X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=flowdata.cpp;h=2891281c9de412a27b2d27229683c8d3bb7cf41b;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=d5adcf7163a14c27c4c783efd05359aa1494e1a7;hpb=08ab48641e3c75cc341971a374f771ad860f6f2b;p=mothur.git

diff --git a/flowdata.cpp b/flowdata.cpp
index d5adcf7..2891281 100644
--- a/flowdata.cpp
+++ b/flowdata.cpp
@@ -40,12 +40,19 @@ FlowData::FlowData(int numFlows, float signal, float noise, int maxHomoP, string
 //**********************************************************************************************************************
 
 bool FlowData::getNext(ifstream& flowFile){
-	
 	try {
+        
         seqName = getSequenceName(flowFile);
-		flowFile >> endFlow;	
+        if (m->debug) {  m->mothurOut("[DEBUG]: flow = " + seqName + " "); }
+		flowFile >> endFlow;
+        if (m->debug) {  m->mothurOut(toString(endFlow) + " "); }
         if (!m->control_pressed) {
-            for(int i=0;i<numFlows;i++)	{	flowFile >> flowData[i]; 	}
+            if (m->debug) {  m->mothurOut(" "); }
+            for(int i=0;i<numFlows;i++)	{
+                flowFile >> flowData[i];
+                if (m->debug) {  m->mothurOut(toString(flowData[i]) + " "); }
+            }
+            if (m->debug) {  m->mothurOut("\n"); }
             updateEndFlow(); 
             translateFlow();
             m->gobble(flowFile);
@@ -68,9 +75,7 @@ string FlowData::getSequenceName(ifstream& flowFile) {
         flowFile >> name;
 		
 		if (name.length() != 0) { 
-            for (int i = 0; i < name.length(); i++) {
-                if (name[i] == ':') { name[i] = '_'; m->changedSeqNames = true; }
-            }
+            m->checkName(name);
         }else{ m->mothurOut("Error in reading your flowfile, at position " + toString(flowFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); m->control_pressed = true;  }
         
 		return name;
@@ -86,7 +91,7 @@ string FlowData::getSequenceName(ifstream& flowFile) {
 void FlowData::updateEndFlow(){
 	try{
 		
-        //if (baseFlow.length() > 4) { return; }
+        if (baseFlow.length() > 4) { return; }
         
 		//int currLength = 0;
 		float maxIntensity = (float) maxHomoP + 0.49;
@@ -192,6 +197,27 @@ void FlowData::capFlows(int mF){
 
 //**********************************************************************************************************************
 
+bool FlowData::hasGoodHomoP(){
+	
+	try{
+        
+        float maxIntensity = (float) maxHomoP + 0.49;
+
+        for(int i=0;i<endFlow;i++){
+            if(flowData[i] > maxIntensity){
+                return 0;
+            }
+        }
+		return 1;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FlowData", "hasMinFlows");
+		exit(1);
+	}
+}
+
+//**********************************************************************************************************************
+
 bool FlowData::hasMinFlows(int minFlows){
 	
 	try{