fixed bug in cluster.split with classify method

[mothur.git] / readtree.cpp

diff --git a/readtree.cpp b/readtree.cpp
index 1df49b5502f405bf29b31ee585fb5d6a264f9cda..c805edc9896bf15b4e7397305c13d8bfbce175d8 100644 (file)
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -287,15 +287,55 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                if (m->control_pressed) { return -1; } 
                
                int c = readNodeChar(f);
-    
+  string k;
+k = c;
+       cout << "at beginning = " << k <<endl;  
                if(c == '('){
-                       int lc = readNewickInt(f, n, T);
-                       if (lc == -1) { return -1; } //reports an error in reading
+               
+                       //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
+                               
+                               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 { string k;
+                       k = f.peek();
+       cout << "in here k = " << k << '\t' << f.tellg() <<endl;
+ }
+                       }
+       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; 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++;
+                       }
                        
-                       readSpecialChar(f,',',"comma");
+                       //to account for extra ++ in looping
+                       n--;
+                       //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     
+                       //int rc = readNewickInt(f, n, T);
+                       //if (rc == -1) { return -1; }  //reports an error in reading   
                        
                        if(f.peek()==')'){      
                                readSpecialChar(f,')',"right parenthesis");     
@@ -303,7 +343,6 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                                c=filehandle.get();
                                while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ c=filehandle.get(); }
                                filehandle.putback(c);
-
                        }                       
                
                        if(f.peek() == ':'){                                                                          
@@ -317,8 +356,10 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                        }                                               
                        
                        //to account for multifurcating trees generated by fasttree, we are forcing them to be bifurcating
-                       while(f.peek() == ','){
-                               
+                       /*while(f.peek() == ','){
+                       string k;
+                       k = f.peek();
+       cout << "in here k = " << k << '\t' << f.tellg() <<endl;
                                //force this node to be left child and read new rc
                                T->tree[n].setChildren(lc,rc);
                                T->tree[lc].setParent(n);
@@ -330,14 +371,11 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                                
                                readSpecialChar(f,',',"comma");
 
-                               int rc = readNewickInt(f, n, T);
-               cout << n << '\t' << lc << '\t' << rc << endl;
+                               rc = readNewickInt(f, n, T);
+               
                                if (rc == -1) { return -1; }  //reports an error in reading     
                                
                                if(f.peek()==')'){      
-                               string k;
-                               k = f.peek();
-               cout << "in here " << k << endl;
                                        readSpecialChar(f,')',"right parenthesis");     
                                        //to pass over labels in trees
                                        c=filehandle.get();
@@ -345,25 +383,26 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                                        filehandle.putback(c);
                                        
                                        if(f.peek() == ':'){                                                                          
-                                       readSpecialChar(f,':',"colon"); 
+                                               readSpecialChar(f,':',"colon"); 
                                        
-                                       if(n >= numNodes){      m->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));
+                                               T->tree[n].setBranchLength(readBranchLength(f));
                                        }else{
                                                T->tree[n].setBranchLength(0.0); 
                                        }                                               
 
                                        break;
                                }                       
-                       }
-       cout << n << '\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;
+                       }*/
+               
+                       //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 = "";