pat's changes to trim.seqs

[mothur.git] / qualityscores.h

diff --git a/qualityscores.h b/qualityscores.h
new file mode 100644 (file)
index 0000000..710200a
--- /dev/null
+++ b/qualityscores.h
@@ -0,0 +1,44 @@
+#ifndef QUALITYSCORES
+#define QUALITYSCORES
+
+/*
+ *  qualityscores.h
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 7/12/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "mothur.h"
+#include "mothurout.h"
+#include "sequence.hpp"
+
+/**************************************************************************************************/
+
+class QualityScores {
+public:
+       QualityScores();
+       QualityScores(ifstream&);
+       string getName();
+       void printQScores(ofstream&);
+       void trimQScores(int, int);
+       void flipQScores();
+       bool stripQualThreshold(Sequence&, double);
+       bool stripQualRollingAverage(Sequence&, double);
+       bool stripQualWindowAverage(Sequence&, int, int, double);
+       bool cullQualAverage(Sequence&, double);
+private:
+       
+       double calculateAverage();
+       MothurOut* m;
+       vector<int> qScores;
+       
+       string seqName;
+       int seqLength;
+};
+       
+/**************************************************************************************************/
+
+#endif