commandfactory.cpp

   1 /*
   2  *  commandfactory.cpp
   3  *
   4  *
   5  *  Created by Pat Schloss on 10/25/08.
   6  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10 #include "command.hpp"
  11 #include "readdistcommand.h"
  12 #include "readtreecommand.h"
  13 #include "readotucommand.h"
  14 #include "clustercommand.h"
  15 #include "parselistcommand.h"
  16 #include "collectcommand.h"
  17 #include "collectsharedcommand.h"
  18 #include "getgroupcommand.h"
  19 #include "getlabelcommand.h"
  20 #include "getlinecommand.h"
  21 #include "rarefactcommand.h"
  22 #include "summarycommand.h"
  23 #include "summarysharedcommand.h"
  24 #include "rarefactsharedcommand.h"
  25 #include "quitcommand.h"
  26 #include "helpcommand.h"
  27 #include "commandfactory.hpp"
  28 #include "deconvolutecommand.h"
  29 #include "parsimonycommand.h"
  30 #include "unifracunweightedcommand.h"
  31 #include "unifracweightedcommand.h"
  32 #include "libshuffcommand.h"
  33 #include "heatmapcommand.h"
  34 #include "heatmapsimcommand.h"
  35 #include "filterseqscommand.h"
  36 #include "mothur.h"
  37 #include "venncommand.h"
  38 #include "nocommands.h"
  39 #include "binsequencecommand.h"
  40 #include "getoturepcommand.h"
  41 #include "treegroupscommand.h"
  42 #include "bootstrapsharedcommand.h"
  43 #include "concensuscommand.h"
  44 #include "distancecommand.h"
  45 #include "aligncommand.h"
  46 #include "matrixoutputcommand.h"
  47 #include "getsabundcommand.h"
  48 #include "getrabundcommand.h"
  49 #include "seqsummarycommand.h"
  50 #include "screenseqscommand.h"
  51 #include "reversecommand.h"
  52 #include "trimseqscommand.h"
  53
  54 /***********************************************************/
  55
  56 /***********************************************************/
  57 CommandFactory::CommandFactory(){
  58         command = new NoCommand();
  59 }
  60 /***********************************************************/
  61
  62 /***********************************************************/
  63 CommandFactory::~CommandFactory(){
  64         delete command;
  65 }
  66
  67 /***********************************************************/
  68
  69 /***********************************************************/
  70 //This function calls the appropriate command fucntions based on user input.
  71 Command* CommandFactory::getCommand(string commandName){
  72         try {
  73                 delete command;   //delete the old command
  74
  75                 if(commandName == "read.dist")                                  {       command = new ReadDistCommand();                        }
  76                 else if(commandName == "read.otu")                              {       command = new ReadOtuCommand();                         }
  77                 else if(commandName == "read.tree")                             {       command = new ReadTreeCommand();                        }
  78                 else if(commandName == "cluster")                               {       command = new ClusterCommand();                         }
  79                 else if(commandName == "unique.seqs")                   {       command = new DeconvoluteCommand();                     }
  80                 else if(commandName == "parsimony")                             {       command = new ParsimonyCommand();                       }
  81                 else if(commandName == "help")                                  {       command = new HelpCommand();                            }
  82                 else if(commandName == "quit")                                  {       command = new QuitCommand();                            }
  83                 else if(commandName == "collect.single")                {       command = new CollectCommand();                         }
  84                 else if(commandName == "collect.shared")                {       command = new CollectSharedCommand();           }
  85                 else if(commandName == "rarefaction.single")    {       command = new RareFactCommand();                        }
  86                 else if(commandName == "rarefaction.shared")    {       command = new RareFactSharedCommand();          }
  87                 else if(commandName == "summary.single")                {       command = new SummaryCommand();                         }
  88                 else if(commandName == "summary.shared")                {       command = new SummarySharedCommand();           }
  89                 else if(commandName == "unifrac.weighted")              {       command = new UnifracWeightedCommand();         }
  90                 else if(commandName == "unifrac.unweighted")    {       command = new UnifracUnweightedCommand();       }
  91                 else if(commandName == "get.group")             {   command = new GetgroupCommand();                    }
  92                 else if(commandName == "get.label")             {   command = new GetlabelCommand();                    }
  93                 else if(commandName == "get.line")              {   command = new GetlineCommand();                             }
  94                 else if(commandName == "get.sabund")            {   command = new GetSAbundCommand();                   }
  95                 else if(commandName == "get.rabund")            {   command = new GetRAbundCommand();                   }
  96                 else if(commandName == "libshuff")              {   command = new LibShuffCommand();                    }
  97                 else if(commandName == "heatmap.bin")                   {   command = new HeatMapCommand();                             }
  98                 else if(commandName == "heatmap.sim")                   {   command = new HeatMapSimCommand();                  }
  99                 else if(commandName == "filter.seqs")                   {   command = new FilterSeqsCommand();          }
 100                 else if(commandName == "venn")                                  {   command = new VennCommand();                                }
 101                 else if(commandName == "bin.seqs")                              {   command = new BinSeqCommand();                              }
 102                 else if(commandName == "get.oturep")                    {   command = new GetOTURepCommand();                   }
 103                 else if(commandName == "tree.shared")                   {   command = new TreeGroupCommand();                   }
 104                 else if(commandName == "dist.shared")                   {   command = new MatrixOutputCommand();                }
 105                 else if(commandName == "bootstrap.shared")              {   command = new BootSharedCommand();                  }
 106                 else if(commandName == "concensus")                             {   command = new ConcensusCommand();                   }
 107                 else if(commandName == "dist.seqs")                             {   command = new DistanceCommand();                    }
 108                 else if(commandName == "align.seqs")                    {   command = new AlignCommand();                               }
 109                 else if(commandName == "summary.seqs")                  {       command = new SeqSummaryCommand();                      }
 110                 else if(commandName == "screen.seqs")                   {       command = new ScreenSeqsCommand();                      }
 111                 else if(commandName == "reverse.seqs")                  {       command = new ReverseSeqsCommand();                     }
 112                 else if(commandName == "trim.seqs")                             {       command = new TrimSeqsCommand();                        }
 113                 else                                                                                    {       command = new NoCommand();                                      }
 114
 115                 return command;
 116         }
 117         catch(exception& e) {
 118                 cout << "Standard Error: " << e.what() << " has occurred in the CommandFactory class Function getCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 119                 exit(1);
 120         }
 121         catch(...) {
 122                 cout << "An unknown error has occurred in the CommandFactory class function getCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 123                 exit(1);
 124         }
 125
 126 }
 127 /***********************************************************/
 128