added ability for user to select which groups to analyze with the collect.shared...

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 8c04545d61fc321382122526bc53e4c2892321eb..c473c2d77e819164d62799095ea6bf849d27c42a 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -31,6 +31,9 @@ CollectSharedCommand::CollectSharedCommand(){
                format = globaldata->getFormat();
                validCalculator = new ValidCalculators();
                
+               //set users groups
+               setGroups();
+               
                int i;
                for (i=0; i<globaldata->Estimators.size(); i++) {
                        if (validCalculator->isValidCalculator("shared", globaldata->Estimators[i]) == true) { 
@@ -143,6 +146,10 @@ int CollectSharedCommand::execute(){
                        if(orderList.count(*i) == 0)
                                cout << "'" << *i << "'" << " is not a valid label.\n";
                for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }       
+               
+               //reset groups parameter
+               globaldata->Groups.clear();  globaldata->setGroups("");
+               
                return 0;
        }
        catch(exception& e) {
@@ -157,3 +164,50 @@ int CollectSharedCommand::execute(){
 
 
 //**********************************************************************************************************************
+void CollectSharedCommand::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) || (globaldata->Groups.size() == 1)) { 
+                                       cout << "When using the groups parameter you must have at least 2 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 CollectSharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the CollectSharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }               
+
+}
+/***********************************************************/
+