X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=a3858639a1f78d633e9c1537054978bac4e4d499;hb=4ba6188707e67c638ea5ee3c787d5d07ccd07e3e;hp=9adf6791505060d7379fbfc387e1ce6f5d9f5afd;hpb=c4fb347858dd8cfea4d2933f429fff4130dca65b;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 9adf679..a385863 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -57,6 +57,9 @@
 #include "secondarystructurecommand.h"
 #include "getsharedotucommand.h"
 #include "getlistcountcommand.h"
+#include "hclustercommand.h"
+#include "classifyseqscommand.h"
+#include "phylotypecommand.h"
 
 /***********************************************************/
 
@@ -110,9 +113,12 @@ 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";
 
 }
 /***********************************************************/
@@ -175,8 +181,11 @@ 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											{	command = new NoCommand(optionString);					}
 
 		return command;
@@ -186,7 +195,22 @@ 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 {