#include "command.hpp"
#include "readdistcommand.h"
#include "readtreecommand.h"
-#include "readsharedcommand.h"
#include "readotucommand.h"
#include "clustercommand.h"
-#include "parselistcommand.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 "nocommand.h"
#include "quitcommand.h"
#include "helpcommand.h"
#include "commandfactory.hpp"
#include "parsimonycommand.h"
#include "unifracunweightedcommand.h"
#include "unifracweightedcommand.h"
-#include <exception>
+#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 "bootstrapsharedcommand.h"
+//#include "consensuscommand.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 "chimeraseqscommand.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 "pcacommand.h"
+#include "otuhierarchycommand.h"
+#include "setdircommand.h"
+#include "parselistscommand.h"
+#include "parsesffcommand.h"
+#include "chimeraccodecommand.h"
+#include "chimeracheckcommand.h"
+#include "chimeraslayercommand.h"
+#include "chimerapintailcommand.h"
+#include "chimerabellerophoncommand.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"
+/*******************************************************/
+
+/******************************************************/
+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(){
- command = new NoCommand();
+ string s = "";
+ m = MothurOut::getInstance();
+
+ command = new NoCommand(s);
+ shellcommand = new NoCommand(s);
+ pipecommand = new NoCommand(s);
+
+ outputDir = ""; inputDir = "";
+ logFileName = "";
+ append = false;
+
+ //initialize list of valid commands
+ commands["read.dist"] = "read.dist";
+ commands["read.otu"] = "read.otu";
+ commands["read.tree"] = "read.tree";
+ commands["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["bootstrap.shared"] = "bootstrap.shared";
+ //commands["consensus"] = "consensus";
+ commands["help"] = "help";
+ commands["reverse.seqs"] = "reverse.seqs";
+ commands["trim.seqs"] = "trim.seqs";
+ commands["list.seqs"] = "list.seqs";
+ commands["get.seqs"] = "get.seqs";
+ commands["remove.seqs"] = "get.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"] = "set.dir";
+ commands["merge.files"] = "merge.files";
+ commands["parse.list"] = "parse.list";
+ commands["parse.sff"] = "parse.sff";
+ 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["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.seqs"] = "chimera.seqs";
+ commands["chimera.ccode"] = "MPIEnabled";
+ commands["chimera.check"] = "MPIEnabled";
+ commands["chimera.slayer"] = "MPIEnabled";
+ commands["chimera.pintail"] = "MPIEnabled";
+ commands["chimera.bellerophon"] = "MPIEnabled";
+ commands["screen.seqs"] = "MPIEnabled";
+ commands["summary.seqs"] = "MPIEnabled";
+ commands["cluster.split"] = "MPIEnabled";
+ commands["sens.spec"] = "sens.spec";
+ commands["seq.error"] = "seq.error";
+ commands["quit"] = "MPIEnabled";
+
}
+/***********************************************************/
+/***********************************************************/
+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;
}
/***********************************************************/
/***********************************************************/
//This function calls the appropriate command fucntions based on user input.
-Command* CommandFactory::getCommand(string commandName){
+Command* CommandFactory::getCommand(string commandName, string optionString){
try {
delete command; //delete the old command
+
+ //user has opted to redirect output from dir where input files are located to some other place
+ if (outputDir != "") {
+ if (optionString != "") { optionString += ", outputdir=" + outputDir; }
+ else { optionString += "outputdir=" + outputDir; }
+ }
+
+ //user has opted to redirect input from dir where mothur.exe is located to some other place
+ if (inputDir != "") {
+ if (optionString != "") { optionString += ", inputdir=" + inputDir; }
+ else { optionString += "inputdir=" + inputDir; }
+ }
+
+ if(commandName == "read.dist") { command = new ReadDistCommand(optionString); }
+ else if(commandName == "read.otu") { command = new ReadOtuCommand(optionString); }
+ else if(commandName == "read.tree") { command = new ReadTreeCommand(optionString); }
+ else 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 == "bootstrap.shared") { command = new BootSharedCommand(optionString); }
+ else if(commandName == "consensus") { command = new ConcensusCommand(optionString); }
+ else if(commandName == "dist.seqs") { command = new DistanceCommand(optionString); }
+ else if(commandName == "align.seqs") { command = new AlignCommand(optionString); }
+ else if(commandName == "summary.seqs") { command = new SeqSummaryCommand(optionString); }
+ else if(commandName == "screen.seqs") { command = new ScreenSeqsCommand(optionString); }
+ else if(commandName == "reverse.seqs") { command = new ReverseSeqsCommand(optionString); }
+ else if(commandName == "trim.seqs") { command = new TrimSeqsCommand(optionString); }
+ else if(commandName == "chimera.seqs") { command = new ChimeraSeqsCommand(optionString); }
+ else if(commandName == "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.pintail") { command = new ChimeraPintailCommand(optionString); }
+ else if(commandName == "chimera.bellerophon") { command = new ChimeraBellerophonCommand(optionString); }
+ else if(commandName == "phylotype") { command = new PhylotypeCommand(optionString); }
+ else if(commandName == "mgcluster") { command = new MGClusterCommand(optionString); }
+ else if(commandName == "pre.cluster") { command = new PreClusterCommand(optionString); }
+ else if(commandName == "pcoa") { command = new PCACommand(optionString); }
+ else if(commandName == "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 == "parse.sff") { command = new ParseSFFCommand(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 == "fastq.info") { command = new ParseFastaQCommand(optionString); }
+ else if(commandName == "pipeline.pds") { command = new PipelineCommand(optionString); }
+ else if(commandName == "deunique.seqs") { command = new DeUniqueSeqsCommand(optionString); }
+ else if(commandName == "pairwise.seqs") { command = new PairwiseSeqsCommand(optionString); }
+ else { command = new NoCommand(optionString); }
- if(commandName == "read.dist") { command = new ReadDistCommand(); }
- else if(commandName == "read.otu") { command = new ReadOtuCommand(); }
- else if(commandName == "read.tree") { command = new ReadTreeCommand(); }
- else if(commandName == "read.shared") { command = new ReadSharedCommand(); }
- else if(commandName == "cluster") { command = new ClusterCommand(); }
- else if(commandName == "deconvolute") { command = new DeconvoluteCommand(); }
- else if(commandName == "parsimony") { command = new ParsimonyCommand(); }
- else if(commandName == "help") { command = new HelpCommand(); }
- else if(commandName == "quit") { command = new QuitCommand(); }
- else if(commandName == "collect.single") { command = new CollectCommand(); }
- else if(commandName == "collect.shared") { command = new CollectSharedCommand(); }
- else if(commandName == "rarefaction.single") { command = new RareFactCommand(); }
- else if(commandName == "rarefaction.shared") { command = new RareFactSharedCommand(); }
- else if(commandName == "summary.single") { command = new SummaryCommand(); }
- else if(commandName == "summary.shared") { command = new SummarySharedCommand(); }
- else if(commandName == "unifrac.weighted") { command = new UnifracWeightedCommand(); }
- else if(commandName == "unifrac.unweighted") { command = new UnifracUnweightedCommand(); }
- else { command = new NoCommand(); }
-
return command;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the CommandFactory class Function getCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "CommandFactory", "getCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the CommandFactory class function getCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/***********************************************************/
+
+/***********************************************************/
+//This function calls the appropriate command fucntions based on user input.
+Command* CommandFactory::getCommand(string commandName, string optionString, string mode){
+ try {
+ delete pipecommand; //delete the old command
+
+ //user has opted to redirect output from dir where input files are located to some other place
+ if (outputDir != "") {
+ if (optionString != "") { optionString += ", outputdir=" + outputDir; }
+ else { optionString += "outputdir=" + outputDir; }
+ }
+
+ //user has opted to redirect input from dir where mothur.exe is located to some other place
+ if (inputDir != "") {
+ if (optionString != "") { optionString += ", inputdir=" + inputDir; }
+ else { optionString += "inputdir=" + inputDir; }
+ }
+
+ if(commandName == "read.dist") { pipecommand = new ReadDistCommand(optionString); }
+ else if(commandName == "read.otu") { pipecommand = new ReadOtuCommand(optionString); }
+ else if(commandName == "read.tree") { pipecommand = new ReadTreeCommand(optionString); }
+ else if(commandName == "cluster") { pipecommand = new ClusterCommand(optionString); }
+ else if(commandName == "unique.seqs") { pipecommand = new DeconvoluteCommand(optionString); }
+ else if(commandName == "parsimony") { pipecommand = new ParsimonyCommand(optionString); }
+ else if(commandName == "help") { pipecommand = new HelpCommand(optionString); }
+ else if(commandName == "quit") { pipecommand = new QuitCommand(optionString); }
+ else if(commandName == "collect.single") { pipecommand = new CollectCommand(optionString); }
+ else if(commandName == "collect.shared") { pipecommand = new CollectSharedCommand(optionString); }
+ else if(commandName == "rarefaction.single") { pipecommand = new RareFactCommand(optionString); }
+ else if(commandName == "rarefaction.shared") { pipecommand = new RareFactSharedCommand(optionString); }
+ else if(commandName == "summary.single") { pipecommand = new SummaryCommand(optionString); }
+ else if(commandName == "summary.shared") { pipecommand = new SummarySharedCommand(optionString); }
+ else if(commandName == "unifrac.weighted") { pipecommand = new UnifracWeightedCommand(optionString); }
+ else if(commandName == "unifrac.unweighted") { pipecommand = new UnifracUnweightedCommand(optionString); }
+ else if(commandName == "get.group") { pipecommand = new GetgroupCommand(optionString); }
+ else if(commandName == "get.label") { pipecommand = new GetlabelCommand(optionString); }
+ else if(commandName == "get.sabund") { pipecommand = new GetSAbundCommand(optionString); }
+ else if(commandName == "get.rabund") { pipecommand = new GetRAbundCommand(optionString); }
+ else if(commandName == "libshuff") { pipecommand = new LibShuffCommand(optionString); }
+ else if(commandName == "heatmap.bin") { pipecommand = new HeatMapCommand(optionString); }
+ else if(commandName == "heatmap.sim") { pipecommand = new HeatMapSimCommand(optionString); }
+ else if(commandName == "filter.seqs") { pipecommand = new FilterSeqsCommand(optionString); }
+ else if(commandName == "venn") { pipecommand = new VennCommand(optionString); }
+ else if(commandName == "bin.seqs") { pipecommand = new BinSeqCommand(optionString); }
+ else if(commandName == "get.oturep") { pipecommand = new GetOTURepCommand(optionString); }
+ else if(commandName == "tree.shared") { pipecommand = new TreeGroupCommand(optionString); }
+ else if(commandName == "dist.shared") { pipecommand = new MatrixOutputCommand(optionString); }
+ else if(commandName == "bootstrap.shared") { pipecommand = new BootSharedCommand(optionString); }
+ else if(commandName == "consensus") { pipecommand = new ConcensusCommand(optionString); }
+ else if(commandName == "dist.seqs") { pipecommand = new DistanceCommand(optionString); }
+ else if(commandName == "align.seqs") { pipecommand = new AlignCommand(optionString); }
+ else if(commandName == "summary.seqs") { pipecommand = new SeqSummaryCommand(optionString); }
+ else if(commandName == "screen.seqs") { pipecommand = new ScreenSeqsCommand(optionString); }
+ else if(commandName == "reverse.seqs") { pipecommand = new ReverseSeqsCommand(optionString); }
+ else if(commandName == "trim.seqs") { pipecommand = new TrimSeqsCommand(optionString); }
+ else if(commandName == "chimera.seqs") { pipecommand = new ChimeraSeqsCommand(optionString); }
+ else if(commandName == "list.seqs") { pipecommand = new ListSeqsCommand(optionString); }
+ else if(commandName == "get.seqs") { pipecommand = new GetSeqsCommand(optionString); }
+ else if(commandName == "remove.seqs") { pipecommand = new RemoveSeqsCommand(optionString); }
+ else if(commandName == "merge.files") { pipecommand = new MergeFileCommand(optionString); }
+ else if(commandName == "system") { pipecommand = new SystemCommand(optionString); }
+ else if(commandName == "align.check") { pipecommand = new AlignCheckCommand(optionString); }
+ else if(commandName == "get.sharedseqs") { pipecommand = new GetSharedOTUCommand(optionString); }
+ else if(commandName == "get.otulist") { pipecommand = new GetListCountCommand(optionString); }
+ else if(commandName == "hcluster") { pipecommand = new HClusterCommand(optionString); }
+ else if(commandName == "classify.seqs") { pipecommand = new ClassifySeqsCommand(optionString); }
+ else if(commandName == "chimera.ccode") { pipecommand = new ChimeraCcodeCommand(optionString); }
+ else if(commandName == "chimera.check") { pipecommand = new ChimeraCheckCommand(optionString); }
+ else if(commandName == "chimera.slayer") { pipecommand = new ChimeraSlayerCommand(optionString); }
+ else if(commandName == "chimera.pintail") { pipecommand = new ChimeraPintailCommand(optionString); }
+ else if(commandName == "chimera.bellerophon") { pipecommand = new ChimeraBellerophonCommand(optionString); }
+ else if(commandName == "phylotype") { pipecommand = new PhylotypeCommand(optionString); }
+ else if(commandName == "mgcluster") { pipecommand = new MGClusterCommand(optionString); }
+ else if(commandName == "pre.cluster") { pipecommand = new PreClusterCommand(optionString); }
+ else if(commandName == "pcoa") { pipecommand = new PCACommand(optionString); }
+ else if(commandName == "otu.hierarchy") { pipecommand = new OtuHierarchyCommand(optionString); }
+ else if(commandName == "set.dir") { pipecommand = new SetDirectoryCommand(optionString); }
+ else if(commandName == "set.logfile") { pipecommand = new SetLogFileCommand(optionString); }
+ else if(commandName == "parse.list") { pipecommand = new ParseListCommand(optionString); }
+ else if(commandName == "parse.sff") { pipecommand = new ParseSFFCommand(optionString); }
+ else if(commandName == "phylo.diversity") { pipecommand = new PhyloDiversityCommand(optionString); }
+ else if(commandName == "make.group") { pipecommand = new MakeGroupCommand(optionString); }
+ else if(commandName == "chop.seqs") { pipecommand = new ChopSeqsCommand(optionString); }
+ else if(commandName == "clearcut") { pipecommand = new ClearcutCommand(optionString); }
+ else if(commandName == "catchall") { pipecommand = new CatchAllCommand(optionString); }
+ else if(commandName == "split.abund") { pipecommand = new SplitAbundCommand(optionString); }
+ else if(commandName == "cluster.split") { pipecommand = new ClusterSplitCommand(optionString); }
+ else if(commandName == "classify.otu") { pipecommand = new ClassifyOtuCommand(optionString); }
+ else if(commandName == "degap.seqs") { pipecommand = new DegapSeqsCommand(optionString); }
+ else if(commandName == "get.relabund") { pipecommand = new GetRelAbundCommand(optionString); }
+ else if(commandName == "sens.spec") { pipecommand = new SensSpecCommand(optionString); }
+ else if(commandName == "seq.error") { pipecommand = new SeqErrorCommand(optionString); }
+ else if(commandName == "sffinfo") { pipecommand = new SffInfoCommand(optionString); }
+ else if(commandName == "normalize.shared") { pipecommand = new NormalizeSharedCommand(optionString); }
+ else if(commandName == "metastats") { pipecommand = new MetaStatsCommand(optionString); }
+ else if(commandName == "split.groups") { pipecommand = new SplitGroupCommand(optionString); }
+ else if(commandName == "cluster.fragments") { pipecommand = new ClusterFragmentsCommand(optionString); }
+ else if(commandName == "get.lineage") { pipecommand = new GetLineageCommand(optionString); }
+ else if(commandName == "remove.lineage") { pipecommand = new RemoveLineageCommand(optionString); }
+ else if(commandName == "fastq.info") { pipecommand = new ParseFastaQCommand(optionString); }
+ else if(commandName == "deunique.seqs") { pipecommand = new DeUniqueSeqsCommand(optionString); }
+ else if(commandName == "pairwise.seqs") { pipecommand = new PairwiseSeqsCommand(optionString); }
+ else { pipecommand = new NoCommand(optionString); }
+
+ return pipecommand;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CommandFactory", "getCommand");
exit(1);
}
-
}
/***********************************************************/
+/***********************************************************/
+//This function calls the appropriate command fucntions based on user input, this is used by the pipeline command to check a users piepline for errors before running
+Command* CommandFactory::getCommand(string commandName){
+ try {
+ delete shellcommand; //delete the old command
+
+ if(commandName == "read.dist") { shellcommand = new ReadDistCommand(); }
+ else if(commandName == "read.otu") { shellcommand = new ReadOtuCommand(); }
+ else if(commandName == "read.tree") { shellcommand = new ReadTreeCommand(); }
+ else if(commandName == "cluster") { shellcommand = new ClusterCommand(); }
+ else if(commandName == "unique.seqs") { shellcommand = new DeconvoluteCommand(); }
+ else if(commandName == "parsimony") { shellcommand = new ParsimonyCommand(); }
+ else if(commandName == "help") { shellcommand = new HelpCommand(); }
+ else if(commandName == "quit") { shellcommand = new QuitCommand(); }
+ else if(commandName == "collect.single") { shellcommand = new CollectCommand(); }
+ else if(commandName == "collect.shared") { shellcommand = new CollectSharedCommand(); }
+ else if(commandName == "rarefaction.single") { shellcommand = new RareFactCommand(); }
+ else if(commandName == "rarefaction.shared") { shellcommand = new RareFactSharedCommand(); }
+ else if(commandName == "summary.single") { shellcommand = new SummaryCommand(); }
+ else if(commandName == "summary.shared") { shellcommand = new SummarySharedCommand(); }
+ else if(commandName == "unifrac.weighted") { shellcommand = new UnifracWeightedCommand(); }
+ else if(commandName == "unifrac.unweighted") { shellcommand = new UnifracUnweightedCommand(); }
+ else if(commandName == "get.group") { shellcommand = new GetgroupCommand(); }
+ else if(commandName == "get.label") { shellcommand = new GetlabelCommand(); }
+ else if(commandName == "get.sabund") { shellcommand = new GetSAbundCommand(); }
+ else if(commandName == "get.rabund") { shellcommand = new GetRAbundCommand(); }
+ else if(commandName == "libshuff") { shellcommand = new LibShuffCommand(); }
+ else if(commandName == "heatmap.bin") { shellcommand = new HeatMapCommand(); }
+ else if(commandName == "heatmap.sim") { shellcommand = new HeatMapSimCommand(); }
+ else if(commandName == "filter.seqs") { shellcommand = new FilterSeqsCommand(); }
+ else if(commandName == "venn") { shellcommand = new VennCommand(); }
+ else if(commandName == "bin.seqs") { shellcommand = new BinSeqCommand(); }
+ else if(commandName == "get.oturep") { shellcommand = new GetOTURepCommand(); }
+ else if(commandName == "tree.shared") { shellcommand = new TreeGroupCommand(); }
+ else if(commandName == "dist.shared") { shellcommand = new MatrixOutputCommand(); }
+ else if(commandName == "bootstrap.shared") { shellcommand = new BootSharedCommand(); }
+ else if(commandName == "consensus") { shellcommand = new ConcensusCommand(); }
+ else if(commandName == "dist.seqs") { shellcommand = new DistanceCommand(); }
+ else if(commandName == "align.seqs") { shellcommand = new AlignCommand(); }
+ else if(commandName == "summary.seqs") { shellcommand = new SeqSummaryCommand(); }
+ else if(commandName == "screen.seqs") { shellcommand = new ScreenSeqsCommand(); }
+ else if(commandName == "reverse.seqs") { shellcommand = new ReverseSeqsCommand(); }
+ else if(commandName == "trim.seqs") { shellcommand = new TrimSeqsCommand(); }
+ else if(commandName == "chimera.seqs") { shellcommand = new ChimeraSeqsCommand(); }
+ else if(commandName == "list.seqs") { shellcommand = new ListSeqsCommand(); }
+ else if(commandName == "get.seqs") { shellcommand = new GetSeqsCommand(); }
+ else if(commandName == "remove.seqs") { shellcommand = new RemoveSeqsCommand(); }
+ else if(commandName == "merge.files") { shellcommand = new MergeFileCommand(); }
+ else if(commandName == "system") { shellcommand = new SystemCommand(); }
+ else if(commandName == "align.check") { shellcommand = new AlignCheckCommand(); }
+ else if(commandName == "get.sharedseqs") { shellcommand = new GetSharedOTUCommand(); }
+ else if(commandName == "get.otulist") { shellcommand = new GetListCountCommand(); }
+ else if(commandName == "hcluster") { shellcommand = new HClusterCommand(); }
+ else if(commandName == "classify.seqs") { shellcommand = new ClassifySeqsCommand(); }
+ else if(commandName == "chimera.ccode") { shellcommand = new ChimeraCcodeCommand(); }
+ else if(commandName == "chimera.check") { shellcommand = new ChimeraCheckCommand(); }
+ else if(commandName == "chimera.slayer") { shellcommand = new ChimeraSlayerCommand(); }
+ else if(commandName == "chimera.pintail") { shellcommand = new ChimeraPintailCommand(); }
+ else if(commandName == "chimera.bellerophon") { shellcommand = new ChimeraBellerophonCommand(); }
+ else if(commandName == "phylotype") { shellcommand = new PhylotypeCommand(); }
+ else if(commandName == "mgcluster") { shellcommand = new MGClusterCommand(); }
+ else if(commandName == "pre.cluster") { shellcommand = new PreClusterCommand(); }
+ else if(commandName == "pcoa") { shellcommand = new PCACommand(); }
+ else if(commandName == "otu.hierarchy") { shellcommand = new OtuHierarchyCommand(); }
+ else if(commandName == "set.dir") { shellcommand = new SetDirectoryCommand(); }
+ else if(commandName == "set.logfile") { shellcommand = new SetLogFileCommand(); }
+ else if(commandName == "parse.list") { shellcommand = new ParseListCommand(); }
+ else if(commandName == "parse.sff") { shellcommand = new ParseSFFCommand(); }
+ else if(commandName == "phylo.diversity") { shellcommand = new PhyloDiversityCommand(); }
+ else if(commandName == "make.group") { shellcommand = new MakeGroupCommand(); }
+ else if(commandName == "chop.seqs") { shellcommand = new ChopSeqsCommand(); }
+ else if(commandName == "clearcut") { shellcommand = new ClearcutCommand(); }
+ else if(commandName == "catchall") { shellcommand = new CatchAllCommand(); }
+ else if(commandName == "split.abund") { shellcommand = new SplitAbundCommand(); }
+ else if(commandName == "cluster.split") { shellcommand = new ClusterSplitCommand(); }
+ else if(commandName == "classify.otu") { shellcommand = new ClassifyOtuCommand(); }
+ else if(commandName == "degap.seqs") { shellcommand = new DegapSeqsCommand(); }
+ else if(commandName == "get.relabund") { shellcommand = new GetRelAbundCommand(); }
+ else if(commandName == "sens.spec") { shellcommand = new SensSpecCommand(); }
+ else if(commandName == "seq.error") { shellcommand = new SeqErrorCommand(); }
+ else if(commandName == "sffinfo") { shellcommand = new SffInfoCommand(); }
+ else if(commandName == "normalize.shared") { shellcommand = new NormalizeSharedCommand(); }
+ else if(commandName == "metastats") { shellcommand = new MetaStatsCommand(); }
+ else if(commandName == "split.groups") { shellcommand = new SplitGroupCommand(); }
+ else if(commandName == "cluster.fragments") { shellcommand = new ClusterFragmentsCommand(); }
+ else if(commandName == "get.lineage") { shellcommand = new GetLineageCommand(); }
+ else if(commandName == "remove.lineage") { shellcommand = new RemoveLineageCommand(); }
+ else if(commandName == "fastq.info") { shellcommand = new ParseFastaQCommand(); }
+ else if(commandName == "deunique.seqs") { shellcommand = new DeUniqueSeqsCommand(); }
+ else if(commandName == "pairwise.seqs") { shellcommand = new PairwiseSeqsCommand(); }
+ else { shellcommand = new NoCommand(); }
+
+ return shellcommand;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CommandFactory", "getCommand");
+ exit(1);
+ }
+}
+/***********************************************************
+//This function is used to interrupt a command
+Command* CommandFactory::getCommand(){
+ try {
+ 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);
+ }
+}
+/***********************************************************************/
+
+
+
+
projects / mothur.git / blobdiff