flowdata.cpp

   1 /*
   2  *  flowdata.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 12/22/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "flowdata.h"
  11
  12 //**********************************************************************************************************************
  13
  14 FlowData::FlowData(){}
  15
  16 //**********************************************************************************************************************
  17
  18 FlowData::~FlowData(){  /*      do nothing      */      }
  19
  20 //**********************************************************************************************************************
  21
  22 FlowData::FlowData(int numFlows, float signal, float noise, int maxHomoP, string baseFlow) :
  23                         numFlows(numFlows), signalIntensity(signal), noiseIntensity(noise), maxHomoP(maxHomoP), baseFlow(baseFlow){
  24
  25         try {
  26                 m = MothurOut::getInstance();
  27
  28                 flowData.assign(numFlows, 0);
  29 //              baseFlow = "TACG";
  30                 seqName = "";
  31                 locationString = "";
  32         }
  33         catch(exception& e) {
  34                 m->errorOut(e, "FlowData", "FlowData");
  35                 exit(1);
  36         }
  37
  38 }
  39
  40 //**********************************************************************************************************************
  41
  42 bool FlowData::getNext(ifstream& flowFile){
  43
  44         try {
  45         seqName = getSequenceName(flowFile);
  46                 flowFile >> endFlow;
  47         if (!m->control_pressed) {
  48             for(int i=0;i<numFlows;i++) {       flowFile >> flowData[i];        }
  49             updateEndFlow();
  50             translateFlow();
  51             m->gobble(flowFile);
  52                 }
  53
  54                 if(flowFile){   return 1;       }
  55                 else            {       return 0;       }
  56         }
  57         catch(exception& e) {
  58                 m->errorOut(e, "FlowData", "getNext");
  59                 exit(1);
  60         }
  61
  62 }
  63 //********************************************************************************************************************
  64 string FlowData::getSequenceName(ifstream& flowFile) {
  65         try {
  66                 string name = "";
  67
  68         flowFile >> name;
  69
  70                 if (name.length() != 0) {
  71             for (int i = 0; i < name.length(); i++) {
  72                 if (name[i] == ':') { name[i] = '_'; m->changedSeqNames = true; }
  73             }
  74         }else{ m->mothurOut("Error in reading your flowfile, at position " + toString(flowFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); m->control_pressed = true;  }
  75
  76                 return name;
  77         }
  78         catch(exception& e) {
  79                 m->errorOut(e, "FlowData", "getSequenceName");
  80                 exit(1);
  81         }
  82 }
  83
  84 //**********************************************************************************************************************
  85
  86 void FlowData::updateEndFlow(){
  87         try{
  88
  89         if (baseFlow.length() > 4) { return; }
  90
  91                 //int currLength = 0;
  92                 float maxIntensity = (float) maxHomoP + 0.49;
  93
  94                 int deadSpot = 0;
  95
  96                 while(deadSpot < endFlow){
  97                         int signal = 0;
  98                         int noise = 0;
  99
 100                         for(int i=0;i<baseFlow.length();i++){
 101                                 float intensity = flowData[i + deadSpot];
 102                                 if(intensity > signalIntensity){
 103                                         signal++;
 104
 105                                         if(intensity  < noiseIntensity || intensity > maxIntensity){
 106                                                 noise++;
 107                                         }
 108                                 }
 109                         }
 110
 111                         if(noise > 0 || signal == 0){
 112                                 break;
 113                         }
 114
 115                         deadSpot += baseFlow.length();
 116                 }
 117                 endFlow = deadSpot;
 118
 119         }
 120         catch(exception& e) {
 121                 m->errorOut(e, "FlowData", "findDeadSpot");
 122                 exit(1);
 123         }
 124 }
 125
 126 //**********************************************************************************************************************
 127 //TATGCT
 128 //1 0 0 0 0 1
 129 //then the second positive flow is for a T, but you saw a T between the last and previous flow adn it wasn't positive, so something is missing
 130 //Becomes TNT
 131 void FlowData::translateFlow(){
 132         try{
 133         sequence = "";
 134         set<char> charInMiddle;
 135         int oldspot = -1;
 136         bool updateOld = false;
 137
 138         for(int i=0;i<endFlow;i++){
 139                         int intensity = (int)(flowData[i] + 0.5);
 140                         char base = baseFlow[i % baseFlow.length()];
 141
 142             if (intensity == 0) { //are we in the middle
 143                 if (oldspot != -1) { charInMiddle.insert(base); }
 144             }else if (intensity >= 1) {
 145                 if (oldspot == -1) { updateOld = true;  }
 146                 else {  //check for bases inbetween two 1's
 147                     if (charInMiddle.count(base) != 0) { //we want to covert to an N
 148                         sequence = sequence.substr(0, oldspot+1);
 149                         sequence += 'N';
 150                     }
 151                     updateOld = true;
 152                     charInMiddle.clear();
 153                 }
 154             }
 155
 156                         for(int j=0;j<intensity;j++){
 157                                 sequence += base;
 158                         }
 159
 160             if (updateOld) { oldspot = sequence.length()-1;  updateOld = false; }
 161                 }
 162
 163                 if(sequence.size() > 4){
 164                         sequence = sequence.substr(4);
 165                 }
 166                 else{
 167                         sequence = "NNNN";
 168                 }
 169     }
 170         catch(exception& e) {
 171                 m->errorOut(e, "FlowData", "translateFlow");
 172                 exit(1);
 173         }
 174 }
 175
 176 //**********************************************************************************************************************
 177
 178 void FlowData::capFlows(int mF){
 179
 180         try{
 181
 182                 maxFlows = mF;
 183                 if(endFlow > maxFlows){ endFlow = maxFlows;     }
 184         translateFlow();
 185
 186         }
 187         catch(exception& e) {
 188                 m->errorOut(e, "FlowData", "capFlows");
 189                 exit(1);
 190         }
 191 }
 192
 193 //**********************************************************************************************************************
 194
 195 bool FlowData::hasMinFlows(int minFlows){
 196
 197         try{
 198                 bool pastMin = 0;
 199                 if(endFlow >= minFlows){        pastMin = 1;    }
 200
 201                 return pastMin;
 202         }
 203         catch(exception& e) {
 204                 m->errorOut(e, "FlowData", "hasMinFlows");
 205                 exit(1);
 206         }
 207 }
 208
 209 //**********************************************************************************************************************
 210
 211 Sequence FlowData::getSequence(){
 212
 213         try{
 214                 return Sequence(seqName, sequence);
 215         }
 216         catch(exception& e) {
 217                 m->errorOut(e, "FlowData", "getSequence");
 218                 exit(1);
 219         }
 220 }
 221
 222 //**********************************************************************************************************************
 223
 224 void FlowData::printFlows(ofstream& outFlowFile){
 225         try{
 226 //      outFlowFile << '>' << seqName << locationString << " length=" << seqLength << " numflows=" << maxFlows << endl;
 227                 outFlowFile << seqName << ' ' << endFlow << ' ' << setprecision(2);
 228
 229                 for(int i=0;i<maxFlows;i++){
 230                         outFlowFile << flowData[i] << ' ';
 231                 }
 232                 outFlowFile << endl;
 233         }
 234         catch(exception& e) {
 235                 m->errorOut(e, "FlowData", "printFlows");
 236                 exit(1);
 237         }
 238 }
 239
 240 //**********************************************************************************************************************
 241
 242 void FlowData::printFlows(ofstream& outFlowFile, string scrapCode){
 243         try{
 244                 outFlowFile << seqName << '|' << scrapCode << ' ' << endFlow << ' ' << setprecision(2);
 245
 246                 for(int i=0;i<numFlows;i++){
 247                         outFlowFile << flowData[i] << ' ';
 248                 }
 249                 outFlowFile << endl;
 250         }
 251         catch(exception& e) {
 252                 m->errorOut(e, "FlowData", "printFlows");
 253                 exit(1);
 254         }
 255 }
 256
 257 //**********************************************************************************************************************
 258
 259 string FlowData::getName(){
 260
 261         try{
 262                 return seqName;
 263         }
 264         catch(exception& e) {
 265                 m->errorOut(e, "FlowData", "getName");
 266                 exit(1);
 267         }
 268 }
 269
 270 //**********************************************************************************************************************