X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtree.cpp;h=1dd77f9152b241321f6658d0e0efc025c01a1a71;hb=ccaad73f103d8f105264d65491ce19e5df80477d;hp=1df49b5502f405bf29b31ee585fb5d6a264f9cda;hpb=6de5adaae66b28aa60a75f123005cede410c156c;p=mothur.git

diff --git a/readtree.cpp b/readtree.cpp
index 1df49b5..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;
 	
 	}
@@ -287,23 +292,50 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 		if (m->control_pressed) { return -1; } 
 		
 		int c = readNodeChar(f);
-    
+
 		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
+		//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 {;}
+			}
+	//cout << childrenNodes.size() << endl;		
+			if (childrenNodes.size() < 2) {  m->mothurOut("Error in tree, please correct."); m->mothurOutEndLine(); return -1; }
 			
-			readSpecialChar(f,',',"comma");
-
-			int rc = readNewickInt(f, n, T);
-			if (rc == -1) { return -1; }  //reports an error in reading	
+			//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-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;
+				n++;
+			}
+			
+			//to account for extra ++ in looping
+			n--;
 			
 			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);
-
 			}			
 		
 			if(f.peek() == ':'){									      
@@ -316,54 +348,13 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 				T->tree[n].setBranchLength(0.0); 
 			}						
 			
-			//to account for multifurcating trees generated by fasttree, we are forcing them to be bifurcating
-			while(f.peek() == ','){
-				
-				//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");
-
-				int rc = readNewickInt(f, n, T);
-		cout << n << '\t' << lc << '\t' << rc << endl;
-				if (rc == -1) { return -1; }  //reports an error in reading	
-				
-				if(f.peek()==')'){	
-				string k;
-				k = f.peek();
-		cout << "in here " << k << endl;
-					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;
-				}			
-			}
-	cout << n << '\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->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 = "";
@@ -372,7 +363,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 				name += d;
 				d=f.get();
 			}
-		cout << name << endl;
+//cout << name << endl;
 			int blen = 0;
 			if(d == ':')	{		blen = 1;	}		
 		
@@ -416,6 +407,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 			}
 		
 			while((c=f.get())!=0 && (c != ':' && c != ',' && c!=')') )		{;}		
+	
 			f.putback(c);
 		
 			return n1;