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

[mothur.git] / pintail.cpp

diff --git a/pintail.cpp b/pintail.cpp
index e92e19f519fb31ec9833736e1223f3f76c9281f3..2698fe48b278fff835ec9c1a5c40dfe8dc76a9f3 100644 (file)
--- a/pintail.cpp
+++ b/pintail.cpp
@@ -74,7 +74,7 @@ void Pintail::print(ostream& out) {
 }
 
 //***************************************************************************************************************
-void Pintail::getChimeras() {
+int Pintail::getChimeras() {
        try {
                
                //read in query sequences and subject sequences
@@ -85,6 +85,8 @@ void Pintail::getChimeras() {
                
                int numSeqs = querySeqs.size();
                
+               if (unaligned) { mothurOut("Your sequences need to be aligned when you use the pintail method."); mothurOutEndLine(); return 1;  }
+               
                obsDistance.resize(numSeqs);
                expectedDistance.resize(numSeqs);
                seqCoef.resize(numSeqs);
@@ -382,6 +384,8 @@ void Pintail::getChimeras() {
                        
                delete distcalculator;
                delete decalc;
+               
+               return 0;
        }
        catch(exception& e) {
                errorOut(e, "Pintail", "getChimeras");