X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtree.cpp;h=d3790df170ab0651c24987bc3541b62f48197c5f;hb=d873f7bf94309317a08c8757e0d0d60b06fbd473;hp=59239c8af0d24e089bfc7eade92ed055ffaa6e64;hpb=ef2b771b08a9753db3800b06b9860317204dad5b;p=mothur.git

diff --git a/readtree.cpp b/readtree.cpp
index 59239c8..d3790df 100644
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -100,31 +100,42 @@ float ReadTree::readBranchLength(istream& f) {
 	}		
 }
 
-
 /***********************************************************************/
 /***********************************************************************/
 
-
 //Child Classes Below
 
 /***********************************************************************/
 /***********************************************************************/
 //This class reads a file in Newick form and stores it in a tree.
 
-void ReadNewickTree::read() {
+int ReadNewickTree::read() {
 	try {
-		int c;
+		holder = "";
+		int c, error;
 		int comment = 0;
 		
 		//if you are not a nexus file 
 		if ((c = filehandle.peek()) != '#') {  
 			while((c = filehandle.peek()) != EOF) { 
+				while ((c = filehandle.peek()) != EOF) {
+					// get past comments
+					if(c == '[') {
+						comment = 1;
+					}
+					if(c == ']'){
+						comment = 0;
+					}
+					if((c == '(') && (comment != 1)){ break; }
+					filehandle.get();
+				}
+
 				//make new tree
 				T = new Tree(); 
 				numNodes = T->getNumNodes();
 				numLeaves = T->getNumLeaves();
 				
-				readTreeString(); 
+				error = readTreeString(); 
 				
 				//save trees for later commands
 				globaldata->gTree.push_back(T); 
@@ -158,12 +169,15 @@ void ReadNewickTree::read() {
 				numLeaves = T->getNumLeaves();
 				
 				//read tree info
-				readTreeString(); 
+				error = readTreeString(); 
 				 
 				//save trees for later commands
 				globaldata->gTree.push_back(T); 
 			}
 		}
+		
+		if (error != 0) { readOk = error; } 
+		return readOk;
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the ReadNewickTree class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -221,7 +235,7 @@ void ReadNewickTree::nexusTranslation() {
 }
 
 /**************************************************************************************************/
-void ReadNewickTree::readTreeString() {
+int ReadNewickTree::readTreeString() {
 	try {
 		
 		int n = 0;
@@ -235,6 +249,7 @@ void 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) { cout << "error with lc" << endl; return -1; } //reports an error in reading
 		
 			if(filehandle.peek()==','){							
 				readSpecialChar(filehandle,',',"comma");
@@ -245,6 +260,7 @@ void ReadNewickTree::readTreeString() {
 			}												
 			if(rooted != 1){								
 				rc = readNewickInt(filehandle, n, T);
+				if (rc == -1) { cout << "error with rc" << endl; return -1; } //reports an error in reading
 				if(filehandle.peek() == ')'){					
 					readSpecialChar(filehandle,')',"right parenthesis");
 				}											
@@ -261,7 +277,8 @@ void ReadNewickTree::readTreeString() {
 
 			if(n!=0){
 				cerr << "Internal error: The only taxon is not taxon 0.\n";
-				exit(1);
+				//exit(1);
+				readOk = -1; return -1;
 			}
 			lc = rc = -1;
 		} 
@@ -274,6 +291,7 @@ void ReadNewickTree::readTreeString() {
 			if(lc!=-1){		T->tree[lc].setParent(n);		}
 			if(rc!=-1){		T->tree[rc].setParent(n);		}
 		}
+		return 0;
 	
 	}
 	catch(exception& e) {
@@ -294,16 +312,20 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
     
 		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);		
+			int rc = readNewickInt(f, n, T);
+			if (rc == -1) { return -1; }  //reports an error in reading	
 			if(f.peek()==')'){	
-				readSpecialChar(f,')',"right parenthesis");					
+				readSpecialChar(f,')',"right parenthesis");	
 			}			
 		
 			if(f.peek() == ':'){									      
-				readSpecialChar(f,':',"colon");							
-				if(n >= numNodes){	cerr << "Error: Too many nodes in input tree\n";  exit(1); }
+				readSpecialChar(f,':',"colon");	
+										
+				if(n >= numNodes){	cerr << "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); }						
 		
@@ -322,7 +344,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 			}
 		
 			int blen = 0;
-			if(d == ':')	{		blen = 1;			}		
+			if(d == ':')	{		blen = 1;	}		
 		
 			f.putback(d);
 		
@@ -333,12 +355,11 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 			int n1 = T->getIndex(name);
 			
 			//adds sequence names that are not in group file to the "xxx" group
-			if(n1 == -1) {
-				cerr << "Name: " << name << " not found in your groupfile.. \n"; exit(1);
+			if(group == "not found") {
+				cout << "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";
-				globaldata->gTreemap->treemap[name].vectorIndex = (globaldata->gTreemap->namesOfSeqs.size() - 1);
 				
 				map<string, int>::iterator it;
 				it = globaldata->gTreemap->seqsPerGroup.find("xxx");
@@ -349,19 +370,14 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 					globaldata->gTreemap->seqsPerGroup["xxx"]++;
 				}
 				
-				//find index in tree of name
-				n1 = T->getIndex(name);
 				group = "xxx";
-				numLeaves++;
-				numNodes = 2*numLeaves - 1;
-				//T->resetTree();
 			}
 			
 			T->tree[n1].setGroup(group);
 			T->tree[n1].setChildren(-1,-1);
 		
 			if(blen == 1){	
-				f.get();		
+				f.get();
 				T->tree[n1].setBranchLength(readBranchLength(f));
 			}else{
 				T->tree[n1].setBranchLength(0.0);