*** empty log message ***

[mothur.git] / collectcommand.cpp

diff --git a/collectcommand.cpp b/collectcommand.cpp
index 62258a85661b4983ee787262f655440992087f6e..d317a06aff4ebf68557a081475cd15a4df58c86a 100644 (file)
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -22,6 +22,12 @@
 #include "logsd.h"
 #include "bergerparker.h"
 #include "bstick.h"
+#include "goodscoverage.h"
+#include "efron.h"
+#include "boneh.h"
+#include "solow.h"
+#include "shen.h"
+#include "coverage.h"
 
 
 //**********************************************************************************************************************
@@ -40,6 +46,8 @@ CollectCommand::CollectCommand(){
                                        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] == "coverage") { 
+                                       cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
                                }else if (globaldata->Estimators[i] == "ace") { 
                                        convert(globaldata->getAbund(), abund);
                                        cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
@@ -53,16 +61,30 @@ CollectCommand::CollectCommand(){
                                        cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
                                }else if (globaldata->Estimators[i] == "bootstrap") { 
                                        cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
-                               }else if (globaldata->Estimators[i] == "geom") { 
-                                       cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geom")));
+                               }else if (globaldata->Estimators[i] == "geometric") { 
+                                       cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
                                }else if (globaldata->Estimators[i] == "qstat") { 
                                        cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
-                               }else if (globaldata->Estimators[i] == "logsd") { 
-                                       cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logsd")));
+                               }else if (globaldata->Estimators[i] == "logseries") { 
+                                       cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
                                }else if (globaldata->Estimators[i] == "bergerparker") { 
                                        cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
                                }else if (globaldata->Estimators[i] == "bstick") { 
-                                       cDisplays.push_back(new CollectDisplay(new BStick(), new OneColumnFile(fileNameRoot+"bstick")));
+                                       cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick")));
+                               }else if (globaldata->Estimators[i] == "goodscoverage") { 
+                                       cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage")));
+                               }else if (globaldata->Estimators[i] == "efron") {
+                                       convert(globaldata->getSize(), size); 
+                                       cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron")));
+                               }else if (globaldata->Estimators[i] == "boneh") {
+                                       convert(globaldata->getSize(), size); 
+                                       cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh")));
+                               }else if (globaldata->Estimators[i] == "solow") {
+                                       convert(globaldata->getSize(), size); 
+                                       cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow")));
+                               }else if (globaldata->Estimators[i] == "shen") {
+                                       convert(globaldata->getSize(), size); 
+                                       cDisplays.push_back(new CollectDisplay(new Shen(size), new OneColumnFile(fileNameRoot+"shen")));
                                }
                        }
                }
@@ -118,6 +140,8 @@ int CollectCommand::execute(){
                        
                                cout << order->getLabel() << '\t' << count << endl;
                        }
+                       
+                       delete order;
                        order = (input->getOrderVector());
                        count++;
                }