added code to check path for uchime and catchall executables

[mothur.git] / flowdata.cpp

diff --git a/flowdata.cpp b/flowdata.cpp
index a172a03337303f287c64ed0f8e7352cdfde3db57..1420f84b992a54ed6dfb6d3a28d8452a083691de 100644 (file)
--- a/flowdata.cpp
+++ b/flowdata.cpp
@@ -19,14 +19,14 @@ FlowData::~FlowData(){      /*      do nothing      */      }
 
 //**********************************************************************************************************************
 
-FlowData::FlowData(int numFlows, float signal, float noise, int maxHomoP) : 
-                       numFlows(numFlows), signalIntensity(signal), noiseIntensity(noise), maxHomoP(maxHomoP){
+FlowData::FlowData(int numFlows, float signal, float noise, int maxHomoP, string baseFlow) : 
+                       numFlows(numFlows), signalIntensity(signal), noiseIntensity(noise), maxHomoP(maxHomoP), baseFlow(baseFlow){
 
        try {
                m = MothurOut::getInstance();
 
                flowData.assign(numFlows, 0);
-               baseFlow = "TACG";
+//             baseFlow = "TACG";
                seqName = "";
                locationString = "";
        }
@@ -42,14 +42,11 @@ FlowData::FlowData(int numFlows, float signal, float noise, int maxHomoP) :
 bool FlowData::getNext(ifstream& flowFile){
        
        try {
-               
-               string lengthString;
-               string flowString;
-               
-               flowFile >> seqName >> endFlow;         
-               for(int i=0;i<numFlows;i++)     {       flowFile >> flowData[i];        }
-               
-               updateEndFlow();
+               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);
@@ -68,7 +65,7 @@ bool FlowData::getNext(ifstream& flowFile){
 void FlowData::updateEndFlow(){
        try{
                
-               int currLength = 0;
+               //int currLength = 0;
                float maxIntensity = (float) maxHomoP + 0.49;
                
                int deadSpot = 0;
@@ -138,7 +135,8 @@ void FlowData::capFlows(int mF){
        try{
                
                maxFlows = mF;
-               if(endFlow > maxFlows){ endFlow = maxFlows;     }               
+               if(endFlow > maxFlows){ endFlow = maxFlows;     }       
+        translateFlow();
                
        }
        catch(exception& e) {
@@ -212,3 +210,16 @@ void FlowData::printFlows(ofstream& outFlowFile, string scrapCode){
 }
 
 //**********************************************************************************************************************
+
+string FlowData::getName(){
+       
+       try{
+               return seqName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "FlowData", "getName");
+               exit(1);
+       }
+}
+
+//**********************************************************************************************************************