X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=ae59a8dcef9c43927b08759108c65f4c63d6a0cb;hb=d04f948b1a2a1a2984fc4a45d04403b8c121c5bc;hp=917ab96e69afa7cf7ad76d2cf85bbb79401e8db4;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 917ab96..ae59a8d 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -61,11 +61,10 @@
 #include "phylotypecommand.h"
 #include "mgclustercommand.h"
 #include "preclustercommand.h"
-#include "pcacommand.h"
+#include "pcoacommand.h"
 #include "otuhierarchycommand.h"
 #include "setdircommand.h"
 #include "parselistscommand.h"
-#include "parsesffcommand.h"
 #include "chimeraccodecommand.h"
 #include "chimeracheckcommand.h"
 #include "chimeraslayercommand.h"
@@ -93,6 +92,21 @@
 #include "removelineagecommand.h"
 #include "parsefastaqcommand.h"
 #include "pipelinepdscommand.h"
+#include "deuniqueseqscommand.h"
+#include "pairwiseseqscommand.h"
+#include "clusterdoturcommand.h"
+#include "subsamplecommand.h"
+#include "removegroupscommand.h"
+#include "getgroupscommand.h"
+#include "getotuscommand.h"
+#include "removeotuscommand.h"
+#include "indicatorcommand.h"
+#include "consensusseqscommand.h"
+#include "trimflowscommand.h"
+#include "corraxescommand.h"
+#include "shhhercommand.h"
+#include "pcacommand.h"
+#include "nmdscommand.h"
 
 /*******************************************************/
 
@@ -156,6 +170,7 @@ CommandFactory::CommandFactory(){
 	commands["help"]				= "help";
 	commands["reverse.seqs"]		= "reverse.seqs";
 	commands["trim.seqs"]			= "trim.seqs";
+	commands["trim.flows"]			= "trim.flows";
 	commands["list.seqs"]			= "list.seqs";
 	commands["get.seqs"]			= "get.seqs";
 	commands["remove.seqs"]			= "get.seqs";
@@ -172,7 +187,6 @@ CommandFactory::CommandFactory(){
 	commands["set.dir"]				= "set.dir";
 	commands["merge.files"]			= "merge.files";
 	commands["parse.list"]			= "parse.list";
-	commands["parse.sff"]			= "parse.sff";
 	commands["set.logfile"]			= "set.logfile";
 	commands["phylo.diversity"]		= "phylo.diversity";
 	commands["make.group"]			= "make.group";
@@ -191,6 +205,19 @@ CommandFactory::CommandFactory(){
 	commands["get.lineage"]			= "get.lineage";
 	commands["remove.lineage"]		= "remove.lineage";
 	commands["fastq.info"]			= "fastq.info";
+	commands["deunique.seqs"]		= "deunique.seqs";
+	commands["cluster.classic"]		= "cluster.classic";
+	commands["sub.sample"]			= "sub.sample";
+	commands["remove.groups"]		= "remove.groups";
+	commands["get.groups"]			= "get.groups";
+	commands["get.otus"]			= "get.otus";
+	commands["remove.otus"]			= "remove.otus";
+	commands["indicator"]			= "indicator";
+	commands["consensus.seqs"]		= "consensus.seqs";
+	commands["corr.axes"]			= "corr.axes";
+	commands["pca"]					= "pca";
+	commands["nmds"]				= "nmds";
+	commands["pairwise.seqs"]		= "MPIEnabled";
 	commands["pipeline.pds"]		= "MPIEnabled";
 	commands["classify.seqs"]		= "MPIEnabled"; 
 	commands["dist.seqs"]			= "MPIEnabled";
@@ -205,6 +232,7 @@ CommandFactory::CommandFactory(){
 	commands["screen.seqs"]			= "MPIEnabled";
 	commands["summary.seqs"]		= "MPIEnabled";
 	commands["cluster.split"]		= "MPIEnabled";
+	commands["shhh.seqs"]			= "MPIEnabled";
 	commands["sens.spec"]			= "sens.spec";
 	commands["seq.error"]			= "seq.error";
 	commands["quit"]				= "MPIEnabled"; 
@@ -288,6 +316,8 @@ Command* CommandFactory::getCommand(string commandName, string 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 == "trim.flows")			{	command = new TrimFlowsCommand(optionString);				}
+		else if(commandName == "shhh.seqs")				{	command = new ShhherCommand(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);					}
@@ -307,12 +337,13 @@ 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 == "pcoa")					{	command = new PCACommand(optionString);						}
+		else if(commandName == "pcoa")					{	command = new PCOACommand(optionString);					}
+		else if(commandName == "pca")					{	command = new PCACommand(optionString);						}
+		else if(commandName == "nmds")					{	command = new NMDSCommand(optionString);					}
 		else if(commandName == "otu.hierarchy")			{	command = new OtuHierarchyCommand(optionString);			}
 		else if(commandName == "set.dir")				{	command = new SetDirectoryCommand(optionString);			}
 		else if(commandName == "set.logfile")			{	command = new SetLogFileCommand(optionString);				}
 		else if(commandName == "parse.list")			{	command = new ParseListCommand(optionString);				}
-		else if(commandName == "parse.sff")				{	command = new ParseSFFCommand(optionString);				}
 		else if(commandName == "phylo.diversity")		{	command = new PhyloDiversityCommand(optionString);			}
 		else if(commandName == "make.group")			{	command = new MakeGroupCommand(optionString);				}
 		else if(commandName == "chop.seqs")				{	command = new ChopSeqsCommand(optionString);				}
@@ -332,8 +363,19 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "cluster.fragments")		{	command = new ClusterFragmentsCommand(optionString);		}
 		else if(commandName == "get.lineage")			{	command = new GetLineageCommand(optionString);				}
 		else if(commandName == "remove.lineage")		{	command = new RemoveLineageCommand(optionString);			}
+		else if(commandName == "get.groups")			{	command = new GetGroupsCommand(optionString);				}
+		else if(commandName == "remove.groups")			{	command = new RemoveGroupsCommand(optionString);			}
+		else if(commandName == "get.otus")				{	command = new GetOtusCommand(optionString);					}
+		else if(commandName == "remove.otus")			{	command = new RemoveOtusCommand(optionString);				}
 		else if(commandName == "fastq.info")			{	command = new ParseFastaQCommand(optionString);				}
 		else if(commandName == "pipeline.pds")			{	command = new PipelineCommand(optionString);				}
+		else if(commandName == "deunique.seqs")			{	command = new DeUniqueSeqsCommand(optionString);			}
+		else if(commandName == "pairwise.seqs")			{	command = new PairwiseSeqsCommand(optionString);			}
+		else if(commandName == "cluster.classic")		{	command = new ClusterDoturCommand(optionString);			}
+		else if(commandName == "sub.sample")			{	command = new SubSampleCommand(optionString);				}
+		else if(commandName == "indicator")				{	command = new IndicatorCommand(optionString);				}
+		else if(commandName == "consensus.seqs")		{	command = new ConsensusSeqsCommand(optionString);			}
+		else if(commandName == "corr.axes")				{	command = new CorrAxesCommand(optionString);				}
 		else											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -400,6 +442,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 		else if(commandName == "screen.seqs")			{	pipecommand = new ScreenSeqsCommand(optionString);				}
 		else if(commandName == "reverse.seqs")			{	pipecommand = new ReverseSeqsCommand(optionString);				}
 		else if(commandName == "trim.seqs")				{	pipecommand = new TrimSeqsCommand(optionString);				}
+		else if(commandName == "trim.flows")			{	pipecommand = new TrimFlowsCommand(optionString);				}
+		else if(commandName == "shhh.seqs")				{	pipecommand = new ShhherCommand(optionString);					}
 		else if(commandName == "chimera.seqs")			{	pipecommand = new ChimeraSeqsCommand(optionString);				}
 		else if(commandName == "list.seqs")				{	pipecommand = new ListSeqsCommand(optionString);				}
 		else if(commandName == "get.seqs")				{	pipecommand = new GetSeqsCommand(optionString);					}
@@ -419,12 +463,13 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 		else if(commandName == "phylotype")				{	pipecommand = new PhylotypeCommand(optionString);				}
 		else if(commandName == "mgcluster")				{	pipecommand = new MGClusterCommand(optionString);				}
 		else if(commandName == "pre.cluster")			{	pipecommand = new PreClusterCommand(optionString);				}
-		else if(commandName == "pcoa")					{	pipecommand = new PCACommand(optionString);						}
+		else if(commandName == "pcoa")					{	pipecommand = new PCOACommand(optionString);					}
+		else if(commandName == "pca")					{	pipecommand = new PCACommand(optionString);						}
+		else if(commandName == "nmds")					{	pipecommand = new NMDSCommand(optionString);					}
 		else if(commandName == "otu.hierarchy")			{	pipecommand = new OtuHierarchyCommand(optionString);			}
 		else if(commandName == "set.dir")				{	pipecommand = new SetDirectoryCommand(optionString);			}
 		else if(commandName == "set.logfile")			{	pipecommand = new SetLogFileCommand(optionString);				}
 		else if(commandName == "parse.list")			{	pipecommand = new ParseListCommand(optionString);				}
-		else if(commandName == "parse.sff")				{	pipecommand = new ParseSFFCommand(optionString);				}
 		else if(commandName == "phylo.diversity")		{	pipecommand = new PhyloDiversityCommand(optionString);			}
 		else if(commandName == "make.group")			{	pipecommand = new MakeGroupCommand(optionString);				}
 		else if(commandName == "chop.seqs")				{	pipecommand = new ChopSeqsCommand(optionString);				}
@@ -443,8 +488,19 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 		else if(commandName == "split.groups")			{	pipecommand = new SplitGroupCommand(optionString);				}
 		else if(commandName == "cluster.fragments")		{	pipecommand = new ClusterFragmentsCommand(optionString);		}
 		else if(commandName == "get.lineage")			{	pipecommand = new GetLineageCommand(optionString);				}
+		else if(commandName == "get.groups")			{	pipecommand = new GetGroupsCommand(optionString);				}
 		else if(commandName == "remove.lineage")		{	pipecommand = new RemoveLineageCommand(optionString);			}
+		else if(commandName == "remove.groups")			{	pipecommand = new RemoveGroupsCommand(optionString);			}
+		else if(commandName == "get.otus")				{	pipecommand = new GetOtusCommand(optionString);					}
+		else if(commandName == "remove.otus")			{	pipecommand = new RemoveOtusCommand(optionString);				}
 		else if(commandName == "fastq.info")			{	pipecommand = new ParseFastaQCommand(optionString);				}
+		else if(commandName == "deunique.seqs")			{	pipecommand = new DeUniqueSeqsCommand(optionString);			}
+		else if(commandName == "pairwise.seqs")			{	pipecommand = new PairwiseSeqsCommand(optionString);			}
+		else if(commandName == "cluster.classic")		{	pipecommand = new ClusterDoturCommand(optionString);			}
+		else if(commandName == "sub.sample")			{	pipecommand = new SubSampleCommand(optionString);				}
+		else if(commandName == "indicator")				{	pipecommand = new IndicatorCommand(optionString);				}
+		else if(commandName == "consensus.seqs")		{	pipecommand = new ConsensusSeqsCommand(optionString);			}
+		else if(commandName == "corr.axes")				{	pipecommand = new CorrAxesCommand(optionString);				}
 		else											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -499,6 +555,8 @@ Command* CommandFactory::getCommand(string commandName){
 		else if(commandName == "screen.seqs")			{	shellcommand = new ScreenSeqsCommand();				}
 		else if(commandName == "reverse.seqs")			{	shellcommand = new ReverseSeqsCommand();			}
 		else if(commandName == "trim.seqs")				{	shellcommand = new TrimSeqsCommand();				}
+		else if(commandName == "trim.flows")			{	shellcommand = new TrimFlowsCommand();				}
+		else if(commandName == "shhh.seqs")				{	shellcommand = new ShhherCommand();					}
 		else if(commandName == "chimera.seqs")			{	shellcommand = new ChimeraSeqsCommand();			}
 		else if(commandName == "list.seqs")				{	shellcommand = new ListSeqsCommand();				}
 		else if(commandName == "get.seqs")				{	shellcommand = new GetSeqsCommand();				}
@@ -518,12 +576,13 @@ Command* CommandFactory::getCommand(string commandName){
 		else if(commandName == "phylotype")				{	shellcommand = new PhylotypeCommand();				}
 		else if(commandName == "mgcluster")				{	shellcommand = new MGClusterCommand();				}
 		else if(commandName == "pre.cluster")			{	shellcommand = new PreClusterCommand();				}
-		else if(commandName == "pcoa")					{	shellcommand = new PCACommand();					}
+		else if(commandName == "pcoa")					{	shellcommand = new PCOACommand();					}
+		else if(commandName == "pca")					{	shellcommand = new PCACommand();					}
+		else if(commandName == "nmds")					{	shellcommand = new NMDSCommand();					}
 		else if(commandName == "otu.hierarchy")			{	shellcommand = new OtuHierarchyCommand();			}
 		else if(commandName == "set.dir")				{	shellcommand = new SetDirectoryCommand();			}
 		else if(commandName == "set.logfile")			{	shellcommand = new SetLogFileCommand();				}
 		else if(commandName == "parse.list")			{	shellcommand = new ParseListCommand();				}
-		else if(commandName == "parse.sff")				{	shellcommand = new ParseSFFCommand();				}
 		else if(commandName == "phylo.diversity")		{	shellcommand = new PhyloDiversityCommand();			}
 		else if(commandName == "make.group")			{	shellcommand = new MakeGroupCommand();				}
 		else if(commandName == "chop.seqs")				{	shellcommand = new ChopSeqsCommand();				}
@@ -543,7 +602,18 @@ Command* CommandFactory::getCommand(string commandName){
 		else if(commandName == "cluster.fragments")		{	shellcommand = new ClusterFragmentsCommand();		}
 		else if(commandName == "get.lineage")			{	shellcommand = new GetLineageCommand();				}
 		else if(commandName == "remove.lineage")		{	shellcommand = new RemoveLineageCommand();			}
+		else if(commandName == "get.groups")			{	shellcommand = new GetGroupsCommand();				}
+		else if(commandName == "remove.groups")			{	shellcommand = new RemoveGroupsCommand();			}
+		else if(commandName == "get.otus")				{	shellcommand = new GetOtusCommand();				}
+		else if(commandName == "remove.otus")			{	shellcommand = new RemoveOtusCommand();				}
 		else if(commandName == "fastq.info")			{	shellcommand = new ParseFastaQCommand();			}
+		else if(commandName == "deunique.seqs")			{	shellcommand = new DeUniqueSeqsCommand();			}
+		else if(commandName == "pairwise.seqs")			{	shellcommand = new PairwiseSeqsCommand();			}
+		else if(commandName == "cluster.classic")		{	shellcommand = new ClusterDoturCommand();			}
+		else if(commandName == "sub.sample")			{	shellcommand = new SubSampleCommand();				}
+		else if(commandName == "indicator")				{	shellcommand = new IndicatorCommand();				}
+		else if(commandName == "consensus.seqs")		{	shellcommand = new ConsensusSeqsCommand();			}
+		else if(commandName == "corr.axes")				{	shellcommand = new CorrAxesCommand();				}
 		else											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;