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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 "treegroupscommand.h"
#include "distancecommand.h"
#include "aligncommand.h"
#include "matrixoutputcommand.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 "secondarystructurecommand.h"
#include "getsharedotucommand.h"
#include "getlistcountcommand.h"
#include "hclustercommand.h"
#include "classifyseqscommand.h"
#include "phylotypecommand.h"
#include "mgclustercommand.h"
#include "preclustercommand.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"
#include "createdatabasecommand.h"
#include "makebiomcommand.h"
#include "getcoremicrobiomecommand.h"
#include "listotulabelscommand.h"
#include "getotulabelscommand.h"
#include "removeotulabelscommand.h"
#include "makecontigscommand.h"
#include "loadlogfilecommand.h"
#include "sffmultiplecommand.h"
#include "classifyrfsharedcommand.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"
/*******************************************************/
/******************************************************/
CommandFactory* CommandFactory::getInstance() {
if( _uniqueInstance == 0) {
_uniqueInstance = new CommandFactory();
}
return _uniqueInstance;
}
/***********************************************************/
/***********************************************************/
//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["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["hcluster"] = "hcluster";
commands["phylotype"] = "phylotype";
commands["mgcluster"] = "mgcluster";
commands["pre.cluster"] = "pre.cluster";
commands["pcoa"] = "pcoa";
commands["otu.hierarchy"] = "otu.hierarchy";
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["create.database"] = "create.database";
commands["make.biom"] = "make.biom";
commands["get.coremicrobiome"] = "get.coremicrobiome";
commands["list.otulabels"] = "list.otulabels";
commands["get.otulabels"] = "get.otulabels";
commands["remove.otulabels"] = "remove.otulabels";
commands["make.contigs"] = "make.contigs";
commands["load.logfile"] = "load.logfile";
commands["make.table"] = "make.table";
commands["sff.multiple"] = "sff.multiple";
commands["quit"] = "MPIEnabled";
commands["classify.rf"] = "classify.rf";
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["sra"] = "sra";
commands["merge.sfffiles"] = "merge.sfffiles";
}
/***********************************************************/
/***********************************************************/
bool CommandFactory::MPIEnabled(string commandName) {
bool mpi = false;
it = commands.find(commandName);
if (it != commands.end()) {
if (it->second == "MPIEnabled") { return true; }
}
return mpi;
}
/***********************************************************/
/***********************************************************/
CommandFactory::~CommandFactory(){
_uniqueInstance = 0;
delete command;
delete shellcommand;
delete pipecommand;
}
/***********************************************************/
/***********************************************************/
int CommandFactory::checkForRedirects(string optionString) {
try {
int pos = 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(m->dirCheck(outputOption)){
setOutputDirectory(outputOption);
m->mothurOut("Setting output directory to: " + outputOption); m->mothurOutEndLine();
}
}
pos = 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(m->dirCheck(intputOption)){
setInputDirectory(intputOption);
m->mothurOut("Setting input directory to: " + intputOption); m->mothurOutEndLine();
}
}
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 {
delete command; //delete the old command
checkForRedirects(optionString);
//user has opted to redirect output from dir where input files are located to some other place
if (outputDir != "") {
if (optionString != "") { optionString += ", outputdir=" + outputDir; }
else { optionString += "outputdir=" + outputDir; }
}
//user has opted to redirect input from dir where mothur.exe is located to some other place
if (inputDir != "") {
if (optionString != "") { optionString += ", inputdir=" + inputDir; }
else { optionString += "inputdir=" + inputDir; }
}
if(commandName == "cluster") { command = new ClusterCommand(optionString); }
else if(commandName == "unique.seqs") { command = new DeconvoluteCommand(optionString); }
else if(commandName == "parsimony") { command = new ParsimonyCommand(optionString); }
else if(commandName == "help") { command = new HelpCommand(optionString); }
else if(commandName == "quit") { command = new QuitCommand(optionString); }
else if(commandName == "collect.single") { command = new CollectCommand(optionString); }
else if(commandName == "collect.shared") { command = new CollectSharedCommand(optionString); }
else if(commandName == "rarefaction.single") { command = new RareFactCommand(optionString); }
else if(commandName == "rarefaction.shared") { command = new RareFactSharedCommand(optionString); }
else if(commandName == "summary.single") { command = new SummaryCommand(optionString); }
else if(commandName == "summary.shared") { command = new SummarySharedCommand(optionString); }
else if(commandName == "unifrac.weighted") { command = new UnifracWeightedCommand(optionString); }
else if(commandName == "unifrac.unweighted") { command = new UnifracUnweightedCommand(optionString); }
else if(commandName == "get.group") { command = new GetgroupCommand(optionString); }
else if(commandName == "get.label") { command = new GetlabelCommand(optionString); }
else if(commandName == "get.sabund") { command = new GetSAbundCommand(optionString); }
else if(commandName == "get.rabund") { command = new GetRAbundCommand(optionString); }
else if(commandName == "libshuff") { command = new LibShuffCommand(optionString); }
else if(commandName == "heatmap.bin") { command = new HeatMapCommand(optionString); }
else if(commandName == "heatmap.sim") { command = new HeatMapSimCommand(optionString); }
else if(commandName == "filter.seqs") { command = new FilterSeqsCommand(optionString); }
else if(commandName == "venn") { command = new VennCommand(optionString); }
else if(commandName == "bin.seqs") { command = new BinSeqCommand(optionString); }
else if(commandName == "get.oturep") { command = new GetOTURepCommand(optionString); }
else if(commandName == "tree.shared") { command = new TreeGroupCommand(optionString); }
else if(commandName == "dist.shared") { command = new MatrixOutputCommand(optionString); }
else if(commandName == "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 == "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 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") || (commandName == "make.table")) { 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 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 == "list.otulabels") { command = new ListOtuLabelsCommand(optionString); }
else if(commandName == "get.otulabels") { command = new GetOtuLabelsCommand(optionString); }
else if(commandName == "remove.otulabels") { command = new RemoveOtuLabelsCommand(optionString); }
else if(commandName == "make.contigs") { command = new MakeContigsCommand(optionString); }
else if(commandName == "load.logfile") { command = new LoadLogfileCommand(optionString); }
else if(commandName == "sff.multiple") { command = new SffMultipleCommand(optionString); }
else if(commandName == "classify.rf") { command = new ClassifyRFSharedCommand(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 == "sra") { command = new SRACommand(optionString); }
else if(commandName == "merge.sfffiles") { command = new MergeSfffilesCommand(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 {
delete pipecommand; //delete the old command
checkForRedirects(optionString);
//user has opted to redirect output from dir where input files are located to some other place
if (outputDir != "") {
if (optionString != "") { optionString += ", outputdir=" + outputDir; }
else { optionString += "outputdir=" + outputDir; }
}
//user has opted to redirect input from dir where mothur.exe is located to some other place
if (inputDir != "") {
if (optionString != "") { optionString += ", inputdir=" + inputDir; }
else { optionString += "inputdir=" + inputDir; }
}
if(commandName == "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 == "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") || (commandName == "make.table")) { 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 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 == "list.otulabels") { pipecommand = new ListOtuLabelsCommand(optionString); }
else if(commandName == "get.otulabels") { pipecommand = new GetOtuLabelsCommand(optionString); }
else if(commandName == "remove.otulabels") { pipecommand = new RemoveOtuLabelsCommand(optionString); }
else if(commandName == "make.contigs") { pipecommand = new MakeContigsCommand(optionString); }
else if(commandName == "load.logfile") { pipecommand = new LoadLogfileCommand(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 == "sra") { pipecommand = new SRACommand(optionString); }
else if(commandName == "merge.sfffiles") { pipecommand = new MergeSfffilesCommand(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 == "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 == "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") || (commandName == "make.table")) { 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 if(commandName == "create.database") { shellcommand = new CreateDatabaseCommand(); }
else if(commandName == "make.biom") { shellcommand = new MakeBiomCommand(); }
else if(commandName == "get.coremicrobiome") { shellcommand = new GetCoreMicroBiomeCommand(); }
else if(commandName == "list.otulabels") { shellcommand = new ListOtuLabelsCommand(); }
else if(commandName == "get.otulabels") { shellcommand = new GetOtuLabelsCommand(); }
else if(commandName == "remove.otulabels") { shellcommand = new RemoveOtuLabelsCommand(); }
else if(commandName == "make.contigs") { shellcommand = new MakeContigsCommand(); }
else if(commandName == "load.logfile") { shellcommand = new LoadLogfileCommand(); }
else if(commandName == "sff.multiple") { shellcommand = new SffMultipleCommand(); }
else if(commandName == "classify.rf") { shellcommand = new ClassifyRFSharedCommand(); }
else if(commandName == "filter.shared") { shellcommand = new FilterSharedCommand(); }
else if(commandName == "primer.design") { shellcommand = new PrimerDesignCommand(); }
else if(commandName == "get.dists") { shellcommand = new GetDistsCommand(); }
else if(commandName == "remove.dists") { shellcommand = new RemoveDistsCommand(); }
else if(commandName == "merge.taxsummary") { shellcommand = new MergeTaxSummaryCommand(); }
else if(commandName == "get.communitytype") { shellcommand = new GetMetaCommunityCommand(); }
else if(commandName == "sparcc") { shellcommand = new SparccCommand(); }
else if(commandName == "make.lookup") { shellcommand = new MakeLookupCommand(); }
else if(commandName == "rename.seqs") { shellcommand = new RenameSeqsCommand(); }
else if(commandName == "make.lefse") { shellcommand = new MakeLefseCommand(); }
else if(commandName == "lefse") { shellcommand = new LefseCommand(); }
else if(commandName == "kruskal.wallis") { shellcommand = new KruskalWallisCommand(); }
else if(commandName == "sra") { shellcommand = new SRACommand(); }
else if(commandName == "merge.sfffiles") { shellcommand = new MergeSfffilesCommand(); }
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 {
delete command; //delete the old command
string s = "";
command = new NoCommand(s);
return command;
}
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 {
out << "Valid commands are: ";
for (it = commands.begin(); 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);
//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++) {
out << itCat->first << " commmands include: " << itCat->second << endl;
}
}
catch(exception& e) {
m->errorOut(e, "CommandFactory", "printCommandsCategories");
exit(1);
}
}
/***********************************************************************/
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