more calculator edits and added coverage and whittaker

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 41dc573bee5d8ea1a1ff1a13d02e022b15176ddf..bc0609ef539e119addffbb531d7f8f54f44f747b 100644 (file)
--- 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"
@@ -54,7 +54,7 @@ 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")));
@@ -70,8 +70,8 @@ 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") { 
@@ -127,14 +127,14 @@ int CollectSharedCommand::execute(){
                if (cDisplays.size() == 0) { return 0; }
                
                if (format == "sharedfile") {
-                       read = new ReadPhilFile(globaldata->inputFileName);     
+                       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 = new ReadOTUFile(globaldata->inputFileName);      
                        read->read(&*globaldata); 
                
                        input = globaldata->ginput;