ReadOTUFile::ReadOTUFile(string pf): philFile(pf){
- openInputFile(philFile, fileHandle);
+ //openInputFile(philFile, fileHandle);
}
/***********************************************************************/
//This function reads the list, rabund or sabund files to be used by collect and rarefact command.
void ReadOTUFile::read(GlobalData* globaldata){
try {
+
if (globaldata->getOrderFile() == "") {
//you have two inputs because in the next if statement if you only have one then it moves ahead in the same file.
//So when you run the collect or summary commands you miss a line.
}else {//there is an orderfile
input = new InputData(philFile, globaldata->getOrderFile(), globaldata->getFormat());
}
-
+//cout << "made it here" << endl;
//memory leak prevention
//if (globaldata->ginput != NULL) { delete globaldata->ginput; }
globaldata->ginput = input; //saving to be used by collector and rarefact commands.
-
+//cout << "after input" << endl;
if ((globaldata->getFormat() == "list") || (globaldata->getFormat() == "rabund") || (globaldata->getFormat() == "sabund")) {//you are reading a list, rabund or sabund file for collect, rarefaction or summary.
order = input->getOrderVector();
//memory leak prevention
//if (globaldata->gorder != NULL) { delete globaldata->gorder; }
globaldata->gorder = order; //saving to be used by collect and rarefact commands.
sabund = inputSabund->getSAbundVector();
+ //if (globaldata->sabund != NULL) { delete globaldata->sabund; }
globaldata->sabund = sabund; //saving to be used by summary command.
rabund = inputRabund->getRAbundVector();
+ //if (globaldata->rabund != NULL) { delete globaldata->rabund; }
globaldata->rabund = rabund; //saving to be used by heatmap.bin command.
list = inputList->getListVector();
+ //if (globaldata->gListVector != NULL) { delete globaldata->gListVector; }
globaldata->gListVector = list;
+
}else if (globaldata->getFormat() == "shared") {
SharedList = input->getSharedListVector(); //you are reading for collect.shared, rarefaction.shared, summary.shared, parselist command, or shared commands.
//memory leak prevention