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|
/*
* commandfactory.cpp
*
*
* Created by Pat Schloss on 10/25/08.
* Copyright 2008 Patrick D. Schloss. All rights reserved.
*
*/
#include "command.hpp"
#include "clustercommand.h"
#include "collectcommand.h"
#include "collectsharedcommand.h"
#include "getgroupcommand.h"
#include "getlabelcommand.h"
#include "rarefactcommand.h"
#include "summarycommand.h"
#include "summarysharedcommand.h"
#include "rarefactsharedcommand.h"
#include "quitcommand.h"
#include "helpcommand.h"
#include "commandfactory.hpp"
#include "deconvolutecommand.h"
#include "parsimonycommand.h"
#include "unifracunweightedcommand.h"
#include "unifracweightedcommand.h"
#include "libshuffcommand.h"
#include "heatmapcommand.h"
#include "heatmapsimcommand.h"
#include "filterseqscommand.h"
#include "venncommand.h"
#include "nocommands.h"
#include "binsequencecommand.h"
#include "getoturepcommand.h"
#include "treesharedcommand.h"
#include "distancecommand.h"
#include "aligncommand.h"
#include "distsharedcommand.h"
#include "getsabundcommand.h"
#include "getrabundcommand.h"
#include "seqsummarycommand.h"
#include "screenseqscommand.h"
#include "reversecommand.h"
#include "trimseqscommand.h"
#include "mergefilecommand.h"
#include "listseqscommand.h"
#include "getseqscommand.h"
#include "removeseqscommand.h"
#include "systemcommand.h"
#include "aligncheckcommand.h"
#include "getsharedotucommand.h"
#include "getlistcountcommand.h"
#include "classifyseqscommand.h"
#include "phylotypecommand.h"
#include "mgclustercommand.h"
#include "preclustercommand.h"
#include "pcoacommand.h"
#include "otuhierarchycommand.h"
#include "setdircommand.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 "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 "deuniqueseqscommand.h"
#include "pairwiseseqscommand.h"
#include "clusterdoturcommand.h"
#include "subsamplecommand.h"
#include "removegroupscommand.h"
#include "getgroupscommand.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 "makesharedcommand.h"
#include "deuniquetreecommand.h"
#include "countseqscommand.h"
#include "countgroupscommand.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"
#include "createdatabasecommand.h"
#include "makebiomcommand.h"
#include "getcoremicrobiomecommand.h"
#include "listotuscommand.h"
#include "getotuscommand.h"
#include "removeotuscommand.h"
#include "makecontigscommand.h"
#include "sffmultiplecommand.h"
#include "classifysvmsharedcommand.h"
#include "filtersharedcommand.h"
#include "primerdesigncommand.h"
#include "getdistscommand.h"
#include "removedistscommand.h"
#include "mergetaxsummarycommand.h"
#include "getmetacommunitycommand.h"
#include "sparcccommand.h"
#include "makelookupcommand.h"
#include "renameseqscommand.h"
#include "makelefsecommand.h"
#include "lefsecommand.h"
#include "kruskalwalliscommand.h"
#include "sracommand.h"
#include "mergesfffilecommand.h"
#include "getmimarkspackagecommand.h"
#include "mimarksattributescommand.h"
#include "setseedcommand.h"
#include "makefilecommand.h"
#include "biominfocommand.h"
#include "renamefilecommand.h"
#include "chimeravsearchcommand.h"
#include "mergecountcommand.hpp"
#include "clusterfitcommand.hpp"
#include "mergeotuscommand.hpp"
#include "diversityestimatorcommand.hpp"
#include "srainfocommand.hpp"
#include "makeclrcommand.hpp"
/*******************************************************/
/******************************************************/
CommandFactory* CommandFactory::getInstance() {
if( _uniqueInstance == 0) {
_uniqueInstance = new CommandFactory();
}
return _uniqueInstance;
}
/***********************************************************/
/***********************************************************/
CommandFactory::CommandFactory(){
string s = "";
m = MothurOut::getInstance();
current = CurrentFile::getInstance();
current->setOutputDir(""); current->setInputDir("");
append = false;
//initialize list of valid commands
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.shared"] = "dist.shared";
commands["collect.single"] = "collect.single";
commands["collect.shared"] = "collect.shared";
commands["rarefaction.single"] = "rarefaction.single";
commands["rarefaction.shared"] = "rarefaction.shared";
commands["summary.single"] = "summary.single";
commands["summary.shared"] = "summary.shared";
commands["parsimony"] = "parsimony";
commands["unifrac.weighted"] = "unifrac.weighted";
commands["unifrac.unweighted"] = "unifrac.unweighted";
commands["libshuff"] = "libshuff";
commands["tree.shared"] = "tree.shared";
commands["heatmap.bin"] = "heatmap.bin";
commands["heatmap.sim"] = "heatmap.sim";
commands["venn"] = "venn";
commands["get.group"] = "get.group";
commands["get.label"] = "get.label";
commands["get.sabund"] = "get.sabund";
commands["get.rabund"] = "get.rabund";
commands["help"] = "help";
commands["reverse.seqs"] = "reverse.seqs";
commands["trim.seqs"] = "trim.seqs";
commands["trim.flows"] = "trim.flows";
commands["list.seqs"] = "list.seqs";
commands["get.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["phylotype"] = "phylotype";
commands["mgcluster"] = "mgcluster";
commands["pre.cluster"] = "pre.cluster";
commands["pcoa"] = "pcoa";
commands["otu.hierarchy"] = "otu.hierarchy";
commands["set.dir"] = "set.dir";
commands["merge.files"] = "merge.files";
commands["set.logfile"] = "set.logfile";
commands["phylo.diversity"] = "phylo.diversity";
commands["make.group"] = "make.group";
commands["chop.seqs"] = "chop.seqs";
commands["clearcut"] = "clearcut";
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"] = "get.current";
commands["set.current"] = "set.current";
commands["deunique.tree"] = "deunique.tree";
commands["count.seqs"] = "count.seqs";
commands["count.groups"] = "count.groups";
commands["pairwise.seqs"] = "pairwise.seqs";
commands["classify.seqs"] = "classify.seqs";
commands["dist.seqs"] = "dist.seqs";
commands["filter.seqs"] = "filter.seqs";
commands["align.seqs"] = "align.seqs";
commands["chimera.ccode"] = "chimera.ccode";
commands["chimera.check"] = "chimera.check";
commands["chimera.slayer"] = "chimera.slayer";
commands["chimera.uchime"] = "chimera.uchime";
commands["chimera.perseus"] = "chimera.perseus";
commands["chimera.pintail"] = "chimera.pintail";
commands["chimera.bellerophon"] = "chimera.bellerophon";
commands["chimera.vsearch"] = "chimera.vsearch";
commands["screen.seqs"] = "screen.seqs";
commands["summary.seqs"] = "summary.seqs";
commands["cluster.split"] = "cluster.split";
commands["shhh.flows"] = "shhh.flows";
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["create.database"] = "create.database";
commands["make.biom"] = "make.biom";
commands["get.coremicrobiome"] = "get.coremicrobiome";
commands["list.otus"] = "list.otus";
commands["list.otulabels"] = "list.otulabels";
commands["get.otulabels"] = "get.otulabels";
commands["remove.otulabels"] = "remove.otulabels";
commands["make.contigs"] = "make.contigs";
commands["make.table"] = "make.table";
commands["sff.multiple"] = "sff.multiple";
commands["quit"] = "quit";
commands["classify.svm"] = "classify.svm";
commands["filter.shared"] = "filter.shared";
commands["primer.design"] = "primer.design";
commands["get.dists"] = "get.dists";
commands["remove.dists"] = "remove.dists";
commands["merge.taxsummary"] = "merge.taxsummary";
commands["get.communitytype"] = "get.communitytype";
commands["sparcc"] = "sparcc";
commands["make.lookup"] = "make.lookup";
commands["rename.seqs"] = "rename.seqs";
commands["make.lefse"] = "make.lefse";
commands["lefse"] = "lefse";
commands["kruskal.wallis"] = "kruskal.wallis";
commands["make.sra"] = "make.sra";
commands["merge.sfffiles"] = "merge.sfffiles";
commands["get.mimarkspackage"] = "get.mimarkspackage";
commands["mimarks.attributes"] = "mimarks.attributes";
commands["make.file"] = "make.file";
commands["biom.info"] = "biom.info";
commands["set.seed"] = "set.seed";
commands["rename.file"] = "rename.file";
commands["merge.count"] = "merge.count";
commands["cluster.fit"] = "cluster.fit";
commands["merge.otus"] = "merge.otus";
commands["estimator.single"] = "estimator.single";
commands["sra.info"] = "sra.info";
commands["make.clr"] = "make.clr";
}
/***********************************************************/
CommandFactory::~CommandFactory(){
_uniqueInstance = 0;
}
/***********************************************************/
/***********************************************************/
int CommandFactory::checkForRedirects(string optionString) {
try {
Utils util;
int pos = (int)optionString.find("outputdir");
if (pos != string::npos) { //user has set outputdir in command option string
string outputOption = "";
bool foundEquals = false;
for(int i=pos;i<optionString.length();i++){
if(optionString[i] == ',') { break; }
else if(optionString[i] == '=') { foundEquals = true; }
if (foundEquals) { outputOption += optionString[i]; }
}
if (outputOption[0] == '=') { outputOption = outputOption.substr(1); }
outputOption = util.trimWhiteSpace(outputOption);
outputOption = util.removeQuotes(outputOption);
if(util.mkDir(outputOption)){
current->setOutputDir(outputOption);
m->mothurOut("Setting output directory to: " + outputOption); m->mothurOutEndLine();
}
}
pos = (int)optionString.find("inputdir");
if (pos != string::npos) { //user has set inputdir in command option string
string intputOption = "";
bool foundEquals = false;
for(int i=pos;i<optionString.length();i++){
if(optionString[i] == ',') { break; }
else if(optionString[i] == '=') { foundEquals = true; }
if (foundEquals) { intputOption += optionString[i]; }
}
if (intputOption[0] == '=') { intputOption = intputOption.substr(1); }
intputOption = util.trimWhiteSpace(intputOption);
intputOption = util.removeQuotes(intputOption);
if(util.dirCheck(intputOption)){
current->setInputDir(intputOption);
m->mothurOut("Setting input directory to: " + intputOption); m->mothurOutEndLine();
}
}
pos = (int)optionString.find("seed=");
if (pos != string::npos) { //user has set seed in command option string
string intputOption = "";
bool foundEquals = false;
for(int i=pos;i<optionString.length();i++){
if(optionString[i] == ',') { break; }
else if(optionString[i] == '=') { foundEquals = true; }
if (foundEquals) { intputOption += optionString[i]; }
}
if (intputOption[0] == '=') { intputOption = intputOption.substr(1); }
bool seed = false; int random;
if (intputOption == "clear") {
random = (int)time(NULL);
seed = true;
}else {
if (util.isNumeric1(intputOption)) { util.mothurConvert(intputOption, random); seed=true; }
else { m->mothurOut("[ERROR]: Seed must be an integer.\n"); seed = false;}
}
if (seed) { m->mothurOut("Setting random seed to " + toString(random) + ".\n\n"); m->setRandomSeed(random); }
}
pos = (int)optionString.find("mothurcalling=true");
if (pos != string::npos) { //user has set seed in command option string
current->setMothurCalling(true);
}else { current->setMothurCalling(false); }
return 0;
}
catch(exception& e) {
m->errorOut(e, "CommandFactory", "getCommand");
exit(1);
}
}
/***********************************************************/
/***********************************************************/
//This function calls the appropriate command fucntions based on user input.
Command* CommandFactory::getCommand(string commandName, string optionString){
try {
Command* command = NULL;
if (commandName != "help") { checkForRedirects(optionString); }
if(commandName == "cluster") { command = new ClusterCommand(optionString); }
else if(commandName == "unique.seqs") { command = new DeconvoluteCommand(optionString); }
else if(commandName == "parsimony") { command = new ParsimonyCommand(optionString); }
else if(commandName == "help") { command = new HelpCommand(optionString); }
else if(commandName == "quit") { command = new QuitCommand(optionString); }
else if(commandName == "collect.single") { command = new CollectCommand(optionString); }
else if(commandName == "collect.shared") { command = new CollectSharedCommand(optionString); }
else if(commandName == "rarefaction.single") { command = new RareFactCommand(optionString); }
else if(commandName == "rarefaction.shared") { command = new RareFactSharedCommand(optionString); }
else if(commandName == "summary.single") { command = new SummaryCommand(optionString); }
else if(commandName == "summary.shared") { command = new SummarySharedCommand(optionString); }
else if(commandName == "unifrac.weighted") { command = new UnifracWeightedCommand(optionString); }
else if(commandName == "unifrac.unweighted") { command = new UnifracUnweightedCommand(optionString); }
else if(commandName == "get.group") { command = new GetgroupCommand(optionString); }
else if(commandName == "get.label") { command = new GetlabelCommand(optionString); }
else if(commandName == "get.sabund") { command = new GetSAbundCommand(optionString); }
else if(commandName == "get.rabund") { command = new GetRAbundCommand(optionString); }
else if(commandName == "libshuff") { command = new LibShuffCommand(optionString); }
else if(commandName == "heatmap.bin") { command = new HeatMapCommand(optionString); }
else if(commandName == "heatmap.sim") { command = new HeatMapSimCommand(optionString); }
else if(commandName == "filter.seqs") { command = new FilterSeqsCommand(optionString); }
else if(commandName == "venn") { command = new VennCommand(optionString); }
else if(commandName == "bin.seqs") { command = new BinSeqCommand(optionString); }
else if(commandName == "get.oturep") { command = new GetOTURepCommand(optionString); }
else if(commandName == "tree.shared") { command = new TreeSharedCommand(optionString); }
else if(commandName == "dist.shared") { command = new DistSharedCommand(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 == "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 == "merge.files") { command = new MergeFileCommand(optionString); }
else if(commandName == "system") { command = new SystemCommand(optionString); }
else if(commandName == "align.check") { command = new AlignCheckCommand(optionString); }
else if(commandName == "get.sharedseqs") { command = new GetSharedOTUCommand(optionString); }
else if(commandName == "get.otulist") { command = new GetListCountCommand(optionString); }
else if(commandName == "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 == "chimera.vsearch") { command = new ChimeraVsearchCommand(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 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 == "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 == "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") || (commandName == "get.otulabels")) { command = new GetOtusCommand(optionString); }
else if((commandName == "remove.otus") || (commandName == "remove.otulabels")) { command = new RemoveOtusCommand(optionString); }
else if((commandName == "list.otus") ||(commandName == "list.otulabels")) { command = new ListOtusCommand(optionString); }
else if(commandName == "fastq.info") { command = new ParseFastaQCommand(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 == "merge.count") { command = new MergeCountCommand(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 == "deunique.tree") { command = new DeuniqueTreeCommand(optionString); }
else if((commandName == "count.seqs") || (commandName == "make.table")) { command = new CountSeqsCommand(optionString); }
else if(commandName == "count.groups") { command = new CountGroupsCommand(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 if(commandName == "create.database") { command = new CreateDatabaseCommand(optionString); }
else if(commandName == "make.biom") { command = new MakeBiomCommand(optionString); }
else if(commandName == "get.coremicrobiome") { command = new GetCoreMicroBiomeCommand(optionString); }
else if(commandName == "make.contigs") { command = new MakeContigsCommand(optionString); }
else if(commandName == "sff.multiple") { command = new SffMultipleCommand(optionString); }
else if(commandName == "classify.svm") { command = new ClassifySvmSharedCommand(optionString); }
else if(commandName == "filter.shared") { command = new FilterSharedCommand(optionString); }
else if(commandName == "primer.design") { command = new PrimerDesignCommand(optionString); }
else if(commandName == "get.dists") { command = new GetDistsCommand(optionString); }
else if(commandName == "remove.dists") { command = new RemoveDistsCommand(optionString); }
else if(commandName == "merge.taxsummary") { command = new MergeTaxSummaryCommand(optionString); }
else if(commandName == "get.communitytype") { command = new GetMetaCommunityCommand(optionString); }
else if(commandName == "sparcc") { command = new SparccCommand(optionString); }
else if(commandName == "make.lookup") { command = new MakeLookupCommand(optionString); }
else if(commandName == "rename.seqs") { command = new RenameSeqsCommand(optionString); }
else if(commandName == "make.lefse") { command = new MakeLefseCommand(optionString); }
else if(commandName == "lefse") { command = new LefseCommand(optionString); }
else if(commandName == "kruskal.wallis") { command = new KruskalWallisCommand(optionString); }
else if(commandName == "make.sra") { command = new SRACommand(optionString); }
else if(commandName == "merge.sfffiles") { command = new MergeSfffilesCommand(optionString); }
else if(commandName == "get.mimarkspackage") { command = new GetMIMarksPackageCommand(optionString); }
else if(commandName == "mimarks.attributes") { command = new MimarksAttributesCommand(optionString); }
else if(commandName == "set.seed") { command = new SetSeedCommand(optionString); }
else if(commandName == "make.file") { command = new MakeFileCommand(optionString); }
else if(commandName == "biom.info") { command = new BiomInfoCommand(optionString); }
else if(commandName == "rename.file") { command = new RenameFileCommand(optionString); }
else if(commandName == "cluster.fit") { command = new ClusterFitCommand(optionString); }
else if(commandName == "merge.otus") { command = new MergeOTUsCommand(optionString); }
else if(commandName == "estimator.single") { command = new EstimatorSingleCommand(optionString); }
else if(commandName == "sra.info") { command = new SRAInfoCommand(optionString); }
else if(commandName == "make.clr") { command = new MakeCLRCommand(optionString); }
else { command = new NoCommand(optionString); }
return command;
}
catch(exception& e) {
m->errorOut(e, "CommandFactory", "getCommand");
exit(1);
}
}
/***********************************************************/
/***********************************************************/
//This function calls the appropriate command fucntions based on user input.
Command* CommandFactory::getCommand(string commandName, string optionString, string mode){
try {
Command* pipecommand = NULL; //delete the old command
if (commandName != "help") {
checkForRedirects(optionString);
//user has opted to redirect output from dir where input files are located to some other place
if (current->getOutputDir() != "") {
if (optionString != "") { optionString += ", outputdir=" + current->getOutputDir(); }
else { optionString += "outputdir=" + current->getOutputDir(); }
}
//user has opted to redirect input from dir where mothur.exe is located to some other place
if (current->getInputDir() != "") {
if (optionString != "") { optionString += ", inputdir=" + current->getInputDir(); }
else { optionString += "inputdir=" + current->getInputDir(); }
}
}
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 TreeSharedCommand(optionString); }
else if(commandName == "dist.shared") { pipecommand = new DistSharedCommand(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 == "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 == "chimera.vsearch") { pipecommand = new ChimeraVsearchCommand(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 == "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 == "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") || (commandName == "get.otulabels")) { pipecommand = new GetOtusCommand(optionString); }
else if((commandName == "remove.otus") || (commandName == "remove.otulabels")) { pipecommand = new RemoveOtusCommand(optionString); }
else if((commandName == "list.otus") ||(commandName == "list.otulabels")) { pipecommand = new ListOtusCommand(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 == "merge.count") { pipecommand = new MergeCountCommand(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 == "deunique.tree") { pipecommand = new DeuniqueTreeCommand(optionString); }
else if((commandName == "count.seqs") || (commandName == "make.table")) { pipecommand = new CountSeqsCommand(optionString); }
else if(commandName == "count.groups") { pipecommand = new CountGroupsCommand(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 if(commandName == "create.database") { pipecommand = new CreateDatabaseCommand(optionString); }
else if(commandName == "make.biom") { pipecommand = new MakeBiomCommand(optionString); }
else if(commandName == "get.coremicrobiome") { pipecommand = new GetCoreMicroBiomeCommand(optionString); }
else if(commandName == "make.contigs") { pipecommand = new MakeContigsCommand(optionString); }
else if(commandName == "sff.multiple") { pipecommand = new SffMultipleCommand(optionString); }
//else if(commandName == "classify.rf") { pipecommand = new ClassifyRFSharedCommand(optionString); }
else if(commandName == "filter.shared") { pipecommand = new FilterSharedCommand(optionString); }
else if(commandName == "primer.design") { pipecommand = new PrimerDesignCommand(optionString); }
else if(commandName == "get.dists") { pipecommand = new GetDistsCommand(optionString); }
else if(commandName == "remove.dists") { pipecommand = new RemoveDistsCommand(optionString); }
else if(commandName == "merge.taxsummary") { pipecommand = new MergeTaxSummaryCommand(optionString); }
else if(commandName == "get.communitytype") { pipecommand = new GetMetaCommunityCommand(optionString); }
else if(commandName == "sparcc") { pipecommand = new SparccCommand(optionString); }
else if(commandName == "make.lookup") { pipecommand = new MakeLookupCommand(optionString); }
else if(commandName == "rename.seqs") { pipecommand = new RenameSeqsCommand(optionString); }
else if(commandName == "make.lefse") { pipecommand = new MakeLefseCommand(optionString); }
else if(commandName == "lefse") { pipecommand = new LefseCommand(optionString); }
else if(commandName == "kruskal.wallis") { pipecommand = new KruskalWallisCommand(optionString); }
else if(commandName == "make.sra") { pipecommand = new SRACommand(optionString); }
else if(commandName == "merge.sfffiles") { pipecommand = new MergeSfffilesCommand(optionString); }
else if(commandName == "classify.svm") { pipecommand = new ClassifySvmSharedCommand(optionString); }
else if(commandName == "get.mimarkspackage") { pipecommand = new GetMIMarksPackageCommand(optionString); }
else if(commandName == "mimarks.attributes") { pipecommand = new MimarksAttributesCommand(optionString); }
else if(commandName == "set.seed") { pipecommand = new SetSeedCommand(optionString); }
else if(commandName == "make.file") { pipecommand = new MakeFileCommand(optionString); }
else if(commandName == "biom.info") { pipecommand = new BiomInfoCommand(optionString); }
else if(commandName == "rename.file") { pipecommand = new RenameFileCommand(optionString); }
else if(commandName == "cluster.fit") { pipecommand = new ClusterFitCommand(optionString); }
else if(commandName == "merge.otus") { pipecommand = new MergeOTUsCommand(optionString); }
else if(commandName == "estimator.single") { pipecommand = new EstimatorSingleCommand(optionString); }
else if(commandName == "sra.info") { pipecommand = new SRAInfoCommand(optionString); }
else if(commandName == "make.clr") { pipecommand = new MakeCLRCommand(optionString); }
else { pipecommand = new NoCommand(optionString); }
return pipecommand;
}
catch(exception& e) {
m->errorOut(e, "CommandFactory", "getCommand");
exit(1);
}
}
/***********************************************************************/
bool CommandFactory::isValidCommand(string command) {
try {
//is the command in the map
if ((commands.find(command)) != (commands.end())) {
return true;
}else{
m->mothurOut(command + " is not a valid command in Mothur. Valid commands are ");
for (it = commands.begin(); it != commands.end(); it++) {
m->mothurOut(it->first + ", ");
}
m->mothurOutEndLine();
return false;
}
}
catch(exception& e) {
m->errorOut(e, "CommandFactory", "isValidCommand");
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 {
it = commands.begin();
out << "Valid commands are: " << it->first << ", ";
it++;
out << it->first;
it++;
for (; it != commands.end(); it++) { out << ", " << it->first; }
out << "." << endl;
}
catch(exception& e) {
m->errorOut(e, "CommandFactory", "printCommands");
exit(1);
}
}
/***********************************************************************/
void CommandFactory::printCommandsCategories(ostream& out) {
try {
map<string, string> commands = getListCommands();
map<string, string>::iterator it;
map<string, string> categories;
map<string, string>::iterator itCat;
//loop through each command outputting info
for (it = commands.begin(); it != commands.end(); it++) {
Command* thisCommand = getCommand(it->first, "category");
//don't add hidden commands
if (thisCommand->getCommandCategory() != "Hidden") {
itCat = categories.find(thisCommand->getCommandCategory());
if (itCat == categories.end()) {
categories[thisCommand->getCommandCategory()] = thisCommand->getCommandName();
}else {
categories[thisCommand->getCommandCategory()] += ", " + thisCommand->getCommandName();
}
}
}
for (itCat = categories.begin(); itCat != categories.end(); itCat++) {
#if defined NON_WINDOWS
out << BOLDMAGENTA << endl << itCat->first << " commmands include: " << RESET << itCat->second << endl;
#else
out << endl << itCat->first << " commmands include: " << itCat->second << endl;
#endif
}
}
catch(exception& e) {
m->errorOut(e, "CommandFactory", "printCommandsCategories");
exit(1);
}
}
/***********************************************************************/
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