X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=refchimeratest.h;h=41df4ebba55842eae2c36ff9f02af303d20b64c7;hb=4458418562cc9dfc9a29ed4f8f6cfc7bfb927d40;hp=d4983e05c07ca3b134811f5595290a472af477a4;hpb=f06fdb807822f8e06db003ed809c87250905cfc8;p=mothur.git

diff --git a/refchimeratest.h b/refchimeratest.h
index d4983e0..41df4eb 100644
--- a/refchimeratest.h
+++ b/refchimeratest.h
@@ -16,7 +16,7 @@
 class RefChimeraTest {
 	
 public:
-	RefChimeraTest(vector<Sequence>&);
+	RefChimeraTest(vector<Sequence>&, bool);
 	int printHeader(ofstream&);
 	int analyzeQuery(string, string, ofstream&);
 	int getClosestRefIndex();
@@ -34,7 +34,8 @@ private:
 	int alignLength;
 	int bestMatch;
 	//ofstream chimeraReportFile;
-	
+	bool aligned;
+    
 	MothurOut* m;
 };