X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=224ad217dd103dcb419466978e384cd40941f5b3;hb=8f909cf6870cc2e4d8ed8cff69a203f6f83a160b;hp=0bca8c0ee3db3706404b3fc5c4ff42b8c8f99388;hpb=725a3d4ff2442c79bfde0a75ed3e0904edcf03b7;p=mothur.git diff --git a/commandfactory.cpp b/commandfactory.cpp index 0bca8c0..224ad21 100644 --- a/commandfactory.cpp +++ b/commandfactory.cpp @@ -79,6 +79,23 @@ #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" + /*******************************************************/ @@ -103,6 +120,8 @@ CommandFactory::CommandFactory(){ m = MothurOut::getInstance(); command = new NoCommand(s); + shellcommand = new NoCommand(s); + pipecommand = new NoCommand(s); outputDir = ""; inputDir = ""; logFileName = ""; @@ -164,7 +183,20 @@ CommandFactory::CommandFactory(){ commands["clearcut"] = "clearcut"; commands["catchall"] = "catchall"; commands["split.abund"] = "split.abund"; - commands["cluster.split"] = "cluster.split"; + 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["pairwise.seqs"] = "MPIEnabled"; + commands["pipeline.pds"] = "MPIEnabled"; commands["classify.seqs"] = "MPIEnabled"; commands["dist.seqs"] = "MPIEnabled"; commands["filter.seqs"] = "MPIEnabled"; @@ -177,6 +209,9 @@ CommandFactory::CommandFactory(){ commands["chimera.bellerophon"] = "MPIEnabled"; commands["screen.seqs"] = "MPIEnabled"; commands["summary.seqs"] = "MPIEnabled"; + commands["cluster.split"] = "MPIEnabled"; + commands["sens.spec"] = "sens.spec"; + commands["seq.error"] = "seq.error"; commands["quit"] = "MPIEnabled"; } @@ -197,6 +232,8 @@ bool CommandFactory::MPIEnabled(string commandName) { CommandFactory::~CommandFactory(){ _uniqueInstance = 0; delete command; + delete shellcommand; + delete pipecommand; } /***********************************************************/ @@ -249,7 +286,7 @@ 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); } @@ -288,6 +325,22 @@ Command* CommandFactory::getCommand(string commandName, string 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 == "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 { command = new NoCommand(optionString); } return command; @@ -298,6 +351,220 @@ 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 == "chimera.seqs") { pipecommand = new ChimeraSeqsCommand(optionString); } + else if(commandName == "list.seqs") { pipecommand = new ListSeqsCommand(optionString); } + else if(commandName == "get.seqs") { pipecommand = new GetSeqsCommand(optionString); } + else if(commandName == "remove.seqs") { pipecommand = new RemoveSeqsCommand(optionString); } + else if(commandName == "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.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 PCACommand(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 == "parse.sff") { pipecommand = new ParseSFFCommand(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 == "remove.lineage") { pipecommand = new RemoveLineageCommand(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 { 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 == "chimera.seqs") { shellcommand = new ChimeraSeqsCommand(); } + else if(commandName == "list.seqs") { shellcommand = new ListSeqsCommand(); } + else if(commandName == "get.seqs") { shellcommand = new GetSeqsCommand(); } + else if(commandName == "remove.seqs") { shellcommand = new RemoveSeqsCommand(); } + else if(commandName == "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.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 PCACommand(); } + 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 == "parse.sff") { shellcommand = new ParseSFFCommand(); } + 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 == "fastq.info") { shellcommand = new ParseFastaQCommand(); } + else if(commandName == "deunique.seqs") { shellcommand = new DeUniqueSeqsCommand(); } + else if(commandName == "pairwise.seqs") { shellcommand = new PairwiseSeqsCommand(); } + 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 { @@ -335,13 +602,29 @@ 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; }