#include "binsequencecommand.h"
#include "getoturepcommand.h"
#include "treegroupscommand.h"
-#include "bootstrapsharedcommand.h"
-//#include "consensuscommand.h"
#include "distancecommand.h"
#include "aligncommand.h"
#include "matrixoutputcommand.h"
#include "countgroupscommand.h"
#include "clearmemorycommand.h"
#include "summarytaxcommand.h"
+#include "chimeraperseuscommand.h"
+#include "shhhseqscommand.h"
+#include "summaryqualcommand.h"
+#include "otuassociationcommand.h"
+#include "sortseqscommand.h"
+#include "classifytreecommand.h"
+#include "cooccurrencecommand.h"
+#include "pcrseqscommand.h"
+#include "createdatabasecommand.h"
/*******************************************************/
commands["get.label"] = "get.label";
commands["get.sabund"] = "get.sabund";
commands["get.rabund"] = "get.rabund";
- commands["bootstrap.shared"] = "bootstrap.shared";
- //commands["consensus"] = "consensus";
commands["help"] = "help";
commands["reverse.seqs"] = "reverse.seqs";
commands["trim.seqs"] = "trim.seqs";
commands["pre.cluster"] = "pre.cluster";
commands["pcoa"] = "pcoa";
commands["otu.hierarchy"] = "otu.hierarchy";
- commands["set.dir"] = "set.dir";
+ commands["set.dir"] = "MPIEnabled";
commands["merge.files"] = "merge.files";
commands["parse.list"] = "parse.list";
commands["set.logfile"] = "set.logfile";
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.current"] = "MPIEnabled";
+ commands["set.current"] = "MPIEnabled";
commands["get.commandinfo"] = "get.commandinfo";
commands["deunique.tree"] = "deunique.tree";
commands["count.seqs"] = "count.seqs";
commands["chimera.check"] = "MPIEnabled";
commands["chimera.slayer"] = "MPIEnabled";
commands["chimera.uchime"] = "chimera.uchime";
+ commands["chimera.perseus"] = "chimera.perseus";
commands["chimera.pintail"] = "MPIEnabled";
commands["chimera.bellerophon"] = "MPIEnabled";
commands["screen.seqs"] = "MPIEnabled";
commands["shhh.flows"] = "MPIEnabled";
commands["sens.spec"] = "sens.spec";
commands["seq.error"] = "seq.error";
- commands["seq.error"] = "summary.tax";
+ commands["summary.tax"] = "summary.tax";
+ commands["summary.qual"] = "summary.qual";
+ commands["shhh.seqs"] = "shhh.seqs";
+ commands["otu.association"] = "otu.association";
+ commands["sort.seqs"] = "sort.seqs";
+ commands["classify.tree"] = "classify.tree";
+ commands["cooccurrence"] = "cooccurrence";
+ commands["pcr.seqs"] = "pcr.seqs";
+ commands["create.database"] = "create.database";
commands["quit"] = "MPIEnabled";
}
//This function calls the appropriate command fucntions based on user input.
Command* CommandFactory::getCommand(string commandName, string optionString){
try {
+
delete command; //delete the old command
//user has opted to redirect output from dir where input files are located to some other place
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 == "count.groups") { command = new CountGroupsCommand(optionString); }
else if(commandName == "clear.memory") { command = new ClearMemoryCommand(optionString); }
else if(commandName == "summary.tax") { command = new SummaryTaxCommand(optionString); }
+ else if(commandName == "summary.qual") { command = new SummaryQualCommand(optionString); }
+ else if(commandName == "chimera.perseus") { command = new ChimeraPerseusCommand(optionString); }
+ else if(commandName == "shhh.seqs") { command = new ShhhSeqsCommand(optionString); }
+ else if(commandName == "otu.association") { command = new OTUAssociationCommand(optionString); }
+ else if(commandName == "sort.seqs") { command = new SortSeqsCommand(optionString); }
+ else if(commandName == "classify.tree") { command = new ClassifyTreeCommand(optionString); }
+ else if(commandName == "cooccurrence") { command = new CooccurrenceCommand(optionString); }
+ else if(commandName == "pcr.seqs") { command = new PcrSeqsCommand(optionString); }
+ else if(commandName == "create.database") { command = new CreateDatabaseCommand(optionString); }
else { command = new NoCommand(optionString); }
return command;
else if(commandName == "get.oturep") { pipecommand = new GetOTURepCommand(optionString); }
else if(commandName == "tree.shared") { pipecommand = new TreeGroupCommand(optionString); }
else if(commandName == "dist.shared") { pipecommand = new MatrixOutputCommand(optionString); }
- else if(commandName == "bootstrap.shared") { pipecommand = new BootSharedCommand(optionString); }
- else if(commandName == "consensus") { pipecommand = new ConcensusCommand(optionString); }
else if(commandName == "dist.seqs") { pipecommand = new DistanceCommand(optionString); }
else if(commandName == "align.seqs") { pipecommand = new AlignCommand(optionString); }
else if(commandName == "summary.seqs") { pipecommand = new SeqSummaryCommand(optionString); }
else if(commandName == "count.groups") { pipecommand = new CountGroupsCommand(optionString); }
else if(commandName == "clear.memory") { pipecommand = new ClearMemoryCommand(optionString); }
else if(commandName == "summary.tax") { pipecommand = new SummaryTaxCommand(optionString); }
+ else if(commandName == "summary.qual") { pipecommand = new SummaryQualCommand(optionString); }
+ else if(commandName == "chimera.perseus") { pipecommand = new ChimeraPerseusCommand(optionString); }
+ else if(commandName == "shhh.seqs") { pipecommand = new ShhhSeqsCommand(optionString); }
+ else if(commandName == "otu.association") { pipecommand = new OTUAssociationCommand(optionString); }
+ else if(commandName == "sort.seqs") { pipecommand = new SortSeqsCommand(optionString); }
+ else if(commandName == "classify.tree") { pipecommand = new ClassifyTreeCommand(optionString); }
+ else if(commandName == "cooccurrence") { pipecommand = new CooccurrenceCommand(optionString); }
+ else if(commandName == "pcr.seqs") { pipecommand = new PcrSeqsCommand(optionString); }
+ else if(commandName == "create.database") { pipecommand = new CreateDatabaseCommand(optionString); }
else { pipecommand = new NoCommand(optionString); }
return pipecommand;
else if(commandName == "get.oturep") { shellcommand = new GetOTURepCommand(); }
else if(commandName == "tree.shared") { shellcommand = new TreeGroupCommand(); }
else if(commandName == "dist.shared") { shellcommand = new MatrixOutputCommand(); }
- else if(commandName == "bootstrap.shared") { shellcommand = new BootSharedCommand(); }
- else if(commandName == "consensus") { shellcommand = new ConcensusCommand(); }
else if(commandName == "dist.seqs") { shellcommand = new DistanceCommand(); }
else if(commandName == "align.seqs") { shellcommand = new AlignCommand(); }
else if(commandName == "summary.seqs") { shellcommand = new SeqSummaryCommand(); }
else if(commandName == "count.groups") { shellcommand = new CountGroupsCommand(); }
else if(commandName == "clear.memory") { shellcommand = new ClearMemoryCommand(); }
else if(commandName == "summary.tax") { shellcommand = new SummaryTaxCommand(); }
+ else if(commandName == "summary.qual") { shellcommand = new SummaryQualCommand(); }
+ else if(commandName == "chimera.perseus") { shellcommand = new ChimeraPerseusCommand(); }
+ else if(commandName == "shhh.seqs") { shellcommand = new ShhhSeqsCommand(); }
+ else if(commandName == "otu.association") { shellcommand = new OTUAssociationCommand(); }
+ else if(commandName == "sort.seqs") { shellcommand = new SortSeqsCommand(); }
+ else if(commandName == "classify.tree") { shellcommand = new ClassifyTreeCommand(); }
+ else if(commandName == "cooccurrence") { shellcommand = new CooccurrenceCommand(); }
+ else if(commandName == "pcr.seqs") { shellcommand = new PcrSeqsCommand(); }
+ else if(commandName == "create.database") { shellcommand = new CreateDatabaseCommand(); }
else { shellcommand = new NoCommand(); }
return shellcommand;
exit(1);
}
}
-/***********************************************************************/
+***********************************************************************/
bool CommandFactory::isValidCommand(string command) {
try {
projects / mothur.git / blobdiff