#include "reversecommand.h"
#include "trimseqscommand.h"
#include "mergefilecommand.h"
-#include "chimeraseqscommand.h"
#include "listseqscommand.h"
#include "getseqscommand.h"
#include "removeseqscommand.h"
#include "chimeraslayercommand.h"
#include "chimerapintailcommand.h"
#include "chimerabellerophoncommand.h"
+#include "chimerauchimecommand.h"
#include "setlogfilecommand.h"
#include "phylodiversitycommand.h"
#include "makegroupcommand.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"
/*******************************************************/
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";
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";
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["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.pintail"] = "MPIEnabled";
commands["chimera.bellerophon"] = "MPIEnabled";
commands["screen.seqs"] = "MPIEnabled";
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 == "chimera.seqs") { command = new ChimeraSeqsCommand(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 == "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 == "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") { command = new CountSeqsCommand(optionString); }
+ else if(commandName == "count.groups") { command = new CountGroupsCommand(optionString); }
+ else if(commandName == "clear.memory") { command = new ClearMemoryCommand(optionString); }
else { command = new NoCommand(optionString); }
return command;
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 == "chimera.seqs") { pipecommand = new ChimeraSeqsCommand(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 == "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 == "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") { pipecommand = new CountSeqsCommand(optionString); }
+ else if(commandName == "count.groups") { pipecommand = new CountGroupsCommand(optionString); }
+ else if(commandName == "clear.memory") { pipecommand = new ClearMemoryCommand(optionString); }
else { pipecommand = new NoCommand(optionString); }
return pipecommand;
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 == "chimera.seqs") { shellcommand = new ChimeraSeqsCommand(); }
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 == "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 == "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") { shellcommand = new CountSeqsCommand(); }
+ else if(commandName == "count.groups") { shellcommand = new CountGroupsCommand(); }
+ else if(commandName == "clear.memory") { shellcommand = new ClearMemoryCommand(); }
else { shellcommand = new NoCommand(); }
return shellcommand;
projects / mothur.git / blobdiff