added sorted parameter to get.oturep, added error checking to chimera classes in...

[mothur.git] / bellerophon.cpp

diff --git a/bellerophon.cpp b/bellerophon.cpp
index 9aa4f7ac7aa566f39a9b68c7b9e0103f516e0ba4..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); }
@@ -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
@@ -220,6 +223,8 @@ void Bellerophon::getChimeras() {
                
                //sort Preferences highest to lowest
                sort(pref.begin(), pref.end(), comparePref);
+               
+               return 0;
 
        }
        catch(exception& e) {