#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"
/*******************************************************/
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"] = "get.current";
+ commands["set.current"] = "set.current";
commands["pairwise.seqs"] = "MPIEnabled";
commands["pipeline.pds"] = "MPIEnabled";
commands["classify.seqs"] = "MPIEnabled";
else if(commandName == "pre.cluster") { command = new PreClusterCommand(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 == "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 { command = new NoCommand(optionString); }
return command;
else if(commandName == "pre.cluster") { pipecommand = new PreClusterCommand(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 == "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 { pipecommand = new NoCommand(optionString); }
return pipecommand;
else if(commandName == "pre.cluster") { shellcommand = new PreClusterCommand(); }
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 == "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 { shellcommand = new NoCommand(); }
return shellcommand;