fixed bug with aligner and longest base. added deunique.seqs command.

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 917ab96e69afa7cf7ad76d2cf85bbb79401e8db4..a4d6506df3128579158f2f1ff5ee99f67bfc9bc2 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -93,6 +93,8 @@
 #include "removelineagecommand.h"
 #include "parsefastaqcommand.h"
 #include "pipelinepdscommand.h"
+#include "deuniqueseqscommand.h"
+
 
 /*******************************************************/
 
@@ -191,6 +193,7 @@ CommandFactory::CommandFactory(){
        commands["get.lineage"]                 = "get.lineage";
        commands["remove.lineage"]              = "remove.lineage";
        commands["fastq.info"]                  = "fastq.info";
+       commands["deunique.seqs"]               = "deunique.seqs";
        commands["pipeline.pds"]                = "MPIEnabled";
        commands["classify.seqs"]               = "MPIEnabled"; 
        commands["dist.seqs"]                   = "MPIEnabled";
@@ -334,6 +337,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "remove.lineage")                {       command = new RemoveLineageCommand(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                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -445,6 +449,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "get.lineage")                   {       pipecommand = new GetLineageCommand(optionString);                              }
                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                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -544,6 +549,7 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "get.lineage")                   {       shellcommand = new GetLineageCommand();                         }
                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                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;