*/
#include "command.hpp"
-#include "readdistcommand.h"
-#include "readtreecommand.h"
-#include "readotucommand.h"
#include "clustercommand.h"
#include "collectcommand.h"
#include "collectsharedcommand.h"
#include "createdatabasecommand.h"
#include "makebiomcommand.h"
#include "getcoremicrobiomecommand.h"
+#include "listotulabelscommand.h"
+#include "getotulabelscommand.h"
+#include "removeotulabelscommand.h"
+#include "makecontigscommand.h"
+#include "loadlogfilecommand.h"
+#include "sffmultiplecommand.h"
+#include "classifyrfsharedcommand.h"
+#include "filtersharedcommand.h"
+#include "primerdesigncommand.h"
+#include "getdistscommand.h"
+#include "removedistscommand.h"
+#include "mergetaxsummarycommand.h"
+#include "getmetacommunitycommand.h"
+#include "sparcccommand.h"
+#include "makelookupcommand.h"
+#include "renameseqscommand.h"
+#include "makelefsecommand.h"
+#include "lefsecommand.h"
+#include "kruskalwalliscommand.h"
+#include "sracommand.h"
+#include "mergesfffilecommand.h"
/*******************************************************/
append = false;
//initialize list of valid commands
- 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["pcr.seqs"] = "pcr.seqs";
commands["create.database"] = "create.database";
commands["make.biom"] = "make.biom";
- commands["get.coremicrobiome"] = "get.coremicrobiome";
+ commands["get.coremicrobiome"] = "get.coremicrobiome";
+ commands["list.otulabels"] = "list.otulabels";
+ commands["get.otulabels"] = "get.otulabels";
+ commands["remove.otulabels"] = "remove.otulabels";
+ commands["make.contigs"] = "make.contigs";
+ commands["load.logfile"] = "load.logfile";
+ commands["make.table"] = "make.table";
+ commands["sff.multiple"] = "sff.multiple";
commands["quit"] = "MPIEnabled";
+ commands["classify.rf"] = "classify.rf";
+ commands["filter.shared"] = "filter.shared";
+ commands["primer.design"] = "primer.design";
+ commands["get.dists"] = "get.dists";
+ commands["remove.dists"] = "remove.dists";
+ commands["merge.taxsummary"] = "merge.taxsummary";
+ commands["get.communitytype"] = "get.communitytype";
+ commands["sparcc"] = "sparcc";
+ commands["make.lookup"] = "make.lookup";
+ commands["rename.seqs"] = "rename.seqs";
+ commands["make.lefse"] = "make.lefse";
+ commands["lefse"] = "lefse";
+ commands["kruskal.wallis"] = "kruskal.wallis";
+ commands["sra"] = "sra";
+ commands["merge.sfffiles"] = "merge.sfffiles";
+
}
/***********************************************************/
else { optionString += "inputdir=" + inputDir; }
}
- if(commandName == "read.dist") { command = new ReadDistCommand(optionString); }
- else if(commandName == "read.otu") { command = new ReadOtuCommand(optionString); }
- else if(commandName == "read.tree") { command = new ReadTreeCommand(optionString); }
- else if(commandName == "cluster") { command = new ClusterCommand(optionString); }
+ if(commandName == "cluster") { command = new ClusterCommand(optionString); }
else if(commandName == "unique.seqs") { command = new DeconvoluteCommand(optionString); }
else if(commandName == "parsimony") { command = new ParsimonyCommand(optionString); }
else if(commandName == "help") { command = new HelpCommand(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.seqs") || (commandName == "make.table")) { command = new CountSeqsCommand(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 == "create.database") { command = new CreateDatabaseCommand(optionString); }
else if(commandName == "make.biom") { command = new MakeBiomCommand(optionString); }
else if(commandName == "get.coremicrobiome") { command = new GetCoreMicroBiomeCommand(optionString); }
+ else if(commandName == "list.otulabels") { command = new ListOtuLabelsCommand(optionString); }
+ else if(commandName == "get.otulabels") { command = new GetOtuLabelsCommand(optionString); }
+ else if(commandName == "remove.otulabels") { command = new RemoveOtuLabelsCommand(optionString); }
+ else if(commandName == "make.contigs") { command = new MakeContigsCommand(optionString); }
+ else if(commandName == "load.logfile") { command = new LoadLogfileCommand(optionString); }
+ else if(commandName == "sff.multiple") { command = new SffMultipleCommand(optionString); }
+ else if(commandName == "classify.rf") { command = new ClassifyRFSharedCommand(optionString); }
+ else if(commandName == "filter.shared") { command = new FilterSharedCommand(optionString); }
+ else if(commandName == "primer.design") { command = new PrimerDesignCommand(optionString); }
+ else if(commandName == "get.dists") { command = new GetDistsCommand(optionString); }
+ else if(commandName == "remove.dists") { command = new RemoveDistsCommand(optionString); }
+ else if(commandName == "merge.taxsummary") { command = new MergeTaxSummaryCommand(optionString); }
+ else if(commandName == "get.communitytype") { command = new GetMetaCommunityCommand(optionString); }
+ else if(commandName == "sparcc") { command = new SparccCommand(optionString); }
+ else if(commandName == "make.lookup") { command = new MakeLookupCommand(optionString); }
+ else if(commandName == "rename.seqs") { command = new RenameSeqsCommand(optionString); }
+ else if(commandName == "make.lefse") { command = new MakeLefseCommand(optionString); }
+ else if(commandName == "lefse") { command = new LefseCommand(optionString); }
+ else if(commandName == "kruskal.wallis") { command = new KruskalWallisCommand(optionString); }
+ else if(commandName == "sra") { command = new SRACommand(optionString); }
+ else if(commandName == "merge.sfffiles") { command = new MergeSfffilesCommand(optionString); }
else { command = new NoCommand(optionString); }
return command;
else { optionString += "inputdir=" + inputDir; }
}
- if(commandName == "read.dist") { pipecommand = new ReadDistCommand(optionString); }
- else if(commandName == "read.otu") { pipecommand = new ReadOtuCommand(optionString); }
- else if(commandName == "read.tree") { pipecommand = new ReadTreeCommand(optionString); }
- else if(commandName == "cluster") { pipecommand = new ClusterCommand(optionString); }
+ if(commandName == "cluster") { pipecommand = new ClusterCommand(optionString); }
else if(commandName == "unique.seqs") { pipecommand = new DeconvoluteCommand(optionString); }
else if(commandName == "parsimony") { pipecommand = new ParsimonyCommand(optionString); }
else if(commandName == "help") { pipecommand = new HelpCommand(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.seqs") || (commandName == "make.table")) { pipecommand = new CountSeqsCommand(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 == "create.database") { pipecommand = new CreateDatabaseCommand(optionString); }
else if(commandName == "make.biom") { pipecommand = new MakeBiomCommand(optionString); }
else if(commandName == "get.coremicrobiome") { pipecommand = new GetCoreMicroBiomeCommand(optionString); }
+ else if(commandName == "list.otulabels") { pipecommand = new ListOtuLabelsCommand(optionString); }
+ else if(commandName == "get.otulabels") { pipecommand = new GetOtuLabelsCommand(optionString); }
+ else if(commandName == "remove.otulabels") { pipecommand = new RemoveOtuLabelsCommand(optionString); }
+ else if(commandName == "make.contigs") { pipecommand = new MakeContigsCommand(optionString); }
+ else if(commandName == "load.logfile") { pipecommand = new LoadLogfileCommand(optionString); }
+ else if(commandName == "sff.multiple") { pipecommand = new SffMultipleCommand(optionString); }
+ else if(commandName == "classify.rf") { pipecommand = new ClassifyRFSharedCommand(optionString); }
+ else if(commandName == "filter.shared") { pipecommand = new FilterSharedCommand(optionString); }
+ else if(commandName == "primer.design") { pipecommand = new PrimerDesignCommand(optionString); }
+ else if(commandName == "get.dists") { pipecommand = new GetDistsCommand(optionString); }
+ else if(commandName == "remove.dists") { pipecommand = new RemoveDistsCommand(optionString); }
+ else if(commandName == "merge.taxsummary") { pipecommand = new MergeTaxSummaryCommand(optionString); }
+ else if(commandName == "get.communitytype") { pipecommand = new GetMetaCommunityCommand(optionString); }
+ else if(commandName == "sparcc") { pipecommand = new SparccCommand(optionString); }
+ else if(commandName == "make.lookup") { pipecommand = new MakeLookupCommand(optionString); }
+ else if(commandName == "rename.seqs") { pipecommand = new RenameSeqsCommand(optionString); }
+ else if(commandName == "make.lefse") { pipecommand = new MakeLefseCommand(optionString); }
+ else if(commandName == "lefse") { pipecommand = new LefseCommand(optionString); }
+ else if(commandName == "kruskal.wallis") { pipecommand = new KruskalWallisCommand(optionString); }
+ else if(commandName == "sra") { pipecommand = new SRACommand(optionString); }
+ else if(commandName == "merge.sfffiles") { pipecommand = new MergeSfffilesCommand(optionString); }
else { pipecommand = new NoCommand(optionString); }
return pipecommand;
try {
delete shellcommand; //delete the old command
- if(commandName == "read.dist") { shellcommand = new ReadDistCommand(); }
- else if(commandName == "read.otu") { shellcommand = new ReadOtuCommand(); }
- else if(commandName == "read.tree") { shellcommand = new ReadTreeCommand(); }
- else if(commandName == "cluster") { shellcommand = new ClusterCommand(); }
+ if(commandName == "cluster") { shellcommand = new ClusterCommand(); }
else if(commandName == "unique.seqs") { shellcommand = new DeconvoluteCommand(); }
else if(commandName == "parsimony") { shellcommand = new ParsimonyCommand(); }
else if(commandName == "help") { shellcommand = new HelpCommand(); }
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.seqs") || (commandName == "make.table")) { shellcommand = new CountSeqsCommand(); }
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 == "create.database") { shellcommand = new CreateDatabaseCommand(); }
else if(commandName == "make.biom") { shellcommand = new MakeBiomCommand(); }
else if(commandName == "get.coremicrobiome") { shellcommand = new GetCoreMicroBiomeCommand(); }
+ else if(commandName == "list.otulabels") { shellcommand = new ListOtuLabelsCommand(); }
+ else if(commandName == "get.otulabels") { shellcommand = new GetOtuLabelsCommand(); }
+ else if(commandName == "remove.otulabels") { shellcommand = new RemoveOtuLabelsCommand(); }
+ else if(commandName == "make.contigs") { shellcommand = new MakeContigsCommand(); }
+ else if(commandName == "load.logfile") { shellcommand = new LoadLogfileCommand(); }
+ else if(commandName == "sff.multiple") { shellcommand = new SffMultipleCommand(); }
+ else if(commandName == "classify.rf") { shellcommand = new ClassifyRFSharedCommand(); }
+ else if(commandName == "filter.shared") { shellcommand = new FilterSharedCommand(); }
+ else if(commandName == "primer.design") { shellcommand = new PrimerDesignCommand(); }
+ else if(commandName == "get.dists") { shellcommand = new GetDistsCommand(); }
+ else if(commandName == "remove.dists") { shellcommand = new RemoveDistsCommand(); }
+ else if(commandName == "merge.taxsummary") { shellcommand = new MergeTaxSummaryCommand(); }
+ else if(commandName == "get.communitytype") { shellcommand = new GetMetaCommunityCommand(); }
+ else if(commandName == "sparcc") { shellcommand = new SparccCommand(); }
+ else if(commandName == "make.lookup") { shellcommand = new MakeLookupCommand(); }
+ else if(commandName == "rename.seqs") { shellcommand = new RenameSeqsCommand(); }
+ else if(commandName == "make.lefse") { shellcommand = new MakeLefseCommand(); }
+ else if(commandName == "lefse") { shellcommand = new LefseCommand(); }
+ else if(commandName == "kruskal.wallis") { shellcommand = new KruskalWallisCommand(); }
+ else if(commandName == "sra") { shellcommand = new SRACommand(); }
+ else if(commandName == "merge.sfffiles") { shellcommand = new MergeSfffilesCommand(); }
else { shellcommand = new NoCommand(); }
return shellcommand;
}
}
/***********************************************************************/
+void CommandFactory::printCommandsCategories(ostream& out) {
+ try {
+ map<string, string> commands = getListCommands();
+ map<string, string>::iterator it;
+
+ map<string, string> categories;
+ map<string, string>::iterator itCat;
+ //loop through each command outputting info
+ for (it = commands.begin(); it != commands.end(); it++) {
+
+ Command* thisCommand = getCommand(it->first);
+
+ //don't add hidden commands
+ if (thisCommand->getCommandCategory() != "Hidden") {
+ itCat = categories.find(thisCommand->getCommandCategory());
+ if (itCat == categories.end()) {
+ categories[thisCommand->getCommandCategory()] = thisCommand->getCommandName();
+ }else {
+ categories[thisCommand->getCommandCategory()] += ", " + thisCommand->getCommandName();
+ }
+ }
+ }
+
+ for (itCat = categories.begin(); itCat != categories.end(); itCat++) {
+ out << itCat->first << " commmands include: " << itCat->second << endl;
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CommandFactory", "printCommandsCategories");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
projects / mothur.git / blobdiff