added nseqs and sharednseqs calculators, removed excess tabs in output files.

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 18470d0df300f3b37249b9e4fc7fb05a8211518f..9e2c6681afbad503c02f7116bf797ccd99d5e488 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -11,6 +11,7 @@
 #include "sharedsobscollectsummary.h"
 #include "sharedchao1.h"
 #include "sharedace.h"
+#include "sharednseqs.h"
 #include "sharedjabund.h"
 #include "sharedsorabund.h"
 #include "sharedjclass.h"
@@ -56,6 +57,8 @@ SummarySharedCommand::SummarySharedCommand(){
                                        sumCalculators.push_back(new SharedThetaYC());
                                }else if (globaldata->Estimators[i] == "sharedthetan") { 
                                        sumCalculators.push_back(new SharedThetaN());
+                               }else if (globaldata->Estimators[i] == "sharednseqs") { 
+                                       sumCalculators.push_back(new SharedNSeqs());
                                }
                        }
                }
@@ -128,7 +131,15 @@ 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' << (lookup[k]->getGroup() + lookup[l]->getGroup()) << '\t' << '\t'; //print out label and group
+                                               outputFileHandle << order->getLabel() << '\t';
+                                               
+                                               //sort groups to be alphanumeric
+                                               if (lookup[k]->getGroup() > lookup[l]->getGroup()) {
+                                                       outputFileHandle << (lookup[l]->getGroup() +'\t' + lookup[k]->getGroup()) << '\t'; //print out groups
+                                               }else{
+                                                       outputFileHandle << (lookup[k]->getGroup() +'\t' + lookup[l]->getGroup()) << '\t'; //print out groups
+                                               }
+                                               
                                                for(int i=0;i<sumCalculators.size();i++){
                                                        sumCalculators[i]->getValues(lookup[k], lookup[l]); //saves the calculator outputs
                                                        outputFileHandle << '\t';