fixed trim.seqs bug with qtrim parameter and added num=1 special case to database...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 7d47491f7e32a3dc2adf518aa5d97cc2265f7121..ae59a8dcef9c43927b08759108c65f4c63d6a0cb 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -61,11 +61,10 @@
 #include "phylotypecommand.h"
 #include "mgclustercommand.h"
 #include "preclustercommand.h"
-#include "pcacommand.h"
+#include "pcoacommand.h"
 #include "otuhierarchycommand.h"
 #include "setdircommand.h"
 #include "parselistscommand.h"
-#include "parsesffcommand.h"
 #include "chimeraccodecommand.h"
 #include "chimeracheckcommand.h"
 #include "chimeraslayercommand.h"
@@ -106,6 +105,8 @@
 #include "trimflowscommand.h"
 #include "corraxescommand.h"
 #include "shhhercommand.h"
+#include "pcacommand.h"
+#include "nmdscommand.h"
 
 /*******************************************************/
 
@@ -186,7 +187,6 @@ CommandFactory::CommandFactory(){
        commands["set.dir"]                             = "set.dir";
        commands["merge.files"]                 = "merge.files";
        commands["parse.list"]                  = "parse.list";
-       commands["parse.sff"]                   = "parse.sff";
        commands["set.logfile"]                 = "set.logfile";
        commands["phylo.diversity"]             = "phylo.diversity";
        commands["make.group"]                  = "make.group";
@@ -215,6 +215,8 @@ CommandFactory::CommandFactory(){
        commands["indicator"]                   = "indicator";
        commands["consensus.seqs"]              = "consensus.seqs";
        commands["corr.axes"]                   = "corr.axes";
+       commands["pca"]                                 = "pca";
+       commands["nmds"]                                = "nmds";
        commands["pairwise.seqs"]               = "MPIEnabled";
        commands["pipeline.pds"]                = "MPIEnabled";
        commands["classify.seqs"]               = "MPIEnabled"; 
@@ -335,12 +337,13 @@ 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 == "pca")                                   {       command = new PCACommand(optionString);                                         }
+               else if(commandName == "nmds")                                  {       command = new NMDSCommand(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);                          }
                else if(commandName == "parse.list")                    {       command = new ParseListCommand(optionString);                           }
-               else if(commandName == "parse.sff")                             {       command = new ParseSFFCommand(optionString);                            }
                else if(commandName == "phylo.diversity")               {       command = new PhyloDiversityCommand(optionString);                      }
                else if(commandName == "make.group")                    {       command = new MakeGroupCommand(optionString);                           }
                else if(commandName == "chop.seqs")                             {       command = new ChopSeqsCommand(optionString);                            }
@@ -460,12 +463,13 @@ 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 == "pca")                                   {       pipecommand = new PCACommand(optionString);                                             }
+               else if(commandName == "nmds")                                  {       pipecommand = new NMDSCommand(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);                              }
                else if(commandName == "parse.list")                    {       pipecommand = new ParseListCommand(optionString);                               }
-               else if(commandName == "parse.sff")                             {       pipecommand = new ParseSFFCommand(optionString);                                }
                else if(commandName == "phylo.diversity")               {       pipecommand = new PhyloDiversityCommand(optionString);                  }
                else if(commandName == "make.group")                    {       pipecommand = new MakeGroupCommand(optionString);                               }
                else if(commandName == "chop.seqs")                             {       pipecommand = new ChopSeqsCommand(optionString);                                }
@@ -572,12 +576,13 @@ 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 == "pca")                                   {       shellcommand = new PCACommand();                                        }
+               else if(commandName == "nmds")                                  {       shellcommand = new NMDSCommand();                                       }
                else if(commandName == "otu.hierarchy")                 {       shellcommand = new OtuHierarchyCommand();                       }
                else if(commandName == "set.dir")                               {       shellcommand = new SetDirectoryCommand();                       }
                else if(commandName == "set.logfile")                   {       shellcommand = new SetLogFileCommand();                         }
                else if(commandName == "parse.list")                    {       shellcommand = new ParseListCommand();                          }
-               else if(commandName == "parse.sff")                             {       shellcommand = new ParseSFFCommand();                           }
                else if(commandName == "phylo.diversity")               {       shellcommand = new PhyloDiversityCommand();                     }
                else if(commandName == "make.group")                    {       shellcommand = new MakeGroupCommand();                          }
                else if(commandName == "chop.seqs")                             {       shellcommand = new ChopSeqsCommand();                           }