started shared utilities, updates to venn and heatmap added tree.groups command

[mothur.git] / rarefactsharedcommand.cpp

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 6a4fe85b76b56dd5903b98155f0b01121f0f0002..dc71b22b3cab606d13f1e86a743aee1b5bf104a5 100644 (file)
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -20,6 +20,7 @@ RareFactSharedCommand::RareFactSharedCommand(){
                fileNameRoot = getRootName(globaldata->inputFileName);
                format = globaldata->getFormat();
                validCalculator = new ValidCalculators();
+               util = new SharedUtil();
                                
                int i;
                for (i=0; i<globaldata->Estimators.size(); i++) {
@@ -55,6 +56,7 @@ RareFactSharedCommand::~RareFactSharedCommand(){
        delete input;
        delete rCurve;
        delete read;
+       delete util;
 }
 
 //**********************************************************************************************************************
@@ -83,7 +85,7 @@ int RareFactSharedCommand::execute(){
                }
                
                //set users groups
-               setGroups();
+               util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "rarefact");
                
                while(order != NULL){
                
@@ -134,51 +136,3 @@ int RareFactSharedCommand::execute(){
 
 
 //**********************************************************************************************************************
-
-void RareFactSharedCommand::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 RareFactSharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the RareFactSharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
-
-}
-/***********************************************************/
-