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;
-
+ RAbundVector* lastRAbund;
+ vector<SharedRAbundVector*> lastLookup;
+
if (format == "sharedfile") {
//you have groups
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 ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- input = globaldata->ginput;
- SharedList = globaldata->gSharedList;
- order = SharedList->getSharedOrderVector();
+ lookup = input->getSharedRAbundVectors();
+ lastLookup = lookup;
}else if (format == "list") {
//you are using just a list file and have only one group
read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
- ordersingle = globaldata->gorder;
- input = globaldata->ginput;
+ rabund = globaldata->rabund;
+ lastRAbund = globaldata->rabund;
+ input = globaldata->ginput;
}
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> processedLabels;
+ set<string> userLabels = globaldata->labels;
+ set<int> userLines = globaldata->lines;
+
if (format != "list") {
- util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "heat");
- globaldata->setGroups("");
-
-
- while(order != NULL){
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
- 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);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+ userLines.erase(count);
}
-
+
+ if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
+ cout << lastLookup[0]->getLabel() << '\t' << count << endl;
+ heatmap->getPic(lastLookup);
+
+ processedLabels.insert(lastLookup[0]->getLabel());
+ userLabels.erase(lastLookup[0]->getLabel());
+ }
+
+ //prevent memory leak
+ if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
+ lastLookup = lookup;
+
//get next line to process
- if (format == "sharedfile") {
- order = input->getSharedOrderVector();
+ lookup = input->getSharedRAbundVectors();
+ count++;
+ }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ cout << "Your file does not include the label "<< *it;
+ if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
+ cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+ needToRun = true;
}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;
- }
+ cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
}
- count++;
}
+
+ //run last line if you need to
+ if (needToRun == true) {
+ cout << lastLookup[0]->getLabel() << '\t' << count << endl;
+ heatmap->getPic(lastLookup);
+ }
+
+ for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; }
//reset groups parameter
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) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+
+ 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);
+ processedLabels.insert(rabund->getLabel());
+ userLabels.erase(rabund->getLabel());
+ userLines.erase(count);
}
- ordersingle = (input->getOrderVector());
+ if ((anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastRAbund->getLabel()) != 1)) {
+
+ cout << lastRAbund->getLabel() << '\t' << count << endl;
+ heatmap->getPic(lastRAbund);
+
+ processedLabels.insert(lastRAbund->getLabel());
+ userLabels.erase(lastRAbund->getLabel());
+ }
+
+ if (count != 1) { delete lastRAbund; }
+ lastRAbund = rabund;
+
+ rabund = input->getRAbundVector();
count++;
}
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ cout << "Your file does not include the label "<< *it;
+ if (processedLabels.count(lastRAbund->getLabel()) != 1) {
+ cout << ". I will use " << lastRAbund->getLabel() << "." << endl;
+ needToRun = true;
+ }else {
+ cout << ". Please refer to " << lastRAbund->getLabel() << "." << endl;
+ }
+ }
+
+ //run last line if you need to
+ if (needToRun == true) {
+ cout << lastRAbund->getLabel() << '\t' << count << endl;
+ heatmap->getPic(lastRAbund);
+ }
+
+ delete lastRAbund;
+
}
+ globaldata->setGroups("");
return 0;
}
catch(exception& e) {
projects / mothur.git / blobdiff