X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=2417d8dda900fe4aac1cdf0d4ebea36209c2796c;hb=f27b66ce6415eb14c434f9850019c7cf140e023e;hp=db11f8c0dc890dff846787dee0fc48ea8930384a;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index db11f8c..2417d8d 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -12,7 +12,6 @@
 #include "readtreecommand.h"
 #include "readotucommand.h"
 #include "clustercommand.h"
-#include "parselistcommand.h"
 #include "collectcommand.h"
 #include "collectsharedcommand.h"
 #include "getgroupcommand.h"
@@ -39,7 +38,7 @@
 #include "getoturepcommand.h"
 #include "treegroupscommand.h"
 #include "bootstrapsharedcommand.h"
-#include "concensuscommand.h"
+//#include "consensuscommand.h"
 #include "distancecommand.h"
 #include "aligncommand.h"
 #include "matrixoutputcommand.h"
@@ -50,11 +49,35 @@
 #include "reversecommand.h"
 #include "trimseqscommand.h"
 #include "mergefilecommand.h"
+#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"
 
+/*******************************************************/
+
+/******************************************************/
+CommandFactory* CommandFactory::getInstance() {
+	if( _uniqueInstance == 0) {
+		_uniqueInstance = new CommandFactory();
+	}
+	return _uniqueInstance;
+}
 /***********************************************************/
 
 /***********************************************************/
 CommandFactory::CommandFactory(){
+	_uniqueInstance = 0;
 	string s = "";
 	command = new NoCommand(s);
 	
@@ -89,7 +112,7 @@ CommandFactory::CommandFactory(){
 	commands["get.sabund"]          = "get.sabund";
 	commands["get.rabund"]          = "get.rabund";
 	commands["bootstrap.shared"]	= "bootstrap.shared";
-	commands["concensus"]			= "concensus";
+	//commands["consensus"]			= "consensus";
 	commands["help"]				= "help"; 
 	commands["filter.seqs"]			= "filter.seqs";
 	commands["align.seqs"]			= "align.seqs";
@@ -97,7 +120,21 @@ CommandFactory::CommandFactory(){
 	commands["screen.seqs"]			= "screen.seqs";
 	commands["reverse.seqs"]		= "reverse.seqs";
 	commands["trim.seqs"]			= "trim.seqs";
+	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";
 
 }
 /***********************************************************/
@@ -146,14 +183,28 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "tree.shared")			{   command = new TreeGroupCommand(optionString);			}
 		else if(commandName == "dist.shared")			{   command = new MatrixOutputCommand(optionString);		}
 		else if(commandName == "bootstrap.shared")		{   command = new BootSharedCommand(optionString);			}
-		else if(commandName == "concensus")				{   command = new ConcensusCommand(optionString);			}
+		//else if(commandName == "consensus")			{   command = new ConcensusCommand(optionString);			}
 		else if(commandName == "dist.seqs")				{   command = new DistanceCommand(optionString);			}
 		else if(commandName == "align.seqs")			{   command = new AlignCommand(optionString);				}
 		else if(commandName == "summary.seqs")			{	command = new SeqSummaryCommand(optionString);			}
 		else if(commandName == "screen.seqs")			{	command = new ScreenSeqsCommand(optionString);			}
 		else if(commandName == "reverse.seqs")			{	command = new ReverseSeqsCommand(optionString);			}
 		else if(commandName == "trim.seqs")				{	command = new TrimSeqsCommand(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											{	command = new NoCommand(optionString);					}
 
 		return command;
@@ -163,7 +214,22 @@ 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 {