X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactcommand.cpp;h=3c7975749e126645b91b7b0b53755e5f63e35789;hb=154e089bcd37c2c2f773e53ffb88a20170b27037;hp=df33e5d7a01ed9ca053cee3849bd5bd1448bda23;hpb=addc715b6d7ea52440751cec10edad03e1a19b37;p=mothur.git

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index df33e5d..3c79757 100644
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -10,6 +10,7 @@
 #include "rarefactcommand.h"
 #include "ace.h"
 #include "sobs.h"
+#include "nseqs.h"
 #include "chao1.h"
 #include "bootstrap.h"
 #include "simpson.h"
@@ -38,7 +39,7 @@ RareFactCommand::RareFactCommand(){
 					convert(globaldata->getAbund(), abund);
 					if(abund < 5)
 						abund = 10;
-					rDisplays.push_back(new RareDisplay(new Ace(), new ThreeColumnFile(fileNameRoot+"r_ace")));
+					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") { 
@@ -49,6 +50,8 @@ RareFactCommand::RareFactCommand(){
 					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] == "nseqs") { 
+					rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs")));
 				}
 			}
 		}
@@ -86,7 +89,7 @@ int RareFactCommand::execute(){
 		//if the users entered no valid calculators don't execute command
 		if (rDisplays.size() == 0) { return 0; }
 
-		read = new ReadPhilFile(globaldata->inputFileName);	
+		read = new ReadOTUFile(globaldata->inputFileName);	
 		read->read(&*globaldata); 
 
 		order = globaldata->gorder;