added reverse.seqs command

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index a5ec5f12c48059089496af3a39d26b0fedb12f52..a559c81a4fc5a5703858be458d3e472420723f27 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -22,7 +22,6 @@
 #include "summarycommand.h"
 #include "summarysharedcommand.h"
 #include "rarefactsharedcommand.h"
-#include "nocommand.h"
 #include "quitcommand.h"
 #include "helpcommand.h"
 #include "commandfactory.hpp"
@@ -30,8 +29,25 @@
 #include "parsimonycommand.h"
 #include "unifracunweightedcommand.h"
 #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"
+#include "reversecommand.h"
 
 /***********************************************************/
 
@@ -39,7 +55,6 @@
 CommandFactory::CommandFactory(){
        command = new NoCommand();
 }
-
 /***********************************************************/
 
 /***********************************************************/
@@ -55,11 +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();                            }
@@ -71,9 +86,26 @@ Command* CommandFactory::getCommand(string commandName){
                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.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 if(commandName == "reverse.seqs")                  {       command = new ReverseSeqsCommand();                     }
                else                                                                                    {       command = new NoCommand();                                      }
 
                return command;