(); return -1; }
+
+ //then force into 2 node structure
+ for (int i = 1; i < childrenNodes.size(); i++) {
+
+ int lc, rc;
+ if (i == 1) { lc = childrenNodes[i-1]; rc = childrenNodes[i]; }
+ else { lc = n; rc = childrenNodes[i]; }
+ cout << i << '\t' << lc << '\t' << rc << endl;
+ T->tree[n].setChildren(lc,rc);
+ T->tree[lc].setParent(n);
+ T->tree[rc].setParent(n);
+
+ T->printTree(); cout << endl;
+ n++;
+ }
+
+ //to account for extra ++ in looping
+ n--;
+ //int lc = readNewickInt(f, n, T);
+ //if (lc == -1) { return -1; } //reports an error in reading
- readSpecialChar(f,',',"comma");
+ //readSpecialChar(f,',',"comma");
- int rc = readNewickInt(f, n, T);
- if (rc == -1) { return -1; } //reports an error in reading
+ //int rc = readNewickInt(f, n, T);
+ //if (rc == -1) { return -1; } //reports an error in reading
+
if(f.peek()==')'){
readSpecialChar(f,')',"right parenthesis");
//to pass over labels in trees
c=filehandle.get();
while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ c=filehandle.get(); }
filehandle.putback(c);
-
}
if(f.peek() == ':'){
}else{
T->tree[n].setBranchLength(0.0);
}
+
+ //to account for multifurcating trees generated by fasttree, we are forcing them to be bifurcating
+ /*while(f.peek() == ','){
+ string k;
+ k = f.peek();
+ cout << "in here k = " << k << '\t' << f.tellg() <<endl;
+ //force this node to be left child and read new rc
+ T->tree[n].setChildren(lc,rc);
+ T->tree[lc].setParent(n);
+ T->tree[rc].setParent(n);
+
+ T->printTree(); cout << endl;
+ lc = n;
+ n++;
+
+ readSpecialChar(f,',',"comma");
+
+ rc = readNewickInt(f, n, T);
- T->tree[n].setChildren(lc,rc);
- T->tree[lc].setParent(n);
- T->tree[rc].setParent(n);
+ if (rc == -1) { return -1; } //reports an error in reading
+
+ if(f.peek()==')'){
+ readSpecialChar(f,')',"right parenthesis");
+ //to pass over labels in trees
+ c=filehandle.get();
+ while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ c=filehandle.get(); }
+ filehandle.putback(c);
+
+ if(f.peek() == ':'){
+ readSpecialChar(f,':',"colon");
+
+ if(n >= numNodes){ m->mothurOut("Error: Too many nodes in input tree\n"); readOk = -1; return -1; }
+
+ T->tree[n].setBranchLength(readBranchLength(f));
+ }else{
+ T->tree[n].setBranchLength(0.0);
+ }
+
+ break;
+ }
+ }*/
+ //T->tree[n].setChildren(lc,rc);
+ //T->tree[lc].setParent(n);
+ //T->tree[rc].setParent(n);
+ //T->printTree(); cout << endl;
+
return n++;
+
}else{
f.putback(c);
string name = "";
name += d;
d=f.get();
}
-
+ cout << name << endl;
int blen = 0;
if(d == ':') { blen = 1; }