X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=flowdata.h;h=cfe349c6e53a14180d521ae6401ed07381c0cd9f;hp=dafeab3e034b419ba7d4efcc998095cd984e014a;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=d635b39347cd81943ea50de7b813a0a5d743b0c0

diff --git a/flowdata.h b/flowdata.h
index dafeab3..cfe349c 100644
--- a/flowdata.h
+++ b/flowdata.h
@@ -18,25 +18,29 @@ class FlowData {
 
 public:
 	FlowData();
-	FlowData(ifstream&, float, float, int);
-	~FlowData(){};
+	FlowData(int, float, float, int, string);
+	~FlowData();
+	bool getNext(ifstream&);
+	string getName();
 	void capFlows(int);
 	bool hasMinFlows(int);
+    bool hasGoodHomoP();
+
 	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;
+    string getSequenceName(ifstream&);
 };
 
 #endif