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