X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=b361b6600655ff57a987cf7bce9b2b543d96c854;hb=c82900be3ceed3d9bc491bdc98b1819ef85c1af7;hp=48a363336be3bea3a482471608cf7e0ce2300b3e;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 48a3633..b361b66 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"
@@ -33,14 +32,13 @@
 #include "heatmapcommand.h"
 #include "heatmapsimcommand.h"
 #include "filterseqscommand.h"
-#include "mothur.h"
 #include "venncommand.h"
 #include "nocommands.h"
 #include "binsequencecommand.h"
 #include "getoturepcommand.h"
 #include "treegroupscommand.h"
 #include "bootstrapsharedcommand.h"
-#include "concensuscommand.h"
+//#include "consensuscommand.h"
 #include "distancecommand.h"
 #include "aligncommand.h"
 #include "matrixoutputcommand.h"
@@ -50,13 +48,90 @@
 #include "screenseqscommand.h"
 #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"
 
+/*******************************************************/
+
+/******************************************************/
+CommandFactory* CommandFactory::getInstance() {
+	if( _uniqueInstance == 0) {
+		_uniqueInstance = new CommandFactory();
+	}
+	return _uniqueInstance;
+}
 /***********************************************************/
 
 /***********************************************************/
 CommandFactory::CommandFactory(){
+	_uniqueInstance = 0;
 	string s = "";
 	command = new NoCommand(s);
+	
+	
+	//initialize list of valid commands
+	commands["read.dist"]			= "read.dist"; 
+	commands["read.otu"]			= "read.otu";
+	commands["read.tree"]			= "read.tree"; 
+	commands["bin.seqs"]			= "bin.seqs"; 
+	commands["get.oturep"]			= "get.oturep";
+	commands["cluster"]				= "cluster"; 
+	commands["unique.seqs"]			= "unique.seqs"; 
+	commands["dist.seqs"]			= "dist.seqs";
+	commands["dist.shared"]			= "dist.shared";
+	commands["collect.single"]		= "collect.single"; 
+	commands["collect.shared"]		= "collect.shared"; 
+	commands["rarefaction.single"]	= "rarefaction.single"; 
+	commands["rarefaction.shared"]	= "rarefaction.shared"; 
+	commands["summary.single"]		= "summary.single"; 
+	commands["summary.shared"]		= "summary.shared"; 
+	commands["parsimony"]			= "parsimony";
+	commands["unifrac.weighted"]	= "unifrac.weighted"; 
+	commands["unifrac.unweighted"]	= "unifrac.unweighted"; 
+	commands["libshuff"]			= "libshuff";
+	commands["tree.shared"]			= "tree.shared";
+	commands["heatmap.bin"]			= "heatmap.bin";
+	commands["heatmap.sim"]			= "heatmap.sim";
+	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";
+	//commands["consensus"]			= "consensus";
+	commands["help"]				= "help"; 
+	commands["filter.seqs"]			= "filter.seqs";
+	commands["align.seqs"]			= "align.seqs";
+	commands["summary.seqs"]		= "summary.seqs";
+	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";
+
 }
 /***********************************************************/
 
@@ -104,26 +179,90 @@ 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											{	command = new NoCommand(optionString);					}
 
 		return command;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the CommandFactory class Function getCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "CommandFactory", "getCommand");
+		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);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the CommandFactory class function getCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/***********************************************************************/
+bool CommandFactory::isValidCommand(string command) {
+	try {	
+	
+		//is the command in the map
+		if ((commands.find(command)) != (commands.end())) {
+			return true;
+		}else{
+			mothurOut(command + " is not a valid command in Mothur.  Valid commands are ");
+			for (it = commands.begin(); it != commands.end(); it++) {
+				mothurOut(it->first + ", ");
+			}
+			mothurOutEndLine();
+			return false;
+		}
+		
+	}
+	catch(exception& e) {
+		errorOut(e, "CommandFactory", "isValidCommand");
 		exit(1);
 	}
+}
 
+/***********************************************************************/
+void CommandFactory::printCommands(ostream& out) {
+	try {	
+		out << "Valid commands are ";
+		for (it = commands.begin(); it != commands.end(); it++) {
+			out << it->first << ", ";
+		}
+		out << endl;
+	}
+	catch(exception& e) {
+		errorOut(e, "CommandFactory", "printCommands");
+		exit(1);
+	}
 }
-/***********************************************************/
+/***********************************************************************/
+
+
+