setcurrentcommand.cpp

   1 /*
   2  *  setcurrentcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 3/16/11.
   6  *  Copyright 2011 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "setcurrentcommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> SetCurrentCommand::getValidParameters(){
  14         try {
  15                 string Array[] =  {"outputdir","inputdir","clear", "phylip", "column", "list","rabund","sabund","name","group",
  16                         "design","order","tree","shared","ordergroup","relabund","fasta","qfile","sff","oligos","accnos","taxonomy"};
  17                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  18                 return myArray;
  19         }
  20         catch(exception& e) {
  21                 m->errorOut(e, "SetCurrentCommand", "getValidParameters");
  22                 exit(1);
  23         }
  24 }
  25 //**********************************************************************************************************************
  26 SetCurrentCommand::SetCurrentCommand(){
  27         try {
  28                 abort = true; calledHelp = true;
  29         }
  30         catch(exception& e) {
  31                 m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand");
  32                 exit(1);
  33         }
  34 }
  35 //**********************************************************************************************************************
  36 vector<string> SetCurrentCommand::getRequiredParameters(){
  37         try {
  38                 vector<string> myArray;
  39                 return myArray;
  40         }
  41         catch(exception& e) {
  42                 m->errorOut(e, "SetCurrentCommand", "getRequiredParameters");
  43                 exit(1);
  44         }
  45 }
  46 //**********************************************************************************************************************
  47 vector<string> SetCurrentCommand::getRequiredFiles(){
  48         try {
  49                 vector<string> myArray;
  50                 return myArray;
  51         }
  52         catch(exception& e) {
  53                 m->errorOut(e, "SetCurrentCommand", "getRequiredFiles");
  54                 exit(1);
  55         }
  56 }
  57 //**********************************************************************************************************************
  58 SetCurrentCommand::SetCurrentCommand(string option)  {
  59         try {
  60                 abort = false; calledHelp = false;
  61
  62                 //allow user to run help
  63                 if(option == "help") { help(); abort = true; calledHelp = true; }
  64
  65                 else {
  66                         //valid paramters for this command
  67                         string Array[] =  {"outputdir","inputdir","clear", "phylip", "column", "list","rabund","sabund","name","group",
  68                                 "design","order","tree","shared","ordergroup","relabund","fasta","qfile","sff","oligos","accnos","taxonomy"};
  69                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  70
  71                         OptionParser parser(option);
  72                         map<string,string> parameters = parser.getParameters();
  73
  74                         ValidParameters validParameter;
  75                         map<string,string>::iterator it;
  76                         //check to make sure all parameters are valid for command
  77                         for (it = parameters.begin(); it != parameters.end(); it++) {
  78                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  79                         }
  80
  81
  82                         //if the user changes the input directory command factory will send this info to us in the output parameter
  83                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  84                         if (inputDir == "not found"){   inputDir = "";          }
  85                         else {
  86                                 string path;
  87                                 it = parameters.find("phylip");
  88                                 //user has given a template file
  89                                 if(it != parameters.end()){
  90                                         path = m->hasPath(it->second);
  91                                         //if the user has not given a path then, add inputdir. else leave path alone.
  92                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
  93                                 }
  94
  95                                 it = parameters.find("column");
  96                                 //user has given a template file
  97                                 if(it != parameters.end()){
  98                                         path = m->hasPath(it->second);
  99                                         //if the user has not given a path then, add inputdir. else leave path alone.
 100                                         if (path == "") {       parameters["column"] = inputDir + it->second;           }
 101                                 }
 102
 103                                 it = parameters.find("fasta");
 104                                 //user has given a template file
 105                                 if(it != parameters.end()){
 106                                         path = m->hasPath(it->second);
 107                                         //if the user has not given a path then, add inputdir. else leave path alone.
 108                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 109                                 }
 110
 111                                 it = parameters.find("list");
 112                                 //user has given a template file
 113                                 if(it != parameters.end()){
 114                                         path = m->hasPath(it->second);
 115                                         //if the user has not given a path then, add inputdir. else leave path alone.
 116                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 117                                 }
 118
 119                                 it = parameters.find("rabund");
 120                                 //user has given a template file
 121                                 if(it != parameters.end()){
 122                                         path = m->hasPath(it->second);
 123                                         //if the user has not given a path then, add inputdir. else leave path alone.
 124                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 125                                 }
 126
 127                                 it = parameters.find("sabund");
 128                                 //user has given a template file
 129                                 if(it != parameters.end()){
 130                                         path = m->hasPath(it->second);
 131                                         //if the user has not given a path then, add inputdir. else leave path alone.
 132                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 133                                 }
 134
 135                                 it = parameters.find("name");
 136                                 //user has given a template file
 137                                 if(it != parameters.end()){
 138                                         path = m->hasPath(it->second);
 139                                         //if the user has not given a path then, add inputdir. else leave path alone.
 140                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 141                                 }
 142
 143                                 it = parameters.find("group");
 144                                 //user has given a template file
 145                                 if(it != parameters.end()){
 146                                         path = m->hasPath(it->second);
 147                                         //if the user has not given a path then, add inputdir. else leave path alone.
 148                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 149                                 }
 150
 151                                 it = parameters.find("design");
 152                                 //user has given a template file
 153                                 if(it != parameters.end()){
 154                                         path = m->hasPath(it->second);
 155                                         //if the user has not given a path then, add inputdir. else leave path alone.
 156                                         if (path == "") {       parameters["design"] = inputDir + it->second;           }
 157                                 }
 158
 159                                 it = parameters.find("order");
 160                                 //user has given a template file
 161                                 if(it != parameters.end()){
 162                                         path = m->hasPath(it->second);
 163                                         //if the user has not given a path then, add inputdir. else leave path alone.
 164                                         if (path == "") {       parameters["order"] = inputDir + it->second;            }
 165                                 }
 166
 167                                 it = parameters.find("tree");
 168                                 //user has given a template file
 169                                 if(it != parameters.end()){
 170                                         path = m->hasPath(it->second);
 171                                         //if the user has not given a path then, add inputdir. else leave path alone.
 172                                         if (path == "") {       parameters["tree"] = inputDir + it->second;             }
 173                                 }
 174
 175                                 it = parameters.find("shared");
 176                                 //user has given a template file
 177                                 if(it != parameters.end()){
 178                                         path = m->hasPath(it->second);
 179                                         //if the user has not given a path then, add inputdir. else leave path alone.
 180                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 181                                 }
 182
 183                                 it = parameters.find("ordergroup");
 184                                 //user has given a template file
 185                                 if(it != parameters.end()){
 186                                         path = m->hasPath(it->second);
 187                                         //if the user has not given a path then, add inputdir. else leave path alone.
 188                                         if (path == "") {       parameters["ordergroup"] = inputDir + it->second;               }
 189                                 }
 190
 191                                 it = parameters.find("relabund");
 192                                 //user has given a template file
 193                                 if(it != parameters.end()){
 194                                         path = m->hasPath(it->second);
 195                                         //if the user has not given a path then, add inputdir. else leave path alone.
 196                                         if (path == "") {       parameters["relabund"] = inputDir + it->second;         }
 197                                 }
 198
 199                                 it = parameters.find("fasta");
 200                                 //user has given a template file
 201                                 if(it != parameters.end()){
 202                                         path = m->hasPath(it->second);
 203                                         //if the user has not given a path then, add inputdir. else leave path alone.
 204                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 205                                 }
 206
 207                                 it = parameters.find("qfile");
 208                                 //user has given a template file
 209                                 if(it != parameters.end()){
 210                                         path = m->hasPath(it->second);
 211                                         //if the user has not given a path then, add inputdir. else leave path alone.
 212                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 213                                 }
 214
 215                                 it = parameters.find("sff");
 216                                 //user has given a template file
 217                                 if(it != parameters.end()){
 218                                         path = m->hasPath(it->second);
 219                                         //if the user has not given a path then, add inputdir. else leave path alone.
 220                                         if (path == "") {       parameters["sff"] = inputDir + it->second;              }
 221                                 }
 222
 223                                 it = parameters.find("oligos");
 224                                 //user has given a template file
 225                                 if(it != parameters.end()){
 226                                         path = m->hasPath(it->second);
 227                                         //if the user has not given a path then, add inputdir. else leave path alone.
 228                                         if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
 229                                 }
 230
 231                                 it = parameters.find("accnos");
 232                                 //user has given a template file
 233                                 if(it != parameters.end()){
 234                                         path = m->hasPath(it->second);
 235                                         //if the user has not given a path then, add inputdir. else leave path alone.
 236                                         if (path == "") {       parameters["accnos"] = inputDir + it->second;           }
 237                                 }
 238
 239                                 it = parameters.find("taxonomy");
 240                                 //user has given a template file
 241                                 if(it != parameters.end()){
 242                                         path = m->hasPath(it->second);
 243                                         //if the user has not given a path then, add inputdir. else leave path alone.
 244                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 245                                 }
 246                         }
 247
 248                         //check for parameters
 249                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 250                         if (phylipfile == "not open") { m->mothurOut("Ignoring: " + parameters["phylip"]); m->mothurOutEndLine(); phylipfile = ""; }
 251                         else if (phylipfile == "not found") {  phylipfile = "";  }
 252                         if (phylipfile != "") { m->setPhylipFile(phylipfile); }
 253
 254                         columnfile = validParameter.validFile(parameters, "column", true);
 255                         if (columnfile == "not open") { m->mothurOut("Ignoring: " + parameters["column"]); m->mothurOutEndLine(); columnfile = ""; }
 256                         else if (columnfile == "not found") {  columnfile = "";  }
 257                         if (columnfile != "") { m->setColumnFile(columnfile); }
 258
 259                         listfile = validParameter.validFile(parameters, "list", true);
 260                         if (listfile == "not open") { m->mothurOut("Ignoring: " + parameters["list"]); m->mothurOutEndLine(); listfile = ""; }
 261                         else if (listfile == "not found") {  listfile = "";  }
 262                         if (listfile != "") { m->setListFile(listfile); }
 263
 264                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 265                         if (rabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["rabund"]); m->mothurOutEndLine(); rabundfile = ""; }
 266                         else if (rabundfile == "not found") {  rabundfile = "";  }
 267                         if (rabundfile != "") { m->setRabundFile(rabundfile); }
 268
 269                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 270                         if (sabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["sabund"]); m->mothurOutEndLine(); sabundfile = ""; }
 271                         else if (sabundfile == "not found") {  sabundfile = "";  }
 272                         if (sabundfile != "") { m->setSabundFile(sabundfile); }
 273
 274                         namefile = validParameter.validFile(parameters, "name", true);
 275                         if (namefile == "not open") { m->mothurOut("Ignoring: " + parameters["name"]); m->mothurOutEndLine(); namefile = ""; }
 276                         else if (namefile == "not found") {  namefile = "";  }
 277                         if (namefile != "") { m->setNameFile(namefile); }
 278
 279                         groupfile = validParameter.validFile(parameters, "group", true);
 280                         if (groupfile == "not open") { m->mothurOut("Ignoring: " + parameters["group"]); m->mothurOutEndLine(); groupfile = ""; }
 281                         else if (groupfile == "not found") {  groupfile = "";  }
 282                         if (groupfile != "") { m->setGroupFile(groupfile); }
 283
 284                         designfile = validParameter.validFile(parameters, "design", true);
 285                         if (designfile == "not open") { m->mothurOut("Ignoring: " + parameters["design"]); m->mothurOutEndLine(); designfile = ""; }
 286                         else if (designfile == "not found") {  designfile = "";  }
 287                         if (designfile != "") { m->setDesignFile(designfile); }
 288
 289                         orderfile = validParameter.validFile(parameters, "order", true);
 290                         if (orderfile == "not open") { m->mothurOut("Ignoring: " + parameters["order"]); m->mothurOutEndLine(); orderfile = ""; }
 291                         else if (orderfile == "not found") {  orderfile = "";  }
 292                         if (orderfile != "") { m->setOrderFile(orderfile); }
 293
 294                         treefile = validParameter.validFile(parameters, "tree", true);
 295                         if (treefile == "not open") { m->mothurOut("Ignoring: " + parameters["tree"]); m->mothurOutEndLine(); treefile = ""; }
 296                         else if (treefile == "not found") {  treefile = "";  }
 297                         if (treefile != "") { m->setTreeFile(treefile); }
 298
 299                         sharedfile = validParameter.validFile(parameters, "shared", true);
 300                         if (sharedfile == "not open") { m->mothurOut("Ignoring: " + parameters["shared"]); m->mothurOutEndLine(); sharedfile = ""; }
 301                         else if (sharedfile == "not found") {  sharedfile = "";  }
 302                         if (sharedfile != "") { m->setSharedFile(sharedfile); }
 303
 304                         ordergroupfile = validParameter.validFile(parameters, "ordergroup", true);
 305                         if (ordergroupfile == "not open") { m->mothurOut("Ignoring: " + parameters["ordergroup"]); m->mothurOutEndLine(); ordergroupfile = ""; }
 306                         else if (ordergroupfile == "not found") {  ordergroupfile = "";  }
 307                         if (ordergroupfile != "") { m->setOrderGroupFile(ordergroupfile); }
 308
 309                         relabundfile = validParameter.validFile(parameters, "relabund", true);
 310                         if (relabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["relabund"]); m->mothurOutEndLine(); relabundfile = ""; }
 311                         else if (relabundfile == "not found") {  relabundfile = "";  }
 312                         if (relabundfile != "") { m->setRelAbundFile(relabundfile); }
 313
 314                         fastafile = validParameter.validFile(parameters, "fasta", true);
 315                         if (fastafile == "not open") { m->mothurOut("Ignoring: " + parameters["fasta"]); m->mothurOutEndLine(); fastafile = ""; }
 316                         else if (fastafile == "not found") {  fastafile = "";  }
 317                         if (fastafile != "") { m->setFastaFile(fastafile); }
 318
 319                         qualfile = validParameter.validFile(parameters, "qfile", true);
 320                         if (qualfile == "not open") { m->mothurOut("Ignoring: " + parameters["qfile"]); m->mothurOutEndLine(); qualfile = ""; }
 321                         else if (qualfile == "not found") {  qualfile = "";  }
 322                         if (qualfile != "") { m->setQualFile(qualfile); }
 323
 324                         sfffile = validParameter.validFile(parameters, "sff", true);
 325                         if (sfffile == "not open") { m->mothurOut("Ignoring: " + parameters["sff"]); m->mothurOutEndLine(); sfffile = ""; }
 326                         else if (sfffile == "not found") {  sfffile = "";  }
 327                         if (sfffile != "") { m->setSFFFile(sfffile); }
 328
 329                         oligosfile = validParameter.validFile(parameters, "oligos", true);
 330                         if (oligosfile == "not open") { m->mothurOut("Ignoring: " + parameters["oligos"]); m->mothurOutEndLine(); oligosfile = ""; }
 331                         else if (oligosfile == "not found") {  oligosfile = "";  }
 332                         if (oligosfile != "") { m->setOligosFile(oligosfile); }
 333
 334                         accnosfile = validParameter.validFile(parameters, "accnos", true);
 335                         if (accnosfile == "not open") { m->mothurOut("Ignoring: " + parameters["accnos"]); m->mothurOutEndLine(); accnosfile = ""; }
 336                         else if (accnosfile == "not found") {  accnosfile = "";  }
 337                         if (accnosfile != "") { m->setAccnosFile(accnosfile); }
 338
 339                         taxonomyfile = validParameter.validFile(parameters, "taxonomy", true);
 340                         if (taxonomyfile == "not open") { m->mothurOut("Ignoring: " + parameters["taxonomy"]); m->mothurOutEndLine(); taxonomyfile = ""; }
 341                         else if (taxonomyfile == "not found") {  taxonomyfile = "";  }
 342                         if (taxonomyfile != "") { m->setTaxonomyFile(taxonomyfile); }
 343
 344                         clearTypes = validParameter.validFile(parameters, "clear", false);
 345                         if (clearTypes == "not found") { clearTypes = ""; }
 346                         else { m->splitAtDash(clearTypes, types);       }
 347                 }
 348
 349         }
 350         catch(exception& e) {
 351                 m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand");
 352                 exit(1);
 353         }
 354 }
 355 //**********************************************************************************************************************
 356
 357 void SetCurrentCommand::help(){
 358         try {
 359                 m->mothurOut("The set.current command allows you to set the current files saved by mothur.\n");
 360                 m->mothurOut("The set.current command parameters are: clear, phylip, column, list, rabund, sabund, name, group, design, order, tree, shared, ordergroup, relabund, fasta, qfile, sff, oligos, accnos, taxonomy.\n");
 361                 m->mothurOut("The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n");
 362                 m->mothurOut("The set.current command should be in the following format: \n");
 363                 m->mothurOut("set.current(fasta=yourFastaFile) or set.current(fasta=amazon.fasta, clear=name-accnos)\n");
 364
 365         }
 366         catch(exception& e) {
 367                 m->errorOut(e, "SetCurrentCommand", "help");
 368                 exit(1);
 369         }
 370 }
 371
 372 //**********************************************************************************************************************
 373 SetCurrentCommand::~SetCurrentCommand(){}
 374 //**********************************************************************************************************************
 375
 376 int SetCurrentCommand::execute(){
 377         try {
 378
 379                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 380
 381                 //user wants to clear a type
 382                 if (types.size() != 0) {
 383                         for (int i = 0; i < types.size(); i++) {
 384
 385                                 if (m->control_pressed) { break; }
 386
 387                                 //look for file types
 388                                 if (types[i] == "fasta") {
 389                                         m->setFastaFile("");
 390                                 }else if (types[i] == "qfile") {
 391                                         m->setQualFile("");
 392                                 }else if (types[i] == "phylip") {
 393                                         m->setPhylipFile("");
 394                                 }else if (types[i] == "column") {
 395                                         m->setColumnFile("");
 396                                 }else if (types[i] == "list") {
 397                                         m->setListFile("");
 398                                 }else if (types[i] == "rabund") {
 399                                         m->setRabundFile("");
 400                                 }else if (types[i] == "sabund") {
 401                                         m->setSabundFile("");
 402                                 }else if (types[i] == "name") {
 403                                         m->setNameFile("");
 404                                 }else if (types[i] == "group") {
 405                                         m->setGroupFile("");
 406                                 }else if (types[i] == "order") {
 407                                         m->setOrderFile("");
 408                                 }else if (types[i] == "ordergroup") {
 409                                         m->setOrderGroupFile("");
 410                                 }else if (types[i] == "tree") {
 411                                         m->setTreeFile("");
 412                                 }else if (types[i] == "shared") {
 413                                         m->setSharedFile("");
 414                                 }else if (types[i] == "relabund") {
 415                                         m->setRelAbundFile("");
 416                                 }else if (types[i] == "design") {
 417                                         m->setDesignFile("");
 418                                 }else if (types[i] == "sff") {
 419                                         m->setSFFFile("");
 420                                 }else if (types[i] == "oligos") {
 421                                         m->setOligosFile("");
 422                                 }else if (types[i] == "accnos") {
 423                                         m->setAccnosFile("");
 424                                 }else if (types[i] == "taxonomy") {
 425                                         m->setTaxonomyFile("");
 426                                 }else if (types[i] == "all") {
 427                                         m->clearCurrentFiles();
 428                                 }else {
 429                                         m->mothurOut("[ERROR]: mothur does not save a current file for " + types[i]); m->mothurOutEndLine();
 430                                 }
 431                         }
 432                 }
 433
 434                 m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
 435                 m->printCurrentFiles();
 436
 437                 return 0;
 438         }
 439
 440         catch(exception& e) {
 441                 m->errorOut(e, "SetCurrentCommand", "execute");
 442                 exit(1);
 443         }
 444 }
 445
 446 //**********************************************************************************************************************
 447
 448
 449