X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=fbafe572582194ca455074a4c4fab0887a21bf0c;hb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;hp=5d9679a498f70eea896664bad38c057710fd01bd;hpb=d635b39347cd81943ea50de7b813a0a5d743b0c0;p=mothur.git diff --git a/commandfactory.cpp b/commandfactory.cpp index 5d9679a..fbafe57 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" @@ -61,11 +60,10 @@ #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" @@ -105,6 +103,20 @@ #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" /*******************************************************/ @@ -140,6 +152,7 @@ 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"; @@ -185,7 +198,6 @@ 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"; @@ -214,13 +226,24 @@ CommandFactory::CommandFactory(){ 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["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"; @@ -229,6 +252,7 @@ CommandFactory::CommandFactory(){ 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"; @@ -313,7 +337,7 @@ Command* CommandFactory::getCommand(string commandName, string 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 == "chimera.seqs") { command = new ChimeraSeqsCommand(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); } @@ -332,12 +356,13 @@ Command* CommandFactory::getCommand(string commandName, string 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); } @@ -370,6 +395,17 @@ Command* CommandFactory::getCommand(string commandName, string 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 { command = new NoCommand(optionString); } return command; @@ -437,7 +473,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str 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 == "chimera.seqs") { pipecommand = new ChimeraSeqsCommand(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); } @@ -456,12 +492,13 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str 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); } @@ -493,6 +530,17 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str 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 { pipecommand = new NoCommand(optionString); } return pipecommand; @@ -548,7 +596,7 @@ Command* CommandFactory::getCommand(string commandName){ 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 == "chimera.seqs") { shellcommand = new ChimeraSeqsCommand(); } + 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(); } @@ -567,12 +615,13 @@ Command* CommandFactory::getCommand(string commandName){ 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(); } @@ -604,6 +653,17 @@ Command* CommandFactory::getCommand(string commandName){ 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 { shellcommand = new NoCommand(); } return shellcommand;