moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / flowdata.cpp

diff --git a/flowdata.cpp b/flowdata.cpp
deleted file mode 100644 (file)
index 1420f84..0000000
--- a/flowdata.cpp
+++ /dev/null
@@ -1,225 +0,0 @@
-/*
- *  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);
-       }
-}
-
-//**********************************************************************************************************************