X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarycommand.cpp;h=e7fda2e5dedcd8052b3c610931964377e356a7af;hb=a8f5a612bba54ceb74e17efc027d3a7f5aa93c9a;hp=8c8a2aadf93440ab0e6271381e641bdae2167686;hpb=eb1c88346fb246e95a6b38935b103f95e38b82ca;p=mothur.git

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 8c8a2aa..e7fda2e 100644
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -22,6 +22,12 @@
 #include "qstat.h"
 #include "bergerparker.h"
 #include "bstick.h"
+#include "goodscoverage.h"
+#include "coverage.h"
+#include "efron.h"
+#include "boneh.h"
+#include "solow.h"
+#include "shen.h"
 
 //**********************************************************************************************************************
 
@@ -33,14 +39,15 @@ SummaryCommand::SummaryCommand(){
 		
 		for (i=0; i<globaldata->Estimators.size(); i++) {
 			if (validCalculator->isValidCalculator("summary", globaldata->Estimators[i]) == true) { 
-			
 				if(globaldata->Estimators[i] == "sobs"){
 					sumCalculators.push_back(new Sobs());
 				}else if(globaldata->Estimators[i] == "chao"){
 					sumCalculators.push_back(new Chao1());
-				}else if(globaldata->Estimators[i] == "geom"){
+				}else if(globaldata->Estimators[i] == "coverage"){
+					sumCalculators.push_back(new Coverage());
+				}else if(globaldata->Estimators[i] == "geometric"){
 					sumCalculators.push_back(new Geom());
-				}else if(globaldata->Estimators[i] == "logsd"){
+				}else if(globaldata->Estimators[i] == "logseries"){
 					sumCalculators.push_back(new LogSD());
 				}else if(globaldata->Estimators[i] == "qstat"){
 					sumCalculators.push_back(new QStat());
@@ -65,6 +72,20 @@ SummaryCommand::SummaryCommand(){
 					sumCalculators.push_back(new Bootstrap());
 				}else if (globaldata->Estimators[i] == "nseqs") { 
 					sumCalculators.push_back(new NSeqs());
+				}else if (globaldata->Estimators[i] == "goodscoverage") { 
+					sumCalculators.push_back(new GoodsCoverage());
+				}else if (globaldata->Estimators[i] == "efron") { 
+					convert(globaldata->getSize(), size);
+					sumCalculators.push_back(new Efron(size));
+				}else if (globaldata->Estimators[i] == "boneh") { 
+					convert(globaldata->getSize(), size);
+					sumCalculators.push_back(new Boneh(size));
+				}else if (globaldata->Estimators[i] == "solow") { 
+					convert(globaldata->getSize(), size);
+					sumCalculators.push_back(new Solow(size));
+				}else if (globaldata->Estimators[i] == "shen") { 
+					convert(globaldata->getSize(), size);
+					sumCalculators.push_back(new Shen(size));
 				}
 			}
 		}
@@ -94,7 +115,8 @@ SummaryCommand::~SummaryCommand(){
 
 int SummaryCommand::execute(){
 	try {
-	
+		int count = 1;
+		
 		//if the users entered no valid calculators don't execute command
 		if (sumCalculators.size() == 0) { return 0; }
 
@@ -102,9 +124,13 @@ int SummaryCommand::execute(){
 		openOutputFile(outputFileName, outputFileHandle);
 		outputFileHandle << "label";
 	
-		read = new ReadPhilFile(globaldata->inputFileName);	
+		read = new ReadOTUFile(globaldata->inputFileName);	
 		read->read(&*globaldata); 
-
+		
+		sabund = globaldata->sabund;
+		SAbundVector* lastSAbund = sabund;
+		input = globaldata->ginput;
+		
 		for(int i=0;i<sumCalculators.size();i++){
 			if(sumCalculators[i]->getCols() == 1){
 				outputFileHandle << '\t' << sumCalculators[i]->getName();
@@ -115,28 +141,76 @@ int SummaryCommand::execute(){
 		}
 		outputFileHandle << endl;
 		
-		sabund = globaldata->sabund;
-		input = globaldata->ginput;
-		int count = 1;
-		while(sabund != NULL){
+		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+		set<string> processedLabels;
+		set<string> userLabels = globaldata->labels;
 		
+		while((sabund != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+			
 			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){			
 	
 				cout << sabund->getLabel() << '\t' << count << endl;
+				processedLabels.insert(sabund->getLabel());
+				userLabels.erase(sabund->getLabel());
+
 				
 				outputFileHandle << sabund->getLabel();
 				for(int i=0;i<sumCalculators.size();i++){
 					vector<double> data = sumCalculators[i]->getValues(sabund);
 					outputFileHandle << '\t';
-					//sumCalculators[i]->print(outputFileHandle);
+					sumCalculators[i]->print(outputFileHandle);
 				}
-				
 				outputFileHandle << endl;
 			}
+			
+			if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastSAbund->getLabel()) != 1)) {
+
+				cout << lastSAbund->getLabel() << '\t' << count << endl;
+				processedLabels.insert(lastSAbund->getLabel());
+				userLabels.erase(lastSAbund->getLabel());
+				
+				outputFileHandle << lastSAbund->getLabel();
+				for(int i=0;i<sumCalculators.size();i++){
+					vector<double> data = sumCalculators[i]->getValues(lastSAbund);
+					outputFileHandle << '\t';
+					sumCalculators[i]->print(outputFileHandle);
+				}
+				outputFileHandle << endl;
+			}		
+
+			if (count != 1) { delete lastSAbund; }
+			lastSAbund = sabund;			
+
 			sabund = input->getSAbundVector();
 			count++;
 		}
-	
+		
+		//output error messages about any remaining user labels
+		set<string>::iterator it;
+		bool needToRun = false;
+		for (it = userLabels.begin(); it != userLabels.end(); it++) {  
+			cout << "Your file does not include the label "<< *it; 
+			if (processedLabels.count(lastSAbund->getLabel()) != 1) {
+				cout << ". I will use " << lastSAbund->getLabel() << "." << endl;
+				needToRun = true;
+			}else {
+				cout << ". Please refer to " << lastSAbund->getLabel() << "." << endl;
+			}
+		}
+		
+		//run last line if you need to
+		if (needToRun == true)  {
+			cout << lastSAbund->getLabel() << '\t' << count << endl;
+			outputFileHandle << lastSAbund->getLabel();
+			for(int i=0;i<sumCalculators.size();i++){
+				vector<double> data = sumCalculators[i]->getValues(lastSAbund);
+				outputFileHandle << '\t';
+				sumCalculators[i]->print(outputFileHandle);
+			}
+			outputFileHandle << endl;
+		}
+		
+		delete lastSAbund;
 		return 0;
 	}
 	catch(exception& e) {