X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectsharedcommand.cpp;h=4a3a338944958aa8e9342661847898c20e598f3d;hb=fb01d5df390a98313ca095a812fc240dc079d084;hp=41dc573bee5d8ea1a1ff1a13d02e022b15176ddf;hpb=c537597ec5ebd47b4898da87ae03b0c2aeced354;p=mothur.git

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 41dc573..4a3a338 100644
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -20,7 +20,7 @@
 #include "sharedthetayc.h"
 #include "sharedthetan.h"
 #include "sharedkstest.h"
-#include "sharedbdiversity.h"
+#include "whittaker.h"
 #include "sharednseqs.h"
 #include "sharedochiai.h"
 #include "sharedanderbergs.h"
@@ -29,6 +29,8 @@
 #include "sharedlennon.h"
 #include "sharedmorisitahorn.h"
 #include "sharedbraycurtis.h"
+#include "sharedjackknife.h"
+#include "sharedwhittaker.h"
 
 
 
@@ -54,7 +56,7 @@ CollectSharedCommand::CollectSharedCommand(){
 					cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace")));
 				}else if (globaldata->Estimators[i] == "jabund") { 	
 					cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(fileNameRoot+"jabund")));
-				}else if (globaldata->Estimators[i] == "sorensonabund") { 
+				}else if (globaldata->Estimators[i] == "sorabund") { 
 					cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(fileNameRoot+"sorabund")));
 				}else if (globaldata->Estimators[i] == "jclass") { 
 					cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(fileNameRoot+"jclass")));
@@ -70,10 +72,11 @@ CollectSharedCommand::CollectSharedCommand(){
 					cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(fileNameRoot+"thetan")));
 				}else if (globaldata->Estimators[i] == "kstest") { 
 					cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(fileNameRoot+"kstest")));
-				}else if (globaldata->Estimators[i] == "bdiversity") { 
-					cDisplays.push_back(new CollectDisplay(new BDiversity(), new SharedOneColumnFile(fileNameRoot+"bdiversity")));
+				}else if (globaldata->Estimators[i] == "whittaker") { 
+					cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(fileNameRoot+"whittaker")));
 				}else if (globaldata->Estimators[i] == "sharednseqs") { 
 					cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs")));
+
 				}else if (globaldata->Estimators[i] == "ochiai") { 
 					cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(fileNameRoot+"ochiai")));
 				}else if (globaldata->Estimators[i] == "anderberg") { 
@@ -126,21 +129,12 @@ int CollectSharedCommand::execute(){
 		//if the users entered no valid calculators don't execute command
 		if (cDisplays.size() == 0) { return 0; }
 		
-		if (format == "sharedfile") {
-			read = new ReadPhilFile(globaldata->inputFileName);	
-			read->read(&*globaldata); 
+		read = new ReadOTUFile(globaldata->inputFileName);	
+		read->read(&*globaldata); 
 			
-			input = globaldata->ginput;
-			order = input->getSharedOrderVector();
-		}else {
-			//you are using a list and a groupfile
-			read = new ReadPhilFile(globaldata->inputFileName);	
-			read->read(&*globaldata); 
+		input = globaldata->ginput;
+		order = input->getSharedOrderVector();
 		
-			input = globaldata->ginput;
-			SharedList = globaldata->gSharedList;
-			order = SharedList->getSharedOrderVector();
-		}
 		set<string> orderList;
 		
 		//set users groups
@@ -148,8 +142,11 @@ int CollectSharedCommand::execute(){
 		util->updateGroupIndex(globaldata->Groups, globaldata->gGroupmap->groupIndex);
 
 		while(order != NULL){
+		
 			orderList.insert(order->getLabel());
+			
 			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
+				
 				//create collectors curve
 				cCurve = new Collect(order, cDisplays);
 				convert(globaldata->getFreq(), freq);
@@ -161,24 +158,15 @@ int CollectSharedCommand::execute(){
 			}
 			
 			//get next line to process
-			if (format == "sharedfile") {
-				order = input->getSharedOrderVector();
-			}else {
-				//you are using a list and a groupfile
-				SharedList = input->getSharedListVector(); //get new list vector to process
-				if (SharedList != NULL) {
-					order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
-				}else {
-					break;
-				}
-			}
-			
+			delete order;
+			order = input->getSharedOrderVector();
 			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];	}	
 		
 		//reset groups parameter