X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=a401177f74a97a3c61f9373a6390c249f24403a7;hb=5334a314651228c55fd0f206dec0209bc3148b24;hp=5a7b23712c3c3503c44e31e2276123fb7b5c3c56;hpb=3b137af694d322b7162e97275c070c41b42597a3;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 5a7b237..a401177 100644
--- 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"
@@ -105,6 +105,15 @@
 #include "trimflowscommand.h"
 #include "corraxescommand.h"
 #include "shhhercommand.h"
+#include "pcacommand.h"
+#include "nmdscommand.h"
+#include "removerarecommand.h"
+#include "mergegroupscommand.h"
+#include "amovacommand.h"
+#include "homovacommand.h"
+#include "mantelcommand.h"
+#include "makefastqcommand.h"
+#include "anosimcommand.h"
 
 /*******************************************************/
 
@@ -213,6 +222,15 @@ CommandFactory::CommandFactory(){
 	commands["indicator"]			= "indicator";
 	commands["consensus.seqs"]		= "consensus.seqs";
 	commands["corr.axes"]			= "corr.axes";
+	commands["pca"]					= "pca";
+	commands["nmds"]				= "nmds";
+	commands["remove.rare"]			= "remove.rare";
+	commands["amova"]				= "amova";
+	commands["homova"]				= "homova";
+	commands["mantel"]				= "mantel";
+	commands["anosim"]				= "anosim";
+	commands["make.fastq"]			= "make.fastq";
+	commands["merge.groups"]		= "merge.groups";
 	commands["pairwise.seqs"]		= "MPIEnabled";
 	commands["pipeline.pds"]		= "MPIEnabled";
 	commands["classify.seqs"]		= "MPIEnabled"; 
@@ -333,7 +351,9 @@ 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);				}
@@ -370,6 +390,13 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "indicator")				{	command = new IndicatorCommand(optionString);				}
 		else if(commandName == "consensus.seqs")		{	command = new ConsensusSeqsCommand(optionString);			}
 		else if(commandName == "corr.axes")				{	command = new CorrAxesCommand(optionString);				}
+		else if(commandName == "remove.rare")			{	command = new RemoveRareCommand(optionString);				}
+		else if(commandName == "merge.groups")			{	command = new MergeGroupsCommand(optionString);				}
+		else if(commandName == "amova")					{	command = new AmovaCommand(optionString);					}
+		else if(commandName == "homova")				{	command = new HomovaCommand(optionString);					}
+		else if(commandName == "mantel")				{	command = new MantelCommand(optionString);					}
+		else if(commandName == "make.fastq")			{	command = new MakeFastQCommand(optionString);				}
+		else if(commandName == "anosim")				{	command = new AnosimCommand(optionString);					}
 		else											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -457,7 +484,9 @@ 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);				}
@@ -493,6 +522,13 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 		else if(commandName == "indicator")				{	pipecommand = new IndicatorCommand(optionString);				}
 		else if(commandName == "consensus.seqs")		{	pipecommand = new ConsensusSeqsCommand(optionString);			}
 		else if(commandName == "corr.axes")				{	pipecommand = new CorrAxesCommand(optionString);				}
+		else if(commandName == "remove.rare")			{	pipecommand = new RemoveRareCommand(optionString);				}
+		else if(commandName == "merge.groups")			{	pipecommand = new MergeGroupsCommand(optionString);				}
+		else if(commandName == "amova")					{	pipecommand = new AmovaCommand(optionString);					}
+		else if(commandName == "homova")				{	pipecommand = new HomovaCommand(optionString);					}
+		else if(commandName == "mantel")				{	pipecommand = new MantelCommand(optionString);					}
+		else if(commandName == "anosim")				{	pipecommand = new AnosimCommand(optionString);					}
+		else if(commandName == "make.fastq")			{	pipecommand = new MakeFastQCommand(optionString);				}
 		else											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -568,7 +604,9 @@ 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();				}
@@ -604,6 +642,13 @@ Command* CommandFactory::getCommand(string commandName){
 		else if(commandName == "indicator")				{	shellcommand = new IndicatorCommand();				}
 		else if(commandName == "consensus.seqs")		{	shellcommand = new ConsensusSeqsCommand();			}
 		else if(commandName == "corr.axes")				{	shellcommand = new CorrAxesCommand();				}
+		else if(commandName == "remove.rare")			{	shellcommand = new RemoveRareCommand();				}
+		else if(commandName == "merge.groups")			{	shellcommand = new MergeGroupsCommand();			}
+		else if(commandName == "amova")					{	shellcommand = new AmovaCommand();					}
+		else if(commandName == "homova")				{	shellcommand = new HomovaCommand();					}
+		else if(commandName == "mantel")				{	shellcommand = new MantelCommand();					}
+		else if(commandName == "anosim")				{	shellcommand = new AnosimCommand();					}
+		else if(commandName == "make.fastq")			{	shellcommand = new MakeFastQCommand();				}
 		else											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;