#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 "removelineagecommand.h"
#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"
/*******************************************************/
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["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["get.lineage"] = "get.lineage";
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["merge.groups"] = "merge.groups";
+ commands["pairwise.seqs"] = "MPIEnabled";
commands["pipeline.pds"] = "MPIEnabled";
commands["classify.seqs"] = "MPIEnabled";
commands["dist.seqs"] = "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";
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); }
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); }
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 { command = new NoCommand(optionString); }
return command;
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); }
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); }
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 { pipecommand = new NoCommand(optionString); }
return pipecommand;
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(); }
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(); }
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 { shellcommand = new NoCommand(); }
return shellcommand;
projects / mothur.git / blobdiff