fixed read.tree so that it can read trees generated by fasttree

[mothur.git] / tree.cpp

diff --git a/tree.cpp b/tree.cpp
index 400a72ae388a88c5b94aa2b8a717471f600b33ed..8e459810589cbc23e9f443884406028382e4e212 100644 (file)
--- a/tree.cpp
+++ b/tree.cpp
@@ -736,20 +736,39 @@ int Tree::readTreeString(ifstream& filehandle)    {
 //cout << " at beginning of while " <<  k << endl;                     
                        if(c == ')')  {    
                                //to pass over labels in trees
-                               string label = readLabel(filehandle);
+                               c=filehandle.get();
+                               while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ c=filehandle.get(); }
+                               filehandle.putback(c);
                        }
-                       
                        if(c == ';') { return 0; }
                        if(c == -1) { return 0; }
-                       
                        //if you are a name
                        if((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space
-                               name = readName(filehandle);
+                               name = "";
+                               c = filehandle.get();
+                       //k = c;
+//cout << k << endl;
+                               while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {                       
+                                       name += c;
+                                       c = filehandle.get();
+                       //k = c;
+//cout << " in name while " << k << endl;
+                               }
+                               
+//cout << "name = " << name << endl;
                                globaldata->Treenames.push_back(name);
+                               filehandle.putback(c);
+//k = c;
+//cout << " after putback" <<  k << endl;
                        } 
                        
                        if(c  == ':') { //read until you reach the end of the branch length
-                               string bl = readBranchLength(filehandle);
+                               while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
+                                       c = filehandle.get();
+       //k = c;
+       //cout << " in branch while " << k << endl;
+                               }
+                               filehandle.putback(c);
                        }
                
                        c = filehandle.get();
@@ -770,68 +789,6 @@ int Tree::readTreeString(ifstream& filehandle)     {
 }      
 
 /*******************************************************/
-string Tree::readLabel(ifstream& filehandle)   {
-       try {
-               
-               string label = "";
-               
-               //to pass over labels in trees
-               int c=filehandle.get();
-               while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ label += c; c=filehandle.get(); }
-               filehandle.putback(c);
-               
-               return label;
-               
-       }
-       catch(exception& e) {
-               m->errorOut(e, "Tree", "readLabel");
-               exit(1);
-       }
-}      
-/*******************************************************/
-string Tree::readName(ifstream& filehandle)    {
-       try {
-               
-               string name = "";
-               int c = filehandle.get();
-               
-               while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {                       
-                       name += c;
-                       c = filehandle.get();
-               }
-                               
-//cout << "name = " << name << endl;
-               filehandle.putback(c);
-               
-               return name;
-               
-       }
-       catch(exception& e) {
-               m->errorOut(e, "Tree", "readName");
-               exit(1);
-       }
-}      
-/*******************************************************/
-string Tree::readBranchLength(ifstream& filehandle)    {
-       try {
-               
-               string br = "";
-               int c;
-               while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
-                       br += c;
-                       c = filehandle.get();
-               }
-               filehandle.putback(c);
-               
-               return br;
-               
-       }
-       catch(exception& e) {
-               m->errorOut(e, "Tree", "readBranchLength");
-               exit(1);
-       }
-}      
 
 /*******************************************************/
-/*******************************************************/