X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=refchimeratest.h;h=d4983e05c07ca3b134811f5595290a472af477a4;hb=f06fdb807822f8e06db003ed809c87250905cfc8;hp=6b648fb9703d255a690fec9924dd439efd28df17;hpb=ec1b5bc7460ac8ad40f54f0729900d9ed98e7292;p=mothur.git

diff --git a/refchimeratest.h b/refchimeratest.h
index 6b648fb..d4983e0 100644
--- a/refchimeratest.h
+++ b/refchimeratest.h
@@ -16,8 +16,9 @@
 class RefChimeraTest {
 	
 public:
-	RefChimeraTest(vector<Sequence>&, string);
-	int analyzeQuery(string, string);
+	RefChimeraTest(vector<Sequence>&);
+	int printHeader(ofstream&);
+	int analyzeQuery(string, string, ofstream&);
 	int getClosestRefIndex();
 private:
 	int getMismatches(string&, vector<vector<int> >&, vector<vector<int> >&, int&);
@@ -32,7 +33,7 @@ private:
 	int numRefSeqs;
 	int alignLength;
 	int bestMatch;
-	ofstream chimeraReportFile;
+	//ofstream chimeraReportFile;
 	
 	MothurOut* m;
 };