globaldata = GlobalData::getInstance();
heatmap = new HeatMap();
format = globaldata->getFormat();
+ util = new SharedUtil();
}
catch(exception& e) {
delete input;
delete read;
delete heatmap;
+ delete util;
}
//**********************************************************************************************************************
ordersingle = globaldata->gorder;
input = globaldata->ginput;
}
-
+
if (format != "list") {
-
- setGroups();
-
+
+ util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "heat");
+ globaldata->setGroups("");
+
+
while(order != NULL){
if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
}
//reset groups parameter
- globaldata->Groups.clear(); globaldata->setGroups("");
+ globaldata->Groups.clear();
}else{
while(ordersingle != NULL){
}
//**********************************************************************************************************************
-void HeatMapCommand::setGroups() {
- try {
- //if the user has not entered specific groups to analyze then do them all
- if (globaldata->Groups.size() != 0) {
- if (globaldata->Groups[0] != "all") {
- //check that groups are valid
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
- cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
- // erase the invalid group from globaldata->Groups
- globaldata->Groups.erase(globaldata->Groups.begin()+i);
- }
- }
-
- //if the user only entered invalid groups
- if (globaldata->Groups.size() == 0) {
- cout << "When using the groups parameter you must have at least 1 valid groups. I will run the command using all the groups in your groupfile." << endl;
- for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
- }
- }
- }else{//user has enter "all" and wants the default groups
- globaldata->Groups.clear();
- for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
- }
- globaldata->setGroups("");
- }
- }else {
- for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
- }
- }
-
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the HeatMapCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-/***********************************************************/