added pairwise.seqs

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index a4d6506df3128579158f2f1ff5ee99f67bfc9bc2..224ad217dd103dcb419466978e384cd40941f5b3 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -94,6 +94,7 @@
 #include "parsefastaqcommand.h"
 #include "pipelinepdscommand.h"
 #include "deuniqueseqscommand.h"
+#include "pairwiseseqscommand.h"
 
 
 /*******************************************************/
@@ -194,6 +195,7 @@ CommandFactory::CommandFactory(){
        commands["remove.lineage"]              = "remove.lineage";
        commands["fastq.info"]                  = "fastq.info";
        commands["deunique.seqs"]               = "deunique.seqs";
+       commands["pairwise.seqs"]               = "MPIEnabled";
        commands["pipeline.pds"]                = "MPIEnabled";
        commands["classify.seqs"]               = "MPIEnabled"; 
        commands["dist.seqs"]                   = "MPIEnabled";
@@ -338,6 +340,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "fastq.info")                    {       command = new ParseFastaQCommand(optionString);                         }
                else if(commandName == "pipeline.pds")                  {       command = new PipelineCommand(optionString);                            }
                else if(commandName == "deunique.seqs")                 {       command = new DeUniqueSeqsCommand(optionString);                        }
+               else if(commandName == "pairwise.seqs")                 {       command = new PairwiseSeqsCommand(optionString);                        }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -450,6 +453,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "remove.lineage")                {       pipecommand = new RemoveLineageCommand(optionString);                   }
                else if(commandName == "fastq.info")                    {       pipecommand = new ParseFastaQCommand(optionString);                             }
                else if(commandName == "deunique.seqs")                 {       pipecommand = new DeUniqueSeqsCommand(optionString);                    }
+               else if(commandName == "pairwise.seqs")                 {       pipecommand = new PairwiseSeqsCommand(optionString);                    }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -550,6 +554,7 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "remove.lineage")                {       shellcommand = new RemoveLineageCommand();                      }
                else if(commandName == "fastq.info")                    {       shellcommand = new ParseFastaQCommand();                        }
                else if(commandName == "deunique.seqs")                 {       shellcommand = new DeUniqueSeqsCommand();                       }
+               else if(commandName == "pairwise.seqs")                 {       shellcommand = new PairwiseSeqsCommand();                       }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;