X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=flowdata.cpp;h=5dc7dc3e6c780171f1ee5cacdb1d766864f18a18;hb=14cddf859d97118481161bf3e85a647976020758;hp=1420f84b992a54ed6dfb6d3a28d8452a083691de;hpb=09207a049d2ec77f56ac98960c6525be084fa090;p=mothur.git

diff --git a/flowdata.cpp b/flowdata.cpp
index 1420f84..5dc7dc3 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;	}
 	}
@@ -59,6 +60,26 @@ 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);
+	}
+}
 
 //**********************************************************************************************************************