globaldata = GlobalData::getInstance();
heatmap = new HeatMap();
format = globaldata->getFormat();
- util = new SharedUtil();
-
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function HeatMapCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
delete input;
delete read;
delete heatmap;
- delete util;
}
//**********************************************************************************************************************
int HeatMapCommand::execute(){
try {
int count = 1;
-
+
if (format == "sharedfile") {
//you have groups
- read = new ReadPhilFile(globaldata->inputFileName);
+ read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
input = globaldata->ginput;
- order = input->getSharedOrderVector();
- }else if (format == "shared") {
- //you are using a list and a groupfile
- read = new ReadPhilFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- input = globaldata->ginput;
- SharedList = globaldata->gSharedList;
- order = SharedList->getSharedOrderVector();
+ lookup = input->getSharedRAbundVectors();
}else if (format == "list") {
//you are using just a list file and have only one group
- read = new ReadPhilFile(globaldata->inputFileName);
+ read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
-
- ordersingle = globaldata->gorder;
- input = globaldata->ginput;
+
+ rabund = globaldata->rabund;
+ input = globaldata->ginput;
}
-
if (format != "list") {
- util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "heat");
- globaldata->setGroups("");
-
-
- while(order != NULL){
+ while(lookup[0] != NULL){
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
+ if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
- cout << order->getLabel() << '\t' << count << endl;
- heatmap->getPic(order);
-
+ cout << lookup[0]->getLabel() << '\t' << count << endl;
+ heatmap->getPic(lookup);
}
//get next line to process
- if (format == "sharedfile") {
- order = input->getSharedOrderVector();
- }else {
- //you are using a list and a groupfile
- SharedList = input->getSharedListVector(); //get new list vector to process
- if (SharedList != NULL) {
- order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
- }else {
- break;
- }
- }
+ lookup = input->getSharedRAbundVectors();
count++;
}
globaldata->Groups.clear();
}else{
- while(ordersingle != NULL){
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(ordersingle->getLabel()) == 1){
+ while(rabund != NULL){
+
+ if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(rabund->getLabel()) == 1){
- cout << ordersingle->getLabel() << '\t' << count << endl;
- heatmap->getPic(ordersingle);
-
+ cout << rabund->getLabel() << '\t' << count << endl;
+ heatmap->getPic(rabund);
}
- ordersingle = (input->getOrderVector());
+ rabund = input->getRAbundVector();
count++;
}
}
+ globaldata->setGroups("");
return 0;
}
catch(exception& e) {