fixed bug in read.tree updates help and validparameters strings, added ability for...

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 18470d0df300f3b37249b9e4fc7fb05a8211518f..526cd8292e2082eccf96c2c25f82c8a4709267e5 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"
@@ -19,6 +20,15 @@
 #include "sharedsorest.h"
 #include "sharedthetayc.h"
 #include "sharedthetan.h"
+#include "sharedkstest.h"
+#include "sharedbdiversity.h"
+#include "sharedochiai.h"
+#include "sharedanderbergs.h"
+#include "sharedkulczynski.h"
+#include "sharedkulczynskicody.h"
+#include "sharedlennon.h"
+#include "sharedmorisitahorn.h"
+#include "sharedbraycurtis.h"
 
 
 //**********************************************************************************************************************
@@ -56,10 +66,31 @@ SummarySharedCommand::SummarySharedCommand(){
                                        sumCalculators.push_back(new SharedThetaYC());
                                }else if (globaldata->Estimators[i] == "sharedthetan") { 
                                        sumCalculators.push_back(new SharedThetaN());
+                               }else if (globaldata->Estimators[i] == "sharedkstest") { 
+                                       sumCalculators.push_back(new SharedKSTest());
+                               }else if (globaldata->Estimators[i] == "sharednseqs") { 
+                                       sumCalculators.push_back(new SharedNSeqs());
+                               }else if (globaldata->Estimators[i] == "sharedochiai") { 
+                                       sumCalculators.push_back(new SharedOchiai());
+                               }else if (globaldata->Estimators[i] == "sharedanderberg") { 
+                                       sumCalculators.push_back(new SharedAnderberg());
+                               }else if (globaldata->Estimators[i] == "sharedkulczynski") { 
+                                       sumCalculators.push_back(new SharedKulczynski());
+                               }else if (globaldata->Estimators[i] == "sharedkulczynskicody") { 
+                                       sumCalculators.push_back(new SharedKulczynskiCody());
+                               }else if (globaldata->Estimators[i] == "sharedlennon") { 
+                                       sumCalculators.push_back(new SharedLennon());
+                               }else if (globaldata->Estimators[i] == "sharedmorisitahorn") { 
+                                       sumCalculators.push_back(new SharedMorHorn());
+                               }else if (globaldata->Estimators[i] == "sharedbraycurtis") { 
+                                       sumCalculators.push_back(new SharedBrayCurtis());
                                }
+                               else if (globaldata->Estimators[i] == "sharedbdiversity") { 
+                                       sumCalculators.push_back(new SharedBDiversity());
+                               }
+                               
                        }
                }
-               
                //reset calc for next command
                globaldata->setCalc("");
 
@@ -129,6 +160,15 @@ int SummarySharedCommand::execute(){
                                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';