X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectcommand.cpp;h=233b7bef963a22bdc0ab9a2e524699bc49e4366c;hb=599af78a6ea4916919d460a131e2d0dffa28d35e;hp=4687c6e8dcb35fa3b19296f2fe5cc0d39745d582;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/collectcommand.cpp b/collectcommand.cpp
index 4687c6e..233b7be 100644
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -10,42 +10,73 @@
 #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();
 		string fileNameRoot;
 		fileNameRoot = getRootName(globaldata->inputFileName);
 		int i;
-		for (i=0; i<globaldata->singleEstimators.size(); i++) {
-			if (globaldata->singleEstimators[i] == "sobs") { 
-				cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
-			}else if (globaldata->singleEstimators[i] == "chao") { 
-				cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
-			}else if (globaldata->singleEstimators[i] == "ace") { 
-				cDisplays.push_back(new CollectDisplay(new Ace(), new ThreeColumnFile(fileNameRoot+"ace")));
-			}else if (globaldata->singleEstimators[i] == "jack") { 
-				cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
-			}else if (globaldata->singleEstimators[i] == "shannon") { 
-				cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
-			}else if (globaldata->singleEstimators[i] == "npshannon") { 
-				cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
-			}else if (globaldata->singleEstimators[i] == "simpson") { 
-				cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
-			}else if (globaldata->singleEstimators[i] == "bootstrap") { 
-				cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
+		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);
+					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")));
+				}else if (globaldata->Estimators[i] == "shannon") { 
+					cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
+				}else if (globaldata->Estimators[i] == "npshannon") { 
+					cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
+				}else if (globaldata->Estimators[i] == "simpson") { 
+					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")));
+				}
 			}
 		}
+		
+		//reset calc for next command
+		globaldata->setCalc("");
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -72,16 +103,21 @@ CollectCommand::~CollectCommand(){
 int CollectCommand::execute(){
 	try {
 		int count = 1;
-		read = new ReadPhilFile(globaldata->inputFileName);	
+		
+		//if the users entered no valid calculators don't execute command
+		if (cDisplays.size() == 0) { return 0; }
+
+		read = new ReadOTUFile(globaldata->inputFileName);	
 		read->read(&*globaldata); 
 		
 		order = globaldata->gorder;
 		input = globaldata->ginput;
-			
+		set<string> orderList;	
+		
 		while(order != NULL){
 		
+			orderList.insert(order->getLabel());
 			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
-			
 				cCurve = new Collect(order, cDisplays);
 				convert(globaldata->getFreq(), freq);
 				cCurve->getCurve(freq);
@@ -90,12 +126,15 @@ int CollectCommand::execute(){
 			
 				cout << order->getLabel() << '\t' << count << endl;
 			}
-		
+			
+			delete order;
 			order = (input->getOrderVector());
 			count++;
-		
 		}
-	
+		set<string>::iterator i;
+		for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
+			if(orderList.count(*i) == 0)
+				cout << "'" << *i << "'" << " is not a valid label.\n";
 		for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}	
 		return 0;
 	}