fixed bug in read.tree

[mothur.git] / readtree.cpp

diff --git a/readtree.cpp b/readtree.cpp
index c33617fca57a483da46f179e384497661e205878..029164452c49d2247bd97262369a649cfbd3d190 100644 (file)
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -32,12 +32,12 @@ int ReadTree::readSpecialChar(istream& f, char c, string name) {
                char d = f.get();
        
                if(d == EOF){
-                       cerr << "Error: Input file ends prematurely, expecting a " << name << "\n";  return -1;
-                       //exit(1);
+                       cerr << "Error: Input file ends prematurely, expecting a " << name << "\n";
+                       exit(1);
                }
                if(d != c){
-                       cerr << "Error: Expected " << name << " in input file.  Found " << d << ".\n";  return -1;
-                       //exit(1);
+                       cerr << "Error: Expected " << name << " in input file.  Found " << d << ".\n";
+                       exit(1);
                }
                if(d == ')' && f.peek() == '\n'){
                        gobble(f);
@@ -62,8 +62,8 @@ int ReadTree::readNodeChar(istream& f) {
                char d = f.get();
 
                if(d == EOF){
-                       cerr << "Error: Input file ends prematurely, expecting a left parenthesis\n";  return -1;
-                       //exit(1);
+                       cerr << "Error: Input file ends prematurely, expecting a left parenthesis\n";
+                       exit(1);
                }
                return d;
        }
@@ -84,8 +84,8 @@ float ReadTree::readBranchLength(istream& f) {
                float b;
        
                if(!(f >> b)){
-                       cerr << "Error: Missing branch length in input tree.\n";  return -1;
-                       //exit(1);
+                       cerr << "Error: Missing branch length in input tree.\n";
+                       exit(1);
                }
                gobble(f);
                return b;
@@ -226,7 +226,7 @@ int ReadNewickTree::readTreeString() {
        try {
                
                int n = 0;
-               int lc, rc, error; 
+               int lc, rc; 
                
                int rooted = 0;
        
@@ -239,8 +239,7 @@ int ReadNewickTree::readTreeString() {
                        if (lc == -1) { return -1; } //reports an error in reading
                
                        if(filehandle.peek()==','){                                                     
-                               error = readSpecialChar(filehandle,',',"comma");
-                               if (error == -1) { readOk = -1; return -1; }
+                               readSpecialChar(filehandle,',',"comma");
                        }
                        // ';' means end of tree.                                                                                               
                        else if((ch=filehandle.peek())==';' || ch=='['){                
@@ -250,8 +249,7 @@ int ReadNewickTree::readTreeString() {
                                rc = readNewickInt(filehandle, n, T);
                                if (rc == -1) { return -1; } //reports an error in reading
                                if(filehandle.peek() == ')'){                                   
-                                       error = readSpecialChar(filehandle,')',"right parenthesis");
-                                       if (error == -1) { readOk = -1; return -1; }
+                                       readSpecialChar(filehandle,')',"right parenthesis");
                                }                                                                                       
                        }                                                                                               
                }
@@ -297,31 +295,25 @@ int ReadNewickTree::readTreeString() {
 
 int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
        try {
-               int error;
-               
                int c = readNodeChar(f);
-               if (c == -1) { readOk = -1; return -1; }
     
                if(c == '('){
                        int lc = readNewickInt(f, n, T);
                        if (lc == -1) { return -1; } //reports an error in reading
-                       error = readSpecialChar(f,',',"comma");
-                       if (error == -1) { readOk = -1; return -1; }
+                       readSpecialChar(f,',',"comma");
 
                        int rc = readNewickInt(f, n, T);
                        if (rc == -1) { return -1; }  //reports an error in reading     
                        if(f.peek()==')'){      
-                               error = readSpecialChar(f,')',"right parenthesis");     
-                               if (error == -1) { readOk = -1; return -1; }                            
+                               readSpecialChar(f,')',"right parenthesis");     
                        }                       
                
                        if(f.peek() == ':'){                                                                          
-                               error = readSpecialChar(f,':',"colon"); 
-                               if (error == -1) { readOk = -1; return -1; }                                            
+                               readSpecialChar(f,':',"colon"); 
+                                                                               
                                if(n >= numNodes){      cerr << "Error: Too many nodes in input tree\n";  readOk = -1; return -1; }
-                               error = readBranchLength(f);
-                               if (error == -1) { readOk = -1; return -1; }
-                               T->tree[n].setBranchLength(error);
+                               
+                               T->tree[n].setBranchLength(readBranchLength(f));
                        }else{T->tree[n].setBranchLength(0.0); }                                                
                
                        T->tree[n].setChildren(lc,rc);
@@ -378,9 +370,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                
                        if(blen == 1){  
                                f.get();
-                               error = readBranchLength(f);    
-                               if (error == -1) { readOk = -1; return -1; }    
-                               T->tree[n1].setBranchLength(error);
+                               T->tree[n1].setBranchLength(readBranchLength(f));
                        }else{
                                T->tree[n1].setBranchLength(0.0);
                        }