bool FlowData::getNext(ifstream& flowFile){
try {
-
- string lengthString;
- string flowString;
-
- flowFile >> seqName >> endFlow;
- for(int i=0;i<numFlows;i++) { flowFile >> flowData[i]; }
-
- updateEndFlow();
- translateFlow();
-
- m->gobble(flowFile);
+ seqName = getSequenceName(flowFile);
+ flowFile >> endFlow;
+ if (!m->control_pressed) {
+ for(int i=0;i<numFlows;i++) { flowFile >> flowData[i]; }
+ updateEndFlow();
+ translateFlow();
+ m->gobble(flowFile);
+ }
+
if(flowFile){ return 1; }
else { return 0; }
}
}
}
+//********************************************************************************************************************
+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<4;i++){
+ for(int i=0;i<baseFlow.length();i++){
float intensity = flowData[i + deadSpot];
if(intensity > signalIntensity){
signal++;
break;
}
- deadSpot += 4;
+ deadSpot += baseFlow.length();
}
endFlow = deadSpot;
}
//**********************************************************************************************************************
-
+//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 = "";
- for(int i=0;i<endFlow;i++){
+ 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 % 4];
+ 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);
try{
maxFlows = mF;
- if(endFlow > maxFlows){ endFlow = maxFlows; }
+ if(endFlow > maxFlows){ endFlow = maxFlows; }
+ translateFlow();
}
catch(exception& e) {