X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=baef2164942f5e637f43d8b3b6431091ef13ca63;hb=a218321731df14d231bbc08e79906f757cf1540d;hp=0da5986187ec2a3d4c2920c854cd34d101529528;hpb=ee4dd201fa4f2c4ede5b2e525c82cce0a37de363;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 0da5986..baef216 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -16,7 +16,6 @@
 #include "collectsharedcommand.h"
 #include "getgroupcommand.h"
 #include "getlabelcommand.h"
-#include "getlinecommand.h"
 #include "rarefactcommand.h"
 #include "summarycommand.h"
 #include "summarysharedcommand.h"
@@ -64,6 +63,8 @@
 #include "preclustercommand.h"
 #include "pcacommand.h"
 #include "otuhierarchycommand.h"
+#include "setdircommand.h"
+#include "parselistscommand.h"
 
 /*******************************************************/
 
@@ -78,10 +79,10 @@ CommandFactory* CommandFactory::getInstance() {
 
 /***********************************************************/
 CommandFactory::CommandFactory(){
-	_uniqueInstance = 0;
 	string s = "";
 	command = new NoCommand(s);
 	
+	outputDir = ""; inputDir = "";
 	
 	//initialize list of valid commands
 	commands["read.dist"]			= "read.dist"; 
@@ -109,7 +110,6 @@ CommandFactory::CommandFactory(){
 	commands["venn"]				= "venn";
 	commands["get.group"]           = "get.group";
 	commands["get.label"]           = "get.label";
-	commands["get.line"]            = "get.line";
 	commands["get.sabund"]          = "get.sabund";
 	commands["get.rabund"]          = "get.rabund";
 	commands["bootstrap.shared"]	= "bootstrap.shared";
@@ -135,14 +135,17 @@ 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";
+	commands["merge.files"]			= "merge.files";
+	commands["parse.list"]			= "parse.list";
 }
 /***********************************************************/
 
 /***********************************************************/
 CommandFactory::~CommandFactory(){
+	_uniqueInstance = 0;
 	delete command;
 }
 
@@ -153,7 +156,19 @@ CommandFactory::~CommandFactory(){
 Command* CommandFactory::getCommand(string commandName, string optionString){
 	try {
 		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 != "") { 
+			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 != "") { 
+			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);				}
 		else if(commandName == "read.tree")				{	command = new ReadTreeCommand(optionString);			}
@@ -172,7 +187,6 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "unifrac.unweighted")	{	command = new UnifracUnweightedCommand(optionString);	}
 		else if(commandName == "get.group")             {   command = new GetgroupCommand(optionString);			}
 		else if(commandName == "get.label")             {   command = new GetlabelCommand(optionString);			}
-		else if(commandName == "get.line")              {   command = new GetlineCommand(optionString);				}
 		else if(commandName == "get.sabund")            {   command = new GetSAbundCommand(optionString);			}
 		else if(commandName == "get.rabund")            {   command = new GetRAbundCommand(optionString);			}
 		else if(commandName == "libshuff")              {   command = new LibShuffCommand(optionString);			}
@@ -206,8 +220,10 @@ 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 if(commandName == "parse.list")			{	command = new ParseListCommand(optionString);			}
 		else											{	command = new NoCommand(optionString);					}
 
 		return command;