X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtree.cpp;h=e98524b45e9ec513fe171c5a342ab381a68fcacc;hb=fd5f17bcbe5fadab2c525f3d1fcfd1d79a60ae72;hp=51f44e217899c3acebc1a34879b31d6624389191;hpb=2a7d1455e8cfe4f67a7173f3a7249762c5436217;p=mothur.git

diff --git a/readtree.cpp b/readtree.cpp
index 51f44e2..e98524b 100644
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -25,7 +25,7 @@ ReadTree::ReadTree() {
 int ReadTree::readSpecialChar(istream& f, char c, string name) {
     try {
 	
-		gobble(f);
+		m->gobble(f);
 		char d = f.get();
 	
 		if(d == EOF){
@@ -37,7 +37,7 @@ int ReadTree::readSpecialChar(istream& f, char c, string name) {
 			exit(1);
 		}
 		if(d == ')' && f.peek() == '\n'){
-			gobble(f);
+			m->gobble(f);
 		}	
 		return d;
 	}
@@ -51,7 +51,7 @@ int ReadTree::readSpecialChar(istream& f, char c, string name) {
 int ReadTree::readNodeChar(istream& f) {
 	try {
 //		while(isspace(d=f.get()))		{;}
-		gobble(f);
+		m->gobble(f);
 		char d = f.get();
 
 		if(d == EOF){
@@ -76,7 +76,7 @@ float ReadTree::readBranchLength(istream& f) {
 			m->mothurOut("Error: Missing branch length in input tree.\n");
 			exit(1);
 		}
-		gobble(f);
+		m->gobble(f);
 		return b;
 	}
 	catch(exception& e) {
@@ -125,7 +125,7 @@ int ReadNewickTree::read() {
 				
 				//save trees for later commands
 				globaldata->gTree.push_back(T); 
-				gobble(filehandle);
+				m->gobble(filehandle);
 			}
 		//if you are a nexus file
 		}else if ((c = filehandle.peek()) == '#') {
@@ -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;
 	
 	}
@@ -287,53 +292,69 @@ 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; }
+			
+			//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--;
 			
-			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);
-
 			}			
 		
 			if(f.peek() == ':'){									      
 				readSpecialChar(f,':',"colon");	
 										
-				if(n >= numNodes){	m->mothurOut("Error: Too many nodes in input tree\n");  readOk = -1; return -1; }
+				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); 
 			}						
 			
-			//to account for multifurcating trees generated by fasttree, we are forcing them to be bifurcating
-		/*	if(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);
-				
-				n++;
-				
-
+			//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);
-		
 			return n++;
+		
 		}else{
 			f.putback(c);
 			string name = "";
@@ -342,7 +363,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 				name += d;
 				d=f.get();
 			}
-		
+//cout << name << endl;
 			int blen = 0;
 			if(d == ':')	{		blen = 1;	}		
 		
@@ -386,6 +407,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 			}
 		
 			while((c=f.get())!=0 && (c != ':' && c != ',' && c!=')') )		{;}		
+	
 			f.putback(c);
 		
 			return n1;