added order=A or order=B to trim.flows and shhh.flows commands. added load balancing...

[mothur.git] / flowdata.cpp

diff --git a/flowdata.cpp b/flowdata.cpp
index 5dc7dc3e6c780171f1ee5cacdb1d766864f18a18..f4605b6dbe1613fdb3e1a6beb1929a3585ff5fe7 100644 (file)
--- a/flowdata.cpp
+++ b/flowdata.cpp
@@ -50,7 +50,7 @@ bool FlowData::getNext(ifstream& flowFile){
             translateFlow();
             m->gobble(flowFile);
                }
-            
+           
                if(flowFile){   return 1;       }
                else            {       return 0;       }
        }
@@ -86,16 +86,18 @@ string FlowData::getSequenceName(ifstream& flowFile) {
 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++;
@@ -110,7 +112,7 @@ void FlowData::updateEndFlow(){
                                break;
                        }
                
-                       deadSpot += 4;
+                       deadSpot += baseFlow.length();
                }
                endFlow = deadSpot;
 
@@ -129,13 +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);
                }