X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=commandfactory.cpp;h=387ee10833323300a66a0e6d1161a64bff6fb9ee;hp=a4d6506df3128579158f2f1ff5ee99f67bfc9bc2;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=f09bacac01a842a74c1c1b69070852cc969ff506

diff --git a/commandfactory.cpp b/commandfactory.cpp
index a4d6506..387ee10 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -8,9 +8,6 @@
  */
 
 #include "command.hpp"
-#include "readdistcommand.h"
-#include "readtreecommand.h"
-#include "readotucommand.h"
 #include "clustercommand.h"
 #include "collectcommand.h"
 #include "collectsharedcommand.h"
@@ -36,8 +33,6 @@
 #include "binsequencecommand.h"
 #include "getoturepcommand.h"
 #include "treegroupscommand.h"
-#include "bootstrapsharedcommand.h"
-//#include "consensuscommand.h"
 #include "distancecommand.h"
 #include "aligncommand.h"
 #include "matrixoutputcommand.h"
@@ -48,7 +43,6 @@
 #include "reversecommand.h"
 #include "trimseqscommand.h"
 #include "mergefilecommand.h"
-#include "chimeraseqscommand.h"
 #include "listseqscommand.h"
 #include "getseqscommand.h"
 #include "removeseqscommand.h"
@@ -61,16 +55,16 @@
 #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"
 #include "chimerapintailcommand.h"
 #include "chimerabellerophoncommand.h"
+#include "chimerauchimecommand.h"
 #include "setlogfilecommand.h"
 #include "phylodiversitycommand.h"
 #include "makegroupcommand.h"
@@ -94,7 +88,62 @@
 #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"
+#include "removerarecommand.h"
+#include "mergegroupscommand.h"
+#include "amovacommand.h"
+#include "homovacommand.h"
+#include "mantelcommand.h"
+#include "makefastqcommand.h"
+#include "anosimcommand.h"
+#include "getcurrentcommand.h"
+#include "setcurrentcommand.h"
+#include "sharedcommand.h"
+#include "getcommandinfocommand.h"
+#include "deuniquetreecommand.h"
+#include "countseqscommand.h"
+#include "countgroupscommand.h"
+#include "clearmemorycommand.h"
+#include "summarytaxcommand.h"
+#include "chimeraperseuscommand.h"
+#include "shhhseqscommand.h"
+#include "summaryqualcommand.h"
+#include "otuassociationcommand.h"
+#include "sortseqscommand.h"
+#include "classifytreecommand.h"
+#include "cooccurrencecommand.h"
+#include "pcrseqscommand.h"
+#include "createdatabasecommand.h"
+#include "makebiomcommand.h"
+#include "getcoremicrobiomecommand.h"
+#include "listotulabelscommand.h"
+#include "getotulabelscommand.h"
+#include "removeotulabelscommand.h"
+#include "makecontigscommand.h"
+#include "loadlogfilecommand.h"
+#include "sffmultiplecommand.h"
+#include "classifysharedcommand.h"
+#include "filtersharedcommand.h"
+#include "primerdesigncommand.h"
+#include "getdistscommand.h"
+#include "removedistscommand.h"
+#include "mergetaxsummarycommand.h"
+#include "getmetacommunitycommand.h"
+#include "sparcccommand.h"
+#include "makelookupcommand.h"
 
 /*******************************************************/
 
@@ -127,9 +176,7 @@ CommandFactory::CommandFactory(){
 	append = false;
 	
 	//initialize list of valid commands
-	commands["read.dist"]			= "read.dist"; 
-	commands["read.otu"]			= "read.otu";
-	commands["read.tree"]			= "read.tree"; 
+	commands["make.shared"]			= "make.shared"; 
 	commands["bin.seqs"]			= "bin.seqs"; 
 	commands["get.oturep"]			= "get.oturep";
 	commands["cluster"]				= "cluster"; 
@@ -153,14 +200,13 @@ CommandFactory::CommandFactory(){
 	commands["get.label"]           = "get.label";
 	commands["get.sabund"]          = "get.sabund";
 	commands["get.rabund"]          = "get.rabund";
-	commands["bootstrap.shared"]	= "bootstrap.shared";
-	//commands["consensus"]			= "consensus";
 	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";
+	commands["remove.seqs"]			= "remove.seqs";
 	commands["system"]				= "system";
 	commands["align.check"]			= "align.check";
 	commands["get.sharedseqs"]		= "get.sharedseqs";
@@ -171,10 +217,9 @@ CommandFactory::CommandFactory(){
 	commands["pre.cluster"]			= "pre.cluster";
 	commands["pcoa"]				= "pcoa";
 	commands["otu.hierarchy"]		= "otu.hierarchy";
-	commands["set.dir"]				= "set.dir";
+	commands["set.dir"]				= "MPIEnabled";
 	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";
@@ -194,23 +239,79 @@ CommandFactory::CommandFactory(){
 	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["remove.rare"]			= "remove.rare";
+	commands["amova"]				= "amova";
+	commands["homova"]				= "homova";
+	commands["mantel"]				= "mantel";
+	commands["anosim"]				= "anosim";
+	commands["make.fastq"]			= "make.fastq";
+	commands["merge.groups"]		= "merge.groups";
+	commands["get.current"]			= "MPIEnabled";
+	commands["set.current"]			= "MPIEnabled";
+	commands["get.commandinfo"]		= "get.commandinfo";
+	commands["deunique.tree"]		= "deunique.tree";
+	commands["count.seqs"]			= "count.seqs";
+	commands["count.groups"]		= "count.groups";
+	commands["clear.memory"]		= "clear.memory";
+	commands["pairwise.seqs"]		= "MPIEnabled";
 	commands["pipeline.pds"]		= "MPIEnabled";
 	commands["classify.seqs"]		= "MPIEnabled"; 
 	commands["dist.seqs"]			= "MPIEnabled";
 	commands["filter.seqs"]			= "MPIEnabled";
 	commands["align.seqs"]			= "MPIEnabled";
-	commands["chimera.seqs"]		= "chimera.seqs";
 	commands["chimera.ccode"]		= "MPIEnabled";
 	commands["chimera.check"]		= "MPIEnabled";
 	commands["chimera.slayer"]		= "MPIEnabled";
+	commands["chimera.uchime"]		= "chimera.uchime";
+	commands["chimera.perseus"]		= "chimera.perseus";
 	commands["chimera.pintail"]		= "MPIEnabled";
 	commands["chimera.bellerophon"]	= "MPIEnabled";
 	commands["screen.seqs"]			= "MPIEnabled";
 	commands["summary.seqs"]		= "MPIEnabled";
 	commands["cluster.split"]		= "MPIEnabled";
+	commands["shhh.flows"]			= "MPIEnabled";
 	commands["sens.spec"]			= "sens.spec";
 	commands["seq.error"]			= "seq.error";
+	commands["summary.tax"]			= "summary.tax";
+	commands["summary.qual"]		= "summary.qual";
+	commands["shhh.seqs"]			= "shhh.seqs";
+	commands["otu.association"]		= "otu.association";
+    commands["sort.seqs"]           = "sort.seqs";
+    commands["classify.tree"]       = "classify.tree";
+    commands["cooccurrence"]        = "cooccurrence";
+    commands["pcr.seqs"]            = "pcr.seqs";
+    commands["create.database"]     = "create.database";
+    commands["make.biom"]           = "make.biom";
+    commands["get.coremicrobiome"]  = "get.coremicrobiome";
+    commands["list.otulabels"]      = "list.otulabels";
+    commands["get.otulabels"]       = "get.otulabels";
+    commands["remove.otulabels"]    = "remove.otulabels";
+    commands["make.contigs"]        = "make.contigs";
+    commands["load.logfile"]        = "load.logfile";
+    commands["make.table"]          = "make.table";
+    commands["sff.multiple"]        = "sff.multiple";
 	commands["quit"]				= "MPIEnabled"; 
+    commands["classify.shared"]		= "classify.shared"; 
+    commands["filter.shared"]		= "filter.shared"; 
+    commands["primer.design"]		= "primer.design";
+    commands["get.dists"]           = "get.dists";
+    commands["remove.dists"]        = "remove.dists";
+    commands["merge.taxsummary"]    = "merge.taxsummary";
+    commands["get.metacommunity"]   = "get.metacommunity";
+    commands["sparcc"]              = "sparcc";
+    commands["make.lookup"]         = "make.lookup";
+    
 
 }
 /***********************************************************/
@@ -233,15 +334,60 @@ CommandFactory::~CommandFactory(){
 	delete shellcommand;
 	delete pipecommand;
 }
+/***********************************************************/
 
+/***********************************************************/
+int CommandFactory::checkForRedirects(string optionString) {
+    try {
+        
+        int pos = optionString.find("outputdir");
+        if (pos != string::npos) { //user has set outputdir in command option string
+            string outputOption = "";
+            bool foundEquals = false;
+            for(int i=pos;i<optionString.length();i++){
+                if(optionString[i] == ',')       { break;               }		
+                else if(optionString[i] == '=')  { foundEquals = true;	}
+                if (foundEquals)       {   outputOption += optionString[i]; }
+            }
+            if(m->dirCheck(outputOption)){ 
+                setOutputDirectory(outputOption); 
+                m->mothurOut("Setting output directory to: " + outputOption); m->mothurOutEndLine();
+            }
+        }
+        
+        pos = optionString.find("inputdir");
+        if (pos != string::npos) { //user has set inputdir in command option string
+            string intputOption = "";
+            bool foundEquals = false;
+            for(int i=pos;i<optionString.length();i++){
+                if(optionString[i] == ',')       { break;               }		
+                else if(optionString[i] == '=')  { foundEquals = true;	}
+                if (foundEquals)       {   intputOption += optionString[i]; }
+            }
+            if(m->dirCheck(intputOption)){ 
+                setInputDirectory(intputOption); 
+                m->mothurOut("Setting input directory to: " + intputOption); m->mothurOutEndLine();
+            }
+        }
+        
+        return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "CommandFactory", "getCommand");
+		exit(1);
+	}
+}
 /***********************************************************/
 
 /***********************************************************/
 //This function calls the appropriate command fucntions based on user input.
 Command* CommandFactory::getCommand(string commandName, string optionString){
 	try {
+        
 		delete command;   //delete the old command
-		
+        
+        checkForRedirects(optionString);
+        		
 		//user has opted to redirect output from dir where input files are located to some other place
 		if (outputDir != "") { 
 			if (optionString != "") { optionString += ", outputdir=" + outputDir; }
@@ -254,10 +400,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 			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);				}
-		else if(commandName == "cluster")				{	command = new ClusterCommand(optionString);					}
+		if(commandName == "cluster")				{	command = new ClusterCommand(optionString);					}
 		else if(commandName == "unique.seqs")			{	command = new DeconvoluteCommand(optionString);				}
 		else if(commandName == "parsimony")				{	command = new ParsimonyCommand(optionString);				}
 		else if(commandName == "help")					{	command = new HelpCommand(optionString);					}
@@ -283,15 +426,14 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "get.oturep")			{   command = new GetOTURepCommand(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 == "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 == "trim.flows")			{	command = new TrimFlowsCommand(optionString);				}
+		else if(commandName == "shhh.flows")			{	command = new ShhherCommand(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);				}
@@ -305,17 +447,19 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "chimera.ccode")			{	command = new ChimeraCcodeCommand(optionString);			}
 		else if(commandName == "chimera.check")			{	command = new ChimeraCheckCommand(optionString);			}
 		else if(commandName == "chimera.slayer")		{	command = new ChimeraSlayerCommand(optionString);			}
+		else if(commandName == "chimera.uchime")		{	command = new ChimeraUchimeCommand(optionString);			}
 		else if(commandName == "chimera.pintail")		{	command = new ChimeraPintailCommand(optionString);			}
 		else if(commandName == "chimera.bellerophon")	{	command = new ChimeraBellerophonCommand(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);				}
@@ -335,9 +479,61 @@ 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 if(commandName == "remove.rare")			{	command = new RemoveRareCommand(optionString);				}
+		else if(commandName == "merge.groups")			{	command = new MergeGroupsCommand(optionString);				}
+		else if(commandName == "amova")					{	command = new AmovaCommand(optionString);					}
+		else if(commandName == "homova")				{	command = new HomovaCommand(optionString);					}
+		else if(commandName == "mantel")				{	command = new MantelCommand(optionString);					}
+		else if(commandName == "make.fastq")			{	command = new MakeFastQCommand(optionString);				}
+		else if(commandName == "get.current")			{	command = new GetCurrentCommand(optionString);				}
+		else if(commandName == "set.current")			{	command = new SetCurrentCommand(optionString);				}
+		else if(commandName == "anosim")				{	command = new AnosimCommand(optionString);					}
+		else if(commandName == "make.shared")			{	command = new SharedCommand(optionString);					}
+		else if(commandName == "get.commandinfo")		{	command = new GetCommandInfoCommand(optionString);			}
+		else if(commandName == "deunique.tree")			{	command = new DeuniqueTreeCommand(optionString);			}
+		else if((commandName == "count.seqs") || (commandName == "make.table"))			{	command = new CountSeqsCommand(optionString);				}
+		else if(commandName == "count.groups")			{	command = new CountGroupsCommand(optionString);				}
+		else if(commandName == "clear.memory")			{	command = new ClearMemoryCommand(optionString);				}
+		else if(commandName == "summary.tax")			{	command = new SummaryTaxCommand(optionString);				}
+		else if(commandName == "summary.qual")			{	command = new SummaryQualCommand(optionString);				}
+		else if(commandName == "chimera.perseus")		{	command = new ChimeraPerseusCommand(optionString);			}
+		else if(commandName == "shhh.seqs")				{	command = new ShhhSeqsCommand(optionString);				}
+		else if(commandName == "otu.association")		{	command = new OTUAssociationCommand(optionString);			}
+        else if(commandName == "sort.seqs")             {	command = new SortSeqsCommand(optionString);                }
+        else if(commandName == "classify.tree")         {	command = new ClassifyTreeCommand(optionString);            }
+        else if(commandName == "cooccurrence")          {	command = new CooccurrenceCommand(optionString);            }
+        else if(commandName == "pcr.seqs")              {	command = new PcrSeqsCommand(optionString);                 }
+        else if(commandName == "create.database")       {	command = new CreateDatabaseCommand(optionString);          }
+        else if(commandName == "make.biom")             {	command = new MakeBiomCommand(optionString);                }
+        else if(commandName == "get.coremicrobiome")    {	command = new GetCoreMicroBiomeCommand(optionString);       }
+        else if(commandName == "list.otulabels")        {	command = new ListOtuLabelsCommand(optionString);           }
+        else if(commandName == "get.otulabels")         {	command = new GetOtuLabelsCommand(optionString);            }
+        else if(commandName == "remove.otulabels")      {	command = new RemoveOtuLabelsCommand(optionString);         }
+        else if(commandName == "make.contigs")          {	command = new MakeContigsCommand(optionString);             }
+        else if(commandName == "load.logfile")          {	command = new LoadLogfileCommand(optionString);             }
+        else if(commandName == "sff.multiple")          {	command = new SffMultipleCommand(optionString);             }
+        else if(commandName == "classify.shared")       {	command = new ClassifySharedCommand(optionString);          }
+        else if(commandName == "filter.shared")         {	command = new FilterSharedCommand(optionString);            }
+        else if(commandName == "primer.design")         {	command = new PrimerDesignCommand(optionString);            }
+        else if(commandName == "get.dists")             {	command = new GetDistsCommand(optionString);                }
+        else if(commandName == "remove.dists")          {	command = new RemoveDistsCommand(optionString);             }
+        else if(commandName == "merge.taxsummary")      {	command = new MergeTaxSummaryCommand(optionString);         }
+        else if(commandName == "get.metacommunity")     {	command = new GetMetaCommunityCommand(optionString);        }
+        else if(commandName == "sparcc")                {	command = new SparccCommand(optionString);                  }
+        else if(commandName == "make.lookup")			{	command = new MakeLookupCommand(optionString);				}
 		else											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -355,6 +551,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 	try {
 		delete pipecommand;   //delete the old command
 		
+        checkForRedirects(optionString);
+        
 		//user has opted to redirect output from dir where input files are located to some other place
 		if (outputDir != "") { 
 			if (optionString != "") { optionString += ", outputdir=" + outputDir; }
@@ -367,10 +565,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 			else { optionString += "inputdir=" + inputDir; }
 		}
 		
-		if(commandName == "read.dist")					{	pipecommand = new ReadDistCommand(optionString);				}
-		else if(commandName == "read.otu")				{	pipecommand = new ReadOtuCommand(optionString);					}
-		else if(commandName == "read.tree")				{	pipecommand = new ReadTreeCommand(optionString);				}
-		else if(commandName == "cluster")				{	pipecommand = new ClusterCommand(optionString);					}
+		if(commandName == "cluster")				{	pipecommand = new ClusterCommand(optionString);					}
 		else if(commandName == "unique.seqs")			{	pipecommand = new DeconvoluteCommand(optionString);				}
 		else if(commandName == "parsimony")				{	pipecommand = new ParsimonyCommand(optionString);				}
 		else if(commandName == "help")					{	pipecommand = new HelpCommand(optionString);					}
@@ -396,15 +591,14 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 		else if(commandName == "get.oturep")			{   pipecommand = new GetOTURepCommand(optionString);				}
 		else if(commandName == "tree.shared")			{   pipecommand = new TreeGroupCommand(optionString);				}
 		else if(commandName == "dist.shared")			{   pipecommand = new MatrixOutputCommand(optionString);			}
-		else if(commandName == "bootstrap.shared")		{   pipecommand = new BootSharedCommand(optionString);				}
-		else if(commandName == "consensus")				{   pipecommand = new ConcensusCommand(optionString);				}
 		else if(commandName == "dist.seqs")				{   pipecommand = new DistanceCommand(optionString);				}
 		else if(commandName == "align.seqs")			{   pipecommand = new AlignCommand(optionString);					}
 		else if(commandName == "summary.seqs")			{	pipecommand = new SeqSummaryCommand(optionString);				}
 		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 == "chimera.seqs")			{	pipecommand = new ChimeraSeqsCommand(optionString);				}
+		else if(commandName == "trim.flows")			{	pipecommand = new TrimFlowsCommand(optionString);				}
+		else if(commandName == "shhh.flows")			{	pipecommand = new ShhherCommand(optionString);					}
 		else if(commandName == "list.seqs")				{	pipecommand = new ListSeqsCommand(optionString);				}
 		else if(commandName == "get.seqs")				{	pipecommand = new GetSeqsCommand(optionString);					}
 		else if(commandName == "remove.seqs")			{	pipecommand = new RemoveSeqsCommand(optionString);				}
@@ -417,18 +611,20 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 		else if(commandName == "classify.seqs")			{	pipecommand = new ClassifySeqsCommand(optionString);			}
 		else if(commandName == "chimera.ccode")			{	pipecommand = new ChimeraCcodeCommand(optionString);			}
 		else if(commandName == "chimera.check")			{	pipecommand = new ChimeraCheckCommand(optionString);			}
+		else if(commandName == "chimera.uchime")		{	pipecommand = new ChimeraUchimeCommand(optionString);			}
 		else if(commandName == "chimera.slayer")		{	pipecommand = new ChimeraSlayerCommand(optionString);			}
 		else if(commandName == "chimera.pintail")		{	pipecommand = new ChimeraPintailCommand(optionString);			}
 		else if(commandName == "chimera.bellerophon")	{	pipecommand = new ChimeraBellerophonCommand(optionString);		}
 		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);				}
@@ -447,9 +643,61 @@ 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 if(commandName == "remove.rare")			{	pipecommand = new RemoveRareCommand(optionString);				}
+		else if(commandName == "merge.groups")			{	pipecommand = new MergeGroupsCommand(optionString);				}
+		else if(commandName == "amova")					{	pipecommand = new AmovaCommand(optionString);					}
+		else if(commandName == "homova")				{	pipecommand = new HomovaCommand(optionString);					}
+		else if(commandName == "mantel")				{	pipecommand = new MantelCommand(optionString);					}
+		else if(commandName == "anosim")				{	pipecommand = new AnosimCommand(optionString);					}
+		else if(commandName == "make.fastq")			{	pipecommand = new MakeFastQCommand(optionString);				}
+		else if(commandName == "get.current")			{	pipecommand = new GetCurrentCommand(optionString);				}
+		else if(commandName == "set.current")			{	pipecommand = new SetCurrentCommand(optionString);				}
+		else if(commandName == "make.shared")			{	pipecommand = new SharedCommand(optionString);					}
+		else if(commandName == "get.commandinfo")		{	pipecommand = new GetCommandInfoCommand(optionString);			}
+		else if(commandName == "deunique.tree")			{	pipecommand = new DeuniqueTreeCommand(optionString);			}
+		else if((commandName == "count.seqs") || (commandName == "make.table"))			{	pipecommand = new CountSeqsCommand(optionString);				}
+		else if(commandName == "count.groups")			{	pipecommand = new CountGroupsCommand(optionString);				}
+		else if(commandName == "clear.memory")			{	pipecommand = new ClearMemoryCommand(optionString);				}
+		else if(commandName == "summary.tax")			{	pipecommand = new SummaryTaxCommand(optionString);				}
+		else if(commandName == "summary.qual")			{	pipecommand = new SummaryQualCommand(optionString);				}
+		else if(commandName == "chimera.perseus")		{	pipecommand = new ChimeraPerseusCommand(optionString);			}
+		else if(commandName == "shhh.seqs")				{	pipecommand = new ShhhSeqsCommand(optionString);				}
+		else if(commandName == "otu.association")		{	pipecommand = new OTUAssociationCommand(optionString);			}
+        else if(commandName == "sort.seqs")             {	pipecommand = new SortSeqsCommand(optionString);                }
+        else if(commandName == "classify.tree")         {	pipecommand = new ClassifyTreeCommand(optionString);            }
+        else if(commandName == "cooccurrence")          {	pipecommand = new CooccurrenceCommand(optionString);            }
+        else if(commandName == "pcr.seqs")              {	pipecommand = new PcrSeqsCommand(optionString);                 }
+        else if(commandName == "create.database")       {	pipecommand = new CreateDatabaseCommand(optionString);          }
+        else if(commandName == "make.biom")             {	pipecommand = new MakeBiomCommand(optionString);                }
+        else if(commandName == "get.coremicrobiome")    {	pipecommand = new GetCoreMicroBiomeCommand(optionString);       }
+        else if(commandName == "list.otulabels")        {	pipecommand = new ListOtuLabelsCommand(optionString);           }
+        else if(commandName == "get.otulabels")         {	pipecommand = new GetOtuLabelsCommand(optionString);            }
+        else if(commandName == "remove.otulabels")      {	pipecommand = new RemoveOtuLabelsCommand(optionString);         }
+        else if(commandName == "make.contigs")          {	pipecommand = new MakeContigsCommand(optionString);             }
+        else if(commandName == "load.logfile")          {	pipecommand = new LoadLogfileCommand(optionString);             }
+        else if(commandName == "sff.multiple")          {	pipecommand = new SffMultipleCommand(optionString);             }
+        else if(commandName == "classify.shared")       {	pipecommand = new ClassifySharedCommand(optionString);          }
+        else if(commandName == "filter.shared")         {	pipecommand = new FilterSharedCommand(optionString);            }
+        else if(commandName == "primer.design")         {	pipecommand = new PrimerDesignCommand(optionString);            }
+        else if(commandName == "get.dists")             {	pipecommand = new GetDistsCommand(optionString);                }
+        else if(commandName == "remove.dists")          {	pipecommand = new RemoveDistsCommand(optionString);             }
+        else if(commandName == "merge.taxsummary")      {	pipecommand = new MergeTaxSummaryCommand(optionString);         }
+        else if(commandName == "get.metacommunity")     {	pipecommand = new GetMetaCommunityCommand(optionString);        }
+        else if(commandName == "sparcc")                {	pipecommand = new SparccCommand(optionString);                  }
+        else if(commandName == "make.lookup")			{	pipecommand = new MakeLookupCommand(optionString);				}
 		else											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -467,10 +715,7 @@ Command* CommandFactory::getCommand(string commandName){
 	try {
 		delete shellcommand;   //delete the old command
 		
-		if(commandName == "read.dist")					{	shellcommand = new ReadDistCommand();				}
-		else if(commandName == "read.otu")				{	shellcommand = new ReadOtuCommand();				}
-		else if(commandName == "read.tree")				{	shellcommand = new ReadTreeCommand();				}
-		else if(commandName == "cluster")				{	shellcommand = new ClusterCommand();				}
+		if(commandName == "cluster")				{	shellcommand = new ClusterCommand();				}
 		else if(commandName == "unique.seqs")			{	shellcommand = new DeconvoluteCommand();			}
 		else if(commandName == "parsimony")				{	shellcommand = new ParsimonyCommand();				}
 		else if(commandName == "help")					{	shellcommand = new HelpCommand();					}
@@ -496,15 +741,14 @@ Command* CommandFactory::getCommand(string commandName){
 		else if(commandName == "get.oturep")			{   shellcommand = new GetOTURepCommand();				}
 		else if(commandName == "tree.shared")			{   shellcommand = new TreeGroupCommand();				}
 		else if(commandName == "dist.shared")			{   shellcommand = new MatrixOutputCommand();			}
-		else if(commandName == "bootstrap.shared")		{   shellcommand = new BootSharedCommand();				}
-		else if(commandName == "consensus")				{   shellcommand = new ConcensusCommand();				}
 		else if(commandName == "dist.seqs")				{   shellcommand = new DistanceCommand();				}
 		else if(commandName == "align.seqs")			{   shellcommand = new AlignCommand();					}
 		else if(commandName == "summary.seqs")			{	shellcommand = new SeqSummaryCommand();				}
 		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 == "chimera.seqs")			{	shellcommand = new ChimeraSeqsCommand();			}
+		else if(commandName == "trim.flows")			{	shellcommand = new TrimFlowsCommand();				}
+		else if(commandName == "shhh.flows")			{	shellcommand = new ShhherCommand();					}
 		else if(commandName == "list.seqs")				{	shellcommand = new ListSeqsCommand();				}
 		else if(commandName == "get.seqs")				{	shellcommand = new GetSeqsCommand();				}
 		else if(commandName == "remove.seqs")			{	shellcommand = new RemoveSeqsCommand();				}
@@ -518,17 +762,19 @@ Command* CommandFactory::getCommand(string commandName){
 		else if(commandName == "chimera.ccode")			{	shellcommand = new ChimeraCcodeCommand();			}
 		else if(commandName == "chimera.check")			{	shellcommand = new ChimeraCheckCommand();			}
 		else if(commandName == "chimera.slayer")		{	shellcommand = new ChimeraSlayerCommand();			}
+		else if(commandName == "chimera.uchime")		{	shellcommand = new ChimeraUchimeCommand();			}
 		else if(commandName == "chimera.pintail")		{	shellcommand = new ChimeraPintailCommand();			}
 		else if(commandName == "chimera.bellerophon")	{	shellcommand = new ChimeraBellerophonCommand();		}
 		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();				}
@@ -548,8 +794,60 @@ 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 if(commandName == "remove.rare")			{	shellcommand = new RemoveRareCommand();				}
+		else if(commandName == "merge.groups")			{	shellcommand = new MergeGroupsCommand();			}
+		else if(commandName == "amova")					{	shellcommand = new AmovaCommand();					}
+		else if(commandName == "homova")				{	shellcommand = new HomovaCommand();					}
+		else if(commandName == "mantel")				{	shellcommand = new MantelCommand();					}
+		else if(commandName == "anosim")				{	shellcommand = new AnosimCommand();					}
+		else if(commandName == "make.fastq")			{	shellcommand = new MakeFastQCommand();				}
+		else if(commandName == "get.current")			{	shellcommand = new GetCurrentCommand();				}
+		else if(commandName == "set.current")			{	shellcommand = new SetCurrentCommand();				}
+		else if(commandName == "make.shared")			{	shellcommand = new SharedCommand();					}
+		else if(commandName == "get.commandinfo")		{	shellcommand = new GetCommandInfoCommand();			}
+		else if(commandName == "deunique.tree")			{	shellcommand = new DeuniqueTreeCommand();			}
+		else if((commandName == "count.seqs") || (commandName == "make.table"))			{	shellcommand = new CountSeqsCommand();				}
+		else if(commandName == "count.groups")			{	shellcommand = new CountGroupsCommand();			}
+		else if(commandName == "clear.memory")			{	shellcommand = new ClearMemoryCommand();			}
+		else if(commandName == "summary.tax")			{	shellcommand = new SummaryTaxCommand();				}
+		else if(commandName == "summary.qual")			{	shellcommand = new SummaryQualCommand();			}
+		else if(commandName == "chimera.perseus")		{	shellcommand = new ChimeraPerseusCommand();			}
+		else if(commandName == "shhh.seqs")				{	shellcommand = new ShhhSeqsCommand();				}
+		else if(commandName == "otu.association")		{	shellcommand = new OTUAssociationCommand();			}
+        else if(commandName == "sort.seqs")             {	shellcommand = new SortSeqsCommand();               }
+        else if(commandName == "classify.tree")         {	shellcommand = new ClassifyTreeCommand();           }
+        else if(commandName == "cooccurrence")          {	shellcommand = new CooccurrenceCommand();           }
+        else if(commandName == "pcr.seqs")              {	shellcommand = new PcrSeqsCommand();                }
+        else if(commandName == "create.database")       {	shellcommand = new CreateDatabaseCommand();         }
+        else if(commandName == "make.biom")             {	shellcommand = new MakeBiomCommand();               }
+        else if(commandName == "get.coremicrobiome")    {	shellcommand = new GetCoreMicroBiomeCommand();      }
+        else if(commandName == "list.otulabels")        {	shellcommand = new ListOtuLabelsCommand();          }
+        else if(commandName == "get.otulabels")         {	shellcommand = new GetOtuLabelsCommand();           }
+        else if(commandName == "remove.otulabels")      {	shellcommand = new RemoveOtuLabelsCommand();        }
+        else if(commandName == "make.contigs")          {	shellcommand = new MakeContigsCommand();            }
+        else if(commandName == "load.logfile")          {	shellcommand = new LoadLogfileCommand();            }
+        else if(commandName == "sff.multiple")          {	shellcommand = new SffMultipleCommand();            }
+        else if(commandName == "classify.shared")       {	shellcommand = new ClassifySharedCommand();         }
+        else if(commandName == "filter.shared")         {	shellcommand = new FilterSharedCommand();           }
+        else if(commandName == "primer.design")         {	shellcommand = new PrimerDesignCommand();           }
+        else if(commandName == "get.dists")             {	shellcommand = new GetDistsCommand();               }
+        else if(commandName == "remove.dists")          {	shellcommand = new RemoveDistsCommand();            }
+        else if(commandName == "merge.taxsummary")      {	shellcommand = new MergeTaxSummaryCommand();        }
+        else if(commandName == "get.metacommunity")     {	shellcommand = new GetMetaCommunityCommand();       }
+        else if(commandName == "sparcc")                {	shellcommand = new SparccCommand();                 }
+        else if(commandName == "make.lookup")			{	shellcommand = new MakeLookupCommand();				}
 		else											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;
@@ -575,7 +873,7 @@ Command* CommandFactory::getCommand(){
 		exit(1);
 	}
 }
-/***********************************************************************/
+***********************************************************************/
 bool CommandFactory::isValidCommand(string command) {
 	try {	
 	
@@ -629,6 +927,41 @@ void CommandFactory::printCommands(ostream& out) {
 	}
 }
 /***********************************************************************/
+void CommandFactory::printCommandsCategories(ostream& out) {
+    try {
+        map<string, string> commands = getListCommands();
+        map<string, string>::iterator it;
+
+        map<string, string> categories;
+        map<string, string>::iterator itCat;
+        //loop through each command outputting info
+        for (it = commands.begin(); it != commands.end(); it++) {
+    
+            Command* thisCommand = getCommand(it->first);
+    
+            //don't add hidden commands
+            if (thisCommand->getCommandCategory() != "Hidden") {
+                itCat = categories.find(thisCommand->getCommandCategory());
+                if (itCat == categories.end()) {
+                    categories[thisCommand->getCommandCategory()] = thisCommand->getCommandName();
+                }else {
+                    categories[thisCommand->getCommandCategory()] += ", " + thisCommand->getCommandName();
+                }
+            }
+        }
+        
+        for (itCat = categories.begin(); itCat != categories.end(); itCat++) {
+            out << itCat->first << " commmands include: " << itCat->second << endl;
+        }
+
+    }
+	catch(exception& e) {
+		m->errorOut(e, "CommandFactory", "printCommandsCategories");
+		exit(1);
+	}
+}      
+
+/***********************************************************************/