X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarysharedcommand.cpp;h=8b3a63f8688e557f290aa9db1acda63ae4de5426;hb=83950cc7a80a36c79dededb484daec5ec26b330f;hp=f31f7e10e1f19e47781d2d47dd9db09ebafa05cf;hpb=09a01fb51eea9e81409d367410c831394193fd86;p=mothur.git

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index f31f7e1..8b3a63f 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 +20,16 @@
 #include "sharedsorest.h"
 #include "sharedthetayc.h"
 #include "sharedthetan.h"
+#include "sharedkstest.h"
+#include "sharedbdiversity.h"
+#include "sharedochiai.h"
+//#include "sharedanderberg.h"
+#include "sharedkulczynski.h"
+#include "sharedkulczynskicody.h"
+#include "sharedlennon.h"
+#include "sharedmorisitahorn.h"
+#include "sharedbraycurtis.h"
+
 
 //**********************************************************************************************************************
 
@@ -55,10 +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("");
 
@@ -104,13 +136,16 @@ 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++){
 			outputFileHandle << '\t' << sumCalculators[i]->getName();
 		}
 		outputFileHandle << endl;
-
+		
 		while(order != NULL){
 		
 			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){			
@@ -125,6 +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';
@@ -150,7 +194,10 @@ int SummarySharedCommand::execute(){
 			}
 			count++;
 		}
-	
+		
+		//reset groups parameter
+		globaldata->Groups.clear();  globaldata->setGroups("");
+
 		return 0;
 	}
 	catch(exception& e) {
@@ -169,10 +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);
 		}
 		
@@ -191,7 +238,6 @@ try {
 					 break;
 				}
 			}
-			
 		}
 	}
 	catch(exception& e) {
@@ -206,3 +252,49 @@ try {
 }
 
 //**********************************************************************************************************************
+void SummarySharedCommand::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 SummarySharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the SummarySharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}		
+
+}
+/***********************************************************/