X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=flowdata.cpp;h=1fe7d7faf1e31ee486890980c4731ddebfdca8fb;hb=f12174bc43f9e8ad536f2a37fb3a763b1ac90ba9;hp=39c1f8317a306c1a49488625725cbea7a4c6bd4e;hpb=902e0fcab76e75009ac43d3f4537e08182628d6f;p=mothur.git

diff --git a/flowdata.cpp b/flowdata.cpp
index 39c1f83..1fe7d7f 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 = "";
 	}
@@ -42,17 +42,16 @@ 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();
-		translateFlow();
-		
-		m->gobble(flowFile);
+		flowFile >> seqName >> endFlow;	
+        if (seqName.length() != 0) {
+            //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);
+		}else{ m->mothurOut("Error in reading your flowfile, at position " + toString(flowFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
+            
 		if(flowFile){	return 1;	}
 		else		{	return 0;	}
 	}
@@ -138,7 +137,8 @@ void FlowData::capFlows(int mF){
 	try{
 		
 		maxFlows = mF;
-		if(endFlow > maxFlows){	endFlow = maxFlows;	}		
+		if(endFlow > maxFlows){	endFlow = maxFlows;	}	
+        translateFlow();
 		
 	}
 	catch(exception& e) {
@@ -219,7 +219,7 @@ string FlowData::getName(){
 		return seqName;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "FlowData", "getSequence");
+		m->errorOut(e, "FlowData", "getName");
 		exit(1);
 	}
 }