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[mothur.git] / flowdata.cpp

diff --git a/flowdata.cpp b/flowdata.cpp
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+/*
+ *  flowdata.cpp
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 12/22/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "flowdata.h"
+
+//**********************************************************************************************************************
+
+FlowData::FlowData(){}
+
+//**********************************************************************************************************************
+
+FlowData::~FlowData(){ /*      do nothing      */      }
+
+//**********************************************************************************************************************
+
+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";
+               seqName = "";
+               locationString = "";
+       }
+       catch(exception& e) {
+               m->errorOut(e, "FlowData", "FlowData");
+               exit(1);
+       }
+       
+}
+
+//**********************************************************************************************************************
+
+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);
+               if(flowFile){   return 1;       }
+               else            {       return 0;       }
+       }
+       catch(exception& e) {
+               m->errorOut(e, "FlowData", "getNext");
+               exit(1);
+       }
+       
+}
+
+//**********************************************************************************************************************
+
+void FlowData::updateEndFlow(){
+       try{
+               
+               //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++){
+                               float intensity = flowData[i + deadSpot];
+                               if(intensity > signalIntensity){
+                                       signal++;
+
+                                       if(intensity  < noiseIntensity || intensity > maxIntensity){
+                                               noise++;
+                                       }
+                               }
+                       }
+
+                       if(noise > 0 || signal == 0){
+                               break;
+                       }
+               
+                       deadSpot += 4;
+               }
+               endFlow = deadSpot;
+
+       }
+       catch(exception& e) {
+               m->errorOut(e, "FlowData", "findDeadSpot");
+               exit(1);
+       }
+}
+
+//**********************************************************************************************************************
+
+void FlowData::translateFlow(){
+       
+       try{
+               sequence = "";
+               for(int i=0;i<endFlow;i++){
+                       int intensity = (int)(flowData[i] + 0.5);
+                       char base = baseFlow[i % 4];
+                       
+                       for(int j=0;j<intensity;j++){
+                               sequence += base;
+                       }
+               }
+
+               if(sequence.size() > 4){
+                       sequence = sequence.substr(4);
+               }
+               else{
+                       sequence = "NNNN";
+               }
+       }
+       catch(exception& e) {
+               m->errorOut(e, "FlowData", "translateFlow");
+               exit(1);
+       }
+}
+
+//**********************************************************************************************************************
+
+void FlowData::capFlows(int mF){
+       
+       try{
+               
+               maxFlows = mF;
+               if(endFlow > maxFlows){ endFlow = maxFlows;     }       
+        translateFlow();
+               
+       }
+       catch(exception& e) {
+               m->errorOut(e, "FlowData", "capFlows");
+               exit(1);
+       }
+}
+
+//**********************************************************************************************************************
+
+bool FlowData::hasMinFlows(int minFlows){
+       
+       try{
+               bool pastMin = 0;
+               if(endFlow >= minFlows){        pastMin = 1;    }
+
+               return pastMin;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "FlowData", "hasMinFlows");
+               exit(1);
+       }
+}
+
+//**********************************************************************************************************************
+
+Sequence FlowData::getSequence(){
+       
+       try{
+               return Sequence(seqName, sequence);
+       }
+       catch(exception& e) {
+               m->errorOut(e, "FlowData", "getSequence");
+               exit(1);
+       }
+}
+
+//**********************************************************************************************************************
+
+void FlowData::printFlows(ofstream& outFlowFile){
+       try{
+//     outFlowFile << '>' << seqName << locationString << " length=" << seqLength << " numflows=" << maxFlows << endl;
+               outFlowFile << seqName << ' ' << endFlow << ' ' << setprecision(2);
+
+               for(int i=0;i<maxFlows;i++){
+                       outFlowFile << flowData[i] << ' ';
+               }
+               outFlowFile << endl;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "FlowData", "printFlows");
+               exit(1);
+       }
+}
+
+//**********************************************************************************************************************
+
+void FlowData::printFlows(ofstream& outFlowFile, string scrapCode){
+       try{
+               outFlowFile << seqName << '|' << scrapCode << ' ' << endFlow << ' ' << setprecision(2);
+               
+               for(int i=0;i<numFlows;i++){
+                       outFlowFile << flowData[i] << ' ';
+               }
+               outFlowFile << endl;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "FlowData", "printFlows");
+               exit(1);
+       }
+}
+
+//**********************************************************************************************************************
+
+string FlowData::getName(){
+       
+       try{
+               return seqName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "FlowData", "getName");
+               exit(1);
+       }
+}
+
+//**********************************************************************************************************************