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 "rarefactcommand.h"
  20 #include "summarycommand.h"
  21 #include "summarysharedcommand.h"
  22 #include "rarefactsharedcommand.h"
  23 #include "quitcommand.h"
  24 #include "helpcommand.h"
  25 #include "commandfactory.hpp"
  26 #include "deconvolutecommand.h"
  27 #include "parsimonycommand.h"
  28 #include "unifracunweightedcommand.h"
  29 #include "unifracweightedcommand.h"
  30 #include "libshuffcommand.h"
  31 #include "heatmapcommand.h"
  32 #include "heatmapsimcommand.h"
  33 #include "filterseqscommand.h"
  34 #include "venncommand.h"
  35 #include "nocommands.h"
  36 #include "binsequencecommand.h"
  37 #include "getoturepcommand.h"
  38 #include "treegroupscommand.h"
  39 #include "bootstrapsharedcommand.h"
  40 //#include "consensuscommand.h"
  41 #include "distancecommand.h"
  42 #include "aligncommand.h"
  43 #include "matrixoutputcommand.h"
  44 #include "getsabundcommand.h"
  45 #include "getrabundcommand.h"
  46 #include "seqsummarycommand.h"
  47 #include "screenseqscommand.h"
  48 #include "reversecommand.h"
  49 #include "trimseqscommand.h"
  50 #include "mergefilecommand.h"
  51 #include "chimeraseqscommand.h"
  52 #include "listseqscommand.h"
  53 #include "getseqscommand.h"
  54 #include "removeseqscommand.h"
  55 #include "systemcommand.h"
  56 #include "secondarystructurecommand.h"
  57 #include "getsharedotucommand.h"
  58 #include "getlistcountcommand.h"
  59 #include "hclustercommand.h"
  60 #include "classifyseqscommand.h"
  61 #include "phylotypecommand.h"
  62 #include "mgclustercommand.h"
  63 #include "preclustercommand.h"
  64 #include "pcacommand.h"
  65 #include "otuhierarchycommand.h"
  66 #include "setdircommand.h"
  67
  68 /*******************************************************/
  69
  70 /******************************************************/
  71 CommandFactory* CommandFactory::getInstance() {
  72         if( _uniqueInstance == 0) {
  73                 _uniqueInstance = new CommandFactory();
  74         }
  75         return _uniqueInstance;
  76 }
  77 /***********************************************************/
  78
  79 /***********************************************************/
  80 CommandFactory::CommandFactory(){
  81         string s = "";
  82         command = new NoCommand(s);
  83
  84         outputDir = ""; inputDir = "";
  85
  86         //initialize list of valid commands
  87         commands["read.dist"]                   = "read.dist";
  88         commands["read.otu"]                    = "read.otu";
  89         commands["read.tree"]                   = "read.tree";
  90         commands["bin.seqs"]                    = "bin.seqs";
  91         commands["get.oturep"]                  = "get.oturep";
  92         commands["cluster"]                             = "cluster";
  93         commands["unique.seqs"]                 = "unique.seqs";
  94         commands["dist.seqs"]                   = "dist.seqs";
  95         commands["dist.shared"]                 = "dist.shared";
  96         commands["collect.single"]              = "collect.single";
  97         commands["collect.shared"]              = "collect.shared";
  98         commands["rarefaction.single"]  = "rarefaction.single";
  99         commands["rarefaction.shared"]  = "rarefaction.shared";
 100         commands["summary.single"]              = "summary.single";
 101         commands["summary.shared"]              = "summary.shared";
 102         commands["parsimony"]                   = "parsimony";
 103         commands["unifrac.weighted"]    = "unifrac.weighted";
 104         commands["unifrac.unweighted"]  = "unifrac.unweighted";
 105         commands["libshuff"]                    = "libshuff";
 106         commands["tree.shared"]                 = "tree.shared";
 107         commands["heatmap.bin"]                 = "heatmap.bin";
 108         commands["heatmap.sim"]                 = "heatmap.sim";
 109         commands["venn"]                                = "venn";
 110         commands["get.group"]           = "get.group";
 111         commands["get.label"]           = "get.label";
 112         commands["get.sabund"]          = "get.sabund";
 113         commands["get.rabund"]          = "get.rabund";
 114         commands["bootstrap.shared"]    = "bootstrap.shared";
 115         //commands["consensus"]                 = "consensus";
 116         commands["help"]                                = "help";
 117         commands["filter.seqs"]                 = "filter.seqs";
 118         commands["align.seqs"]                  = "align.seqs";
 119         commands["summary.seqs"]                = "summary.seqs";
 120         commands["screen.seqs"]                 = "screen.seqs";
 121         commands["reverse.seqs"]                = "reverse.seqs";
 122         commands["trim.seqs"]                   = "trim.seqs";
 123         commands["chimera.seqs"]                = "chimera.seqs";
 124         commands["list.seqs"]                   = "list.seqs";
 125         commands["get.seqs"]                    = "get.seqs";
 126         commands["remove.seqs"]                 = "get.seqs";
 127         commands["system"]                              = "system";
 128         commands["align.check"]                 = "align.check";
 129         commands["get.sharedseqs"]              = "get.sharedseqs";
 130         commands["get.otulist"]                 = "get.otulist";
 131         commands["quit"]                                = "quit";
 132         commands["hcluster"]                    = "hcluster";
 133         commands["classify.seqs"]               = "classify.seqs";
 134         commands["phylotype"]                   = "phylotype";
 135         commands["mgcluster"]                   = "mgcluster";
 136         commands["pre.cluster"]                 = "pre.cluster";
 137         commands["pca"]                                 = "pca";
 138         commands["otu.hierarchy"]               = "otu.hierarchy";
 139         commands["set.dir"]                             = "set.dir";
 140 }
 141 /***********************************************************/
 142
 143 /***********************************************************/
 144 CommandFactory::~CommandFactory(){
 145         _uniqueInstance = 0;
 146         delete command;
 147 }
 148
 149 /***********************************************************/
 150
 151 /***********************************************************/
 152 //This function calls the appropriate command fucntions based on user input.
 153 Command* CommandFactory::getCommand(string commandName, string optionString){
 154         try {
 155                 delete command;   //delete the old command
 156
 157                 //user has opted to redirect output from dir where input files are located to some other place
 158                 if (outputDir != "") {
 159                         if (optionString != "") { optionString += ", outputdir=" + outputDir; }
 160                         else { optionString += "outputdir=" + outputDir; }
 161                 }
 162
 163                 //user has opted to redirect input from dir where mothur.exe is located to some other place
 164                 if (inputDir != "") {
 165                         if (optionString != "") { optionString += ", inputdir=" + inputDir; }
 166                         else { optionString += "inputdir=" + inputDir; }
 167                 }
 168
 169                 if(commandName == "read.dist")                                  {       command = new ReadDistCommand(optionString);                    }
 170                 else if(commandName == "read.otu")                              {       command = new ReadOtuCommand(optionString);                             }
 171                 else if(commandName == "read.tree")                             {       command = new ReadTreeCommand(optionString);                    }
 172                 else if(commandName == "cluster")                               {       command = new ClusterCommand(optionString);                             }
 173                 else if(commandName == "unique.seqs")                   {       command = new DeconvoluteCommand(optionString);                 }
 174                 else if(commandName == "parsimony")                             {       command = new ParsimonyCommand(optionString);                   }
 175                 else if(commandName == "help")                                  {       command = new HelpCommand(optionString);                                }
 176                 else if(commandName == "quit")                                  {       command = new QuitCommand(optionString);                                }
 177                 else if(commandName == "collect.single")                {       command = new CollectCommand(optionString);                             }
 178                 else if(commandName == "collect.shared")                {       command = new CollectSharedCommand(optionString);               }
 179                 else if(commandName == "rarefaction.single")    {       command = new RareFactCommand(optionString);                    }
 180                 else if(commandName == "rarefaction.shared")    {       command = new RareFactSharedCommand(optionString);              }
 181                 else if(commandName == "summary.single")                {       command = new SummaryCommand(optionString);                             }
 182                 else if(commandName == "summary.shared")                {       command = new SummarySharedCommand(optionString);               }
 183                 else if(commandName == "unifrac.weighted")              {       command = new UnifracWeightedCommand(optionString);             }
 184                 else if(commandName == "unifrac.unweighted")    {       command = new UnifracUnweightedCommand(optionString);   }
 185                 else if(commandName == "get.group")             {   command = new GetgroupCommand(optionString);                        }
 186                 else if(commandName == "get.label")             {   command = new GetlabelCommand(optionString);                        }
 187                 else if(commandName == "get.sabund")            {   command = new GetSAbundCommand(optionString);                       }
 188                 else if(commandName == "get.rabund")            {   command = new GetRAbundCommand(optionString);                       }
 189                 else if(commandName == "libshuff")              {   command = new LibShuffCommand(optionString);                        }
 190                 else if(commandName == "heatmap.bin")                   {   command = new HeatMapCommand(optionString);                         }
 191                 else if(commandName == "heatmap.sim")                   {   command = new HeatMapSimCommand(optionString);                      }
 192                 else if(commandName == "filter.seqs")                   {   command = new FilterSeqsCommand(optionString);                      }
 193                 else if(commandName == "venn")                                  {   command = new VennCommand(optionString);                            }
 194                 else if(commandName == "bin.seqs")                              {   command = new BinSeqCommand(optionString);                          }
 195                 else if(commandName == "get.oturep")                    {   command = new GetOTURepCommand(optionString);                       }
 196                 else if(commandName == "tree.shared")                   {   command = new TreeGroupCommand(optionString);                       }
 197                 else if(commandName == "dist.shared")                   {   command = new MatrixOutputCommand(optionString);            }
 198                 else if(commandName == "bootstrap.shared")              {   command = new BootSharedCommand(optionString);                      }
 199                 //else if(commandName == "consensus")                   {   command = new ConcensusCommand(optionString);                       }
 200                 else if(commandName == "dist.seqs")                             {   command = new DistanceCommand(optionString);                        }
 201                 else if(commandName == "align.seqs")                    {   command = new AlignCommand(optionString);                           }
 202                 else if(commandName == "summary.seqs")                  {       command = new SeqSummaryCommand(optionString);                  }
 203                 else if(commandName == "screen.seqs")                   {       command = new ScreenSeqsCommand(optionString);                  }
 204                 else if(commandName == "reverse.seqs")                  {       command = new ReverseSeqsCommand(optionString);                 }
 205                 else if(commandName == "trim.seqs")                             {       command = new TrimSeqsCommand(optionString);                    }
 206                 else if(commandName == "chimera.seqs")                  {       command = new ChimeraSeqsCommand(optionString);                 }
 207                 else if(commandName == "list.seqs")                             {       command = new ListSeqsCommand(optionString);                    }
 208                 else if(commandName == "get.seqs")                              {       command = new GetSeqsCommand(optionString);                             }
 209                 else if(commandName == "remove.seqs")                   {       command = new RemoveSeqsCommand(optionString);                  }
 210                 else if(commandName == "merge.files")                   {       command = new MergeFileCommand(optionString);                   }
 211                 else if(commandName == "system")                                {       command = new SystemCommand(optionString);                              }
 212                 else if(commandName == "align.check")                   {       command = new AlignCheckCommand(optionString);                  }
 213                 else if(commandName == "get.sharedseqs")                {       command = new GetSharedOTUCommand(optionString);                }
 214                 else if(commandName == "get.otulist")                   {       command = new GetListCountCommand(optionString);                }
 215                 else if(commandName == "hcluster")                              {       command = new HClusterCommand(optionString);                    }
 216                 else if(commandName == "classify.seqs")                 {       command = new ClassifySeqsCommand(optionString);                }
 217                 else if(commandName == "phylotype")                             {       command = new PhylotypeCommand(optionString);                   }
 218                 else if(commandName == "mgcluster")                             {       command = new MGClusterCommand(optionString);                   }
 219                 else if(commandName == "pre.cluster")                   {       command = new PreClusterCommand(optionString);                  }
 220                 else if(commandName == "pca")                                   {       command = new PCACommand(optionString);                                 }
 221                 else if(commandName == "otu.hierarchy")                 {       command = new OtuHierarchyCommand(optionString);                }
 222                 else if(commandName == "set.dir")                               {       command = new SetDirectoryCommand(optionString);        }
 223                 else                                                                                    {       command = new NoCommand(optionString);                                  }
 224
 225                 return command;
 226         }
 227         catch(exception& e) {
 228                 errorOut(e, "CommandFactory", "getCommand");
 229                 exit(1);
 230         }
 231 }
 232 /***********************************************************/
 233 //This function is used to interrupt a command
 234 Command* CommandFactory::getCommand(){
 235         try {
 236                 delete command;   //delete the old command
 237
 238                 string s = "";
 239             command = new NoCommand(s);
 240
 241                 return command;
 242         }
 243         catch(exception& e) {
 244                 errorOut(e, "CommandFactory", "getCommand");
 245                 exit(1);
 246         }
 247 }
 248 /***********************************************************************/
 249 bool CommandFactory::isValidCommand(string command) {
 250         try {
 251
 252                 //is the command in the map
 253                 if ((commands.find(command)) != (commands.end())) {
 254                         return true;
 255                 }else{
 256                         mothurOut(command + " is not a valid command in Mothur.  Valid commands are ");
 257                         for (it = commands.begin(); it != commands.end(); it++) {
 258                                 mothurOut(it->first + ", ");
 259                         }
 260                         mothurOutEndLine();
 261                         return false;
 262                 }
 263
 264         }
 265         catch(exception& e) {
 266                 errorOut(e, "CommandFactory", "isValidCommand");
 267                 exit(1);
 268         }
 269 }
 270
 271 /***********************************************************************/
 272 void CommandFactory::printCommands(ostream& out) {
 273         try {
 274                 out << "Valid commands are ";
 275                 for (it = commands.begin(); it != commands.end(); it++) {
 276                         out << it->first << ", ";
 277                 }
 278                 out << endl;
 279         }
 280         catch(exception& e) {
 281                 errorOut(e, "CommandFactory", "printCommands");
 282                 exit(1);
 283         }
 284 }
 285 /***********************************************************************/
 286
 287
 288
 289