/***********************************************************/
CommandFactory::CommandFactory(){
string s = "";
+ m = MothurOut::getInstance();
+
command = new NoCommand(s);
outputDir = ""; inputDir = "";
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); }
- 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 == "quit") { command = new QuitCommand(optionString); }
- else if(commandName == "collect.single") { command = new CollectCommand(optionString); }
- else if(commandName == "collect.shared") { command = new CollectSharedCommand(optionString); }
- else if(commandName == "rarefaction.single") { command = new RareFactCommand(optionString); }
- else if(commandName == "rarefaction.shared") { command = new RareFactSharedCommand(optionString); }
- else if(commandName == "summary.single") { command = new SummaryCommand(optionString); }
- else if(commandName == "summary.shared") { command = new SummarySharedCommand(optionString); }
- else if(commandName == "unifrac.weighted") { command = new UnifracWeightedCommand(optionString); }
- else if(commandName == "unifrac.unweighted") { command = new UnifracUnweightedCommand(optionString); }
- else if(commandName == "get.group") { command = new GetgroupCommand(optionString); }
- else if(commandName == "get.label") { command = new GetlabelCommand(optionString); }
- else if(commandName == "get.sabund") { command = new GetSAbundCommand(optionString); }
- else if(commandName == "get.rabund") { command = new GetRAbundCommand(optionString); }
- else if(commandName == "libshuff") { command = new LibShuffCommand(optionString); }
- else if(commandName == "heatmap.bin") { command = new HeatMapCommand(optionString); }
- else if(commandName == "heatmap.sim") { command = new HeatMapSimCommand(optionString); }
- else if(commandName == "filter.seqs") { command = new FilterSeqsCommand(optionString); }
- else if(commandName == "venn") { command = new VennCommand(optionString); }
- else if(commandName == "bin.seqs") { command = new BinSeqCommand(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 == "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 == "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 == "remove.seqs") { command = new RemoveSeqsCommand(optionString); }
- else if(commandName == "merge.files") { command = new MergeFileCommand(optionString); }
- else if(commandName == "system") { command = new SystemCommand(optionString); }
- else if(commandName == "align.check") { command = new AlignCheckCommand(optionString); }
- else if(commandName == "get.sharedseqs") { command = new GetSharedOTUCommand(optionString); }
- else if(commandName == "get.otulist") { command = new GetListCountCommand(optionString); }
- else if(commandName == "hcluster") { command = new HClusterCommand(optionString); }
- else if(commandName == "classify.seqs") { command = new ClassifySeqsCommand(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 == "otu.hierarchy") { command = new OtuHierarchyCommand(optionString); }
- else if(commandName == "set.dir") { command = new SetDirectoryCommand(optionString); }
- else if(commandName == "parse.list") { command = new ParseListCommand(optionString); }
- else { command = new NoCommand(optionString); }
+ 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); }
+ 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 == "quit") { command = new QuitCommand(optionString); }
+ else if(commandName == "collect.single") { command = new CollectCommand(optionString); }
+ else if(commandName == "collect.shared") { command = new CollectSharedCommand(optionString); }
+ else if(commandName == "rarefaction.single") { command = new RareFactCommand(optionString); }
+ else if(commandName == "rarefaction.shared") { command = new RareFactSharedCommand(optionString); }
+ else if(commandName == "summary.single") { command = new SummaryCommand(optionString); }
+ else if(commandName == "summary.shared") { command = new SummarySharedCommand(optionString); }
+ else if(commandName == "unifrac.weighted") { command = new UnifracWeightedCommand(optionString); }
+ else if(commandName == "unifrac.unweighted") { command = new UnifracUnweightedCommand(optionString); }
+ else if(commandName == "get.group") { command = new GetgroupCommand(optionString); }
+ else if(commandName == "get.label") { command = new GetlabelCommand(optionString); }
+ else if(commandName == "get.sabund") { command = new GetSAbundCommand(optionString); }
+ else if(commandName == "get.rabund") { command = new GetRAbundCommand(optionString); }
+ else if(commandName == "libshuff") { command = new LibShuffCommand(optionString); }
+ else if(commandName == "heatmap.bin") { command = new HeatMapCommand(optionString); }
+ else if(commandName == "heatmap.sim") { command = new HeatMapSimCommand(optionString); }
+ else if(commandName == "filter.seqs") { command = new FilterSeqsCommand(optionString); }
+ else if(commandName == "venn") { command = new VennCommand(optionString); }
+ else if(commandName == "bin.seqs") { command = new BinSeqCommand(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 == "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 == "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 == "remove.seqs") { command = new RemoveSeqsCommand(optionString); }
+ else if(commandName == "merge.files") { command = new MergeFileCommand(optionString); }
+ else if(commandName == "system") { command = new SystemCommand(optionString); }
+ else if(commandName == "align.check") { command = new AlignCheckCommand(optionString); }
+ else if(commandName == "get.sharedseqs") { command = new GetSharedOTUCommand(optionString); }
+ else if(commandName == "get.otulist") { command = new GetListCountCommand(optionString); }
+ else if(commandName == "hcluster") { command = new HClusterCommand(optionString); }
+ else if(commandName == "classify.seqs") { command = new ClassifySeqsCommand(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 == "otu.hierarchy") { command = new OtuHierarchyCommand(optionString); }
+ else if(commandName == "set.dir") { command = new SetDirectoryCommand(optionString); }
+ else if(commandName == "parse.list") { command = new ParseListCommand(optionString); }
+ else { command = new NoCommand(optionString); }
return command;
}
catch(exception& e) {
- errorOut(e, "CommandFactory", "getCommand");
+ m->errorOut(e, "CommandFactory", "getCommand");
exit(1);
}
}
return command;
}
catch(exception& e) {
- errorOut(e, "CommandFactory", "getCommand");
+ m->errorOut(e, "CommandFactory", "getCommand");
exit(1);
}
}
if ((commands.find(command)) != (commands.end())) {
return true;
}else{
- mothurOut(command + " is not a valid command in Mothur. Valid commands are ");
+ m->mothurOut(command + " is not a valid command in Mothur. Valid commands are ");
for (it = commands.begin(); it != commands.end(); it++) {
- mothurOut(it->first + ", ");
+ m->mothurOut(it->first + ", ");
}
- mothurOutEndLine();
+ m->mothurOutEndLine();
return false;
}
}
catch(exception& e) {
- errorOut(e, "CommandFactory", "isValidCommand");
+ m->errorOut(e, "CommandFactory", "isValidCommand");
exit(1);
}
}
out << endl;
}
catch(exception& e) {
- errorOut(e, "CommandFactory", "printCommands");
+ m->errorOut(e, "CommandFactory", "printCommands");
exit(1);
}
}
projects / mothur.git / blobdiff