*/
#include "command.hpp"
-#include "readdistphylipfilecommand.h"
-#include "readdistcolumnfilecommand.h"
-#include "readlistfilecommand.h"
-#include "readrabundfilecommand.h"
-#include "readsabundfilecommand.h"
-#include "readsharedfilecommand.h"
+#include "readdistcommand.h"
+#include "readtreecommand.h"
+#include "readsharedcommand.h"
+#include "readotucommand.h"
#include "clustercommand.h"
#include "parselistcommand.h"
-#include "sharedcommand.h"
#include "collectcommand.h"
#include "collectsharedcommand.h"
#include "rarefactcommand.h"
#include "quitcommand.h"
#include "helpcommand.h"
#include "commandfactory.hpp"
+#include "deconvolutecommand.h"
+#include "parsimonycommand.h"
+#include "unifracunweightedcommand.h"
+#include "unifracweightedcommand.h"
#include <exception>
try {
delete command; //delete the old command
- if(commandName == "read.phylip") { command = new ReadDistPhylipFileCommand(); }
- else if(commandName == "read.column") { command = new ReadDistColumnFileCommand(); }
- else if(commandName == "read.list") { command = new ReadListFileCommand(); }
- else if(commandName == "read.rabund") { command = new ReadRAbundFileCommand(); }
- else if(commandName == "read.sabund") { command = new ReadSAbundFileCommand(); }
- else if(commandName == "read.shared") { command = new ReadSharedFileCommand(); }
- else if(commandName == "cluster") { command = new ClusterCommand(); }
- 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 == "shared") { command = new SharedCommand(); }
- 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 == "parselist") { command = new ParseListCommand(); }
- else { command = new NoCommand(); }
-
+ 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 == "read.shared") { command = new ReadSharedCommand(); }
+ else if(commandName == "cluster") { command = new ClusterCommand(); }
+ else if(commandName == "deconvolute") { 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 { command = new NoCommand(); }
+
return command;
}
catch(exception& e) {
}
/***********************************************************/
-/***********************************************************/
\ No newline at end of file