X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=1f77b71bfb63b0519527bac53cfbf51511fdbb68;hb=e3e0858c684c4608d679840024e5095ddc8e2719;hp=927f3742216529f54ea12a769bae752501b7fe33;hpb=6cf9539162b0fb0b5c0b99673e999df3cd717c55;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 927f374..1f77b71 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -96,6 +96,9 @@
 #include "deuniqueseqscommand.h"
 #include "pairwiseseqscommand.h"
 #include "clusterdoturcommand.h"
+#include "subsamplecommand.h"
+#include "removegroupscommand.h"
+#include "getgroupscommand.h"
 
 
 /*******************************************************/
@@ -197,6 +200,9 @@ CommandFactory::CommandFactory(){
 	commands["fastq.info"]			= "fastq.info";
 	commands["deunique.seqs"]		= "deunique.seqs";
 	commands["cluster.classic"]		= "cluster.classic";
+	commands["sub.sample"]			= "sub.sample";
+	commands["remove.groups"]		= "remove.groups";
+	commands["get.groups"]			= "get.groups";
 	commands["pairwise.seqs"]		= "MPIEnabled";
 	commands["pipeline.pds"]		= "MPIEnabled";
 	commands["classify.seqs"]		= "MPIEnabled"; 
@@ -339,11 +345,14 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "cluster.fragments")		{	command = new ClusterFragmentsCommand(optionString);		}
 		else if(commandName == "get.lineage")			{	command = new GetLineageCommand(optionString);				}
 		else if(commandName == "remove.lineage")		{	command = new RemoveLineageCommand(optionString);			}
+		else if(commandName == "get.groups")			{	command = new GetGroupsCommand(optionString);				}
+		else if(commandName == "remove.groups")			{	command = new RemoveGroupsCommand(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 if(commandName == "cluster.classic")		{	command = new ClusterDoturCommand(optionString);			}
+		else if(commandName == "sub.sample")			{	command = new SubSampleCommand(optionString);				}
 		else											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -453,11 +462,14 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 		else if(commandName == "split.groups")			{	pipecommand = new SplitGroupCommand(optionString);				}
 		else if(commandName == "cluster.fragments")		{	pipecommand = new ClusterFragmentsCommand(optionString);		}
 		else if(commandName == "get.lineage")			{	pipecommand = new GetLineageCommand(optionString);				}
+		else if(commandName == "get.groups")			{	pipecommand = new GetGroupsCommand(optionString);				}
 		else if(commandName == "remove.lineage")		{	pipecommand = new RemoveLineageCommand(optionString);			}
+		else if(commandName == "remove.groups")			{	pipecommand = new RemoveGroupsCommand(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 if(commandName == "cluster.classic")		{	pipecommand = new ClusterDoturCommand(optionString);			}
+		else if(commandName == "sub.sample")			{	pipecommand = new SubSampleCommand(optionString);				}
 		else											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -556,10 +568,13 @@ Command* CommandFactory::getCommand(string commandName){
 		else if(commandName == "cluster.fragments")		{	shellcommand = new ClusterFragmentsCommand();		}
 		else if(commandName == "get.lineage")			{	shellcommand = new GetLineageCommand();				}
 		else if(commandName == "remove.lineage")		{	shellcommand = new RemoveLineageCommand();			}
+		else if(commandName == "get.groups")			{	shellcommand = new GetGroupsCommand();				}
+		else if(commandName == "remove.groups")			{	shellcommand = new RemoveGroupsCommand();			}
 		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 if(commandName == "cluster.classic")		{	shellcommand = new ClusterDoturCommand();			}
+		else if(commandName == "sub.sample")			{	shellcommand = new SubSampleCommand();				}
 		else											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;