//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.
input = new InputData(philFile, globaldata->getFormat()); //format tells you whether philFile is list, rabund, sabund.
- inputSabund = new InputData(philFile, globaldata->getFormat()); //format tells you whether philFile is list, rabund, sabund.
+ inputSabund = new InputData(philFile, globaldata->getFormat()); //format tells you whether philFile is list, rabund, sabund or shared.
}else {//there is an orderfile
input = new InputData(philFile, globaldata->getOrderFile(), globaldata->getFormat());
}
globaldata->ginput = input; //saving to be used by collector and rarefact commands.
- if (globaldata->getGroupFile() == "") {//you are reading a list, rabund or sabund file for collect, rarefaction or summary.
+ 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();
globaldata->gorder = order; //saving to be used by collect and rarefact commands.
sabund = inputSabund->getSAbundVector();
globaldata->sabund = sabund; //saving to be used by summary command.
- }else {
- SharedList = input->getSharedListVector(); //you are reading for parselist command, or shared commands.
+ }else if (globaldata->getFormat() == "shared") {
+ SharedList = input->getSharedListVector(); //you are reading for collect.shared, rarefaction.shared, summary.shared, parselist command, or shared commands.
globaldata->gSharedList = SharedList;
}
}