X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=c787d07e066ae08db298efb849966dcf0782113d;hb=df92022fc75c08b91cefa2c6ca4fd7b23eb480b0;hp=ddb70290936458fdbc5ca85d550fff1bc1d6ea96;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index ddb7029..c787d07 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -134,7 +134,7 @@ CommandFactory::CommandFactory(){
 	commands["phylotype"]			= "phylotype";
 	commands["mgcluster"]			= "mgcluster";
 	commands["pre.cluster"]			= "pre.cluster";
-	commands["pca"]					= "pca";
+	commands["pcoa"]				= "pcoa";
 	commands["otu.hierarchy"]		= "otu.hierarchy";
 	commands["set.dir"]				= "set.dir";
 }
@@ -155,11 +155,16 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		delete command;   //delete the old command
 		
 		//user has opted to redirect output from dir where input files are located to some other place
-		if (outputDir != "") { optionString += ", outputdir=" + outputDir; }
+		if (outputDir != "") { 
+			if (optionString != "") { optionString += ", outputdir=" + outputDir; }
+			else { optionString += "outputdir=" + outputDir; }
+		}
 		
 		//user has opted to redirect input from dir where mothur.exe is located to some other place
-		if (inputDir != "") { optionString += ", inputdir=" + inputDir; }
-
+		if (inputDir != "") { 
+			if (optionString != "") { optionString += ", inputdir=" + inputDir; }
+			else { optionString += "inputdir=" + inputDir; }
+		}
 		
 		if(commandName == "read.dist")					{	command = new ReadDistCommand(optionString);			}
 		else if(commandName == "read.otu")				{	command = new ReadOtuCommand(optionString);				}
@@ -212,7 +217,7 @@ 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 == "pca")					{	command = new PCACommand(optionString);					}
+		else if(commandName == "pcoa")					{	command = new PCACommand(optionString);					}
 		else if(commandName == "otu.hierarchy")			{	command = new OtuHierarchyCommand(optionString);		}
 		else if(commandName == "set.dir")				{	command = new SetDirectoryCommand(optionString);	}
 		else											{	command = new NoCommand(optionString);					}