added pearson coefficient metric to pcoa

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 5a7b23712c3c3503c44e31e2276123fb7b5c3c56..e3eb2b230ebbd11d83311feb3b63336eb928e698 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -61,7 +61,7 @@
 #include "phylotypecommand.h"
 #include "mgclustercommand.h"
 #include "preclustercommand.h"
-#include "pcacommand.h"
+#include "pcoacommand.h"
 #include "otuhierarchycommand.h"
 #include "setdircommand.h"
 #include "parselistscommand.h"
@@ -333,7 +333,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "phylotype")                             {       command = new PhylotypeCommand(optionString);                           }
                else if(commandName == "mgcluster")                             {       command = new MGClusterCommand(optionString);                           }
                else if(commandName == "pre.cluster")                   {       command = new PreClusterCommand(optionString);                          }
-               else if(commandName == "pcoa")                                  {       command = new PCACommand(optionString);                                         }
+               else if(commandName == "pcoa")                                  {       command = new PCOACommand(optionString);                                                }
                else if(commandName == "otu.hierarchy")                 {       command = new OtuHierarchyCommand(optionString);                        }
                else if(commandName == "set.dir")                               {       command = new SetDirectoryCommand(optionString);                        }
                else if(commandName == "set.logfile")                   {       command = new SetLogFileCommand(optionString);                          }
@@ -457,7 +457,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "phylotype")                             {       pipecommand = new PhylotypeCommand(optionString);                               }
                else if(commandName == "mgcluster")                             {       pipecommand = new MGClusterCommand(optionString);                               }
                else if(commandName == "pre.cluster")                   {       pipecommand = new PreClusterCommand(optionString);                              }
-               else if(commandName == "pcoa")                                  {       pipecommand = new PCACommand(optionString);                                             }
+               else if(commandName == "pcoa")                                  {       pipecommand = new PCOACommand(optionString);                                            }
                else if(commandName == "otu.hierarchy")                 {       pipecommand = new OtuHierarchyCommand(optionString);                    }
                else if(commandName == "set.dir")                               {       pipecommand = new SetDirectoryCommand(optionString);                    }
                else if(commandName == "set.logfile")                   {       pipecommand = new SetLogFileCommand(optionString);                              }
@@ -568,7 +568,7 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "phylotype")                             {       shellcommand = new PhylotypeCommand();                          }
                else if(commandName == "mgcluster")                             {       shellcommand = new MGClusterCommand();                          }
                else if(commandName == "pre.cluster")                   {       shellcommand = new PreClusterCommand();                         }
-               else if(commandName == "pcoa")                                  {       shellcommand = new PCACommand();                                        }
+               else if(commandName == "pcoa")                                  {       shellcommand = new PCOACommand();                                       }
                else if(commandName == "otu.hierarchy")                 {       shellcommand = new OtuHierarchyCommand();                       }
                else if(commandName == "set.dir")                               {       shellcommand = new SetDirectoryCommand();                       }
                else if(commandName == "set.logfile")                   {       shellcommand = new SetLogFileCommand();                         }