errorchecking.cpp

   1 /*
   2  *  errorchecking.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/2/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "errorchecking.h"
  11
  12 /*******************************************************/
  13
  14 /******************************************************/
  15
  16 ErrorCheck::ErrorCheck() {
  17         globaldata = GlobalData::getInstance();
  18         validCommand = new ValidCommands();
  19         validParameter = new ValidParameters();
  20         validCalculator = new ValidCalculators();
  21         columnfile = globaldata->getColumnFile();
  22         phylipfile = globaldata->getPhylipFile();
  23         listfile = globaldata->getListFile();
  24         rabundfile = globaldata->getRabundFile();
  25         sabundfile = globaldata->getSabundFile();
  26         namefile = globaldata->getNameFile();
  27         groupfile = globaldata->getGroupFile();
  28         orderfile = globaldata->getOrderFile();
  29         fastafile = globaldata->getFastaFile();
  30         treefile = globaldata->getTreeFile();
  31         cutoff = globaldata->getCutOff();
  32         format = globaldata->getFormat();
  33         method = globaldata->getMethod();
  34
  35 }
  36 /*******************************************************/
  37
  38 /******************************************************/
  39
  40 ErrorCheck::~ErrorCheck() {}
  41
  42 /*******************************************************/
  43
  44 /******************************************************/
  45
  46 bool ErrorCheck::checkInput(string input) {
  47                 errorFree = true;
  48                 clear();
  49
  50                 //get command name and parameters
  51                 int openParen = input.find_first_of('(');
  52                 int closeParen = input.find_last_of(')');
  53
  54                 if(openParen != -1 && closeParen != -1){
  55                         commandName = input.substr(0, openParen);   //commandName contains everything before "("
  56                         optionText = input.substr(openParen+1, closeParen-openParen-1); //optionString contains everything between "(" and ")".
  57                 }else if (openParen == -1) { //there is no parenthesis
  58                         cout << input << " is not a valid command. You are missing the ()." << endl;
  59                         return false;
  60                 }
  61
  62                 //is it a valid command
  63                 if (validCommand->isValidCommand(commandName) != true) { return false; }
  64
  65                 string parameter, value;
  66                 //reads in parameters and values
  67                 if((optionText != "") && (commandName != "help")){
  68                         while((optionText.find_first_of(',') != -1) && (errorFree)) {  //while there are parameters
  69                                 globaldata->splitAtComma(value, optionText);
  70                                 globaldata->splitAtEquals(parameter, value);
  71
  72                                 //is it a valid parameter
  73                                 if (validParameter->isValidParameter(parameter) != true) { return false; }
  74
  75                                 if (parameter == "phylip" )             { phylipfile = value; }
  76                                 if (parameter == "column" )             { columnfile = value; }
  77                                 if (parameter == "list" )               { listfile = value; }
  78                                 if (parameter == "rabund" )             { rabundfile = value; }
  79                                 if (parameter == "sabund" )             { sabundfile = value; }
  80                                 if (parameter == "name" )               { namefile = value; }
  81                                 if (parameter == "order" )              { orderfile = value; }
  82                                 if (parameter == "fasta" )              { fastafile = value; }
  83                                 if (parameter == "treefile" )           { treefile = value; }
  84                                 if (parameter == "group" )              { groupfile = value; }
  85                                 if (parameter == "cutoff" )                     { cutoff = value; }
  86                                 if (parameter == "precision" )          { precision = value; }
  87                                 if (parameter == "iters" )                      { iters = value; }
  88                                 if (parameter == "jumble" )                     { jumble = value; }
  89                                 if (parameter == "freq" )                       { freq = value; }
  90                                 if (parameter == "method" )                     { method = value; }
  91                                 if (parameter == "fileroot" )           { fileroot = value; }
  92                                 if (parameter == "line" )                       { line = value; }
  93                                 if (parameter == "label" )                      { label = value; }
  94
  95                                 if (parameter == "single") {//stores estimators in a vector
  96                                         singleEsimators.clear(); //clears out old values
  97                                         globaldata->splitAtDash(value, singleEsimators);
  98                                         for (int i = 0; i < singleEsimators.size(); i++) { //loop through estimators
  99                                                 //is it a valid calculator
 100                                                 if (validCalculator->isValidCalculator(parameter, singleEsimators[i]) != true) { return false; }
 101                                         }
 102                                 }
 103                                 if (parameter == "rarefaction") {//stores estimators in a vector
 104                                         rareEstimators.clear(); //clears out old values
 105                                         globaldata->splitAtDash(value, rareEstimators);
 106                                         for (int i = 0; i < rareEstimators.size(); i++) { //loop through estimators
 107                                                 //is it a valid calculator
 108                                                 if (validCalculator->isValidCalculator(parameter, rareEstimators[i]) != true) { return false; }
 109                                         }
 110                                 }
 111                                 if (parameter == "shared") {//stores estimators in a vector
 112                                         sharedEstimators.clear(); //clears out old values
 113                                         globaldata->splitAtDash(value, sharedEstimators);
 114                                         for (int i = 0; i < sharedEstimators.size(); i++) { //loop through estimators
 115                                                 //is it a valid calculator
 116                                                 if (validCalculator->isValidCalculator(parameter, sharedEstimators[i]) != true) { return false; }
 117                                         }
 118                                 }
 119                                 if (parameter == "summary") { //stores summaries to be used in a vector
 120                                         summaryEstimators.clear(); //clears out old values
 121                                         globaldata->splitAtDash(value, summaryEstimators);
 122                                         for (int i = 0; i < summaryEstimators.size(); i++) { //loop through estimators
 123                                                 //is it a valid calculator
 124                                                 if (validCalculator->isValidCalculator(parameter, summaryEstimators[i]) != true) { return false; }
 125                                         }
 126                                 }
 127                                 if (parameter == "sharedrarefaction") { //stores summaries to be used in a vector
 128                                         sharedRareEstimators.clear(); //clears out old values
 129                                         globaldata->splitAtDash(value, sharedRareEstimators);
 130                                         for (int i = 0; i < sharedRareEstimators.size(); i++) { //loop through estimators
 131                                                 //is it a valid calculator
 132                                                 if (validCalculator->isValidCalculator(parameter, sharedRareEstimators[i]) != true) { return false; }
 133                                         }
 134                                 }
 135                         }
 136
 137                         //gets the last parameter and value
 138                         if (errorFree)  { //gets the last parameter and value
 139                                 value = optionText;
 140                                 globaldata->splitAtEquals(parameter, value);
 141                                 //is it a valid parameter
 142                                 if (validParameter->isValidParameter(parameter) != true) { return false; }
 143
 144                                 if (parameter == "phylip" )             { phylipfile = value; }
 145                                 if (parameter == "column" )             { columnfile = value; }
 146                                 if (parameter == "list" )               { listfile = value; }
 147                                 if (parameter == "rabund" )             { rabundfile = value; }
 148                                 if (parameter == "sabund" )             { sabundfile = value; }
 149                                 if (parameter == "name" )               { namefile = value; }
 150                                 if (parameter == "order" )              { orderfile = value; }
 151                                 if (parameter == "group" )              { groupfile = value; }
 152                                 if (parameter == "fasta" )              { fastafile = value; }
 153                                 if (parameter == "treefile" )           { treefile = value; }
 154                                 if (parameter == "cutoff" )                     { cutoff = value; }
 155                                 if (parameter == "precision" )          { precision = value; }
 156                                 if (parameter == "iters" )                      { iters = value; }
 157                                 if (parameter == "jumble" )                     { jumble = value; }
 158                                 if (parameter == "freq" )                       { freq = value; }
 159                                 if (parameter == "method" )                     { method = value; }
 160                                 if (parameter == "fileroot" )           { fileroot = value; }
 161                                 if (parameter == "line" )                       { line = value; }
 162                                 if (parameter == "label" )                      { label = value; }
 163
 164                                 if (parameter == "single") {//stores estimators in a vector
 165                                         singleEsimators.clear(); //clears out old values
 166                                         globaldata->splitAtDash(value, singleEsimators);
 167                                         for (int i = 0; i < singleEsimators.size(); i++) { //loop through estimators
 168                                                 //is it a valid calculator
 169                                                 if (validCalculator->isValidCalculator(parameter, singleEsimators[i]) != true) { return false; }
 170                                         }
 171                                 }
 172                                 if (parameter == "rarefaction") {//stores estimators in a vector
 173                                         rareEstimators.clear(); //clears out old values
 174                                         globaldata->splitAtDash(value, rareEstimators);
 175                                         for (int i = 0; i < rareEstimators.size(); i++) { //loop through estimators
 176                                                 //is it a valid calculator
 177                                                 if (validCalculator->isValidCalculator(parameter, rareEstimators[i]) != true) { return false; }
 178                                         }
 179                                 }
 180                                 if (parameter == "shared") {//stores estimators in a vector
 181                                         sharedEstimators.clear(); //clears out old values
 182                                         globaldata->splitAtDash(value, sharedEstimators);
 183                                         for (int i = 0; i < sharedEstimators.size(); i++) { //loop through estimators
 184                                                 //is it a valid calculator
 185                                                 if (validCalculator->isValidCalculator(parameter, sharedEstimators[i]) != true) { return false; }
 186                                         }
 187                                 }
 188                                 if (parameter == "summary") { //stores summaries to be used in a vector
 189                                         summaryEstimators.clear(); //clears out old values
 190                                         globaldata->splitAtDash(value, summaryEstimators);
 191                                         for (int i = 0; i < summaryEstimators.size(); i++) { //loop through estimators
 192                                                 //is it a valid calculator
 193                                                 if (validCalculator->isValidCalculator(parameter, summaryEstimators[i]) != true) { return false; }
 194                                         }
 195                                 }
 196                                 if (parameter == "sharedrarefaction") { //stores summaries to be used in a vector
 197                                         sharedRareEstimators.clear(); //clears out old values
 198                                         globaldata->splitAtDash(value, sharedRareEstimators);
 199                                         for (int i = 0; i < sharedRareEstimators.size(); i++) { //loop through estimators
 200                                                 //is it a valid calculator
 201                                                 if (validCalculator->isValidCalculator(parameter, sharedRareEstimators[i]) != true) { return false; }
 202                                         }
 203                                 }
 204
 205                         }
 206                 }
 207
 208                 //make sure the user does not use both the line and label parameters
 209                 if ((line != "") && (label != "")) { cout << "You may use either the line or label parameters, but not both." << endl; return false; }
 210
 211
 212                 if (commandName == "read.dist") {
 213                         validateReadFiles();
 214                         validateReadDist();
 215                 }else if (commandName == "read.otu") {
 216                         //you want to do shared commands
 217                         if ((listfile != "") && (groupfile != ""))      {
 218                                 validateParseFiles(); //checks the listfile and groupfile parameters
 219                         }else { //you want to do single commands
 220                                 validateReadFiles();
 221                                 validateReadPhil();
 222                         }
 223                 }else if (commandName == "read.tree") {
 224                         validateTreeFiles(); //checks the treefile and groupfile parameters
 225                 }else if (commandName == "deconvolute") {
 226                         if (fastafile == "") { cout << "You must enter a fastafile with the deconvolute() command." << endl; return false; }
 227                         validateReadFiles();
 228                 }
 229
 230                 //are you trying to cluster before you have read something
 231                 if ((commandName == "cluster") && (globaldata->getSparseMatrix() == NULL) ||
 232                         (commandName == "cluster") && (globaldata->getListVector() == NULL)) {
 233                                 cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl;
 234                                 errorFree = false;
 235                 }
 236
 237                 //check for valid method
 238                 if (commandName == "cluster") {
 239                         if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
 240                         else {cout << "Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average." << endl; return false; }
 241                 }
 242
 243                 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single") ){
 244                         if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the collect.single, rarefaction.single or summary.single commands." << endl; return false; }
 245                 }
 246
 247                 if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") ){
 248                         if (globaldata->getListFile() == "") { cout << "You must read a list and a group before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; }
 249                         else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; }
 250                 }
 251
 252
 253                 return errorFree;
 254 }
 255
 256 /*******************************************************/
 257
 258 /******************************************************/
 259 //This function checks to make sure the user entered a file to
 260 // read and that the file exists and can be opened.
 261 void ErrorCheck::validateReadFiles() {
 262         try {
 263                 //Validating files for read
 264                 ifstream filehandle;
 265                 int ableToOpen;
 266
 267                 //are we reading a phylipfile
 268                 if (phylipfile != "") {
 269                         ableToOpen = openInputFile(phylipfile, filehandle);
 270                         filehandle.close();
 271                         //unable to open
 272                         if (ableToOpen == 1) { errorFree = false; }
 273                         else { globaldata->inputFileName = phylipfile; }
 274                 //are we reading a phylipfile
 275                 }else if (columnfile != "") {
 276                         ableToOpen = openInputFile(columnfile, filehandle);
 277                         filehandle.close();
 278                         //unable to open
 279                         if (ableToOpen == 1) { errorFree = false; }
 280                         else { globaldata->inputFileName = columnfile; }
 281                 //are we reading a listfile
 282                 }else if (listfile!= "") {
 283                         ableToOpen = openInputFile(listfile, filehandle);
 284                         filehandle.close();
 285                         //unable to open
 286                         if (ableToOpen == 1) {  errorFree = false; }
 287                         else { globaldata->inputFileName = listfile; }
 288                 //are we reading a rabundfile
 289                 }else if (rabundfile != "") {
 290                         ableToOpen = openInputFile(rabundfile, filehandle);
 291                         filehandle.close();
 292                         //unable to open
 293                         if (ableToOpen == 1) {  errorFree = false; }
 294                         else { globaldata->inputFileName = rabundfile; }
 295                 //are we reading a sabundfile
 296                 }else if (sabundfile != "") {
 297                         ableToOpen = openInputFile(sabundfile, filehandle);
 298                         filehandle.close();
 299                         //unable to open
 300                         if (ableToOpen == 1) {  errorFree = false; }
 301                         else { globaldata->inputFileName = sabundfile; }
 302                 }else if (fastafile != "") {
 303                         ableToOpen = openInputFile(fastafile, filehandle);
 304                         filehandle.close();
 305                         //unable to open
 306                         if (ableToOpen == 1) {  errorFree = false; }
 307                         else { globaldata->inputFileName = fastafile; }
 308                 }else{ //no file given
 309                         errorFree = false;
 310                 }
 311         }
 312         catch(exception& e) {
 313                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 314                 exit(1);
 315         }
 316         catch(...) {
 317                 cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 318                 exit(1);
 319         }
 320
 321 }
 322 /*******************************************************/
 323
 324 /******************************************************/
 325 //This function checks to make sure the user entered appropriate
 326 // format parameters on a distfile read
 327 void ErrorCheck::validateReadDist() {
 328         try {
 329                 ifstream filehandle;
 330                 int ableToOpen;
 331
 332                 if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist you must enter a phylip or a column." << endl; errorFree = false; }
 333                 else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist you must enter ONLY ONE of the following: phylip or column." << endl; errorFree = false; }
 334
 335                 if (columnfile != "") {
 336                         if (namefile == "") {
 337                                 cout << "You need to provide a namefile if you are going to use the column format." << endl;
 338                                 errorFree = false;
 339                         }else {
 340                                 ableToOpen = openInputFile(namefile, filehandle);
 341                                 filehandle.close();
 342                                 //unable to open
 343                                 if (ableToOpen == 1) { errorFree = false; }
 344                         }
 345                 }
 346         }
 347         catch(exception& e) {
 348                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 349                 exit(1);
 350         }
 351         catch(...) {
 352                 cout << "An unknown error has occurred in the ErrorCheck class function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 353                 exit(1);
 354         }
 355 }
 356 /*******************************************************/
 357
 358 /******************************************************/
 359 //This function checks to make sure the user entered appropriate
 360 // format parameters on a parselistcommand
 361 void ErrorCheck::validateParseFiles() {
 362         try {
 363                 ifstream filehandle;
 364                 int ableToOpen;
 365
 366                 //checks for valid files
 367
 368                 if (listfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
 369                 else if (groupfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
 370
 371                 //checks parameters on the read command
 372                 if (listfile != "") {
 373                         ableToOpen = openInputFile(listfile, filehandle);
 374                         filehandle.close();
 375                         if (ableToOpen == 1) { //unable to open
 376                                 errorFree = false;
 377                         }
 378                         if (groupfile != "") {
 379                                 ableToOpen = openInputFile(groupfile, filehandle);
 380                                 filehandle.close();
 381                                 if (ableToOpen == 1) { //unable to open
 382                                         errorFree = false;;
 383                                 }
 384                         }
 385                 }
 386         }
 387         catch(exception& e) {
 388                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 389                 exit(1);
 390         }
 391         catch(...) {
 392                 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 393                 exit(1);
 394         }
 395 }
 396 /*******************************************************/
 397
 398 /******************************************************/
 399 //This function checks to make sure the user entered appropriate
 400 // format parameters on a parselistcommand
 401 void ErrorCheck::validateTreeFiles() {
 402         try {
 403                 ifstream filehandle;
 404                 int ableToOpen;
 405
 406                 //checks for valid files
 407
 408                 if (treefile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
 409                 else if (groupfile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
 410
 411                 //checks parameters on the read command
 412                 if (treefile != "") {
 413                         ableToOpen = openInputFile(treefile, filehandle);
 414                         filehandle.close();
 415                         if (ableToOpen == 1) { //unable to open
 416                                 errorFree = false;
 417                         }
 418                         if (groupfile != "") {
 419                                 ableToOpen = openInputFile(groupfile, filehandle);
 420                                 filehandle.close();
 421                                 if (ableToOpen == 1) { //unable to open
 422                                         errorFree = false;;
 423                                 }
 424                         }
 425                 }
 426         }
 427         catch(exception& e) {
 428                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 429                 exit(1);
 430         }
 431         catch(...) {
 432                 cout << "An unknown error has occurred in the ErrorCheck class function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 433                 exit(1);
 434         }
 435 }
 436
 437 /*******************************************************/
 438
 439 /******************************************************/
 440 //This function checks to make sure the user entered appropriate
 441 // format parameters on a distfile read
 442 void ErrorCheck::validateReadPhil() {
 443         try {
 444                 ifstream filehandle;
 445                 int ableToOpen;
 446
 447                 //checks to make sure only one file type is given
 448                 if (listfile != "") {
 449                         if ((rabundfile != "") || (sabundfile != "")) {
 450                                 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
 451                 }else if (rabundfile != "") {
 452                         if ((listfile != "") || (sabundfile != "")) {
 453                                 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
 454                 }else if (sabundfile != "") {
 455                         if ((listfile != "") || (rabundfile != "")) {
 456                                 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
 457                 }else if ((listfile == "") && (rabundfile == "") && (sabundfile == "")) {
 458                             cout << "When executing a read.otu you must enter one of the following: list, rabund or sabund." << endl; errorFree = false;
 459                 }
 460
 461                 //checks parameters on the read command
 462                 if (orderfile != "") {
 463                         ableToOpen = openInputFile(orderfile, filehandle);
 464                         filehandle.close();
 465                         if (ableToOpen == 1) { //unable to open
 466                                 errorFree = false;
 467                         }
 468                 }
 469         }
 470         catch(exception& e) {
 471                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 472                 exit(1);
 473         }
 474         catch(...) {
 475                 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 476                 exit(1);
 477         }
 478 }
 479 /*******************************************************/
 480
 481 /******************************************************/
 482
 483 void ErrorCheck::clear() {
 484         //option definitions should go here...
 485         phylipfile              =       "";
 486         columnfile              =       "";
 487         listfile                =       "";
 488         rabundfile              =       "";
 489         sabundfile              =       "";
 490         namefile                =       "";
 491         groupfile               =       "";
 492         orderfile               =       "";
 493         line                    =       "";
 494         label                   =       "";
 495         method                  =   "furthest";
 496 }
 497 /*******************************************************/
 498
 499 /******************************************************/
 500