#include "command.hpp"
#include "readdistcommand.h"
#include "readtreecommand.h"
-#include "readsharedcommand.h"
#include "readotucommand.h"
#include "clustercommand.h"
#include "parselistcommand.h"
#include "collectcommand.h"
#include "collectsharedcommand.h"
+#include "getgroupcommand.h"
+#include "getlabelcommand.h"
+#include "getlinecommand.h"
#include "rarefactcommand.h"
#include "summarycommand.h"
#include "summarysharedcommand.h"
#include "rarefactsharedcommand.h"
-#include "nocommand.h"
#include "quitcommand.h"
#include "helpcommand.h"
#include "commandfactory.hpp"
#include "parsimonycommand.h"
#include "unifracunweightedcommand.h"
#include "unifracweightedcommand.h"
-#include <exception>
+#include "libshuffcommand.h"
+#include "heatmapcommand.h"
+#include "filterseqscommand.h"
+#include "mothur.h"
+#include "venncommand.h"
+#include "nocommands.h"
+#include "binsequencecommand.h"
+#include "getoturepcommand.h"
+#include "treegroupscommand.h"
+#include "bootstrapsharedcommand.h"
+#include "concensuscommand.h"
+#include "distancecommand.h"
+#include "aligncommand.h"
+#include "matrixoutputcommand.h"
+#include "getsabundcommand.h"
+#include "getrabundcommand.h"
+#include "seqsummarycommand.h"
+#include "screenseqscommand.h"
/***********************************************************/
CommandFactory::CommandFactory(){
command = new NoCommand();
}
-
/***********************************************************/
/***********************************************************/
try {
delete command; //delete the old command
- if(commandName == "read.dist") { command = new ReadDistCommand(); }
+ 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 == "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 == "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") { command = new HeatMapCommand(); }
+ 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 { command = new NoCommand(); }
-
+
return command;
}
catch(exception& e) {