X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=8e61e6e7ecef2bf38ea19ddb9171312bae3ade7b;hb=c47e480b743d1c242b8c527b6d12f992c68b8c2c;hp=a4d6506df3128579158f2f1ff5ee99f67bfc9bc2;hpb=f09bacac01a842a74c1c1b69070852cc969ff506;p=mothur.git diff --git a/commandfactory.cpp b/commandfactory.cpp index a4d6506..8e61e6e 100644 --- a/commandfactory.cpp +++ b/commandfactory.cpp @@ -48,7 +48,6 @@ #include "reversecommand.h" #include "trimseqscommand.h" #include "mergefilecommand.h" -#include "chimeraseqscommand.h" #include "listseqscommand.h" #include "getseqscommand.h" #include "removeseqscommand.h" @@ -61,16 +60,16 @@ #include "phylotypecommand.h" #include "mgclustercommand.h" #include "preclustercommand.h" -#include "pcacommand.h" +#include "pcoacommand.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 "chimerauchimecommand.h" #include "setlogfilecommand.h" #include "phylodiversitycommand.h" #include "makegroupcommand.h" @@ -94,7 +93,35 @@ #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" /*******************************************************/ @@ -130,6 +157,7 @@ CommandFactory::CommandFactory(){ commands["read.dist"] = "read.dist"; commands["read.otu"] = "read.otu"; commands["read.tree"] = "read.tree"; + commands["make.shared"] = "make.shared"; commands["bin.seqs"] = "bin.seqs"; commands["get.oturep"] = "get.oturep"; commands["cluster"] = "cluster"; @@ -158,9 +186,10 @@ CommandFactory::CommandFactory(){ 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"] = "get.seqs"; + commands["remove.seqs"] = "remove.seqs"; commands["system"] = "system"; commands["align.check"] = "align.check"; commands["get.sharedseqs"] = "get.sharedseqs"; @@ -174,7 +203,6 @@ CommandFactory::CommandFactory(){ 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"; @@ -194,20 +222,47 @@ CommandFactory::CommandFactory(){ commands["remove.lineage"] = "remove.lineage"; commands["fastq.info"] = "fastq.info"; commands["deunique.seqs"] = "deunique.seqs"; + commands["cluster.classic"] = "cluster.classic"; + commands["sub.sample"] = "sub.sample"; + commands["remove.groups"] = "remove.groups"; + commands["get.groups"] = "get.groups"; + commands["get.otus"] = "get.otus"; + commands["remove.otus"] = "remove.otus"; + commands["indicator"] = "indicator"; + commands["consensus.seqs"] = "consensus.seqs"; + commands["corr.axes"] = "corr.axes"; + commands["pca"] = "pca"; + commands["nmds"] = "nmds"; + commands["remove.rare"] = "remove.rare"; + commands["amova"] = "amova"; + commands["homova"] = "homova"; + commands["mantel"] = "mantel"; + commands["anosim"] = "anosim"; + commands["make.fastq"] = "make.fastq"; + commands["merge.groups"] = "merge.groups"; + commands["get.current"] = "get.current"; + commands["set.current"] = "set.current"; + commands["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.seqs"] = "chimera.seqs"; commands["chimera.ccode"] = "MPIEnabled"; commands["chimera.check"] = "MPIEnabled"; commands["chimera.slayer"] = "MPIEnabled"; + commands["chimera.uchime"] = "chimera.uchime"; commands["chimera.pintail"] = "MPIEnabled"; commands["chimera.bellerophon"] = "MPIEnabled"; commands["screen.seqs"] = "MPIEnabled"; commands["summary.seqs"] = "MPIEnabled"; commands["cluster.split"] = "MPIEnabled"; + commands["shhh.seqs"] = "MPIEnabled"; commands["sens.spec"] = "sens.spec"; commands["seq.error"] = "seq.error"; commands["quit"] = "MPIEnabled"; @@ -291,7 +346,8 @@ Command* CommandFactory::getCommand(string commandName, string 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 == "trim.flows") { command = new TrimFlowsCommand(optionString); } + else if(commandName == "shhh.seqs") { 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); } @@ -305,17 +361,19 @@ Command* CommandFactory::getCommand(string commandName, string 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 PCACommand(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 == "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); } @@ -335,9 +393,34 @@ Command* CommandFactory::getCommand(string commandName, string 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") { command = new CountSeqsCommand(optionString); } + else if(commandName == "count.groups") { command = new CountGroupsCommand(optionString); } + else if(commandName == "clear.memory") { command = new ClearMemoryCommand(optionString); } else { command = new NoCommand(optionString); } return command; @@ -404,7 +487,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str 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 == "trim.flows") { pipecommand = new TrimFlowsCommand(optionString); } + else if(commandName == "shhh.seqs") { 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); } @@ -417,18 +501,20 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str 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 PCACommand(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 == "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); } @@ -447,9 +533,34 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str 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") { pipecommand = new CountSeqsCommand(optionString); } + else if(commandName == "count.groups") { pipecommand = new CountGroupsCommand(optionString); } + else if(commandName == "clear.memory") { pipecommand = new ClearMemoryCommand(optionString); } else { pipecommand = new NoCommand(optionString); } return pipecommand; @@ -504,7 +615,8 @@ Command* CommandFactory::getCommand(string commandName){ 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 == "trim.flows") { shellcommand = new TrimFlowsCommand(); } + else if(commandName == "shhh.seqs") { 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(); } @@ -518,17 +630,19 @@ Command* CommandFactory::getCommand(string commandName){ 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 PCACommand(); } + 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 == "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(); } @@ -548,8 +662,33 @@ Command* CommandFactory::getCommand(string commandName){ 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") { shellcommand = new CountSeqsCommand(); } + else if(commandName == "count.groups") { shellcommand = new CountGroupsCommand(); } + else if(commandName == "clear.memory") { shellcommand = new ClearMemoryCommand(); } else { shellcommand = new NoCommand(); } return shellcommand;