X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=flowdata.cpp;h=1420f84b992a54ed6dfb6d3a28d8452a083691de;hb=791f42d21a85f794529fd4c912dcc27d873c25e8;hp=a172a03337303f287c64ed0f8e7352cdfde3db57;hpb=bf83aa09a52403a2faf1a1f82489d1e0c8c32283;p=mothur.git

diff --git a/flowdata.cpp b/flowdata.cpp
index a172a03..1420f84 100644
--- a/flowdata.cpp
+++ b/flowdata.cpp
@@ -19,14 +19,14 @@ FlowData::~FlowData(){	/*	do nothing	*/	}
 
 //**********************************************************************************************************************
 
-FlowData::FlowData(int numFlows, float signal, float noise, int maxHomoP) : 
-			numFlows(numFlows), signalIntensity(signal), noiseIntensity(noise), maxHomoP(maxHomoP){
+FlowData::FlowData(int numFlows, float signal, float noise, int maxHomoP, string baseFlow) : 
+			numFlows(numFlows), signalIntensity(signal), noiseIntensity(noise), maxHomoP(maxHomoP), baseFlow(baseFlow){
 
 	try {
 		m = MothurOut::getInstance();
 
 		flowData.assign(numFlows, 0);
-		baseFlow = "TACG";
+//		baseFlow = "TACG";
 		seqName = "";
 		locationString = "";
 	}
@@ -42,14 +42,11 @@ FlowData::FlowData(int numFlows, float signal, float noise, int maxHomoP) :
 bool FlowData::getNext(ifstream& flowFile){
 	
 	try {
-		
-		string lengthString;
-		string flowString;
-		
-		flowFile >> seqName >> endFlow;		
-		for(int i=0;i<numFlows;i++)	{	flowFile >> flowData[i];	}
-		
-		updateEndFlow();
+		flowFile >> seqName >> endFlow;	
+		//cout << "in Flowdata " + seqName << endl;
+		for(int i=0;i<numFlows;i++)	{	flowFile >> flowData[i]; 	}
+		//cout << "in Flowdata read " << seqName + " done" << endl;
+		updateEndFlow(); 
 		translateFlow();
 		
 		m->gobble(flowFile);
@@ -68,7 +65,7 @@ bool FlowData::getNext(ifstream& flowFile){
 void FlowData::updateEndFlow(){
 	try{
 		
-		int currLength = 0;
+		//int currLength = 0;
 		float maxIntensity = (float) maxHomoP + 0.49;
 		
 		int deadSpot = 0;
@@ -138,7 +135,8 @@ void FlowData::capFlows(int mF){
 	try{
 		
 		maxFlows = mF;
-		if(endFlow > maxFlows){	endFlow = maxFlows;	}		
+		if(endFlow > maxFlows){	endFlow = maxFlows;	}	
+        translateFlow();
 		
 	}
 	catch(exception& e) {
@@ -212,3 +210,16 @@ void FlowData::printFlows(ofstream& outFlowFile, string scrapCode){
 }
 
 //**********************************************************************************************************************
+
+string FlowData::getName(){
+	
+	try{
+		return seqName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FlowData", "getName");
+		exit(1);
+	}
+}
+
+//**********************************************************************************************************************