X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarysharedcommand.cpp;h=526cd8292e2082eccf96c2c25f82c8a4709267e5;hb=2e5ec5cbbd23637ed20da9bdd544d178a3b5d949;hp=040de2067faf9d0dd9d1de74b2b4f6fe2f6a0086;hpb=39ef0543b73cb12dfc64529522b66ad3df7527d0;p=mothur.git

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 040de20..526cd82 100644
--- 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("");
 
@@ -105,6 +136,9 @@ int SummarySharedCommand::execute(){
 			order = SharedList->getSharedOrderVector();
 		}
 		
+		//set users groups
+		setGroups();
+		
 		//output estimator names as column headers
 		outputFileHandle << "label" <<'\t' << "comparison" << '\t'; 
 		for(int i=0;i<sumCalculators.size();i++){
@@ -112,9 +146,6 @@ int SummarySharedCommand::execute(){
 		}
 		outputFileHandle << endl;
 		
-		//set users groups
-		setGroups();
-
 		while(order != NULL){
 		
 			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){			
@@ -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';
@@ -176,10 +216,10 @@ void SummarySharedCommand::getSharedVectors(){
 try {
 		lookup.clear();
 		//create and initialize vector of sharedvectors, one for each group
-		for (int i = 0; i < globaldata->gGroupmap->getNumGroups(); i++) { 
+		for (int i = 0; i < globaldata->Groups.size(); i++) { 
 			SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
 			temp->setLabel(order->getLabel());
-			temp->setGroup(globaldata->gGroupmap->namesOfGroups[i]);
+			temp->setGroup(globaldata->Groups[i]);
 			lookup.push_back(temp);
 		}
 		
@@ -199,14 +239,6 @@ try {
 				}
 			}
 		}
-		
-		//get rid of vectors from groups you don't want to analyze
-		for (int r = 0; r < lookup.size(); r++) { 
-			if (inUsersGroups(lookup[r]->getGroup(), globaldata->Groups) != true) {
-				lookup.erase(lookup.begin()+r);
-			}
-		}
-		
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";