#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"
/*******************************************************/
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["set.logfile"] = "set.logfile";
commands["anosim"] = "anosim";
commands["make.fastq"] = "make.fastq";
commands["merge.groups"] = "merge.groups";
- commands["get.current"] = "get.current";
- commands["set.current"] = "set.current";
+ 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["chimera.ccode"] = "MPIEnabled";
commands["chimera.check"] = "MPIEnabled";
commands["chimera.slayer"] = "MPIEnabled";
- commands["chimera.uchime"] = "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.seqs"] = "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["quit"] = "MPIEnabled";
}
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 == "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); }
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") { 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 { command = new NoCommand(optionString); }
return command;
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 == "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); }
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") { 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 { pipecommand = new NoCommand(optionString); }
return pipecommand;
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 == "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(); }
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") { 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 { shellcommand = new NoCommand(); }
return shellcommand;