X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactcommand.cpp;h=981f077969b1e734b2dc39fb05b372daa2a5f455;hb=599af78a6ea4916919d460a131e2d0dffa28d35e;hp=c2204e7a573969a2f4d1d80f41eb9defb3c53070;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index c2204e7..981f077 100644
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -10,12 +10,14 @@
 #include "rarefactcommand.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 "coverage.h"
 
 //**********************************************************************************************************************
 
@@ -25,28 +27,41 @@ RareFactCommand::RareFactCommand(){
 		globaldata = GlobalData::getInstance();
 		string fileNameRoot;
 		fileNameRoot = getRootName(globaldata->inputFileName);
+		validCalculator = new ValidCalculators();
+		
 		int i;
-		for (i=0; i<globaldata->rareEstimators.size(); i++) {
-			if (globaldata->rareEstimators[i] == "sobs") { 
-				rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction")));
-			}else if (globaldata->rareEstimators[i] == "chao") { 
-				rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao")));
-			}else if (globaldata->rareEstimators[i] == "ace") { 
-				rDisplays.push_back(new RareDisplay(new Ace(), new ThreeColumnFile(fileNameRoot+"r_ace")));
-			}else if (globaldata->rareEstimators[i] == "jack") { 
-				rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
-			}else if (globaldata->rareEstimators[i] == "shannon") { 
-				rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon")));
-			}else if (globaldata->rareEstimators[i] == "npshannon") { 
-				rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
-			}else if (globaldata->rareEstimators[i] == "simpson") { 
-				rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson")));
-			}else if (globaldata->rareEstimators[i] == "bootstrap") { 
-				rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap")));
+		for (i=0; i<globaldata->Estimators.size(); i++) {
+			if (validCalculator->isValidCalculator("rarefaction", globaldata->Estimators[i]) == true) { 
+				if (globaldata->Estimators[i] == "sobs") { 
+					rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction")));
+				}else if (globaldata->Estimators[i] == "chao") { 
+					rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao")));
+				}else if (globaldata->Estimators[i] == "ace") { 
+					convert(globaldata->getAbund(), abund);
+					if(abund < 5)
+						abund = 10;
+					rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"r_ace")));
+				}else if (globaldata->Estimators[i] == "jack") { 
+					rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
+				}else if (globaldata->Estimators[i] == "shannon") { 
+					rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon")));
+				}else if (globaldata->Estimators[i] == "npshannon") { 
+					rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
+				}else if (globaldata->Estimators[i] == "simpson") { 
+					rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson")));
+				}else if (globaldata->Estimators[i] == "bootstrap") { 
+					rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap")));
+				}else if (globaldata->Estimators[i] == "coverage") { 
+					rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(fileNameRoot+"r_coverage")));
+				}else if (globaldata->Estimators[i] == "nseqs") { 
+					rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs")));
+				}
 			}
 		}
-	
-	
+		
+		//reset calc for next command
+		globaldata->setCalc("");
+
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the RareFactCommand class Function RareFactCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -73,7 +88,11 @@ RareFactCommand::~RareFactCommand(){
 int RareFactCommand::execute(){
 	try {
 		int count = 1;
-		read = new ReadPhilFile(globaldata->inputFileName);	
+		
+		//if the users entered no valid calculators don't execute command
+		if (rDisplays.size() == 0) { return 0; }
+
+		read = new ReadOTUFile(globaldata->inputFileName);	
 		read->read(&*globaldata); 
 
 		order = globaldata->gorder;
@@ -92,7 +111,8 @@ int RareFactCommand::execute(){
 			
 				cout << order->getLabel() << '\t' << count << endl;
 			}
-		
+			
+			delete order;
 			order = (input->getOrderVector());
 			count++;