*/
#include "command.hpp"
-#include "readdistcommand.h"
-#include "readtreecommand.h"
-#include "readotucommand.h"
#include "clustercommand.h"
#include "collectcommand.h"
#include "collectsharedcommand.h"
#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 "sharedcommand.h"
#include "getcommandinfocommand.h"
#include "deuniquetreecommand.h"
+#include "countseqscommand.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"
+#include "makebiomcommand.h"
+#include "getcoremicrobiomecommand.h"
+#include "listotulabelscommand.h"
+#include "getotulabelscommand.h"
+#include "removeotulabelscommand.h"
+#include "makecontigscommand.h"
+#include "loadlogfilecommand.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["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["count.groups"] = "count.groups";
+ commands["clear.memory"] = "clear.memory";
commands["pairwise.seqs"] = "MPIEnabled";
commands["pipeline.pds"] = "MPIEnabled";
commands["classify.seqs"] = "MPIEnabled";
commands["chimera.ccode"] = "MPIEnabled";
commands["chimera.check"] = "MPIEnabled";
commands["chimera.slayer"] = "MPIEnabled";
- commands["chimera.uchime"] = "MPIEnabled";
+ commands["chimera.uchime"] = "chimera.uchime";
+ commands["chimera.perseus"] = "chimera.perseus";
commands["chimera.pintail"] = "MPIEnabled";
commands["chimera.bellerophon"] = "MPIEnabled";
commands["screen.seqs"] = "MPIEnabled";
commands["summary.seqs"] = "MPIEnabled";
commands["cluster.split"] = "MPIEnabled";
- commands["shhh.seqs"] = "MPIEnabled";
+ commands["shhh.flows"] = "MPIEnabled";
commands["sens.spec"] = "sens.spec";
commands["seq.error"] = "seq.error";
+ 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["make.biom"] = "make.biom";
+ 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["quit"] = "MPIEnabled";
}
delete shellcommand;
delete pipecommand;
}
+/***********************************************************/
+/***********************************************************/
+int CommandFactory::checkForRedirects(string optionString) {
+ try {
+
+ int pos = optionString.find("outputdir");
+ if (pos != string::npos) { //user has set outputdir in command option string
+ string outputOption = "";
+ bool foundEquals = false;
+ for(int i=pos;i<optionString.length();i++){
+ if(optionString[i] == ',') { break; }
+ else if(optionString[i] == '=') { foundEquals = true; }
+ if (foundEquals) { outputOption += optionString[i]; }
+ }
+ if(m->dirCheck(outputOption)){
+ setOutputDirectory(outputOption);
+ m->mothurOut("Setting output directory to: " + outputOption); m->mothurOutEndLine();
+ }
+ }
+
+ pos = optionString.find("inputdir");
+ if (pos != string::npos) { //user has set inputdir in command option string
+ string intputOption = "";
+ bool foundEquals = false;
+ for(int i=pos;i<optionString.length();i++){
+ if(optionString[i] == ',') { break; }
+ else if(optionString[i] == '=') { foundEquals = true; }
+ if (foundEquals) { intputOption += optionString[i]; }
+ }
+ if(m->dirCheck(intputOption)){
+ setInputDirectory(intputOption);
+ m->mothurOut("Setting input directory to: " + intputOption); m->mothurOutEndLine();
+ }
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CommandFactory", "getCommand");
+ exit(1);
+ }
+}
/***********************************************************/
/***********************************************************/
//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
-
+
+ checkForRedirects(optionString);
+
//user has opted to redirect output from dir where input files are located to some other place
if (outputDir != "") {
if (optionString != "") { optionString += ", outputdir=" + outputDir; }
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 == "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 == "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 == "shhh.flows") { 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); }
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.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 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 { command = new NoCommand(optionString); }
return command;
try {
delete pipecommand; //delete the old command
+ checkForRedirects(optionString);
+
//user has opted to redirect output from dir where input files are located to some other place
if (outputDir != "") {
if (optionString != "") { optionString += ", outputdir=" + outputDir; }
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 == "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 == "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 == "shhh.flows") { 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); }
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.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 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 { 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 == "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 == "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 == "shhh.flows") { 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(); }
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.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 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 { shellcommand = new NoCommand(); }
return shellcommand;
exit(1);
}
}
-/***********************************************************************/
+***********************************************************************/
bool CommandFactory::isValidCommand(string command) {
try {