added out.hierarchy command

[mothur.git] / bellerophon.cpp

diff --git a/bellerophon.cpp b/bellerophon.cpp
index dc021c064c27bf2550da911589cc51fd5f381458..a60a838f0139e741c92db8c1b5edafbdb158ca02 100644 (file)
--- a/bellerophon.cpp
+++ b/bellerophon.cpp
@@ -75,7 +75,7 @@ inline bool comparePref(Preference left, Preference right){
 }
 
 //***************************************************************************************************************
-void Bellerophon::getChimeras() {
+int Bellerophon::getChimeras() {
        try {
                
                //do soft filter
@@ -94,6 +94,8 @@ void Bellerophon::getChimeras() {
                //read in sequences
                seqs = readSeqs(fastafile);
                
+               if (unaligned) { mothurOut("Your sequences need to be aligned when you use the bellerophon method."); mothurOutEndLine(); return 1;  }
+               
                int numSeqs = seqs.size();
                
                if (numSeqs == 0) { mothurOut("Error in reading you sequences."); mothurOutEndLine(); exit(1); }
@@ -115,7 +117,7 @@ void Bellerophon::getChimeras() {
                                
                        }else{ increment = 0; }
                }
-cout << "increment = " << increment << endl;           
+               
                if (increment == 0) { iters = 1; }
                else { iters = ((seqs[0]->getAlignLength() - (2*window)) / increment); }
                
@@ -138,21 +140,22 @@ cout << "increment = " << increment << endl;
                                vector<Sequence> left;  vector<Sequence> right;
                                
                                for (int i = 0; i < seqs.size(); i++) {
-//cout << "whole = " << seqs[i].getAligned() << endl;
+//cout << "midpoint = " << midpoint << "\twindow = " << window << endl;
+//cout << "whole = " << seqs[i]->getAligned().length() << endl;
                                        //save left side
                                        string seqLeft = seqs[i]->getAligned().substr(midpoint-window, window);
                                        Sequence tempLeft;
                                        tempLeft.setName(seqs[i]->getName());
                                        tempLeft.setAligned(seqLeft);
                                        left.push_back(tempLeft);
-//cout << "left = " << tempLeft.getAligned() << endl;                  
+//cout << "left = " << tempLeft.getAligned().length() << endl;                 
                                        //save right side
                                        string seqRight = seqs[i]->getAligned().substr(midpoint, window);
                                        Sequence tempRight;
                                        tempRight.setName(seqs[i]->getName());
                                        tempRight.setAligned(seqRight);
                                        right.push_back(tempRight);
-//cout << "right = " << seqRight << endl;      
+//cout << "right = " << seqRight.length() << endl;     
                                }
                                
                                //adjust midpoint by increment
@@ -193,7 +196,6 @@ cout << "increment = " << increment << endl;
                                delete SparseLeft;
                                delete SparseRight;
                                
-                               
                                //fill preference structure
                                generatePreferences(distMapLeft, distMapRight, midpoint);
                                
@@ -216,13 +218,13 @@ cout << "increment = " << increment << endl;
                        
                        //how much higher or lower is this than expected
                        pref[i].score[0] = pref[i].score[0] / expectedPercent;
-                       
-                       
-                       
+               
                }
                
                //sort Preferences highest to lowest
                sort(pref.begin(), pref.end(), comparePref);
+               
+               return 0;
 
        }
        catch(exception& e) {
@@ -337,7 +339,6 @@ void Bellerophon::generatePreferences(vector<SeqMap> left, vector<SeqMap> right,
                
                  
                //calculate the dme
-               
                int count0 = 0;
                for (int i = 0; i < pref.size(); i++) {  dme += pref[i].score[1];  if (pref[i].score[1] == 0.0) { count0++; }  }