Working on seq.error changes

[mothur.git] / refchimeratest.h

diff --git a/refchimeratest.h b/refchimeratest.h
index d4983e05c07ca3b134811f5595290a472af477a4..41df4ebba55842eae2c36ff9f02af303d20b64c7 100644 (file)
--- 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;
 };