X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtree.cpp;h=1dd77f9152b241321f6658d0e0efc025c01a1a71;hb=28d6f2bddc5c0718ae7f63648be3130a35fb0f02;hp=25fee86518bc6e2177b11824aa7989168c38772f;hpb=ac1da2a793271cb67f2a2155c5558e1fabdd6aba;p=mothur.git

diff --git a/readtree.cpp b/readtree.cpp
index 25fee86..1dd77f9 100644
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -13,10 +13,11 @@
 ReadTree::ReadTree() {
 	try {
 		globaldata = GlobalData::getInstance();
+		m = MothurOut::getInstance();
 		globaldata->gTree.clear();
 	}
 	catch(exception& e) {
-		errorOut(e, "ReadTree", "ReadTree");
+		m->errorOut(e, "ReadTree", "ReadTree");
 		exit(1);
 	}
 }
@@ -28,11 +29,11 @@ int ReadTree::readSpecialChar(istream& f, char c, string name) {
 		char d = f.get();
 	
 		if(d == EOF){
-			mothurOut("Error: Input file ends prematurely, expecting a " + name + "\n");
+			m->mothurOut("Error: Input file ends prematurely, expecting a " + name + "\n");
 			exit(1);
 		}
 		if(d != c){
-			mothurOut("Error: Expected " + name + " in input file.  Found " + toString(d) + ".\n");
+			m->mothurOut("Error: Expected " + name + " in input file.  Found " + toString(d) + ".\n");
 			exit(1);
 		}
 		if(d == ')' && f.peek() == '\n'){
@@ -41,7 +42,7 @@ int ReadTree::readSpecialChar(istream& f, char c, string name) {
 		return d;
 	}
 	catch(exception& e) {
-		errorOut(e, "ReadTree", "readSpecialChar");
+		m->errorOut(e, "ReadTree", "readSpecialChar");
 		exit(1);
 	}
 }
@@ -54,13 +55,13 @@ int ReadTree::readNodeChar(istream& f) {
 		char d = f.get();
 
 		if(d == EOF){
-			mothurOut("Error: Input file ends prematurely, expecting a left parenthesis\n");
+			m->mothurOut("Error: Input file ends prematurely, expecting a left parenthesis\n");
 			exit(1);
 		}
 		return d;
 	}
 	catch(exception& e) {
-		errorOut(e, "ReadTree", "readNodeChar");
+		m->errorOut(e, "ReadTree", "readNodeChar");
 		exit(1);
 	}
 }
@@ -72,14 +73,14 @@ float ReadTree::readBranchLength(istream& f) {
 		float b;
 	
 		if(!(f >> b)){
-			mothurOut("Error: Missing branch length in input tree.\n");
+			m->mothurOut("Error: Missing branch length in input tree.\n");
 			exit(1);
 		}
 		gobble(f);
 		return b;
 	}
 	catch(exception& e) {
-		errorOut(e, "ReadTree", "readBranchLength");
+		m->errorOut(e, "ReadTree", "readBranchLength");
 		exit(1);
 	}
 }
@@ -164,10 +165,11 @@ int ReadNewickTree::read() {
 		if (error != 0) { readOk = error; } 
 		
 		filehandle.close();
+
 		return readOk;
 	}
 	catch(exception& e) {
-		errorOut(e, "ReadNewickTree", "read");
+		m->errorOut(e, "ReadNewickTree", "read");
 		exit(1);
 	}
 }
@@ -208,7 +210,7 @@ void ReadNewickTree::nexusTranslation() {
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "ReadNewickTree", "nexusTranslation");
+		m->errorOut(e, "ReadNewickTree", "nexusTranslation");
 		exit(1);
 	}
 }
@@ -228,22 +230,23 @@ int ReadNewickTree::readTreeString() {
 			n = numLeaves;  //number of leaves / sequences, we want node 1 to start where the leaves left off
 
 			lc = readNewickInt(filehandle, n, T);
-			if (lc == -1) { mothurOut("error with lc"); mothurOutEndLine(); return -1; } //reports an error in reading
-		
+			if (lc == -1) { m->mothurOut("error with lc"); m->mothurOutEndLine(); return -1; } //reports an error in reading
+	
 			if(filehandle.peek()==','){							
 				readSpecialChar(filehandle,',',"comma");
 			}
 			// ';' means end of tree.												
 			else if((ch=filehandle.peek())==';' || ch=='['){		
 				rooted = 1;									
-			}												
+			}	
+		
 			if(rooted != 1){								
 				rc = readNewickInt(filehandle, n, T);
-				if (rc == -1) { mothurOut("error with rc"); mothurOutEndLine(); return -1; } //reports an error in reading
+				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{
@@ -255,14 +258,15 @@ int ReadNewickTree::readTreeString() {
 			n = T->getIndex(name);
 
 			if(n!=0){
-				mothurOut("Internal error: The only taxon is not taxon 0.\n");
+				m->mothurOut("Internal error: The only taxon is not taxon 0.\n");
 				//exit(1);
 				readOk = -1; return -1;
 			}
 			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);
@@ -270,11 +274,13 @@ 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;
 	
 	}
 	catch(exception& e) {
-		errorOut(e, "ReadNewickTree", "readTreeString");
+		m->errorOut(e, "ReadNewickTree", "readTreeString");
 		exit(1);
 	}
 }
@@ -282,39 +288,73 @@ int ReadNewickTree::readTreeString() {
 
 int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 	try {
+		
+		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
-			readSpecialChar(f,',',"comma");
 
-			int rc = readNewickInt(f, n, T);
-			if (rc == -1) { return -1; }  //reports an error in reading	
+		if(c == '('){
+		
+			//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--;
+			
 			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){	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); 
 			}						
-		
-			T->tree[n].setChildren(lc,rc);
-			T->tree[lc].setParent(n);
-			T->tree[rc].setParent(n);
-		
+			
+			//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 = "";
@@ -323,7 +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;	}		
 		
@@ -337,7 +377,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 			
 			//adds sequence names that are not in group file to the "xxx" group
 			if(group == "not found") {
-				mothurOut("Name: " + name + " is not in your groupfile, and will be disregarded. \n");  //readOk = -1; return n1;
+				m->mothurOut("Name: " + name + " is not in your groupfile, and will be disregarded. \n");  //readOk = -1; return n1;
 				
 				globaldata->gTreemap->namesOfSeqs.push_back(name);
 				globaldata->gTreemap->treemap[name].groupname = "xxx";
@@ -354,7 +394,9 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 				group = "xxx";
 			}
 			
-			T->tree[n1].setGroup(group);
+			vector<string> tempGroup; tempGroup.push_back(group);
+			
+			T->tree[n1].setGroup(tempGroup);
 			T->tree[n1].setChildren(-1,-1);
 		
 			if(blen == 1){	
@@ -365,13 +407,14 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 			}
 		
 			while((c=f.get())!=0 && (c != ':' && c != ',' && c!=')') )		{;}		
+	
 			f.putback(c);
 		
 			return n1;
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "ReadNewickTree", "readNewickInt");
+		m->errorOut(e, "ReadNewickTree", "readNewickInt");
 		exit(1);
 	}
 }