#include "reversecommand.h"
#include "trimseqscommand.h"
#include "mergefilecommand.h"
-#include "chimeraseqscommand.h"
#include "listseqscommand.h"
#include "getseqscommand.h"
#include "removeseqscommand.h"
#include "phylotypecommand.h"
#include "mgclustercommand.h"
#include "preclustercommand.h"
-#include "pcacommand.h"
+#include "pcoacommand.h"
#include "otuhierarchycommand.h"
#include "setdircommand.h"
#include "parselistscommand.h"
+#include "chimeraccodecommand.h"
+#include "chimeracheckcommand.h"
+#include "chimeraslayercommand.h"
+#include "chimerapintailcommand.h"
+#include "chimerabellerophoncommand.h"
+#include "chimerauchimecommand.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"
+#include "seqerrorcommand.h"
+#include "normalizesharedcommand.h"
+#include "metastatscommand.h"
+#include "splitgroupscommand.h"
+#include "clusterfragmentscommand.h"
+#include "getlineagecommand.h"
+#include "removelineagecommand.h"
+#include "parsefastaqcommand.h"
+#include "pipelinepdscommand.h"
+#include "deuniqueseqscommand.h"
+#include "pairwiseseqscommand.h"
+#include "clusterdoturcommand.h"
+#include "subsamplecommand.h"
+#include "removegroupscommand.h"
+#include "getgroupscommand.h"
+#include "getotuscommand.h"
+#include "removeotuscommand.h"
+#include "indicatorcommand.h"
+#include "consensusseqscommand.h"
+#include "trimflowscommand.h"
+#include "corraxescommand.h"
+#include "shhhercommand.h"
+#include "pcacommand.h"
+#include "nmdscommand.h"
+#include "removerarecommand.h"
+#include "mergegroupscommand.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"
+#include "summarytaxcommand.h"
+#include "chimeraperseuscommand.h"
+#include "shhhseqscommand.h"
+#include "summaryqualcommand.h"
+#include "otuassociationcommand.h"
+#include "sortseqscommand.h"
+#include "classifytreecommand.h"
+#include "cooccurrencecommand.h"
+#include "pcrseqscommand.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);
+ shellcommand = new NoCommand(s);
+ pipecommand = new NoCommand(s);
outputDir = ""; inputDir = "";
+ logFileName = "";
+ append = false;
//initialize list of valid commands
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["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["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["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["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["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["normalize.shared"] = "normalize.shared";
+ commands["metastats"] = "metastats";
+ commands["split.groups"] = "split.groups";
+ commands["cluster.fragments"] = "cluster.fragments";
+ commands["get.lineage"] = "get.lineage";
+ commands["remove.lineage"] = "remove.lineage";
+ commands["fastq.info"] = "fastq.info";
+ commands["deunique.seqs"] = "deunique.seqs";
+ commands["cluster.classic"] = "cluster.classic";
+ commands["sub.sample"] = "sub.sample";
+ commands["remove.groups"] = "remove.groups";
+ commands["get.groups"] = "get.groups";
+ commands["get.otus"] = "get.otus";
+ commands["remove.otus"] = "remove.otus";
+ commands["indicator"] = "indicator";
+ commands["consensus.seqs"] = "consensus.seqs";
+ commands["corr.axes"] = "corr.axes";
+ commands["pca"] = "pca";
+ commands["nmds"] = "nmds";
+ commands["remove.rare"] = "remove.rare";
+ 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"] = "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["dist.seqs"] = "MPIEnabled";
+ commands["filter.seqs"] = "MPIEnabled";
+ commands["align.seqs"] = "MPIEnabled";
+ commands["chimera.ccode"] = "MPIEnabled";
+ commands["chimera.check"] = "MPIEnabled";
+ commands["chimera.slayer"] = "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.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["sort.seqs"] = "sort.seqs";
+ commands["classify.tree"] = "classify.tree";
+ commands["cooccurrence"] = "cooccurrence";
+ commands["pcr.seqs"] = "pcr.seqs";
+ commands["quit"] = "MPIEnabled";
+
}
/***********************************************************/
CommandFactory::~CommandFactory(){
_uniqueInstance = 0;
delete command;
+ delete shellcommand;
+ delete pipecommand;
}
/***********************************************************/
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 == "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 == "trim.flows") { command = new TrimFlowsCommand(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 == "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.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 == "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 == "pcoa") { command = new PCOACommand(optionString); }
+ else if(commandName == "pca") { command = new PCACommand(optionString); }
+ else if(commandName == "nmds") { command = new NMDSCommand(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 == "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 == "seq.error") { command = new SeqErrorCommand(optionString); }
+ else if(commandName == "sffinfo") { command = new SffInfoCommand(optionString); }
+ else if(commandName == "normalize.shared") { command = new NormalizeSharedCommand(optionString); }
+ else if(commandName == "metastats") { command = new MetaStatsCommand(optionString); }
+ else if(commandName == "split.groups") { command = new SplitGroupCommand(optionString); }
+ else if(commandName == "cluster.fragments") { command = new ClusterFragmentsCommand(optionString); }
+ else if(commandName == "get.lineage") { command = new GetLineageCommand(optionString); }
+ else if(commandName == "remove.lineage") { command = new RemoveLineageCommand(optionString); }
+ else if(commandName == "get.groups") { command = new GetGroupsCommand(optionString); }
+ else if(commandName == "remove.groups") { command = new RemoveGroupsCommand(optionString); }
+ else if(commandName == "get.otus") { command = new GetOtusCommand(optionString); }
+ else if(commandName == "remove.otus") { command = new RemoveOtusCommand(optionString); }
+ else if(commandName == "fastq.info") { command = new ParseFastaQCommand(optionString); }
+ else if(commandName == "pipeline.pds") { command = new PipelineCommand(optionString); }
+ else if(commandName == "deunique.seqs") { command = new DeUniqueSeqsCommand(optionString); }
+ else if(commandName == "pairwise.seqs") { command = new PairwiseSeqsCommand(optionString); }
+ else if(commandName == "cluster.classic") { command = new ClusterDoturCommand(optionString); }
+ else if(commandName == "sub.sample") { command = new SubSampleCommand(optionString); }
+ else if(commandName == "indicator") { command = new IndicatorCommand(optionString); }
+ else if(commandName == "consensus.seqs") { command = new ConsensusSeqsCommand(optionString); }
+ else if(commandName == "corr.axes") { command = new CorrAxesCommand(optionString); }
+ else if(commandName == "remove.rare") { command = new RemoveRareCommand(optionString); }
+ else if(commandName == "merge.groups") { command = new MergeGroupsCommand(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 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 if(commandName == "sort.seqs") { command = new SortSeqsCommand(optionString); }
+ else if(commandName == "classify.tree") { command = new ClassifyTreeCommand(optionString); }
+ else if(commandName == "cooccurrence") { command = new CooccurrenceCommand(optionString); }
+ else if(commandName == "pcr.seqs") { command = new PcrSeqsCommand(optionString); }
else { command = new NoCommand(optionString); }
return command;
}
}
/***********************************************************/
+
+/***********************************************************/
+//This function calls the appropriate command fucntions based on user input.
+Command* CommandFactory::getCommand(string commandName, string optionString, string mode){
+ try {
+ delete pipecommand; //delete the old command
+
+ //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") { pipecommand = new ReadDistCommand(optionString); }
+ else if(commandName == "read.otu") { pipecommand = new ReadOtuCommand(optionString); }
+ else if(commandName == "read.tree") { pipecommand = new ReadTreeCommand(optionString); }
+ else if(commandName == "cluster") { pipecommand = new ClusterCommand(optionString); }
+ else if(commandName == "unique.seqs") { pipecommand = new DeconvoluteCommand(optionString); }
+ else if(commandName == "parsimony") { pipecommand = new ParsimonyCommand(optionString); }
+ else if(commandName == "help") { pipecommand = new HelpCommand(optionString); }
+ else if(commandName == "quit") { pipecommand = new QuitCommand(optionString); }
+ else if(commandName == "collect.single") { pipecommand = new CollectCommand(optionString); }
+ else if(commandName == "collect.shared") { pipecommand = new CollectSharedCommand(optionString); }
+ else if(commandName == "rarefaction.single") { pipecommand = new RareFactCommand(optionString); }
+ else if(commandName == "rarefaction.shared") { pipecommand = new RareFactSharedCommand(optionString); }
+ else if(commandName == "summary.single") { pipecommand = new SummaryCommand(optionString); }
+ else if(commandName == "summary.shared") { pipecommand = new SummarySharedCommand(optionString); }
+ else if(commandName == "unifrac.weighted") { pipecommand = new UnifracWeightedCommand(optionString); }
+ else if(commandName == "unifrac.unweighted") { pipecommand = new UnifracUnweightedCommand(optionString); }
+ else if(commandName == "get.group") { pipecommand = new GetgroupCommand(optionString); }
+ else if(commandName == "get.label") { pipecommand = new GetlabelCommand(optionString); }
+ else if(commandName == "get.sabund") { pipecommand = new GetSAbundCommand(optionString); }
+ else if(commandName == "get.rabund") { pipecommand = new GetRAbundCommand(optionString); }
+ else if(commandName == "libshuff") { pipecommand = new LibShuffCommand(optionString); }
+ else if(commandName == "heatmap.bin") { pipecommand = new HeatMapCommand(optionString); }
+ else if(commandName == "heatmap.sim") { pipecommand = new HeatMapSimCommand(optionString); }
+ else if(commandName == "filter.seqs") { pipecommand = new FilterSeqsCommand(optionString); }
+ else if(commandName == "venn") { pipecommand = new VennCommand(optionString); }
+ else if(commandName == "bin.seqs") { pipecommand = new BinSeqCommand(optionString); }
+ else if(commandName == "get.oturep") { pipecommand = new GetOTURepCommand(optionString); }
+ else if(commandName == "tree.shared") { pipecommand = new TreeGroupCommand(optionString); }
+ else if(commandName == "dist.shared") { pipecommand = new MatrixOutputCommand(optionString); }
+ else if(commandName == "bootstrap.shared") { pipecommand = new BootSharedCommand(optionString); }
+ else if(commandName == "consensus") { pipecommand = new ConcensusCommand(optionString); }
+ else if(commandName == "dist.seqs") { pipecommand = new DistanceCommand(optionString); }
+ else if(commandName == "align.seqs") { pipecommand = new AlignCommand(optionString); }
+ else if(commandName == "summary.seqs") { pipecommand = new SeqSummaryCommand(optionString); }
+ else if(commandName == "screen.seqs") { pipecommand = new ScreenSeqsCommand(optionString); }
+ 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.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 == "merge.files") { pipecommand = new MergeFileCommand(optionString); }
+ else if(commandName == "system") { pipecommand = new SystemCommand(optionString); }
+ else if(commandName == "align.check") { pipecommand = new AlignCheckCommand(optionString); }
+ else if(commandName == "get.sharedseqs") { pipecommand = new GetSharedOTUCommand(optionString); }
+ else if(commandName == "get.otulist") { pipecommand = new GetListCountCommand(optionString); }
+ else if(commandName == "hcluster") { pipecommand = new HClusterCommand(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 == "phylotype") { pipecommand = new PhylotypeCommand(optionString); }
+ else if(commandName == "mgcluster") { pipecommand = new MGClusterCommand(optionString); }
+ else if(commandName == "pre.cluster") { pipecommand = new PreClusterCommand(optionString); }
+ else if(commandName == "pcoa") { pipecommand = new PCOACommand(optionString); }
+ else if(commandName == "pca") { pipecommand = new PCACommand(optionString); }
+ else if(commandName == "nmds") { pipecommand = new NMDSCommand(optionString); }
+ else if(commandName == "otu.hierarchy") { pipecommand = new OtuHierarchyCommand(optionString); }
+ else if(commandName == "set.dir") { pipecommand = new SetDirectoryCommand(optionString); }
+ else if(commandName == "set.logfile") { pipecommand = new SetLogFileCommand(optionString); }
+ else if(commandName == "parse.list") { pipecommand = new ParseListCommand(optionString); }
+ else if(commandName == "phylo.diversity") { pipecommand = new PhyloDiversityCommand(optionString); }
+ else if(commandName == "make.group") { pipecommand = new MakeGroupCommand(optionString); }
+ else if(commandName == "chop.seqs") { pipecommand = new ChopSeqsCommand(optionString); }
+ else if(commandName == "clearcut") { pipecommand = new ClearcutCommand(optionString); }
+ else if(commandName == "catchall") { pipecommand = new CatchAllCommand(optionString); }
+ else if(commandName == "split.abund") { pipecommand = new SplitAbundCommand(optionString); }
+ else if(commandName == "cluster.split") { pipecommand = new ClusterSplitCommand(optionString); }
+ else if(commandName == "classify.otu") { pipecommand = new ClassifyOtuCommand(optionString); }
+ else if(commandName == "degap.seqs") { pipecommand = new DegapSeqsCommand(optionString); }
+ else if(commandName == "get.relabund") { pipecommand = new GetRelAbundCommand(optionString); }
+ else if(commandName == "sens.spec") { pipecommand = new SensSpecCommand(optionString); }
+ else if(commandName == "seq.error") { pipecommand = new SeqErrorCommand(optionString); }
+ else if(commandName == "sffinfo") { pipecommand = new SffInfoCommand(optionString); }
+ else if(commandName == "normalize.shared") { pipecommand = new NormalizeSharedCommand(optionString); }
+ else if(commandName == "metastats") { pipecommand = new MetaStatsCommand(optionString); }
+ else if(commandName == "split.groups") { pipecommand = new SplitGroupCommand(optionString); }
+ else if(commandName == "cluster.fragments") { pipecommand = new ClusterFragmentsCommand(optionString); }
+ else if(commandName == "get.lineage") { pipecommand = new GetLineageCommand(optionString); }
+ else if(commandName == "get.groups") { pipecommand = new GetGroupsCommand(optionString); }
+ else if(commandName == "remove.lineage") { pipecommand = new RemoveLineageCommand(optionString); }
+ else if(commandName == "remove.groups") { pipecommand = new RemoveGroupsCommand(optionString); }
+ else if(commandName == "get.otus") { pipecommand = new GetOtusCommand(optionString); }
+ else if(commandName == "remove.otus") { pipecommand = new RemoveOtusCommand(optionString); }
+ else if(commandName == "fastq.info") { pipecommand = new ParseFastaQCommand(optionString); }
+ else if(commandName == "deunique.seqs") { pipecommand = new DeUniqueSeqsCommand(optionString); }
+ else if(commandName == "pairwise.seqs") { pipecommand = new PairwiseSeqsCommand(optionString); }
+ else if(commandName == "cluster.classic") { pipecommand = new ClusterDoturCommand(optionString); }
+ else if(commandName == "sub.sample") { pipecommand = new SubSampleCommand(optionString); }
+ else if(commandName == "indicator") { pipecommand = new IndicatorCommand(optionString); }
+ else if(commandName == "consensus.seqs") { pipecommand = new ConsensusSeqsCommand(optionString); }
+ else if(commandName == "corr.axes") { pipecommand = new CorrAxesCommand(optionString); }
+ else if(commandName == "remove.rare") { pipecommand = new RemoveRareCommand(optionString); }
+ else if(commandName == "merge.groups") { pipecommand = new MergeGroupsCommand(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 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 if(commandName == "sort.seqs") { pipecommand = new SortSeqsCommand(optionString); }
+ else if(commandName == "classify.tree") { pipecommand = new ClassifyTreeCommand(optionString); }
+ else if(commandName == "cooccurrence") { pipecommand = new CooccurrenceCommand(optionString); }
+ else if(commandName == "pcr.seqs") { pipecommand = new PcrSeqsCommand(optionString); }
+ else { pipecommand = new NoCommand(optionString); }
+
+ return pipecommand;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CommandFactory", "getCommand");
+ exit(1);
+ }
+}
+/***********************************************************/
+
+/***********************************************************/
+//This function calls the appropriate command fucntions based on user input, this is used by the pipeline command to check a users piepline for errors before running
+Command* CommandFactory::getCommand(string commandName){
+ try {
+ delete shellcommand; //delete the old command
+
+ if(commandName == "read.dist") { shellcommand = new ReadDistCommand(); }
+ else if(commandName == "read.otu") { shellcommand = new ReadOtuCommand(); }
+ else if(commandName == "read.tree") { shellcommand = new ReadTreeCommand(); }
+ else if(commandName == "cluster") { shellcommand = new ClusterCommand(); }
+ else if(commandName == "unique.seqs") { shellcommand = new DeconvoluteCommand(); }
+ else if(commandName == "parsimony") { shellcommand = new ParsimonyCommand(); }
+ else if(commandName == "help") { shellcommand = new HelpCommand(); }
+ else if(commandName == "quit") { shellcommand = new QuitCommand(); }
+ else if(commandName == "collect.single") { shellcommand = new CollectCommand(); }
+ else if(commandName == "collect.shared") { shellcommand = new CollectSharedCommand(); }
+ else if(commandName == "rarefaction.single") { shellcommand = new RareFactCommand(); }
+ else if(commandName == "rarefaction.shared") { shellcommand = new RareFactSharedCommand(); }
+ else if(commandName == "summary.single") { shellcommand = new SummaryCommand(); }
+ else if(commandName == "summary.shared") { shellcommand = new SummarySharedCommand(); }
+ else if(commandName == "unifrac.weighted") { shellcommand = new UnifracWeightedCommand(); }
+ else if(commandName == "unifrac.unweighted") { shellcommand = new UnifracUnweightedCommand(); }
+ else if(commandName == "get.group") { shellcommand = new GetgroupCommand(); }
+ else if(commandName == "get.label") { shellcommand = new GetlabelCommand(); }
+ else if(commandName == "get.sabund") { shellcommand = new GetSAbundCommand(); }
+ else if(commandName == "get.rabund") { shellcommand = new GetRAbundCommand(); }
+ else if(commandName == "libshuff") { shellcommand = new LibShuffCommand(); }
+ else if(commandName == "heatmap.bin") { shellcommand = new HeatMapCommand(); }
+ else if(commandName == "heatmap.sim") { shellcommand = new HeatMapSimCommand(); }
+ else if(commandName == "filter.seqs") { shellcommand = new FilterSeqsCommand(); }
+ else if(commandName == "venn") { shellcommand = new VennCommand(); }
+ else if(commandName == "bin.seqs") { shellcommand = new BinSeqCommand(); }
+ else if(commandName == "get.oturep") { shellcommand = new GetOTURepCommand(); }
+ else if(commandName == "tree.shared") { shellcommand = new TreeGroupCommand(); }
+ else if(commandName == "dist.shared") { shellcommand = new MatrixOutputCommand(); }
+ else if(commandName == "bootstrap.shared") { shellcommand = new BootSharedCommand(); }
+ else if(commandName == "consensus") { shellcommand = new ConcensusCommand(); }
+ else if(commandName == "dist.seqs") { shellcommand = new DistanceCommand(); }
+ else if(commandName == "align.seqs") { shellcommand = new AlignCommand(); }
+ else if(commandName == "summary.seqs") { shellcommand = new SeqSummaryCommand(); }
+ else if(commandName == "screen.seqs") { shellcommand = new ScreenSeqsCommand(); }
+ 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.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 == "merge.files") { shellcommand = new MergeFileCommand(); }
+ else if(commandName == "system") { shellcommand = new SystemCommand(); }
+ else if(commandName == "align.check") { shellcommand = new AlignCheckCommand(); }
+ else if(commandName == "get.sharedseqs") { shellcommand = new GetSharedOTUCommand(); }
+ else if(commandName == "get.otulist") { shellcommand = new GetListCountCommand(); }
+ else if(commandName == "hcluster") { shellcommand = new HClusterCommand(); }
+ else if(commandName == "classify.seqs") { shellcommand = new ClassifySeqsCommand(); }
+ 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 == "mgcluster") { shellcommand = new MGClusterCommand(); }
+ else if(commandName == "pre.cluster") { shellcommand = new PreClusterCommand(); }
+ else if(commandName == "pcoa") { shellcommand = new PCOACommand(); }
+ else if(commandName == "pca") { shellcommand = new PCACommand(); }
+ else if(commandName == "nmds") { shellcommand = new NMDSCommand(); }
+ else if(commandName == "otu.hierarchy") { shellcommand = new OtuHierarchyCommand(); }
+ else if(commandName == "set.dir") { shellcommand = new SetDirectoryCommand(); }
+ else if(commandName == "set.logfile") { shellcommand = new SetLogFileCommand(); }
+ else if(commandName == "parse.list") { shellcommand = new ParseListCommand(); }
+ else if(commandName == "phylo.diversity") { shellcommand = new PhyloDiversityCommand(); }
+ else if(commandName == "make.group") { shellcommand = new MakeGroupCommand(); }
+ else if(commandName == "chop.seqs") { shellcommand = new ChopSeqsCommand(); }
+ else if(commandName == "clearcut") { shellcommand = new ClearcutCommand(); }
+ else if(commandName == "catchall") { shellcommand = new CatchAllCommand(); }
+ else if(commandName == "split.abund") { shellcommand = new SplitAbundCommand(); }
+ else if(commandName == "cluster.split") { shellcommand = new ClusterSplitCommand(); }
+ else if(commandName == "classify.otu") { shellcommand = new ClassifyOtuCommand(); }
+ else if(commandName == "degap.seqs") { shellcommand = new DegapSeqsCommand(); }
+ else if(commandName == "get.relabund") { shellcommand = new GetRelAbundCommand(); }
+ else if(commandName == "sens.spec") { shellcommand = new SensSpecCommand(); }
+ else if(commandName == "seq.error") { shellcommand = new SeqErrorCommand(); }
+ else if(commandName == "sffinfo") { shellcommand = new SffInfoCommand(); }
+ else if(commandName == "normalize.shared") { shellcommand = new NormalizeSharedCommand(); }
+ else if(commandName == "metastats") { shellcommand = new MetaStatsCommand(); }
+ else if(commandName == "split.groups") { shellcommand = new SplitGroupCommand(); }
+ else if(commandName == "cluster.fragments") { shellcommand = new ClusterFragmentsCommand(); }
+ else if(commandName == "get.lineage") { shellcommand = new GetLineageCommand(); }
+ else if(commandName == "remove.lineage") { shellcommand = new RemoveLineageCommand(); }
+ else if(commandName == "get.groups") { shellcommand = new GetGroupsCommand(); }
+ else if(commandName == "remove.groups") { shellcommand = new RemoveGroupsCommand(); }
+ else if(commandName == "get.otus") { shellcommand = new GetOtusCommand(); }
+ else if(commandName == "remove.otus") { shellcommand = new RemoveOtusCommand(); }
+ else if(commandName == "fastq.info") { shellcommand = new ParseFastaQCommand(); }
+ else if(commandName == "deunique.seqs") { shellcommand = new DeUniqueSeqsCommand(); }
+ else if(commandName == "pairwise.seqs") { shellcommand = new PairwiseSeqsCommand(); }
+ else if(commandName == "cluster.classic") { shellcommand = new ClusterDoturCommand(); }
+ else if(commandName == "sub.sample") { shellcommand = new SubSampleCommand(); }
+ else if(commandName == "indicator") { shellcommand = new IndicatorCommand(); }
+ else if(commandName == "consensus.seqs") { shellcommand = new ConsensusSeqsCommand(); }
+ else if(commandName == "corr.axes") { shellcommand = new CorrAxesCommand(); }
+ else if(commandName == "remove.rare") { shellcommand = new RemoveRareCommand(); }
+ else if(commandName == "merge.groups") { shellcommand = new MergeGroupsCommand(); }
+ 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 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 if(commandName == "sort.seqs") { shellcommand = new SortSeqsCommand(); }
+ else if(commandName == "classify.tree") { shellcommand = new ClassifyTreeCommand(); }
+ else if(commandName == "cooccurrence") { shellcommand = new CooccurrenceCommand(); }
+ else if(commandName == "pcr.seqs") { shellcommand = new PcrSeqsCommand(); }
+ else { shellcommand = new NoCommand(); }
+
+ return shellcommand;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CommandFactory", "getCommand");
+ exit(1);
+ }
+}
+/***********************************************************
//This function is used to interrupt a command
Command* CommandFactory::getCommand(){
try {
exit(1);
}
}
-/***********************************************************************/
+***********************************************************************/
bool CommandFactory::isValidCommand(string command) {
try {
exit(1);
}
}
-
+/***********************************************************************/
+bool CommandFactory::isValidCommand(string command, string noError) {
+ try {
+
+ //is the command in the map
+ if ((commands.find(command)) != (commands.end())) {
+ return true;
+ }else{
+ return false;
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CommandFactory", "isValidCommand");
+ exit(1);
+ }
+}
/***********************************************************************/
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