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         string s = "";
  59         command = new NoCommand(s);
  60 }
  61 /***********************************************************/
  62
  63 /***********************************************************/
  64 CommandFactory::~CommandFactory(){
  65         delete command;
  66 }
  67
  68 /***********************************************************/
  69
  70 /***********************************************************/
  71 //This function calls the appropriate command fucntions based on user input.
  72 Command* CommandFactory::getCommand(string commandName, string optionString){
  73         try {
  74                 delete command;   //delete the old command
  75
  76                 if(commandName == "read.dist")                                  {       command = new ReadDistCommand(optionString);                    }
  77                 else if(commandName == "read.otu")                              {       command = new ReadOtuCommand(optionString);                             }
  78                 else if(commandName == "read.tree")                             {       command = new ReadTreeCommand(optionString);                    }
  79                 else if(commandName == "cluster")                               {       command = new ClusterCommand(optionString);                             }
  80                 else if(commandName == "unique.seqs")                   {       command = new DeconvoluteCommand(optionString);                 }
  81                 else if(commandName == "parsimony")                             {       command = new ParsimonyCommand(optionString);                   }
  82                 else if(commandName == "help")                                  {       command = new HelpCommand(optionString);                                }
  83                 else if(commandName == "quit")                                  {       command = new QuitCommand(optionString);                                }
  84                 else if(commandName == "collect.single")                {       command = new CollectCommand(optionString);                             }
  85                 else if(commandName == "collect.shared")                {       command = new CollectSharedCommand(optionString);               }
  86                 else if(commandName == "rarefaction.single")    {       command = new RareFactCommand(optionString);                    }
  87                 else if(commandName == "rarefaction.shared")    {       command = new RareFactSharedCommand(optionString);              }
  88                 else if(commandName == "summary.single")                {       command = new SummaryCommand(optionString);                             }
  89                 else if(commandName == "summary.shared")                {       command = new SummarySharedCommand(optionString);               }
  90                 else if(commandName == "unifrac.weighted")              {       command = new UnifracWeightedCommand(optionString);             }
  91                 else if(commandName == "unifrac.unweighted")    {       command = new UnifracUnweightedCommand(optionString);   }
  92                 else if(commandName == "get.group")             {   command = new GetgroupCommand(optionString);                        }
  93                 else if(commandName == "get.label")             {   command = new GetlabelCommand(optionString);                        }
  94                 else if(commandName == "get.line")              {   command = new GetlineCommand(optionString);                         }
  95                 else if(commandName == "get.sabund")            {   command = new GetSAbundCommand(optionString);                       }
  96                 else if(commandName == "get.rabund")            {   command = new GetRAbundCommand(optionString);                       }
  97                 else if(commandName == "libshuff")              {   command = new LibShuffCommand(optionString);                        }
  98                 else if(commandName == "heatmap.bin")                   {   command = new HeatMapCommand(optionString);                         }
  99                 else if(commandName == "heatmap.sim")                   {   command = new HeatMapSimCommand(optionString);                      }
 100                 else if(commandName == "filter.seqs")                   {   command = new FilterSeqsCommand(optionString);                      }
 101                 else if(commandName == "venn")                                  {   command = new VennCommand(optionString);                            }
 102                 else if(commandName == "bin.seqs")                              {   command = new BinSeqCommand(optionString);                          }
 103                 else if(commandName == "get.oturep")                    {   command = new GetOTURepCommand(optionString);                       }
 104                 else if(commandName == "tree.shared")                   {   command = new TreeGroupCommand(optionString);                       }
 105                 else if(commandName == "dist.shared")                   {   command = new MatrixOutputCommand(optionString);            }
 106                 else if(commandName == "bootstrap.shared")              {   command = new BootSharedCommand(optionString);                      }
 107                 else if(commandName == "concensus")                             {   command = new ConcensusCommand(optionString);                       }
 108                 else if(commandName == "dist.seqs")                             {   command = new DistanceCommand(optionString);                        }
 109                 else if(commandName == "align.seqs")                    {   command = new AlignCommand(optionString);                           }
 110                 else if(commandName == "summary.seqs")                  {       command = new SeqSummaryCommand(optionString);                  }
 111                 else if(commandName == "screen.seqs")                   {       command = new ScreenSeqsCommand(optionString);                  }
 112                 else if(commandName == "reverse.seqs")                  {       command = new ReverseSeqsCommand(optionString);                 }
 113                 else if(commandName == "trim.seqs")                             {       command = new TrimSeqsCommand(optionString);                    }
 114                 else                                                                                    {       command = new NoCommand(optionString);                                  }
 115
 116                 return command;
 117         }
 118         catch(exception& e) {
 119                 cout << "Standard Error: " << e.what() << " has occurred in the CommandFactory class Function getCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 120                 exit(1);
 121         }
 122         catch(...) {
 123                 cout << "An unknown error has occurred in the CommandFactory class function getCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 124                 exit(1);
 125         }
 126
 127 }
 128 /***********************************************************/
 129