X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=579abe82cd4019ab265dcce4220d58aea6924e67;hb=57b3c96832667c1b70d4d526331f52e3d49e8237;hp=727f6e821f019ae5c2f7629e1d0afabd33b6e789;hpb=30c1fd8c45b6f0d66c17f2714dbb58b8ddccdce2;p=mothur.git diff --git a/commandfactory.cpp b/commandfactory.cpp index 727f6e8..579abe8 100644 --- a/commandfactory.cpp +++ b/commandfactory.cpp @@ -48,7 +48,6 @@ #include "reversecommand.h" #include "trimseqscommand.h" #include "mergefilecommand.h" -#include "chimeraseqscommand.h" #include "listseqscommand.h" #include "getseqscommand.h" #include "removeseqscommand.h" @@ -61,10 +60,77 @@ #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" /*******************************************************/ @@ -78,23 +144,33 @@ CommandFactory* CommandFactory::getInstance() { /***********************************************************/ /***********************************************************/ +//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"; @@ -116,32 +192,99 @@ CommandFactory::CommandFactory(){ 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"; + } /***********************************************************/ @@ -160,6 +303,8 @@ bool CommandFactory::MPIEnabled(string commandName) { CommandFactory::~CommandFactory(){ _uniqueInstance = 0; delete command; + delete shellcommand; + delete pipecommand; } /***********************************************************/ @@ -212,14 +357,15 @@ Command* CommandFactory::getCommand(string commandName, string 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 == "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); } @@ -230,13 +376,78 @@ Command* CommandFactory::getCommand(string commandName, string 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; @@ -247,6 +458,292 @@ Command* CommandFactory::getCommand(string commandName, string optionString){ } } /***********************************************************/ + +/***********************************************************/ +//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 { @@ -262,7 +759,7 @@ Command* CommandFactory::getCommand(){ exit(1); } } -/***********************************************************************/ +***********************************************************************/ bool CommandFactory::isValidCommand(string command) { try { @@ -284,13 +781,29 @@ bool CommandFactory::isValidCommand(string command) { 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; }