X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=f581b6db86bb7e8727c76ba28abc57dfe98c06f5;hb=37eac2026d91179acda0494c4dcca22f176551b9;hp=b7b49922e48b28ef2f3ae9503dc4b4feb2f62d8a;hpb=3fd6dd6e4f19a458ac2966ee5458787e998a1bde;p=mothur.git diff --git a/commandfactory.cpp b/commandfactory.cpp index b7b4992..f581b6d 100644 --- a/commandfactory.cpp +++ b/commandfactory.cpp @@ -61,11 +61,10 @@ #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" @@ -103,6 +102,10 @@ #include "removeotuscommand.h" #include "indicatorcommand.h" #include "consensusseqscommand.h" +#include "trimflowscommand.h" +#include "corraxescommand.h" +#include "shhhercommand.h" +#include "pcacommand.h" /*******************************************************/ @@ -166,6 +169,7 @@ 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"; @@ -182,7 +186,6 @@ 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"; @@ -210,6 +213,8 @@ CommandFactory::CommandFactory(){ commands["remove.otus"] = "remove.otus"; commands["indicator"] = "indicator"; commands["consensus.seqs"] = "consensus.seqs"; + commands["corr.axes"] = "corr.axes"; + commands["pca"] = "pca"; commands["pairwise.seqs"] = "MPIEnabled"; commands["pipeline.pds"] = "MPIEnabled"; commands["classify.seqs"] = "MPIEnabled"; @@ -225,6 +230,7 @@ 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"; @@ -308,6 +314,8 @@ 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 == "trim.flows") { command = new TrimFlowsCommand(optionString); } + else if(commandName == "shhh.seqs") { command = new ShhherCommand(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); } @@ -327,12 +335,12 @@ 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 == "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); } @@ -364,6 +372,7 @@ Command* CommandFactory::getCommand(string commandName, string 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 { command = new NoCommand(optionString); } return command; @@ -430,6 +439,8 @@ 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 == "trim.flows") { pipecommand = new TrimFlowsCommand(optionString); } + else if(commandName == "shhh.seqs") { pipecommand = new ShhherCommand(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); } @@ -449,12 +460,12 @@ 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 == "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); } @@ -485,6 +496,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str 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 { pipecommand = new NoCommand(optionString); } return pipecommand; @@ -539,6 +551,8 @@ 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 == "trim.flows") { shellcommand = new TrimFlowsCommand(); } + else if(commandName == "shhh.seqs") { shellcommand = new ShhherCommand(); } else if(commandName == "chimera.seqs") { shellcommand = new ChimeraSeqsCommand(); } else if(commandName == "list.seqs") { shellcommand = new ListSeqsCommand(); } else if(commandName == "get.seqs") { shellcommand = new GetSeqsCommand(); } @@ -558,12 +572,12 @@ 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 == "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(); } @@ -594,6 +608,7 @@ Command* CommandFactory::getCommand(string commandName){ 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 { shellcommand = new NoCommand(); } return shellcommand;