X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtree.cpp;h=1dd77f9152b241321f6658d0e0efc025c01a1a71;hb=28d6f2bddc5c0718ae7f63648be3130a35fb0f02;hp=c805edc9896bf15b4e7397305c13d8bfbce175d8;hpb=814675616c10a40911886afb9dfe216f0245e3a2;p=mothur.git

diff --git a/readtree.cpp b/readtree.cpp
index c805edc..1dd77f9 100644
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -165,6 +165,7 @@ int ReadNewickTree::read() {
 		if (error != 0) { readOk = error; } 
 		
 		filehandle.close();
+
 		return readOk;
 	}
 	catch(exception& e) {
@@ -237,14 +238,15 @@ int ReadNewickTree::readTreeString() {
 			// ';' means end of tree.												
 			else if((ch=filehandle.peek())==';' || ch=='['){		
 				rooted = 1;									
-			}												
+			}	
+		
 			if(rooted != 1){								
 				rc = readNewickInt(filehandle, n, T);
 				if (rc == -1) { m->mothurOut("error with rc"); m->mothurOutEndLine(); return -1; } //reports an error in reading
 				if(filehandle.peek() == ')'){					
 					readSpecialChar(filehandle,')',"right parenthesis");
 				}											
-			}												
+			}	
 		}
 		//note: treeclimber had the code below added - not sure why?
 		else{
@@ -263,7 +265,8 @@ int ReadNewickTree::readTreeString() {
 			lc = rc = -1;
 		} 
 		
-		while(((ch=filehandle.get())!=';') && (filehandle.eof() != true)){;}						
+		while(((ch=filehandle.get())!=';') && (filehandle.eof() != true)){;}  	
+							
 		if(rooted != 1){									
 			T->tree[n].setChildren(lc,rc);
 			T->tree[n].setBranchLength(0);
@@ -271,6 +274,8 @@ int ReadNewickTree::readTreeString() {
 			if(lc!=-1){		T->tree[lc].setParent(n);		}
 			if(rc!=-1){		T->tree[rc].setParent(n);		}
 		}
+		
+		//T->printTree(); cout << endl;
 		return 0;
 	
 	}
@@ -287,9 +292,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 		if (m->control_pressed) { return -1; } 
 		
 		int c = readNodeChar(f);
-  string k;
-k = c;
-	cout << "at beginning = " << k <<endl;  
+
 		if(c == '('){
 		
 			//to account for multifurcating trees generated by fasttree, we are forcing them to be bifurcating
@@ -298,18 +301,15 @@ k = c;
 			while(f.peek() != ')'){
 				int child = readNewickInt(f, n, T);
 				if (child == -1) { return -1; } //reports an error in reading
-				
+		//cout << "child = " << child << endl;		
 				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;
- }
+				else {;}
 			}
-	cout << childrenNodes.size() << 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
@@ -317,31 +317,24 @@ k = c;
 			
 				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;	
+				else { lc = n-1; 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;
+				//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");
-
-			//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(); }
+				while((c!=',') && (c != -1) && (c!= ':') && (c!=';')&& (c!=')')){ c=filehandle.get(); }
 				filehandle.putback(c);
 			}			
 		
@@ -355,47 +348,6 @@ k = c;
 				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);
-		
-				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);
@@ -411,7 +363,7 @@ k = c;
 				name += d;
 				d=f.get();
 			}
-		cout << name << endl;
+//cout << name << endl;
 			int blen = 0;
 			if(d == ':')	{		blen = 1;	}		
 		
@@ -455,6 +407,7 @@ k = c;
 			}
 		
 			while((c=f.get())!=0 && (c != ':' && c != ',' && c!=')') )		{;}		
+	
 			f.putback(c);
 		
 			return n1;