X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=5eb4ff5df0eaf4999808925e658e61c1eedccf31;hb=80eb270cc07e78155b82264e16cbb6bc8ade55ce;hp=2783aa3acfe56a38d2479af5696e542f2228693b;hpb=b9456b1087ade74251792e039f4e5021dbf32349;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 2783aa3..5eb4ff5 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"
@@ -52,7 +51,29 @@
 #include "chimeraseqscommand.h"
 #include "listseqscommand.h"
 #include "getseqscommand.h"
+#include "removeseqscommand.h"
+#include "systemcommand.h"
+#include "secondarystructurecommand.h"
+#include "getsharedotucommand.h"
+#include "getlistcountcommand.h"
+#include "hclustercommand.h"
+#include "classifyseqscommand.h"
+#include "phylotypecommand.h"
+#include "mgclustercommand.h"
+#include "preclustercommand.h"
+#include "pcacommand.h"
+#include "otuhierarchycommand.h"
+#include "setdircommand.h"
 
+/*******************************************************/
+
+/******************************************************/
+CommandFactory* CommandFactory::getInstance() {
+	if( _uniqueInstance == 0) {
+		_uniqueInstance = new CommandFactory();
+	}
+	return _uniqueInstance;
+}
 /***********************************************************/
 
 /***********************************************************/
@@ -60,6 +81,7 @@ CommandFactory::CommandFactory(){
 	string s = "";
 	command = new NoCommand(s);
 	
+	outputDir = ""; inputDir = "";
 	
 	//initialize list of valid commands
 	commands["read.dist"]			= "read.dist"; 
@@ -87,7 +109,6 @@ 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";
@@ -102,13 +123,26 @@ CommandFactory::CommandFactory(){
 	commands["chimera.seqs"]		= "chimera.seqs";
 	commands["list.seqs"]			= "list.seqs";
 	commands["get.seqs"]			= "get.seqs";
+	commands["remove.seqs"]			= "get.seqs";
+	commands["system"]				= "system";
+	commands["align.check"]			= "align.check";
+	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";
+	commands["set.dir"]				= "set.dir";
 }
 /***********************************************************/
 
 /***********************************************************/
 CommandFactory::~CommandFactory(){
+	_uniqueInstance = 0;
 	delete command;
 }
 
@@ -119,7 +153,19 @@ 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);			}
@@ -138,7 +184,6 @@ 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);			}
@@ -161,7 +206,20 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "chimera.seqs")			{	command = new ChimeraSeqsCommand(optionString);			}
 		else if(commandName == "list.seqs")				{	command = new ListSeqsCommand(optionString);			}
 		else if(commandName == "get.seqs")				{	command = new GetSeqsCommand(optionString);				}
+		else if(commandName == "remove.seqs")			{	command = new RemoveSeqsCommand(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.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 if(commandName == "set.dir")				{	command = new SetDirectoryCommand(optionString);	}
 		else											{	command = new NoCommand(optionString);					}
 
 		return command;
@@ -171,7 +229,22 @@ 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 {