added out.hierarchy command

[mothur.git] / bellerophon.cpp

diff --git a/bellerophon.cpp b/bellerophon.cpp
index 2ce395189520a83837805a8322f2619a5f227508..a60a838f0139e741c92db8c1b5edafbdb158ca02 100644 (file)
--- a/bellerophon.cpp
+++ b/bellerophon.cpp
@@ -35,7 +35,7 @@ void Bellerophon::print(ostream& out) {
                        out << pref[i].name << '\t' << setprecision(3) << pref[i].score[0] << '\t' << pref[i].leftParent[0] << '\t' << pref[i].rightParent[0] << endl;
                        
                        //calc # of seqs with preference above 1.0
-                       if (pref[i].score[0] > 1.1) { 
+                       if (pref[i].score[0] > 1.0) { 
                                above1++; 
                                mothurOut(pref[i].name + " is a suspected chimera at breakpoint " + toString(pref[i].midpoint)); mothurOutEndLine();
                                mothurOut("It's score is " + toString(pref[i].score[0]) + " with suspected left parent " + pref[i].leftParent[0] + " and right parent " + pref[i].rightParent[0]); mothurOutEndLine();
@@ -44,7 +44,7 @@ void Bellerophon::print(ostream& out) {
                
                //output results to screen
                mothurOutEndLine();
-               mothurOut("Sequence with preference score above 1.1: " + toString(above1)); mothurOutEndLine();
+               mothurOut("Sequence with preference score above 1.0: " + toString(above1)); mothurOutEndLine();
                int spot;
                spot = pref.size()-1;
                mothurOut("Minimum:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
@@ -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); }
@@ -138,21 +140,22 @@ void Bellerophon::getChimeras() {
                                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
@@ -203,7 +206,7 @@ void Bellerophon::getChimeras() {
                delete distCalculator;
                
                //rank preference score to eachother
-               /*float dme = 0.0;
+               float dme = 0.0;
                float expectedPercent = 1 / (float) (pref.size());
                
                for (int i = 0; i < pref.size(); i++) {  dme += pref[i].score[0];  }
@@ -216,10 +219,12 @@ void Bellerophon::getChimeras() {
                        //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) {
@@ -335,24 +340,21 @@ 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++; }  }
+               for (int i = 0; i < pref.size(); i++) {  dme += pref[i].score[1];  if (pref[i].score[1] == 0.0) { count0++; }  }
                
-               //float expectedPercent = 1 / (float) (pref.size() - count0);
+               float expectedPercent = 1 / (float) (pref.size() - count0);
 //cout << endl << "dme = " << dme << endl;
                //recalculate prefernences based on dme
                for (int i = 0; i < pref.size(); i++) {
-//cout << "unadjusted col[i] " << i << " = " << pref[i].score[1] << endl;      
-//cout << i << '\t' <<  (dme / (dme - 2 * pref[i].score[1])) << endl;
-                       
+//cout << "unadjusted pref " << i << " = " << pref[i].score[1] << endl;        
                        // gives the actual percentage of the dme this seq adds
-                       //pref[i].score[1] = pref[i].score[1] / dme;
+                       pref[i].score[1] = pref[i].score[1] / dme;
                        
                        //how much higher or lower is this than expected
-                       //pref[i].score[1] = pref[i].score[1] / expectedPercent;
+                       pref[i].score[1] = pref[i].score[1] / expectedPercent;
+                       
+                       //pref[i].score[1] = dme / (dme - 2 * pref[i].score[1]);
                        
-                       //not 2 * pref[i].score[1] because i only calulate the pref scores once.
-                       pref[i].score[1] = dme / (dme - pref[i].score[1]);
-//cout << i << '\t' << pref[i].score[1] << endl;
                        //so a non chimeric sequence would be around 1, and a chimeric would be signifigantly higher.
 //cout << "adjusted pref " << i << " = " << pref[i].score[1] << endl;                                  
                }