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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 {
seqName = getSequenceName(flowFile);
if (m->debug) { m->mothurOut("[DEBUG]: flow = " + seqName + " "); }
flowFile >> endFlow;
if (m->debug) { m->mothurOut(toString(endFlow) + " "); }
if (!m->control_pressed) {
if (m->debug) { m->mothurOut(" "); }
for(int i=0;i<numFlows;i++) {
flowFile >> flowData[i];
if (m->debug) { m->mothurOut(toString(flowData[i]) + " "); }
}
if (m->debug) { m->mothurOut("\n"); }
updateEndFlow();
translateFlow();
m->gobble(flowFile);
}
if(flowFile){ return 1; }
else { return 0; }
}
catch(exception& e) {
m->errorOut(e, "FlowData", "getNext");
exit(1);
}
}
//********************************************************************************************************************
string FlowData::getSequenceName(ifstream& flowFile) {
try {
string name = "";
flowFile >> name;
if (name.length() != 0) {
m->checkName(name);
}else{ m->mothurOut("Error in reading your flowfile, at position " + toString(flowFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); m->control_pressed = true; }
return name;
}
catch(exception& e) {
m->errorOut(e, "FlowData", "getSequenceName");
exit(1);
}
}
//**********************************************************************************************************************
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<baseFlow.length();i++){
float intensity = flowData[i + deadSpot];
if(intensity > signalIntensity){
signal++;
if(intensity < noiseIntensity || intensity > maxIntensity){
noise++;
}
}
}
if(noise > 0 || signal == 0){
break;
}
deadSpot += baseFlow.length();
}
endFlow = deadSpot;
}
catch(exception& e) {
m->errorOut(e, "FlowData", "findDeadSpot");
exit(1);
}
}
//**********************************************************************************************************************
//TATGCT
//1 0 0 0 0 1
//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
//Becomes TNT
void FlowData::translateFlow(){
try{
sequence = "";
set<char> charInMiddle;
int oldspot = -1;
bool updateOld = false;
for(int i=0;i<endFlow;i++){
int intensity = (int)(flowData[i] + 0.5);
char base = baseFlow[i % baseFlow.length()];
if (intensity == 0) { //are we in the middle
if (oldspot != -1) { charInMiddle.insert(base); }
}else if (intensity >= 1) {
if (oldspot == -1) { updateOld = true; }
else { //check for bases inbetween two 1's
if (charInMiddle.count(base) != 0) { //we want to covert to an N
sequence = sequence.substr(0, oldspot+1);
sequence += 'N';
}
updateOld = true;
charInMiddle.clear();
}
}
for(int j=0;j<intensity;j++){
sequence += base;
}
if (updateOld) { oldspot = sequence.length()-1; updateOld = false; }
}
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::hasGoodHomoP(){
try{
float maxIntensity = (float) maxHomoP + 0.49;
for(int i=0;i<endFlow;i++){
if(flowData[i] > maxIntensity){
return 0;
}
}
return 1;
}
catch(exception& e) {
m->errorOut(e, "FlowData", "hasMinFlows");
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);
}
}
//**********************************************************************************************************************
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