X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=flowdata.cpp;h=f4605b6dbe1613fdb3e1a6beb1929a3585ff5fe7;hb=e0c50fc42e953dbe258feb9bc1d1d7dc10fafff0;hp=1420f84b992a54ed6dfb6d3a28d8452a083691de;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;p=mothur.git

diff --git a/flowdata.cpp b/flowdata.cpp
index 1420f84..f4605b6 100644
--- a/flowdata.cpp
+++ b/flowdata.cpp
@@ -42,14 +42,15 @@ FlowData::FlowData(int numFlows, float signal, float noise, int maxHomoP, string
 bool FlowData::getNext(ifstream& flowFile){
 	
 	try {
-		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);
+        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;	}
 	}
@@ -59,22 +60,44 @@ 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{
 		
+        if (baseFlow.length() > 4) { return; }
+        
 		//int currLength = 0;
 		float maxIntensity = (float) maxHomoP + 0.49;
 		
 		int deadSpot = 0;
-				
+			
 		while(deadSpot < endFlow){
 			int signal = 0;
 			int noise = 0;
 			
-			for(int i=0;i<4;i++){
+			for(int i=0;i<baseFlow.length();i++){
 				float intensity = flowData[i + deadSpot];
 				if(intensity > signalIntensity){
 					signal++;
@@ -89,7 +112,7 @@ void FlowData::updateEndFlow(){
 				break;
 			}
 		
-			deadSpot += 4;
+			deadSpot += baseFlow.length();
 		}
 		endFlow = deadSpot;
 
@@ -108,13 +131,13 @@ void FlowData::translateFlow(){
 		sequence = "";
 		for(int i=0;i<endFlow;i++){
 			int intensity = (int)(flowData[i] + 0.5);
-			char base = baseFlow[i % 4];
+			char base = baseFlow[i % baseFlow.length()];
 			
 			for(int j=0;j<intensity;j++){
 				sequence += base;
 			}
 		}
-
+        
 		if(sequence.size() > 4){
 			sequence = sequence.substr(4);
 		}