changes to blastdb to make filenames given to blast unique, changes to split.abund...

[mothur.git] / tree.cpp

diff --git a/tree.cpp b/tree.cpp
index 8e459810589cbc23e9f443884406028382e4e212..400a72ae388a88c5b94aa2b8a717471f600b33ed 100644 (file)
--- a/tree.cpp
+++ b/tree.cpp
@@ -736,39 +736,20 @@ int Tree::readTreeString(ifstream& filehandle)    {
 //cout << " at beginning of while " <<  k << endl;                     
                        if(c == ')')  {    
                                //to pass over labels in trees
-                               c=filehandle.get();
-                               while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ c=filehandle.get(); }
-                               filehandle.putback(c);
+                               string label = readLabel(filehandle);
                        }
+                       
                        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 = "";
-                               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;
+                               name = readName(filehandle);
                                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
-                               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);
+                               string bl = readBranchLength(filehandle);
                        }
                
                        c = filehandle.get();
@@ -789,6 +770,68 @@ 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);
+       }
+}      
 
 /*******************************************************/
+/*******************************************************/