changed added group output to indicator command. a few changes to work with the guy

[mothur.git] / flowdata.cpp

diff --git a/flowdata.cpp b/flowdata.cpp
index d1769bbed46e34c12a1a8ad4a1f69bebaeca071d..1fe7d7faf1e31ee486890980c4731ddebfdca8fb 100644 (file)
--- a/flowdata.cpp
+++ b/flowdata.cpp
@@ -42,17 +42,16 @@ FlowData::FlowData(int numFlows, float signal, float noise, int maxHomoP, string
 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) {