added screen.seqs command - pds

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index ff156139ea3f3c1d67791d440113177fc261a700..7b3a5c024fa31655a22946f3b5b2a86af6ae5b79 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -31,12 +31,22 @@
 #include "unifracweightedcommand.h"
 #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"
 
 
 /***********************************************************/
@@ -60,7 +70,7 @@ Command* CommandFactory::getCommand(string commandName){
        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 == "cluster")                               {       command = new ClusterCommand();                         }
@@ -79,13 +89,22 @@ Command* CommandFactory::getCommand(string commandName){
                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;