added a few evenness calculators and fixed a couple of bugs in filter.seqs and pre...

[mothur.git] / collectcommand.cpp

diff --git a/collectcommand.cpp b/collectcommand.cpp
index 8c1565b901d5b885ad86b91d31cb7cc041138535..ca48d75d276a274ff5b2259ffe211b653a02f1a9 100644 (file)
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -14,8 +14,13 @@
 #include "chao1.h"
 #include "bootstrap.h"
 #include "simpson.h"
+#include "simpsoneven.h"
+#include "invsimpson.h"
 #include "npshannon.h"
 #include "shannon.h"
+#include "smithwilson.h"
+#include "heip.h"
+#include "shannoneven.h"
 #include "jackknife.h"
 #include "geom.h"
 #include "qstat.h"
@@ -178,12 +183,27 @@ int CollectCommand::execute(){
                                        }else if (Estimators[i] == "shannon") { 
                                                cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
                                                outputNames.push_back(fileNameRoot+"shannon");
+                                       }else if (Estimators[i] == "shannoneven") { 
+                                               cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(fileNameRoot+"shannoneven")));
+                                               outputNames.push_back(fileNameRoot+"shannoneven");
                                        }else if (Estimators[i] == "npshannon") { 
                                                cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
                                                outputNames.push_back(fileNameRoot+"np_shannon");
+                                       }else if (Estimators[i] == "heip") { 
+                                               cDisplays.push_back(new CollectDisplay(new Heip(), new OneColumnFile(fileNameRoot+"heip")));
+                                               outputNames.push_back(fileNameRoot+"heip");
+                                       }else if (Estimators[i] == "smithwilson") { 
+                                               cDisplays.push_back(new CollectDisplay(new SmithWilson(), new OneColumnFile(fileNameRoot+"smithwilson")));
+                                               outputNames.push_back(fileNameRoot+"smithwilson");
                                        }else if (Estimators[i] == "simpson") { 
                                                cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
                                                outputNames.push_back(fileNameRoot+"simpson");
+                                       }else if (Estimators[i] == "simpsoneven") { 
+                                               cDisplays.push_back(new CollectDisplay(new SimpsonEven(), new OneColumnFile(fileNameRoot+"simpsoneven")));
+                                               outputNames.push_back(fileNameRoot+"simpsoneven");
+                                       }else if (Estimators[i] == "invsimpson") { 
+                                               cDisplays.push_back(new CollectDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+"invsimpson")));
+                                               outputNames.push_back(fileNameRoot+"invsimpson");
                                        }else if (Estimators[i] == "bootstrap") { 
                                                cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
                                                outputNames.push_back(fileNameRoot+"bootstrap");