addition of trim.flows

[mothur.git] / flowdata.h

diff --git a/flowdata.h b/flowdata.h
new file mode 100644 (file)
index 0000000..dafeab3
--- /dev/null
+++ b/flowdata.h
@@ -0,0 +1,42 @@
+#ifndef FLOWDATA_H
+#define FLOWDATA_H
+
+/*
+ *  flowdata.h
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 12/22/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "mothur.h"
+#include "mothurout.h"
+#include "sequence.hpp"
+
+class FlowData {
+
+public:
+       FlowData();
+       FlowData(ifstream&, float, float, int);
+       ~FlowData(){};
+       void capFlows(int);
+       bool hasMinFlows(int);
+       Sequence getSequence();
+       
+       int getSeqLength();
+       void printFlows(ofstream&);
+       void printFlows(ofstream&, string);
+       void printFASTA(ofstream&);
+private:
+       MothurOut* m;
+
+       void findDeadSpot(float, float, int);
+       void translateFlow();
+       
+       string seqName, locationString, sequence, baseFlow;
+       int numFlows, seqLength, deadSpot;
+       vector<float> flowData;
+};
+
+#endif