X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=inline;f=summarysharedcommand.cpp;h=f31f7e10e1f19e47781d2d47dd9db09ebafa05cf;hb=dbc9352256135d7b3e2b17dddc5c506770e2df92;hp=b9fd08debd294870af590f5be48fdc4a7c7ba890;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index b9fd08d..f31f7e1 100644
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -8,6 +8,7 @@
  */
 
 #include "summarysharedcommand.h"
+#include "sharedsobscollectsummary.h"
 #include "sharedchao1.h"
 #include "sharedace.h"
 #include "sharedjabund.h"
@@ -24,31 +25,43 @@
 SummarySharedCommand::SummarySharedCommand(){
 	try {
 		globaldata = GlobalData::getInstance();
+		outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary");
+		openOutputFile(outputFileName, outputFileHandle);
+		format = globaldata->getFormat();
+		validCalculator = new ValidCalculators();
 		
 		int i;
-		for (i=0; i<globaldata->sharedSummaryEstimators.size(); i++) {
-			if (globaldata->sharedSummaryEstimators[i] == "sharedChao") { 
-				sumCalculators.push_back(new SharedChao1());
-			}else if (globaldata->sharedSummaryEstimators[i] == "sharedAce") { 
-				sumCalculators.push_back(new SharedAce());
-			}else if (globaldata->sharedSummaryEstimators[i] == "sharedJabund") { 	
-				sumCalculators.push_back(new SharedJAbund());
-			}else if (globaldata->sharedSummaryEstimators[i] == "sharedSorensonAbund") { 
-				sumCalculators.push_back(new SharedSorAbund());
-			}else if (globaldata->sharedSummaryEstimators[i] == "sharedJclass") { 
-				sumCalculators.push_back(new SharedJclass());
-			}else if (globaldata->sharedSummaryEstimators[i] == "sharedSorClass") { 
-				sumCalculators.push_back(new SharedSorClass());
-			}else if (globaldata->sharedSummaryEstimators[i] == "sharedJest") { 
-				sumCalculators.push_back(new SharedJest());
-			}else if (globaldata->sharedSummaryEstimators[i] == "sharedSorEst") { 
-				sumCalculators.push_back(new SharedSorEst());
-			}else if (globaldata->sharedSummaryEstimators[i] == "SharedThetaYC") { 
-				sumCalculators.push_back(new SharedThetaYC());
-			}else if (globaldata->sharedSummaryEstimators[i] == "SharedThetaN") { 
-				sumCalculators.push_back(new SharedThetaN());
+		for (i=0; i<globaldata->Estimators.size(); i++) {
+			if (validCalculator->isValidCalculator("sharedsummary", globaldata->Estimators[i]) == true) { 
+				if (globaldata->Estimators[i] == "sharedsobs") { 
+					sumCalculators.push_back(new SharedSobsCS());
+				}else if (globaldata->Estimators[i] == "sharedchao") { 
+					sumCalculators.push_back(new SharedChao1());
+				}else if (globaldata->Estimators[i] == "sharedace") { 
+					sumCalculators.push_back(new SharedAce());
+				}else if (globaldata->Estimators[i] == "sharedjabund") { 	
+					sumCalculators.push_back(new SharedJAbund());
+				}else if (globaldata->Estimators[i] == "sharedsorensonabund") { 
+					sumCalculators.push_back(new SharedSorAbund());
+				}else if (globaldata->Estimators[i] == "sharedjclass") { 
+					sumCalculators.push_back(new SharedJclass());
+				}else if (globaldata->Estimators[i] == "sharedsorclass") { 
+					sumCalculators.push_back(new SharedSorClass());
+				}else if (globaldata->Estimators[i] == "sharedjest") { 
+					sumCalculators.push_back(new SharedJest());
+				}else if (globaldata->Estimators[i] == "sharedsorest") { 
+					sumCalculators.push_back(new SharedSorEst());
+				}else if (globaldata->Estimators[i] == "sharedthetayc") { 
+					sumCalculators.push_back(new SharedThetaYC());
+				}else if (globaldata->Estimators[i] == "sharedthetan") { 
+					sumCalculators.push_back(new SharedThetaN());
+				}
 			}
 		}
+		
+		//reset calc for next command
+		globaldata->setCalc("");
+
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function SummarySharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -70,24 +83,34 @@ SummarySharedCommand::~SummarySharedCommand(){
 
 int SummarySharedCommand::execute(){
 	try {
-		outputFileName = ((getRootName(globaldata->inputFileName)) + "sharedSummary");
-		openOutputFile(outputFileName, outputFileHandle);
-	
-		read = new ReadPhilFile(globaldata->inputFileName);	
-		read->read(&*globaldata); 
+		int count = 1;	
 		
-		outputFileHandle << '\t' << '\t' << '\t' << '\t'; //pads file for labels and groupnames
+		//if the users entered no valid calculators don't execute command
+		if (sumCalculators.size() == 0) { return 0; }
+
+		if (format == "sharedfile") {
+			read = new ReadPhilFile(globaldata->inputFileName);	
+			read->read(&*globaldata); 
+			
+			input = globaldata->ginput;
+			order = input->getSharedOrderVector();
+		}else {
+			//you are using a list and a groupfile
+			read = new ReadPhilFile(globaldata->inputFileName);	
+			read->read(&*globaldata); 
+		
+			input = globaldata->ginput;
+			SharedList = globaldata->gSharedList;
+			order = SharedList->getSharedOrderVector();
+		}
+		
+		//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;
-		
-		list = globaldata->glist;
-		input = globaldata->ginput;
-		order = list->getSharedOrderVector();
-		getGroupComb();
-		
-		int count = 1;
+
 		while(order != NULL){
 		
 			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){			
@@ -101,7 +124,7 @@ 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'; //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';
@@ -113,13 +136,19 @@ int SummarySharedCommand::execute(){
 				}
 			}
 		
-			list = input->getListVector(); //get new list vector to process
-			if (list != NULL) {
-				order = list->getSharedOrderVector(); //gets new order vector with group info.
-				count++;
+			//get next line to process
+			if (format == "sharedfile") {
+				order = input->getSharedOrderVector();
 			}else {
-				break;
+				//you are using a list and a groupfile
+				SharedList = input->getSharedListVector(); //get new list vector to process
+				if (SharedList != NULL) {
+					order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
+				}else {
+					break;
+				}
 			}
+			count++;
 		}
 	
 		return 0;
@@ -176,28 +205,4 @@ 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);
-	}
-
-}
-
+//**********************************************************************************************************************