X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=ccode.cpp;h=a86e0fda553c664d8175c524ef1f272f9e7de547;hp=0a9214ef39e16b99b31694fb2bff53e9e25fdc80;hb=a5afca18544555fba2d9c3670ad1f8574916b0a0;hpb=4ba6188707e67c638ea5ee3c787d5d07ccd07e3e

diff --git a/ccode.cpp b/ccode.cpp
index 0a9214e..a86e0fd 100644
--- a/ccode.cpp
+++ b/ccode.cpp
@@ -128,7 +128,7 @@ void Ccode::print(ostream& out) {
 }
 
 //***************************************************************************************************************
-void Ccode::getChimeras() {
+int Ccode::getChimeras() {
 	try {
 		
 		//read in query sequences and subject sequences
@@ -139,6 +139,8 @@ void Ccode::getChimeras() {
 		
 		int numSeqs = querySeqs.size();
 		
+		if (unaligned) { mothurOut("Your sequences need to be aligned when you use the bellerophon ccode."); mothurOutEndLine(); return 1;  }
+		
 		closest.resize(numSeqs);
 		
 		refCombo.resize(numSeqs, 0);
@@ -297,7 +299,8 @@ void Ccode::getChimeras() {
 		for (int i = 0; i < lines.size(); i++)					{	delete lines[i];				}
 		delete distCalc;
 		delete decalc;
-			
+		
+		return 0;
 	}
 	catch(exception& e) {
 		errorOut(e, "Ccode", "getChimeras");