#include "collectsharedcommand.h"
#include "getgroupcommand.h"
#include "getlabelcommand.h"
-#include "getlinecommand.h"
#include "rarefactcommand.h"
#include "summarycommand.h"
#include "summarysharedcommand.h"
#include "hclustercommand.h"
#include "classifyseqscommand.h"
#include "phylotypecommand.h"
+#include "mgclustercommand.h"
+#include "preclustercommand.h"
+#include "pcacommand.h"
+#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"
/*******************************************************/
/***********************************************************/
/***********************************************************/
+//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(){
- _uniqueInstance = 0;
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"] = "dist.seqs";
commands["dist.shared"] = "dist.shared";
commands["collect.single"] = "collect.single";
commands["collect.shared"] = "collect.shared";
commands["venn"] = "venn";
commands["get.group"] = "get.group";
commands["get.label"] = "get.label";
- commands["get.line"] = "get.line";
commands["get.sabund"] = "get.sabund";
commands["get.rabund"] = "get.rabund";
commands["bootstrap.shared"] = "bootstrap.shared";
//commands["consensus"] = "consensus";
- commands["help"] = "help";
- commands["filter.seqs"] = "filter.seqs";
- 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"] = "quit";
commands["hcluster"] = "hcluster";
- commands["classify.seqs"] = "classify.seqs";
commands["phylotype"] = "phylotype";
+ commands["mgcluster"] = "mgcluster";
+ commands["pre.cluster"] = "pre.cluster";
+ commands["pcoa"] = "pcoa";
+ commands["otu.hierarchy"] = "otu.hierarchy";
+ 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["cluster.split"] = "cluster.split";
+ 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["quit"] = "MPIEnabled";
}
/***********************************************************/
+/***********************************************************/
+bool CommandFactory::MPIEnabled(string commandName) {
+ bool mpi = false;
+ it = commands.find(commandName);
+ if (it != commands.end()) {
+ if (it->second == "MPIEnabled") { return true; }
+ }
+ return mpi;
+}
+/***********************************************************/
+
/***********************************************************/
CommandFactory::~CommandFactory(){
+ _uniqueInstance = 0;
delete command;
}
Command* CommandFactory::getCommand(string commandName, string optionString){
try {
delete command; //delete the old command
-
- if(commandName == "read.dist") { command = new ReadDistCommand(optionString); }
- else if(commandName == "read.otu") { command = new ReadOtuCommand(optionString); }
- else if(commandName == "read.tree") { command = new ReadTreeCommand(optionString); }
- else if(commandName == "cluster") { command = new ClusterCommand(optionString); }
- else if(commandName == "unique.seqs") { command = new DeconvoluteCommand(optionString); }
- else if(commandName == "parsimony") { command = new ParsimonyCommand(optionString); }
- else if(commandName == "help") { command = new HelpCommand(optionString); }
- else if(commandName == "quit") { command = new QuitCommand(optionString); }
- else if(commandName == "collect.single") { command = new CollectCommand(optionString); }
- else if(commandName == "collect.shared") { command = new CollectSharedCommand(optionString); }
- else if(commandName == "rarefaction.single") { command = new RareFactCommand(optionString); }
- else if(commandName == "rarefaction.shared") { command = new RareFactSharedCommand(optionString); }
- else if(commandName == "summary.single") { command = new SummaryCommand(optionString); }
- else if(commandName == "summary.shared") { command = new SummarySharedCommand(optionString); }
- else if(commandName == "unifrac.weighted") { command = new UnifracWeightedCommand(optionString); }
- else if(commandName == "unifrac.unweighted") { command = new UnifracUnweightedCommand(optionString); }
- else if(commandName == "get.group") { command = new GetgroupCommand(optionString); }
- else if(commandName == "get.label") { command = new GetlabelCommand(optionString); }
- else if(commandName == "get.line") { command = new GetlineCommand(optionString); }
- else if(commandName == "get.sabund") { command = new GetSAbundCommand(optionString); }
- else if(commandName == "get.rabund") { command = new GetRAbundCommand(optionString); }
- else if(commandName == "libshuff") { command = new LibShuffCommand(optionString); }
- else if(commandName == "heatmap.bin") { command = new HeatMapCommand(optionString); }
- else if(commandName == "heatmap.sim") { command = new HeatMapSimCommand(optionString); }
- else if(commandName == "filter.seqs") { command = new FilterSeqsCommand(optionString); }
- else if(commandName == "venn") { command = new VennCommand(optionString); }
- else if(commandName == "bin.seqs") { command = new BinSeqCommand(optionString); }
- else if(commandName == "get.oturep") { command = new GetOTURepCommand(optionString); }
- 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 == "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 == "screen.seqs") { command = new ScreenSeqsCommand(optionString); }
- else if(commandName == "reverse.seqs") { command = new ReverseSeqsCommand(optionString); }
- else if(commandName == "trim.seqs") { command = new TrimSeqsCommand(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 == "merge.files") { command = new MergeFileCommand(optionString); }
- else if(commandName == "system") { command = new SystemCommand(optionString); }
- else if(commandName == "align.check") { command = new AlignCheckCommand(optionString); }
- else if(commandName == "get.sharedseqs") { command = new GetSharedOTUCommand(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 == "phylotype") { command = new PhylotypeCommand(optionString); }
- else { command = new NoCommand(optionString); }
+
+ //user has opted to redirect output from dir where input files are located to some other place
+ if (outputDir != "") {
+ if (optionString != "") { optionString += ", outputdir=" + outputDir; }
+ else { optionString += "outputdir=" + outputDir; }
+ }
+
+ //user has opted to redirect input from dir where mothur.exe is located to some other place
+ if (inputDir != "") {
+ if (optionString != "") { optionString += ", inputdir=" + inputDir; }
+ else { optionString += "inputdir=" + inputDir; }
+ }
+
+ if(commandName == "read.dist") { command = new ReadDistCommand(optionString); }
+ else if(commandName == "read.otu") { command = new ReadOtuCommand(optionString); }
+ else if(commandName == "read.tree") { command = new ReadTreeCommand(optionString); }
+ else if(commandName == "cluster") { command = new ClusterCommand(optionString); }
+ else if(commandName == "unique.seqs") { command = new DeconvoluteCommand(optionString); }
+ else if(commandName == "parsimony") { command = new ParsimonyCommand(optionString); }
+ else if(commandName == "help") { command = new HelpCommand(optionString); }
+ else if(commandName == "quit") { command = new QuitCommand(optionString); }
+ else if(commandName == "collect.single") { command = new CollectCommand(optionString); }
+ else if(commandName == "collect.shared") { command = new CollectSharedCommand(optionString); }
+ else if(commandName == "rarefaction.single") { command = new RareFactCommand(optionString); }
+ else if(commandName == "rarefaction.shared") { command = new RareFactSharedCommand(optionString); }
+ else if(commandName == "summary.single") { command = new SummaryCommand(optionString); }
+ else if(commandName == "summary.shared") { command = new SummarySharedCommand(optionString); }
+ else if(commandName == "unifrac.weighted") { command = new UnifracWeightedCommand(optionString); }
+ else if(commandName == "unifrac.unweighted") { command = new UnifracUnweightedCommand(optionString); }
+ else if(commandName == "get.group") { command = new GetgroupCommand(optionString); }
+ else if(commandName == "get.label") { command = new GetlabelCommand(optionString); }
+ else if(commandName == "get.sabund") { command = new GetSAbundCommand(optionString); }
+ else if(commandName == "get.rabund") { command = new GetRAbundCommand(optionString); }
+ else if(commandName == "libshuff") { command = new LibShuffCommand(optionString); }
+ else if(commandName == "heatmap.bin") { command = new HeatMapCommand(optionString); }
+ else if(commandName == "heatmap.sim") { command = new HeatMapSimCommand(optionString); }
+ else if(commandName == "filter.seqs") { command = new FilterSeqsCommand(optionString); }
+ else if(commandName == "venn") { command = new VennCommand(optionString); }
+ else if(commandName == "bin.seqs") { command = new BinSeqCommand(optionString); }
+ else if(commandName == "get.oturep") { command = new GetOTURepCommand(optionString); }
+ 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 == "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 == "screen.seqs") { command = new ScreenSeqsCommand(optionString); }
+ else if(commandName == "reverse.seqs") { command = new ReverseSeqsCommand(optionString); }
+ else if(commandName == "trim.seqs") { command = new TrimSeqsCommand(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 == "merge.files") { command = new MergeFileCommand(optionString); }
+ else if(commandName == "system") { command = new SystemCommand(optionString); }
+ else if(commandName == "align.check") { command = new AlignCheckCommand(optionString); }
+ else if(commandName == "get.sharedseqs") { command = new GetSharedOTUCommand(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 { command = new NoCommand(optionString); }
return command;
}
catch(exception& e) {
- errorOut(e, "CommandFactory", "getCommand");
+ m->errorOut(e, "CommandFactory", "getCommand");
exit(1);
}
}
return command;
}
catch(exception& e) {
- errorOut(e, "CommandFactory", "getCommand");
+ m->errorOut(e, "CommandFactory", "getCommand");
exit(1);
}
}
if ((commands.find(command)) != (commands.end())) {
return true;
}else{
- mothurOut(command + " is not a valid command in Mothur. Valid commands are ");
+ m->mothurOut(command + " is not a valid command in Mothur. Valid commands are ");
for (it = commands.begin(); it != commands.end(); it++) {
- mothurOut(it->first + ", ");
+ m->mothurOut(it->first + ", ");
}
- mothurOutEndLine();
+ m->mothurOutEndLine();
return false;
}
}
catch(exception& e) {
- errorOut(e, "CommandFactory", "isValidCommand");
+ m->errorOut(e, "CommandFactory", "isValidCommand");
exit(1);
}
}
out << endl;
}
catch(exception& e) {
- errorOut(e, "CommandFactory", "printCommands");
+ m->errorOut(e, "CommandFactory", "printCommands");
exit(1);
}
}
projects / mothur.git / blobdiff