Merge remote-tracking branch 'mothur/master'

[mothur.git] / refchimeratest.h

diff --git a/refchimeratest.h b/refchimeratest.h
index 6b648fb9703d255a690fec9924dd439efd28df17..41df4ebba55842eae2c36ff9f02af303d20b64c7 100644 (file)
--- a/refchimeratest.h
+++ b/refchimeratest.h
@@ -16,8 +16,9 @@
 class RefChimeraTest {
        
 public:
-       RefChimeraTest(vector<Sequence>&, string);
-       int analyzeQuery(string, string);
+       RefChimeraTest(vector<Sequence>&, bool);
+       int printHeader(ofstream&);
+       int analyzeQuery(string, string, ofstream&);
        int getClosestRefIndex();
 private:
        int getMismatches(string&, vector<vector<int> >&, vector<vector<int> >&, int&);
@@ -32,8 +33,9 @@ private:
        int numRefSeqs;
        int alignLength;
        int bestMatch;
-       ofstream chimeraReportFile;
-       
+       //ofstream chimeraReportFile;
+       bool aligned;
+    
        MothurOut* m;
 };