added reverse.seqs command

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index ea43c48e6b84e4c2e83de0c067e081c2a88da49f..a559c81a4fc5a5703858be458d3e472420723f27 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -41,7 +41,13 @@
 #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"
+#include "reversecommand.h"
 
 /***********************************************************/
 
@@ -64,11 +70,11 @@ 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();                         }
-               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();                            }
@@ -83,6 +89,8 @@ 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();          }
@@ -90,9 +98,14 @@ Command* CommandFactory::getCommand(string commandName){
                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 == "distance")                              {   command = new DistanceCommand();                    }
+               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                                                                                    {       command = new NoCommand();                                      }
 
                return command;