added shhh.seqs command

[mothur.git] / flowdata.h

diff --git a/flowdata.h b/flowdata.h
index dafeab3e034b419ba7d4efcc998095cd984e014a..09426f957f9a4ddee425fedd117d03786c9869ad 100644 (file)
--- a/flowdata.h
+++ b/flowdata.h
@@ -18,24 +18,25 @@ class FlowData {
 
 public:
        FlowData();
-       FlowData(ifstream&, float, float, int);
-       ~FlowData(){};
+       FlowData(int, float, float, int);
+       ~FlowData();
+       bool getNext(ifstream&);
+
        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();
        
+       void updateEndFlow();
+       void translateFlow();
+       float signalIntensity, noiseIntensity;
+       int maxHomoP;
        string seqName, locationString, sequence, baseFlow;
-       int numFlows, seqLength, deadSpot;
+       int numFlows, maxFlows, endFlow;
        vector<float> flowData;
 };