X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectcommand.cpp;h=000f85d1d91f3922766f024d71dc157640b2eabe;hb=9ca2caadbeac83bb84b3330d9204b1b659d62941;hp=0f622c49b2a30632f53e4fa3ec0dfc3196113374;hpb=09a01fb51eea9e81409d367410c831394193fd86;p=mothur.git

diff --git a/collectcommand.cpp b/collectcommand.cpp
index 0f622c4..000f85d 100644
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -10,6 +10,7 @@
 #include "collectcommand.h"
 #include "ace.h"
 #include "sobs.h"
+#include "nseqs.h"
 #include "chao1.h"
 #include "bootstrap.h"
 #include "simpson.h"
@@ -35,8 +36,11 @@ CollectCommand::CollectCommand(){
 					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] == "ace") { 
-					cDisplays.push_back(new CollectDisplay(new Ace(), new ThreeColumnFile(fileNameRoot+"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") { 
@@ -88,11 +92,12 @@ int CollectCommand::execute(){
 		
 		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);
@@ -101,12 +106,13 @@ int CollectCommand::execute(){
 			
 				cout << order->getLabel() << '\t' << count << endl;
 			}
-		
 			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;
 	}