X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=9b6411855b19a8cee7a9f5a4489d8fc522a689c8;hb=0024441c1ff9a98467ba53cc7420a37c98f32e86;hp=6e62995c32306cbcd0c9c9259ae0317a8ff706f9;hpb=fd282e6b4be2560f5b1bd154a9e8d24b798eefaf;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 6e62995..9b64118 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -9,21 +9,43 @@
 
 #include "command.hpp"
 #include "readdistcommand.h"
+#include "readtreecommand.h"
 #include "readotucommand.h"
 #include "clustercommand.h"
 #include "parselistcommand.h"
 #include "collectcommand.h"
 #include "collectsharedcommand.h"
+#include "getgroupcommand.h"
+#include "getlabelcommand.h"
+#include "getlinecommand.h"
 #include "rarefactcommand.h"
 #include "summarycommand.h"
 #include "summarysharedcommand.h"
 #include "rarefactsharedcommand.h"
-#include "nocommand.h"
 #include "quitcommand.h"
 #include "helpcommand.h"
 #include "commandfactory.hpp"
 #include "deconvolutecommand.h"
-#include <exception>
+#include "parsimonycommand.h"
+#include "unifracunweightedcommand.h"
+#include "unifracweightedcommand.h"
+#include "libshuffcommand.h"
+#include "heatmapcommand.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 "distancecommand.h"
+#include "aligncommand.h"
+#include "matrixoutputcommand.h"
+#include "getsabundcommand.h"
+#include "getrabundcommand.h"
+#include "seqsummarycommand.h"
 
 
 /***********************************************************/
@@ -32,7 +54,6 @@
 CommandFactory::CommandFactory(){
 	command = new NoCommand();
 }
-
 /***********************************************************/
 
 /***********************************************************/
@@ -48,19 +69,41 @@ Command* CommandFactory::getCommand(string commandName){
 	try {
 		delete command;   //delete the old command
 
-			 if(commandName == "read.dist")				{	command = new ReadDistCommand();		}
-		else if(commandName == "read.otu")				{	command = new ReadOtuCommand();			}
-		else if(commandName == "cluster")				{	command = new ClusterCommand();			}
-		else if(commandName == "deconvolute")			{	command = new DeconvoluteCommand();		}
-		else if(commandName == "help")					{	command = new HelpCommand();			}
-		else if(commandName == "quit")					{	command = new QuitCommand();			}
-		else if(commandName == "collect.single")		{	command = new CollectCommand();			}
-		else if(commandName == "collect.shared")		{	command = new CollectSharedCommand();	}
-		else if(commandName == "rarefaction.single")	{	command = new RareFactCommand();		}
-		else if(commandName == "rarefaction.shared")	{	command = new RareFactSharedCommand();	}
-		else if(commandName == "summary.single")		{	command = new SummaryCommand();			}
-		else if(commandName == "summary.shared")		{	command = new SummarySharedCommand();	}
-		else											{	command = new NoCommand();				}
+			 if(commandName == "read.dist")				{	command = new ReadDistCommand();			}
+		else if(commandName == "read.otu")				{	command = new ReadOtuCommand();				}
+		else if(commandName == "read.tree")				{	command = new ReadTreeCommand();			}
+		else if(commandName == "cluster")				{	command = new ClusterCommand();				}
+		else if(commandName == "deconvolute")			{	command = new DeconvoluteCommand();			}
+		else if(commandName == "parsimony")				{	command = new ParsimonyCommand();			}
+		else if(commandName == "help")					{	command = new HelpCommand();				}
+		else if(commandName == "quit")					{	command = new QuitCommand();				}
+		else if(commandName == "collect.single")		{	command = new CollectCommand();				}
+		else if(commandName == "collect.shared")		{	command = new CollectSharedCommand();		}
+		else if(commandName == "rarefaction.single")	{	command = new RareFactCommand();			}
+		else if(commandName == "rarefaction.shared")	{	command = new RareFactSharedCommand();		}
+		else if(commandName == "summary.single")		{	command = new SummaryCommand();				}
+		else if(commandName == "summary.shared")		{	command = new SummarySharedCommand();		}
+		else if(commandName == "unifrac.weighted")		{	command = new UnifracWeightedCommand();		}
+		else if(commandName == "unifrac.unweighted")	{	command = new UnifracUnweightedCommand();	}
+		else if(commandName == "get.group")             {   command = new GetgroupCommand();			}
+		else if(commandName == "get.label")             {   command = new GetlabelCommand();			}
+		else if(commandName == "get.line")              {   command = new GetlineCommand();				}
+		else if(commandName == "get.sabund")            {   command = new GetSAbundCommand();			}
+		else if(commandName == "get.rabund")            {   command = new GetRAbundCommand();			}
+		else if(commandName == "libshuff")              {   command = new LibShuffCommand();			}
+		else if(commandName == "heatmap")				{   command = new HeatMapCommand();				}
+		else if(commandName == "filter.seqs")			{   command = new FilterSeqsCommand();          }
+		else if(commandName == "venn")					{   command = new VennCommand();				}
+		else if(commandName == "bin.seqs")				{   command = new BinSeqCommand();				}
+		else if(commandName == "get.oturep")			{   command = new GetOTURepCommand();			}
+		else if(commandName == "tree.shared")			{   command = new TreeGroupCommand();			}
+		else if(commandName == "dist.shared")			{   command = new MatrixOutputCommand();		}
+		else if(commandName == "bootstrap.shared")		{   command = new BootSharedCommand();			}
+		else if(commandName == "concensus")				{   command = new ConcensusCommand();			}
+		else if(commandName == "dist.seqs")				{   command = new DistanceCommand();			}
+		else if(commandName == "align.seqs")			{   command = new AlignCommand();				}
+		else if(commandName == "summary.seqs")			{	command = new SeqSummaryCommand();			}
+		else											{	command = new NoCommand();					}
 
 		return command;
 	}
@@ -76,4 +119,3 @@ Command* CommandFactory::getCommand(string commandName){
 }
 /***********************************************************/
 
-/***********************************************************/
\ No newline at end of file