fixed bug with displaying info for collect.shared() and summary.shared().

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 139b74e762734957c95ccb659434e32068289162..c451ef7aeb6ead4065f55a18bea99cb1840b530f 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -8,7 +8,7 @@
  */
 
 #include "summarysharedcommand.h"
-#include "sharedsobs.h"
+#include "sharedsobscollectsummary.h"
 #include "sharedchao1.h"
 #include "sharedace.h"
 #include "sharedjabund.h"
@@ -29,7 +29,7 @@ SummarySharedCommand::SummarySharedCommand(){
                int i;
                for (i=0; i<globaldata->sharedSummaryEstimators.size(); i++) {
                        if (globaldata->sharedSummaryEstimators[i] == "sharedSobs") { 
-                               sumCalculators.push_back(new SharedSobs());
+                               sumCalculators.push_back(new SharedSobsCS());
                        }else if (globaldata->sharedSummaryEstimators[i] == "sharedChao") { 
                                sumCalculators.push_back(new SharedChao1());
                        }else if (globaldata->sharedSummaryEstimators[i] == "sharedAce") { 
@@ -88,7 +88,6 @@ int SummarySharedCommand::execute(){
                SharedList = globaldata->gSharedList;
                input = globaldata->ginput;
                order = SharedList->getSharedOrderVector();
-               getGroupComb();
                
                int count = 1;
                while(order != NULL){
@@ -104,7 +103,7 @@ int SummarySharedCommand::execute(){
                                int n = 1; 
                                for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
                                        for (int l = n; l < lookup.size(); l++) {
-                                               outputFileHandle << order->getLabel() << '\t' << groupComb[n-1] << '\t' << '\t'; //print out label and group
+                                               outputFileHandle << order->getLabel() << '\t' << (lookup[k]->getGroup() + lookup[l]->getGroup()) << '\t' << '\t'; //print out label and group
                                                for(int i=0;i<sumCalculators.size();i++){
                                                        sumCalculators[i]->getValues(lookup[k], lookup[l]); //saves the calculator outputs
                                                        outputFileHandle << '\t';
@@ -179,28 +178,4 @@ try {
 
 }
 
-/**************************************************************************************/
-void SummarySharedCommand::getGroupComb() {
-       try {
-               string group;
-               
-               int n = 1;
-               for (int i = 0; i < (globaldata->gGroupmap->getNumGroups() - 1); i++) {
-                       for (int l = n; l < globaldata->gGroupmap->getNumGroups(); l++) {
-                               group = globaldata->gGroupmap->namesOfGroups[i] + globaldata->gGroupmap->namesOfGroups[l];
-                               groupComb.push_back(group);     
-                       }
-                       n++;
-               }
-       }
-       catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function getGroupComb. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SummarySharedCommand class function getGroupComb. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-
-}
-
+//**********************************************************************************************************************