X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=0bca8c0ee3db3706404b3fc5c4ff42b8c8f99388;hb=725a3d4ff2442c79bfde0a75ed3e0904edcf03b7;hp=c33de86f5c5a97fe9599a8871b190194170e1a6c;hpb=a5afca18544555fba2d9c3670ad1f8574916b0a0;p=mothur.git diff --git a/commandfactory.cpp b/commandfactory.cpp index c33de86..0bca8c0 100644 --- a/commandfactory.cpp +++ b/commandfactory.cpp @@ -16,7 +16,6 @@ #include "collectsharedcommand.h" #include "getgroupcommand.h" #include "getlabelcommand.h" -#include "getlinecommand.h" #include "rarefactcommand.h" #include "summarycommand.h" #include "summarysharedcommand.h" @@ -60,6 +59,26 @@ #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" /*******************************************************/ @@ -73,11 +92,21 @@ CommandFactory* CommandFactory::getInstance() { /***********************************************************/ /***********************************************************/ +//note: This class is resposible for knowing which commands are mpiEnabled, +//If a command is not enabled only process 0 will execute the command. +//This avoids redundant outputs on pieces of code we have not paralellized. +//If you add mpi code to a existing command you need to modify the list below or the code will hang on MPI blocking commands like FIle_open. +//example: commands["dist.seqs"] = "MPIEnabled"; + CommandFactory::CommandFactory(){ - _uniqueInstance = 0; string s = ""; + m = MothurOut::getInstance(); + command = new NoCommand(s); + outputDir = ""; inputDir = ""; + logFileName = ""; + append = false; //initialize list of valid commands commands["read.dist"] = "read.dist"; @@ -87,7 +116,6 @@ CommandFactory::CommandFactory(){ commands["get.oturep"] = "get.oturep"; commands["cluster"] = "cluster"; commands["unique.seqs"] = "unique.seqs"; - commands["dist.seqs"] = "dist.seqs"; commands["dist.shared"] = "dist.shared"; commands["collect.single"] = "collect.single"; commands["collect.shared"] = "collect.shared"; @@ -105,19 +133,13 @@ CommandFactory::CommandFactory(){ commands["venn"] = "venn"; commands["get.group"] = "get.group"; commands["get.label"] = "get.label"; - commands["get.line"] = "get.line"; commands["get.sabund"] = "get.sabund"; commands["get.rabund"] = "get.rabund"; commands["bootstrap.shared"] = "bootstrap.shared"; //commands["consensus"] = "consensus"; - commands["help"] = "help"; - commands["filter.seqs"] = "filter.seqs"; - commands["align.seqs"] = "align.seqs"; - commands["summary.seqs"] = "summary.seqs"; - commands["screen.seqs"] = "screen.seqs"; + commands["help"] = "help"; commands["reverse.seqs"] = "reverse.seqs"; commands["trim.seqs"] = "trim.seqs"; - commands["chimera.seqs"] = "chimera.seqs"; commands["list.seqs"] = "list.seqs"; commands["get.seqs"] = "get.seqs"; commands["remove.seqs"] = "get.seqs"; @@ -125,16 +147,55 @@ CommandFactory::CommandFactory(){ commands["align.check"] = "align.check"; commands["get.sharedseqs"] = "get.sharedseqs"; commands["get.otulist"] = "get.otulist"; - commands["quit"] = "quit"; commands["hcluster"] = "hcluster"; - commands["classify.seqs"] = "classify.seqs"; commands["phylotype"] = "phylotype"; + commands["mgcluster"] = "mgcluster"; + commands["pre.cluster"] = "pre.cluster"; + commands["pcoa"] = "pcoa"; + commands["otu.hierarchy"] = "otu.hierarchy"; + commands["set.dir"] = "set.dir"; + commands["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["cluster.split"] = "cluster.split"; + 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["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; } @@ -145,63 +206,94 @@ CommandFactory::~CommandFactory(){ Command* CommandFactory::getCommand(string commandName, string optionString){ try { delete command; //delete the old command - - 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.line") { command = new GetlineCommand(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 == "phylotype") { command = new PhylotypeCommand(optionString); } - else { command = new NoCommand(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 == "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 { command = new NoCommand(optionString); } return command; } catch(exception& e) { - errorOut(e, "CommandFactory", "getCommand"); + m->errorOut(e, "CommandFactory", "getCommand"); exit(1); } } @@ -217,7 +309,7 @@ Command* CommandFactory::getCommand(){ return command; } catch(exception& e) { - errorOut(e, "CommandFactory", "getCommand"); + m->errorOut(e, "CommandFactory", "getCommand"); exit(1); } } @@ -229,17 +321,17 @@ bool CommandFactory::isValidCommand(string command) { if ((commands.find(command)) != (commands.end())) { return true; }else{ - mothurOut(command + " is not a valid command in Mothur. Valid commands are "); + m->mothurOut(command + " is not a valid command in Mothur. Valid commands are "); for (it = commands.begin(); it != commands.end(); it++) { - mothurOut(it->first + ", "); + m->mothurOut(it->first + ", "); } - mothurOutEndLine(); + m->mothurOutEndLine(); return false; } } catch(exception& e) { - errorOut(e, "CommandFactory", "isValidCommand"); + m->errorOut(e, "CommandFactory", "isValidCommand"); exit(1); } } @@ -254,7 +346,7 @@ void CommandFactory::printCommands(ostream& out) { out << endl; } catch(exception& e) { - errorOut(e, "CommandFactory", "printCommands"); + m->errorOut(e, "CommandFactory", "printCommands"); exit(1); } }