fixed memory leak in rarefact

[mothur.git] / rarefactsharedcommand.cpp

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 9bd8805f4867a6e445b42324d8b13d406471eace..4a25cb3208f2695fc50308a8ff7df83deda163a8 100644 (file)
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -9,6 +9,7 @@
 
 #include "rarefactsharedcommand.h"
 #include "sharedsobs.h"
+#include "sharednseqs.h"
 
 //**********************************************************************************************************************
 
@@ -19,15 +20,17 @@ RareFactSharedCommand::RareFactSharedCommand(){
                fileNameRoot = getRootName(globaldata->inputFileName);
                format = globaldata->getFormat();
                validCalculator = new ValidCalculators();
-               
-               setGroups();
+               util = new SharedUtil();
                                
                int i;
                for (i=0; i<globaldata->Estimators.size(); i++) {
                        if (validCalculator->isValidCalculator("sharedrarefaction", globaldata->Estimators[i]) == true) { 
                                if (globaldata->Estimators[i] == "sharedobserved") { 
                                        rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
+                               }else if (globaldata->Estimators[i] == "sharednseqs") { 
+                                       rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", "")));
                                }
+
                        }
                }
                
@@ -53,6 +56,7 @@ RareFactSharedCommand::~RareFactSharedCommand(){
        delete input;
        delete rCurve;
        delete read;
+       delete util;
 }
 
 //**********************************************************************************************************************
@@ -64,21 +68,14 @@ int RareFactSharedCommand::execute(){
                //if the users entered no valid calculators don't execute command
                if (rDisplays.size() == 0) { return 0; }
 
-               if (format == "sharedfile") {
-                       read = new ReadPhilFile(globaldata->inputFileName);     
-                       read->read(&*globaldata); 
+               read = new ReadOTUFile(globaldata->inputFileName);      
+               read->read(&*globaldata); 
                        
-                       input = globaldata->ginput;
-                       order = input->getSharedOrderVector();
-               }else {
-                       //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();
-               }
+               input = globaldata->ginput;
+               order = input->getSharedOrderVector();
+                               
+               //set users groups
+               util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "rarefact");
                
                while(order != NULL){
                
@@ -95,18 +92,8 @@ int RareFactSharedCommand::execute(){
                        }
                        
                        //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;
-                               }
-                       }
-                       
+                       delete order;
+                       order = input->getSharedOrderVector();
                        count++;
                }
        
@@ -129,51 +116,3 @@ 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);
-       }               
-
-}
-/***********************************************************/
-