#include "otuhierarchycommand.h"
#include "setdircommand.h"
#include "parselistscommand.h"
+#include "parsesffcommand.h"
+#include "chimeraccodecommand.h"
+#include "chimeracheckcommand.h"
+#include "chimeraslayercommand.h"
+#include "chimerapintailcommand.h"
+#include "chimerabellerophoncommand.h"
+#include "setlogfilecommand.h"
+#include "phylodiversitycommand.h"
+#include "makegroupcommand.h"
+#include "chopseqscommand.h"
+#include "clearcutcommand.h"
+#include "catchallcommand.h"
+#include "splitabundcommand.h"
+#include "clustersplitcommand.h"
+#include "classifyotucommand.h"
+#include "degapseqscommand.h"
+#include "getrelabundcommand.h"
+#include "sensspeccommand.h"
+#include "sffinfocommand.h"
/*******************************************************/
/***********************************************************/
/***********************************************************/
+//note: This class is resposible for knowing which commands are mpiEnabled,
+//If a command is not enabled only process 0 will execute the command.
+//This avoids redundant outputs on pieces of code we have not paralellized.
+//If you add mpi code to a existing command you need to modify the list below or the code will hang on MPI blocking commands like FIle_open.
+//example: commands["dist.seqs"] = "MPIEnabled";
+
CommandFactory::CommandFactory(){
string s = "";
m = MothurOut::getInstance();
command = new NoCommand(s);
outputDir = ""; inputDir = "";
+ logFileName = "";
+ append = false;
//initialize list of valid commands
commands["read.dist"] = "read.dist";
commands["get.oturep"] = "get.oturep";
commands["cluster"] = "cluster";
commands["unique.seqs"] = "unique.seqs";
- commands["dist.seqs"] = "MPIEnabled";
commands["dist.shared"] = "dist.shared";
commands["collect.single"] = "collect.single";
commands["collect.shared"] = "collect.shared";
commands["get.rabund"] = "get.rabund";
commands["bootstrap.shared"] = "bootstrap.shared";
//commands["consensus"] = "consensus";
- commands["help"] = "help";
- commands["filter.seqs"] = "MPIEnabled";
- commands["align.seqs"] = "align.seqs";
- commands["summary.seqs"] = "summary.seqs";
- commands["screen.seqs"] = "screen.seqs";
+ commands["help"] = "help";
commands["reverse.seqs"] = "reverse.seqs";
commands["trim.seqs"] = "trim.seqs";
- commands["chimera.seqs"] = "chimera.seqs";
commands["list.seqs"] = "list.seqs";
commands["get.seqs"] = "get.seqs";
commands["remove.seqs"] = "get.seqs";
commands["align.check"] = "align.check";
commands["get.sharedseqs"] = "get.sharedseqs";
commands["get.otulist"] = "get.otulist";
- commands["quit"] = "MPIEnabled";
commands["hcluster"] = "hcluster";
- commands["classify.seqs"] = "classify.seqs";
commands["phylotype"] = "phylotype";
commands["mgcluster"] = "mgcluster";
commands["pre.cluster"] = "pre.cluster";
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["chop.seqs"] = "chop.seqs";
+ commands["clearcut"] = "clearcut";
+ commands["catchall"] = "catchall";
+ commands["split.abund"] = "split.abund";
+ commands["classify.otu"] = "classify.otu";
+ commands["degap.seqs"] = "degap.seqs";
+ commands["get.relabund"] = "get.relabund";
+ commands["sffinfo"] = "sffinfo";
+ 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.pintail"] = "MPIEnabled";
+ commands["chimera.bellerophon"] = "MPIEnabled";
+ commands["screen.seqs"] = "MPIEnabled";
+ commands["summary.seqs"] = "MPIEnabled";
+ commands["cluster.split"] = "MPIEnabled";
+ commands["sens.spec"] = "sens.spec";
+ commands["quit"] = "MPIEnabled";
+
}
/***********************************************************/
else if(commandName == "tree.shared") { command = new TreeGroupCommand(optionString); }
else if(commandName == "dist.shared") { command = new MatrixOutputCommand(optionString); }
else if(commandName == "bootstrap.shared") { command = new BootSharedCommand(optionString); }
- //else if(commandName == "consensus") { command = new ConcensusCommand(optionString); }
+ else if(commandName == "consensus") { command = new ConcensusCommand(optionString); }
else if(commandName == "dist.seqs") { command = new DistanceCommand(optionString); }
else if(commandName == "align.seqs") { command = new AlignCommand(optionString); }
else if(commandName == "summary.seqs") { command = new SeqSummaryCommand(optionString); }
else if(commandName == "get.otulist") { command = new GetListCountCommand(optionString); }
else if(commandName == "hcluster") { command = new HClusterCommand(optionString); }
else if(commandName == "classify.seqs") { command = new ClassifySeqsCommand(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.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 == "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 == "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 == "clearcut") { command = new ClearcutCommand(optionString); }
+ else if(commandName == "catchall") { command = new CatchAllCommand(optionString); }
+ else if(commandName == "split.abund") { command = new SplitAbundCommand(optionString); }
+ else if(commandName == "cluster.split") { command = new ClusterSplitCommand(optionString); }
+ else if(commandName == "classify.otu") { command = new ClassifyOtuCommand(optionString); }
+ else if(commandName == "degap.seqs") { command = new DegapSeqsCommand(optionString); }
+ else if(commandName == "get.relabund") { command = new GetRelAbundCommand(optionString); }
+ else if(commandName == "sens.spec") { command = new SensSpecCommand(optionString); }
+ else if(commandName == "sffinfo") { command = new SffInfoCommand(optionString); }
else { command = new NoCommand(optionString); }
return command;
/***********************************************************************/
void CommandFactory::printCommands(ostream& out) {
try {
- out << "Valid commands are ";
+ out << "Valid commands are: ";
for (it = commands.begin(); it != commands.end(); it++) {
- out << it->first << ", ";
+ out << it->first << ",";
}
out << endl;
}
projects / mothur.git / blobdiff