X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=0da5986187ec2a3d4c2920c854cd34d101529528;hb=ee4dd201fa4f2c4ede5b2e525c82cce0a37de363;hp=030079ed21e3a6d4f35263f45d46a67878715e5b;hpb=63e089e0b3aad1741bab60119ed7ccc784dce347;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 030079e..0da5986 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -59,11 +59,26 @@
 #include "getlistcountcommand.h"
 #include "hclustercommand.h"
 #include "classifyseqscommand.h"
+#include "phylotypecommand.h"
+#include "mgclustercommand.h"
+#include "preclustercommand.h"
+#include "pcacommand.h"
+#include "otuhierarchycommand.h"
 
+/*******************************************************/
+
+/******************************************************/
+CommandFactory* CommandFactory::getInstance() {
+	if( _uniqueInstance == 0) {
+		_uniqueInstance = new CommandFactory();
+	}
+	return _uniqueInstance;
+}
 /***********************************************************/
 
 /***********************************************************/
 CommandFactory::CommandFactory(){
+	_uniqueInstance = 0;
 	string s = "";
 	command = new NoCommand(s);
 	
@@ -112,11 +127,16 @@ CommandFactory::CommandFactory(){
 	commands["remove.seqs"]			= "get.seqs";
 	commands["system"]				= "system";
 	commands["align.check"]			= "align.check";
-	commands["get.sharedotu"]		= "get.sharedotu";
-	commands["get.listcount"]		= "get.listcount";
+	commands["get.sharedseqs"]		= "get.sharedseqs";
+	commands["get.otulist"]			= "get.otulist";
 	commands["quit"]				= "quit"; 
 	commands["hcluster"]			= "hcluster"; 
 	commands["classify.seqs"]		= "classify.seqs"; 
+	commands["phylotype"]			= "phylotype";
+	commands["mgcluster"]			= "mgcluster";
+	commands["pre.cluster"]			= "pre.cluster";
+	commands["pca"]					= "pca";
+	commands["otu.hierarchy"]		= "otu.hierarchy";
 
 }
 /***********************************************************/
@@ -179,10 +199,15 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "merge.files")			{	command = new MergeFileCommand(optionString);			}
 		else if(commandName == "system")				{	command = new SystemCommand(optionString);				}
 		else if(commandName == "align.check")			{	command = new AlignCheckCommand(optionString);			}
-		else if(commandName == "get.sharedotu")			{	command = new GetSharedOTUCommand(optionString);		}
-		else if(commandName == "get.listcount")			{	command = new GetListCountCommand(optionString);		}
+		else if(commandName == "get.sharedseqs")		{	command = new GetSharedOTUCommand(optionString);		}
+		else if(commandName == "get.otulist")			{	command = new GetListCountCommand(optionString);		}
 		else if(commandName == "hcluster")				{	command = new HClusterCommand(optionString);			}
 		else if(commandName == "classify.seqs")			{	command = new ClassifySeqsCommand(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 == "pca")					{	command = new PCACommand(optionString);					}
+		else if(commandName == "otu.hierarchy")			{	command = new OtuHierarchyCommand(optionString);		}
 		else											{	command = new NoCommand(optionString);					}
 
 		return command;
@@ -192,7 +217,22 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		exit(1);
 	}
 }
+/***********************************************************/
+//This function is used to interrupt a command
+Command* CommandFactory::getCommand(){
+	try {
+		delete command;   //delete the old command
 
+		string s = "";
+	    command = new NoCommand(s);
+	
+		return command;
+	}
+	catch(exception& e) {
+		errorOut(e, "CommandFactory", "getCommand");
+		exit(1);
+	}
+}
 /***********************************************************************/
 bool CommandFactory::isValidCommand(string command) {
 	try {