#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 "trimflowscommand.h"
#include "corraxescommand.h"
#include "shhhercommand.h"
+#include "pcacommand.h"
+#include "nmdscommand.h"
/*******************************************************/
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";
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";
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); }
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); }
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(); }