#include "summarytaxcommand.h"
#include "chimeraperseuscommand.h"
#include "shhhseqscommand.h"
#include "summarytaxcommand.h"
#include "chimeraperseuscommand.h"
#include "shhhseqscommand.h"
commands["pre.cluster"] = "pre.cluster";
commands["pcoa"] = "pcoa";
commands["otu.hierarchy"] = "otu.hierarchy";
commands["pre.cluster"] = "pre.cluster";
commands["pcoa"] = "pcoa";
commands["otu.hierarchy"] = "otu.hierarchy";
commands["merge.files"] = "merge.files";
commands["parse.list"] = "parse.list";
commands["set.logfile"] = "set.logfile";
commands["merge.files"] = "merge.files";
commands["parse.list"] = "parse.list";
commands["set.logfile"] = "set.logfile";
commands["anosim"] = "anosim";
commands["make.fastq"] = "make.fastq";
commands["merge.groups"] = "merge.groups";
commands["anosim"] = "anosim";
commands["make.fastq"] = "make.fastq";
commands["merge.groups"] = "merge.groups";
commands["get.commandinfo"] = "get.commandinfo";
commands["deunique.tree"] = "deunique.tree";
commands["count.seqs"] = "count.seqs";
commands["get.commandinfo"] = "get.commandinfo";
commands["deunique.tree"] = "deunique.tree";
commands["count.seqs"] = "count.seqs";
commands["sens.spec"] = "sens.spec";
commands["seq.error"] = "seq.error";
commands["summary.tax"] = "summary.tax";
commands["sens.spec"] = "sens.spec";
commands["seq.error"] = "seq.error";
commands["summary.tax"] = "summary.tax";
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 == "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 == "chimera.perseus") { command = new ChimeraPerseusCommand(optionString); }
else if(commandName == "shhh.seqs") { command = new ShhhSeqsCommand(optionString); }
else if(commandName == "chimera.perseus") { command = new ChimeraPerseusCommand(optionString); }
else if(commandName == "shhh.seqs") { command = new ShhhSeqsCommand(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 == "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 == "chimera.perseus") { pipecommand = new ChimeraPerseusCommand(optionString); }
else if(commandName == "shhh.seqs") { pipecommand = new ShhhSeqsCommand(optionString); }
else if(commandName == "chimera.perseus") { pipecommand = new ChimeraPerseusCommand(optionString); }
else if(commandName == "shhh.seqs") { pipecommand = new ShhhSeqsCommand(optionString); }
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 == "count.groups") { shellcommand = new CountGroupsCommand(); }
else if(commandName == "clear.memory") { shellcommand = new ClearMemoryCommand(); }
else if(commandName == "summary.tax") { shellcommand = new SummaryTaxCommand(); }
else if(commandName == "chimera.perseus") { shellcommand = new ChimeraPerseusCommand(); }
else if(commandName == "shhh.seqs") { shellcommand = new ShhhSeqsCommand(); }
else if(commandName == "chimera.perseus") { shellcommand = new ChimeraPerseusCommand(); }
else if(commandName == "shhh.seqs") { shellcommand = new ShhhSeqsCommand(); }