X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=flowdata.cpp;h=5dc7dc3e6c780171f1ee5cacdb1d766864f18a18;hb=14cddf859d97118481161bf3e85a647976020758;hp=a172a03337303f287c64ed0f8e7352cdfde3db57;hpb=bf83aa09a52403a2faf1a1f82489d1e0c8c32283;p=mothur.git

diff --git a/flowdata.cpp b/flowdata.cpp
index a172a03..5dc7dc3 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 +42,15 @@ 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);
+        seqName = getSequenceName(flowFile);
+		flowFile >> endFlow;	
+        if (!m->control_pressed) {
+            for(int i=0;i<numFlows;i++)	{	flowFile >> flowData[i]; 	}
+            updateEndFlow(); 
+            translateFlow();
+            m->gobble(flowFile);
+		}
+            
 		if(flowFile){	return 1;	}
 		else		{	return 0;	}
 	}
@@ -62,13 +60,33 @@ bool FlowData::getNext(ifstream& flowFile){
 	}
 	
 }
+//********************************************************************************************************************
+string FlowData::getSequenceName(ifstream& flowFile) {
+	try {
+		string name = "";
+		
+        flowFile >> name;
+		
+		if (name.length() != 0) { 
+            for (int i = 0; i < name.length(); i++) {
+                if (name[i] == ':') { name[i] = '_'; m->changedSeqNames = true; }
+            }
+        }else{ m->mothurOut("Error in reading your flowfile, at position " + toString(flowFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); m->control_pressed = true;  }
+        
+		return name;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FlowData", "getSequenceName");
+		exit(1);
+	}
+}
 
 //**********************************************************************************************************************
 
 void FlowData::updateEndFlow(){
 	try{
 		
-		int currLength = 0;
+		//int currLength = 0;
 		float maxIntensity = (float) maxHomoP + 0.49;
 		
 		int deadSpot = 0;
@@ -138,7 +156,8 @@ void FlowData::capFlows(int mF){
 	try{
 		
 		maxFlows = mF;
-		if(endFlow > maxFlows){	endFlow = maxFlows;	}		
+		if(endFlow > maxFlows){	endFlow = maxFlows;	}	
+        translateFlow();
 		
 	}
 	catch(exception& e) {
@@ -212,3 +231,16 @@ void FlowData::printFlows(ofstream& outFlowFile, string scrapCode){
 }
 
 //**********************************************************************************************************************
+
+string FlowData::getName(){
+	
+	try{
+		return seqName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FlowData", "getName");
+		exit(1);
+	}
+}
+
+//**********************************************************************************************************************