X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectcommand.cpp;h=233b7bef963a22bdc0ab9a2e524699bc49e4366c;hb=fb01d5df390a98313ca095a812fc240dc079d084;hp=c716732474da857a38bee138931b4a769cca4aa1;hpb=5e7c1cf6a6dd289a90d27c0eef7eb4675b5e17b7;p=mothur.git

diff --git a/collectcommand.cpp b/collectcommand.cpp
index c716732..233b7be 100644
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -10,17 +10,25 @@
 #include "collectcommand.h"
 #include "ace.h"
 #include "sobs.h"
+#include "nseqs.h"
 #include "chao1.h"
 #include "bootstrap.h"
 #include "simpson.h"
 #include "npshannon.h"
 #include "shannon.h"
 #include "jackknife.h"
+#include "geom.h"
+#include "qstat.h"
+#include "logsd.h"
+#include "bergerparker.h"
+#include "bstick.h"
+#include "goodscoverage.h"
 
 
-//**********************************************************************************************************************
+#include "coverage.h"
 
 
+//**********************************************************************************************************************
 CollectCommand::CollectCommand(){
 	try {
 		globaldata = GlobalData::getInstance();
@@ -28,15 +36,18 @@ CollectCommand::CollectCommand(){
 		fileNameRoot = getRootName(globaldata->inputFileName);
 		int i;
 		validCalculator = new ValidCalculators();
-		
 		for (i=0; i<globaldata->Estimators.size(); i++) {
 			if (validCalculator->isValidCalculator("single", globaldata->Estimators[i]) == true) { 
 				if (globaldata->Estimators[i] == "sobs") { 
 					cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
 				}else if (globaldata->Estimators[i] == "chao") { 
 					cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
+				}else if (globaldata->Estimators[i] == "nseqs") { 
+					cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
+				}else if (globaldata->Estimators[i] == "coverage") { 
+					cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
 				}else if (globaldata->Estimators[i] == "ace") { 
-				convert(globaldata->getAbund(), abund);
+					convert(globaldata->getAbund(), abund);
 					cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
 				}else if (globaldata->Estimators[i] == "jack") { 
 					cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
@@ -48,6 +59,18 @@ CollectCommand::CollectCommand(){
 					cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
 				}else if (globaldata->Estimators[i] == "bootstrap") { 
 					cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
+				}else if (globaldata->Estimators[i] == "geometric") { 
+					cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
+				}else if (globaldata->Estimators[i] == "qstat") { 
+					cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
+				}else if (globaldata->Estimators[i] == "logseries") { 
+					cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
+				}else if (globaldata->Estimators[i] == "bergerparker") { 
+					cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
+				}else if (globaldata->Estimators[i] == "bstick") { 
+					cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick")));
+				}else if (globaldata->Estimators[i] == "goodscoverage") { 
+					cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage")));
 				}
 			}
 		}
@@ -84,7 +107,7 @@ int CollectCommand::execute(){
 		//if the users entered no valid calculators don't execute command
 		if (cDisplays.size() == 0) { return 0; }
 
-		read = new ReadPhilFile(globaldata->inputFileName);	
+		read = new ReadOTUFile(globaldata->inputFileName);	
 		read->read(&*globaldata); 
 		
 		order = globaldata->gorder;
@@ -103,6 +126,8 @@ int CollectCommand::execute(){
 			
 				cout << order->getLabel() << '\t' << count << endl;
 			}
+			
+			delete order;
 			order = (input->getOrderVector());
 			count++;
 		}
@@ -110,7 +135,6 @@ int CollectCommand::execute(){
 		for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
 			if(orderList.count(*i) == 0)
 				cout << "'" << *i << "'" << " is not a valid label.\n";
-		globaldata->clearLabels();
 		for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}	
 		return 0;
 	}