/***********************************************************/
CommandFactory::CommandFactory(){
- command = new NoCommand();
+ string s = "";
+ command = new NoCommand(s);
}
/***********************************************************/
/***********************************************************/
//This function calls the appropriate command fucntions based on user input.
-Command* CommandFactory::getCommand(string commandName){
+Command* CommandFactory::getCommand(string commandName, string optionString){
try {
delete command; //delete the old command
- if(commandName == "read.dist") { command = new ReadDistCommand(); }
- else if(commandName == "read.otu") { command = new ReadOtuCommand(); }
- else if(commandName == "read.tree") { command = new ReadTreeCommand(); }
- else if(commandName == "cluster") { command = new ClusterCommand(); }
- else if(commandName == "unique.seqs") { command = new DeconvoluteCommand(); }
- else if(commandName == "parsimony") { command = new ParsimonyCommand(); }
- else if(commandName == "help") { command = new HelpCommand(); }
- else if(commandName == "quit") { command = new QuitCommand(); }
- else if(commandName == "collect.single") { command = new CollectCommand(); }
- else if(commandName == "collect.shared") { command = new CollectSharedCommand(); }
- else if(commandName == "rarefaction.single") { command = new RareFactCommand(); }
- else if(commandName == "rarefaction.shared") { command = new RareFactSharedCommand(); }
- else if(commandName == "summary.single") { command = new SummaryCommand(); }
- else if(commandName == "summary.shared") { command = new SummarySharedCommand(); }
- else if(commandName == "unifrac.weighted") { command = new UnifracWeightedCommand(); }
- else if(commandName == "unifrac.unweighted") { command = new UnifracUnweightedCommand(); }
- else if(commandName == "get.group") { command = new GetgroupCommand(); }
- else if(commandName == "get.label") { command = new GetlabelCommand(); }
- else if(commandName == "get.line") { command = new GetlineCommand(); }
- else if(commandName == "get.sabund") { command = new GetSAbundCommand(); }
- else if(commandName == "get.rabund") { command = new GetRAbundCommand(); }
- else if(commandName == "libshuff") { command = new LibShuffCommand(); }
- else if(commandName == "heatmap.bin") { command = new HeatMapCommand(); }
- else if(commandName == "heatmap.sim") { command = new HeatMapSimCommand(); }
- else if(commandName == "filter.seqs") { command = new FilterSeqsCommand(); }
- else if(commandName == "venn") { command = new VennCommand(); }
- else if(commandName == "bin.seqs") { command = new BinSeqCommand(); }
- else if(commandName == "get.oturep") { command = new GetOTURepCommand(); }
- else if(commandName == "tree.shared") { command = new TreeGroupCommand(); }
- else if(commandName == "dist.shared") { command = new MatrixOutputCommand(); }
- else if(commandName == "bootstrap.shared") { command = new BootSharedCommand(); }
- else if(commandName == "concensus") { command = new ConcensusCommand(); }
- else if(commandName == "dist.seqs") { command = new DistanceCommand(); }
- else if(commandName == "align.seqs") { command = new AlignCommand(); }
- else if(commandName == "summary.seqs") { command = new SeqSummaryCommand(); }
- else if(commandName == "screen.seqs") { command = new ScreenSeqsCommand(); }
- else if(commandName == "reverse.seqs") { command = new ReverseSeqsCommand(); }
- else if(commandName == "trim.seqs") { command = new TrimSeqsCommand(); }
- else { command = new NoCommand(); }
+ 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.line") { command = new GetlineCommand(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 == "concensus") { 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 { command = new NoCommand(optionString); }
return command;
}
projects / mothur.git / blobdiff