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 "collectcommand.h"
  16 #include "collectsharedcommand.h"
  17 #include "getgroupcommand.h"
  18 #include "getlabelcommand.h"
  19 #include "getlinecommand.h"
  20 #include "rarefactcommand.h"
  21 #include "summarycommand.h"
  22 #include "summarysharedcommand.h"
  23 #include "rarefactsharedcommand.h"
  24 #include "quitcommand.h"
  25 #include "helpcommand.h"
  26 #include "commandfactory.hpp"
  27 #include "deconvolutecommand.h"
  28 #include "parsimonycommand.h"
  29 #include "unifracunweightedcommand.h"
  30 #include "unifracweightedcommand.h"
  31 #include "libshuffcommand.h"
  32 #include "heatmapcommand.h"
  33 #include "heatmapsimcommand.h"
  34 #include "filterseqscommand.h"
  35 #include "venncommand.h"
  36 #include "nocommands.h"
  37 #include "binsequencecommand.h"
  38 #include "getoturepcommand.h"
  39 #include "treegroupscommand.h"
  40 #include "bootstrapsharedcommand.h"
  41 //#include "consensuscommand.h"
  42 #include "distancecommand.h"
  43 #include "aligncommand.h"
  44 #include "matrixoutputcommand.h"
  45 #include "getsabundcommand.h"
  46 #include "getrabundcommand.h"
  47 #include "seqsummarycommand.h"
  48 #include "screenseqscommand.h"
  49 #include "reversecommand.h"
  50 #include "trimseqscommand.h"
  51 #include "mergefilecommand.h"
  52 #include "chimeraseqscommand.h"
  53 #include "listseqscommand.h"
  54 #include "getseqscommand.h"
  55 #include "removeseqscommand.h"
  56 #include "systemcommand.h"
  57 #include "secondarystructurecommand.h"
  58 #include "getsharedotucommand.h"
  59 #include "getlistcountcommand.h"
  60 #include "hclustercommand.h"
  61 #include "classifyseqscommand.h"
  62 #include "phylotypecommand.h"
  63
  64 /***********************************************************/
  65
  66 /***********************************************************/
  67 CommandFactory::CommandFactory(){
  68         string s = "";
  69         command = new NoCommand(s);
  70
  71
  72         //initialize list of valid commands
  73         commands["read.dist"]                   = "read.dist";
  74         commands["read.otu"]                    = "read.otu";
  75         commands["read.tree"]                   = "read.tree";
  76         commands["bin.seqs"]                    = "bin.seqs";
  77         commands["get.oturep"]                  = "get.oturep";
  78         commands["cluster"]                             = "cluster";
  79         commands["unique.seqs"]                 = "unique.seqs";
  80         commands["dist.seqs"]                   = "dist.seqs";
  81         commands["dist.shared"]                 = "dist.shared";
  82         commands["collect.single"]              = "collect.single";
  83         commands["collect.shared"]              = "collect.shared";
  84         commands["rarefaction.single"]  = "rarefaction.single";
  85         commands["rarefaction.shared"]  = "rarefaction.shared";
  86         commands["summary.single"]              = "summary.single";
  87         commands["summary.shared"]              = "summary.shared";
  88         commands["parsimony"]                   = "parsimony";
  89         commands["unifrac.weighted"]    = "unifrac.weighted";
  90         commands["unifrac.unweighted"]  = "unifrac.unweighted";
  91         commands["libshuff"]                    = "libshuff";
  92         commands["tree.shared"]                 = "tree.shared";
  93         commands["heatmap.bin"]                 = "heatmap.bin";
  94         commands["heatmap.sim"]                 = "heatmap.sim";
  95         commands["venn"]                                = "venn";
  96         commands["get.group"]           = "get.group";
  97         commands["get.label"]           = "get.label";
  98         commands["get.line"]            = "get.line";
  99         commands["get.sabund"]          = "get.sabund";
 100         commands["get.rabund"]          = "get.rabund";
 101         commands["bootstrap.shared"]    = "bootstrap.shared";
 102         //commands["consensus"]                 = "consensus";
 103         commands["help"]                                = "help";
 104         commands["filter.seqs"]                 = "filter.seqs";
 105         commands["align.seqs"]                  = "align.seqs";
 106         commands["summary.seqs"]                = "summary.seqs";
 107         commands["screen.seqs"]                 = "screen.seqs";
 108         commands["reverse.seqs"]                = "reverse.seqs";
 109         commands["trim.seqs"]                   = "trim.seqs";
 110         commands["chimera.seqs"]                = "chimera.seqs";
 111         commands["list.seqs"]                   = "list.seqs";
 112         commands["get.seqs"]                    = "get.seqs";
 113         commands["remove.seqs"]                 = "get.seqs";
 114         commands["system"]                              = "system";
 115         commands["align.check"]                 = "align.check";
 116         commands["get.sharedseqs"]              = "get.sharedseqs";
 117         commands["get.otulist"]                 = "get.otulist";
 118         commands["quit"]                                = "quit";
 119         commands["hcluster"]                    = "hcluster";
 120         commands["classify.seqs"]               = "classify.seqs";
 121         commands["phylotype"]                   = "phylotype";
 122
 123 }
 124 /***********************************************************/
 125
 126 /***********************************************************/
 127 CommandFactory::~CommandFactory(){
 128         delete command;
 129 }
 130
 131 /***********************************************************/
 132
 133 /***********************************************************/
 134 //This function calls the appropriate command fucntions based on user input.
 135 Command* CommandFactory::getCommand(string commandName, string optionString){
 136         try {
 137                 delete command;   //delete the old command
 138
 139                 if(commandName == "read.dist")                                  {       command = new ReadDistCommand(optionString);                    }
 140                 else if(commandName == "read.otu")                              {       command = new ReadOtuCommand(optionString);                             }
 141                 else if(commandName == "read.tree")                             {       command = new ReadTreeCommand(optionString);                    }
 142                 else if(commandName == "cluster")                               {       command = new ClusterCommand(optionString);                             }
 143                 else if(commandName == "unique.seqs")                   {       command = new DeconvoluteCommand(optionString);                 }
 144                 else if(commandName == "parsimony")                             {       command = new ParsimonyCommand(optionString);                   }
 145                 else if(commandName == "help")                                  {       command = new HelpCommand(optionString);                                }
 146                 else if(commandName == "quit")                                  {       command = new QuitCommand(optionString);                                }
 147                 else if(commandName == "collect.single")                {       command = new CollectCommand(optionString);                             }
 148                 else if(commandName == "collect.shared")                {       command = new CollectSharedCommand(optionString);               }
 149                 else if(commandName == "rarefaction.single")    {       command = new RareFactCommand(optionString);                    }
 150                 else if(commandName == "rarefaction.shared")    {       command = new RareFactSharedCommand(optionString);              }
 151                 else if(commandName == "summary.single")                {       command = new SummaryCommand(optionString);                             }
 152                 else if(commandName == "summary.shared")                {       command = new SummarySharedCommand(optionString);               }
 153                 else if(commandName == "unifrac.weighted")              {       command = new UnifracWeightedCommand(optionString);             }
 154                 else if(commandName == "unifrac.unweighted")    {       command = new UnifracUnweightedCommand(optionString);   }
 155                 else if(commandName == "get.group")             {   command = new GetgroupCommand(optionString);                        }
 156                 else if(commandName == "get.label")             {   command = new GetlabelCommand(optionString);                        }
 157                 else if(commandName == "get.line")              {   command = new GetlineCommand(optionString);                         }
 158                 else if(commandName == "get.sabund")            {   command = new GetSAbundCommand(optionString);                       }
 159                 else if(commandName == "get.rabund")            {   command = new GetRAbundCommand(optionString);                       }
 160                 else if(commandName == "libshuff")              {   command = new LibShuffCommand(optionString);                        }
 161                 else if(commandName == "heatmap.bin")                   {   command = new HeatMapCommand(optionString);                         }
 162                 else if(commandName == "heatmap.sim")                   {   command = new HeatMapSimCommand(optionString);                      }
 163                 else if(commandName == "filter.seqs")                   {   command = new FilterSeqsCommand(optionString);                      }
 164                 else if(commandName == "venn")                                  {   command = new VennCommand(optionString);                            }
 165                 else if(commandName == "bin.seqs")                              {   command = new BinSeqCommand(optionString);                          }
 166                 else if(commandName == "get.oturep")                    {   command = new GetOTURepCommand(optionString);                       }
 167                 else if(commandName == "tree.shared")                   {   command = new TreeGroupCommand(optionString);                       }
 168                 else if(commandName == "dist.shared")                   {   command = new MatrixOutputCommand(optionString);            }
 169                 else if(commandName == "bootstrap.shared")              {   command = new BootSharedCommand(optionString);                      }
 170                 //else if(commandName == "consensus")                   {   command = new ConcensusCommand(optionString);                       }
 171                 else if(commandName == "dist.seqs")                             {   command = new DistanceCommand(optionString);                        }
 172                 else if(commandName == "align.seqs")                    {   command = new AlignCommand(optionString);                           }
 173                 else if(commandName == "summary.seqs")                  {       command = new SeqSummaryCommand(optionString);                  }
 174                 else if(commandName == "screen.seqs")                   {       command = new ScreenSeqsCommand(optionString);                  }
 175                 else if(commandName == "reverse.seqs")                  {       command = new ReverseSeqsCommand(optionString);                 }
 176                 else if(commandName == "trim.seqs")                             {       command = new TrimSeqsCommand(optionString);                    }
 177                 else if(commandName == "chimera.seqs")                  {       command = new ChimeraSeqsCommand(optionString);                 }
 178                 else if(commandName == "list.seqs")                             {       command = new ListSeqsCommand(optionString);                    }
 179                 else if(commandName == "get.seqs")                              {       command = new GetSeqsCommand(optionString);                             }
 180                 else if(commandName == "remove.seqs")                   {       command = new RemoveSeqsCommand(optionString);                  }
 181                 else if(commandName == "merge.files")                   {       command = new MergeFileCommand(optionString);                   }
 182                 else if(commandName == "system")                                {       command = new SystemCommand(optionString);                              }
 183                 else if(commandName == "align.check")                   {       command = new AlignCheckCommand(optionString);                  }
 184                 else if(commandName == "get.sharedseqs")                {       command = new GetSharedOTUCommand(optionString);                }
 185                 else if(commandName == "get.otulist")                   {       command = new GetListCountCommand(optionString);                }
 186                 else if(commandName == "hcluster")                              {       command = new HClusterCommand(optionString);                    }
 187                 else if(commandName == "classify.seqs")                 {       command = new ClassifySeqsCommand(optionString);                }
 188                 else if(commandName == "phylotype")                             {       command = new PhylotypeCommand(optionString);                   }
 189                 else                                                                                    {       command = new NoCommand(optionString);                                  }
 190
 191                 return command;
 192         }
 193         catch(exception& e) {
 194                 errorOut(e, "CommandFactory", "getCommand");
 195                 exit(1);
 196         }
 197 }
 198 /***********************************************************/
 199 //This function is used to interrupt a command
 200 Command* CommandFactory::getCommand(){
 201         try {
 202                 delete command;   //delete the old command
 203
 204                 string s = "";
 205             command = new NoCommand(s);
 206
 207                 return command;
 208         }
 209         catch(exception& e) {
 210                 errorOut(e, "CommandFactory", "getCommand");
 211                 exit(1);
 212         }
 213 }
 214 /***********************************************************************/
 215 bool CommandFactory::isValidCommand(string command) {
 216         try {
 217
 218                 //is the command in the map
 219                 if ((commands.find(command)) != (commands.end())) {
 220                         return true;
 221                 }else{
 222                         mothurOut(command + " is not a valid command in Mothur.  Valid commands are ");
 223                         for (it = commands.begin(); it != commands.end(); it++) {
 224                                 mothurOut(it->first + ", ");
 225                         }
 226                         mothurOutEndLine();
 227                         return false;
 228                 }
 229
 230         }
 231         catch(exception& e) {
 232                 errorOut(e, "CommandFactory", "isValidCommand");
 233                 exit(1);
 234         }
 235 }
 236
 237 /***********************************************************************/
 238 void CommandFactory::printCommands(ostream& out) {
 239         try {
 240                 out << "Valid commands are ";
 241                 for (it = commands.begin(); it != commands.end(); it++) {
 242                         out << it->first << ", ";
 243                 }
 244                 out << endl;
 245         }
 246         catch(exception& e) {
 247                 errorOut(e, "CommandFactory", "printCommands");
 248                 exit(1);
 249         }
 250 }
 251 /***********************************************************************/
 252
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