fixed bug in read.tree updates help and validparameters strings, added ability for...

[mothur.git] / collectcommand.cpp

diff --git a/collectcommand.cpp b/collectcommand.cpp
index 95a79d5bc69f763688915ecb998bd47cff162f1e..5994af594ae182f63087cd9c08ca6f96ec4a1187 100644 (file)
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -10,17 +10,21 @@
 #include "collectcommand.h"
 #include "ace.h"
 #include "sobs.h"
+#include "nseqs.h"
 #include "chao1.h"
 #include "bootstrap.h"
 #include "simpson.h"
 #include "npshannon.h"
 #include "shannon.h"
 #include "jackknife.h"
+#include "geom.h"
+#include "qstat.h"
+#include "logsd.h"
+#include "bergerparker.h"
+#include "bstick.h"
 
 
 //**********************************************************************************************************************
-
-
 CollectCommand::CollectCommand(){
        try {
                globaldata = GlobalData::getInstance();
@@ -28,15 +32,16 @@ CollectCommand::CollectCommand(){
                fileNameRoot = getRootName(globaldata->inputFileName);
                int i;
                validCalculator = new ValidCalculators();
-               
                for (i=0; i<globaldata->Estimators.size(); i++) {
                        if (validCalculator->isValidCalculator("single", globaldata->Estimators[i]) == true) { 
                                if (globaldata->Estimators[i] == "sobs") { 
                                        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") { 
-                               convert(globaldata->getAbund(), abund);
+                                       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")));
@@ -48,6 +53,16 @@ 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] == "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] == "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")));
                                }
                        }
                }