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 }
  21 /*******************************************************/
  22
  23 /******************************************************/
  24
  25 void ErrorCheck::refresh() {
  26         columnfile = globaldata->getColumnFile();
  27         phylipfile = globaldata->getPhylipFile();
  28         listfile = globaldata->getListFile();
  29         rabundfile = globaldata->getRabundFile();
  30         sabundfile = globaldata->getSabundFile();
  31         namefile = globaldata->getNameFile();
  32         groupfile = globaldata->getGroupFile();
  33         orderfile = globaldata->getOrderFile();
  34         fastafile = globaldata->getFastaFile();
  35         treefile = globaldata->getTreeFile();
  36         cutoff = globaldata->getCutOff();
  37         format = globaldata->getFormat();
  38         method = globaldata->getMethod();
  39
  40
  41         string p[] = {
  42                 "phylip",              //0
  43                 "column",             //1
  44                 "list",               //2
  45                 "rabund",             //3
  46                 "sabund",             //4
  47                 "name",               //5
  48                 "order",              //6
  49                 "group",              //7
  50                 "fasta",              //8
  51                 "treefile",           //9
  52                 "cutoff",             //10
  53                 "precision",          //11
  54                 "iters",              //12
  55                 "jumble",             //13
  56                 "freq",               //14
  57                 "method",             //15
  58                 "fileroot",           //16
  59                 "line",               //17
  60                 "label",              //18
  61                 "single",             //19
  62                 "rarefaction",        //20
  63                 "shared",             //21
  64                 "summary",            //22
  65                 "sharedrarefaction",  //23
  66                 "sharedsummary",      //24
  67                 "groups",                         //25
  68                 "abund",              //26
  69                 };
  70
  71         string c0[] = {p[0],p[5],p[10],p[11]};
  72         string c1[] = {p[2],p[6],p[7]};
  73         string c2[] = {p[10],p[11],p[15]};
  74         string c3[] = {p[8]};
  75         string c4[] = {p[14],p[17],p[18],p[19],p[26]};
  76         string c5[] = {p[13],p[14],p[17],p[18],p[21],p[25]};
  77         string c6[] = {""};
  78         string c7[] = {""};
  79         string c8[] = {""};
  80         string c9[] = {p[12],p[14],p[17],p[18],p[20],p[26]};
  81         string c10[] = {p[12],p[13],p[17],p[18],p[23]};
  82         string c11[] = {p[17],p[18],p[22],p[26]};
  83         string c12[] =  {p[13],p[17],p[18],p[24]};
  84         string c13[] = {""};
  85
  86         vector<string> v0 (c0, c0+sizeof(c0)/sizeof(string));
  87         vector<string> v1 (c1, c1+sizeof(c1)/sizeof(string));
  88         vector<string> v2 (c2, c2+sizeof(c2)/sizeof(string));
  89         vector<string> v3 (c3, c3+sizeof(c3)/sizeof(string));
  90         vector<string> v4 (c4, c4+sizeof(c4)/sizeof(string));
  91         vector<string> v5 (c5, c5+sizeof(c5)/sizeof(string));
  92         vector<string> v6 (c6, c6+sizeof(c6)/sizeof(string));
  93         vector<string> v7 (c7, c7+sizeof(c7)/sizeof(string));
  94         vector<string> v8 (c8, c8+sizeof(c8)/sizeof(string));
  95         vector<string> v9 (c9, c9+sizeof(c9)/sizeof(string));
  96         vector<string> v10 (c10, c10+sizeof(c10)/sizeof(string));
  97         vector<string> v11 (c11, c11+sizeof(c11)/sizeof(string));
  98         vector<string> v12 (c12, c12+sizeof(c12)/sizeof(string));
  99         vector<string> v13 (c13, c13+sizeof(c13)/sizeof(string));
 100
 101         vector<vector<string> > allCommands;
 102         allCommands.push_back(v0);
 103         allCommands.push_back(v1);
 104         allCommands.push_back(v2);
 105         allCommands.push_back(v3);
 106         allCommands.push_back(v4);
 107         allCommands.push_back(v5);
 108         allCommands.push_back(v6);
 109         allCommands.push_back(v7);
 110         allCommands.push_back(v8);
 111         allCommands.push_back(v9);
 112         allCommands.push_back(v10);
 113         allCommands.push_back(v11);
 114         allCommands.push_back(v12);
 115         allCommands.push_back(v13);
 116
 117         string commands[] = {
 118         "read.dist",          //0
 119         "read.otu",           //1
 120         "cluster",            //2
 121         "deconvolute",        //3
 122         "collect.single",     //4
 123         "collect.shared",     //5
 124         "get.group",          //6
 125         "get.label",          //7
 126         "get.line",           //8
 127         "rarefaction.single", //9
 128         "rarefaction.shared", //10
 129         "summary.single",     //11
 130         "summary.shared",     //12
 131         "quit"                //13
 132         };
 133
 134         for(int i = 0; i < allCommands.size(); i++)
 135                 commandParameters[commands[i]] = allCommands.at(i);
 136
 137          //{Lowerbound(piSent if no lowerbound), Upperbound(piSent if no upperbound), 1 if only the first 2 values, 0 if greater than, 0 if less than};
 138         piSent = 3.14159;
 139         double ip0[] = {10, piSent, 0, 1, 0};
 140         double ip1[] = {10, piSent, 0, 1, 0};
 141         double ip2[] = {0, 1, 1, 0, 0};
 142         double ip3[] =  {1, piSent, 0, 0, 0};
 143         double ip4[] = {1, piSent, 0, 1, 0};
 144         double ip5[] = {5, piSent, 0, 1, 0};
 145
 146         vector<double> ipv0 (ip0, ip0+sizeof(ip0)/sizeof(double));
 147         vector<double> ipv1 (ip1, ip1+sizeof(ip1)/sizeof(double));
 148         vector<double> ipv2 (ip2, ip2+sizeof(ip2)/sizeof(double));
 149         vector<double> ipv3 (ip3, ip3+sizeof(ip3)/sizeof(double));
 150         vector<double> ipv4 (ip4, ip4+sizeof(ip4)/sizeof(double));
 151         vector<double> ipv5 (ip5, ip5+sizeof(ip5)/sizeof(double));
 152
 153         intParams[p[11]] = ipv0;
 154         intParams[p[12]] = ipv1;
 155         intParams[p[13]] = ipv2;
 156         intParams[p[14]] = ipv3;
 157         intParams[p[17]] = ipv4;
 158         intParams[p[26]] = ipv5;
 159
 160         randomtree = globaldata->getRandomTree();
 161         sharedfile = globaldata->getSharedFile();
 162 }
 163
 164 /*******************************************************/
 165
 166 /******************************************************/
 167
 168 ErrorCheck::~ErrorCheck() {}
 169
 170 /*******************************************************/
 171
 172 /******************************************************/
 173
 174 bool ErrorCheck::checkInput(string input) {
 175                 errorFree = true;
 176                 clear();
 177
 178                 //refresh variable
 179                 refresh();
 180
 181                 //get command name and parameters
 182                 int openParen = input.find_first_of('(');
 183                 int closeParen = input.find_last_of(')');
 184
 185                 if(openParen != -1 && closeParen != -1){
 186                         commandName = input.substr(0, openParen);   //commandName contains everything before "("
 187                         optionText = input.substr(openParen+1, closeParen-openParen-1); //optionString contains everything between "(" and ")".
 188                 }else if (openParen == -1) { //there is no parenthesis
 189                         cout << input << " is not a valid command. You are missing the ()." << endl;
 190                         return false;
 191                 }
 192
 193                 //is it a valid command
 194                 if (validCommand->isValidCommand(commandName) != true) { return false; }
 195
 196                 string parameter, value;
 197
 198                 //reads in parameters and values
 199                 if((optionText != "") && (commandName != "help")){
 200                         while((optionText.find_first_of(',') != -1) && (errorFree)) {  //while there are parameters
 201                                 splitAtComma(value, optionText);
 202                                 splitAtEquals(parameter, value);
 203
 204                                 //is it a valid parameter
 205                                 if (validParameter->isValidParameter(parameter) != true) { return false; }
 206                                 if(!validCommandParameter(parameter,commandName)) {
 207                                         cout << "'" << parameter << "' is not a valid parameter for the " << commandName << " command.\n";
 208                                         return false;
 209                                 }
 210                                 if(!validParameterValue(value, parameter)) {
 211                                         if(parameter.compare("precision") == 0)
 212                                                 cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n";
 213                                         else {
 214                                         vector<double> bounds = intParams[parameter];
 215                                         double a = bounds.at(0);
 216                                         double b = bounds.at(1);
 217                                         double c = bounds.at(2);
 218                                         double d = bounds.at(3);
 219                                         double e = bounds.at(4);
 220                                         cout << "The '" << parameter << "' parameter needs to be ";
 221                                         if(c == 1)
 222                                                         cout << "either '" << a << "' or '" << b << "'.\n";
 223                                         else
 224                                         {
 225                                                 if(a != piSent)
 226                                                 {
 227                                                         cout << ">";
 228                                                         if(d != 0)
 229                                                                 cout << "=";
 230                                                         cout << " '" << a << "'";
 231                                                 }
 232                                                 if(b == piSent)
 233                                                         cout << ".\n";
 234                                                 else if(a != piSent)
 235                                                         cout << " and ";
 236                                                 if(b != piSent)
 237                                                 {
 238                                                         cout << "<";
 239                                                         if(e != 0)
 240                                                                 cout << "=";
 241                                                         cout << " '" << b << ".\n";
 242                                                 }
 243                                         }
 244                                         }
 245                                         return false;
 246                                 }
 247
 248                                 if (parameter == "phylip" )             { phylipfile = value; }
 249                                 if (parameter == "column" )             { columnfile = value; }
 250                                 if (parameter == "list" )               { listfile = value; }
 251                                 if (parameter == "rabund" )             { rabundfile = value; }
 252                                 if (parameter == "sabund" )             { sabundfile = value; }
 253                                 if (parameter == "name" )               { namefile = value; }
 254                                 if (parameter == "order" )              { orderfile = value; }
 255                                 if (parameter == "fasta" )              { fastafile = value; }
 256                                 if (parameter == "tree" )               { treefile = value; }
 257                                 if (parameter == "group" )              { groupfile = value; }
 258                                 if (parameter == "shared" )             { sharedfile = value; }
 259                                 if (parameter == "cutoff" )                     { cutoff = value; }
 260                                 if (parameter == "precision" )          { precision = value; }
 261                                 if (parameter == "iters" )                      { iters = value; }
 262                                 if (parameter == "jumble" )                     { jumble = value; }
 263                                 if (parameter == "freq" )                       { freq = value; }
 264                                 if (parameter == "method" )                     { method = value; }
 265                                 if (parameter == "fileroot" )           { fileroot = value; }
 266                                 if (parameter == "line" )                       { line = value; }
 267                                 if (parameter == "label" )                      { label = value; }
 268                                 if (parameter == "abund" )          { abund = value; }
 269                                 if (parameter == "random" )                     { randomtree = value;   }
 270                         }
 271
 272                         //gets the last parameter and value
 273                         if (errorFree)  { //gets the last parameter and value
 274                                 value = optionText;
 275                                 splitAtEquals(parameter, value);
 276                                 //is it a valid parameter
 277                                 if (validParameter->isValidParameter(parameter) != true) { return false; }
 278                                 if(!validCommandParameter(parameter,commandName)) {
 279                                         cout << "'" << parameter << "' is not a valid parameter for the " << commandName << " command.\n";
 280                                         return false;
 281                                 }
 282                                 if(!validParameterValue(value, parameter)) {
 283                                         if(parameter.compare("precision") == 0)
 284                                                 cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n";
 285                                         else {
 286                                         vector<double> bounds = intParams[parameter];
 287                                         double a = bounds.at(0);
 288                                         double b = bounds.at(1);
 289                                         double c = bounds.at(2);
 290                                         double d = bounds.at(3);
 291                                         double e = bounds.at(4);
 292                                         cout << "The '" << parameter << "' parameter needs to be ";
 293                                         if(c == 1)
 294                                                         cout << "either '" << a << "' or '" << b << "'.\n";
 295                                         else
 296                                         {
 297                                                 if(a != piSent)
 298                                                 {
 299                                                         cout << ">";
 300                                                         if(d != 0)
 301                                                                 cout << "=";
 302                                                         cout << " '" << a << "'";
 303                                                 }
 304                                                 if(b == piSent)
 305                                                         cout << ".\n";
 306                                                 else if(a != piSent)
 307                                                         cout << " and ";
 308                                                 if(b != piSent)
 309                                                 {
 310                                                         cout << "<";
 311                                                         if(e != 0)
 312                                                                 cout << "=";
 313                                                         cout << " '" << b << ".\n";
 314                                                 }
 315                                         }
 316                                         }
 317                                         return false;
 318                                 }
 319                                 if (parameter == "phylip" )             { phylipfile = value; }
 320                                 if (parameter == "column" )             { columnfile = value; }
 321                                 if (parameter == "list" )               { listfile = value; }
 322                                 if (parameter == "rabund" )             { rabundfile = value; }
 323                                 if (parameter == "sabund" )             { sabundfile = value; }
 324                                 if (parameter == "name" )               { namefile = value; }
 325                                 if (parameter == "order" )              { orderfile = value; }
 326                                 if (parameter == "group" )              { groupfile = value; }
 327                                 if (parameter == "shared" )             { sharedfile = value; }
 328                                 if (parameter == "fasta" )              { fastafile = value; }
 329                                 if (parameter == "tree" )               { treefile = value; }
 330                                 if (parameter == "cutoff" )                     { cutoff = value; }
 331                                 if (parameter == "precision" )          { precision = value; }
 332                                 if (parameter == "iters" )                      { iters = value; }
 333                                 if (parameter == "jumble" )                     { jumble = value; }
 334                                 if (parameter == "freq" )                       { freq = value; }
 335                                 if (parameter == "method" )                     { method = value; }
 336                                 if (parameter == "fileroot" )           { fileroot = value; }
 337                                 if (parameter == "line" )                       { line = value; }
 338                                 if (parameter == "label" )                      { label = value; }
 339                                 if (parameter == "random" )                     { randomtree = value;   }
 340                                 if (parameter == "abund" )          { abund = value; }
 341                         }
 342                 }
 343
 344                 //make sure the user does not use both the line and label parameters
 345                 if ((line != "") && (label != "")) { cout << "You may use either the line or label parameters, but not both." << endl; return false; }
 346
 347                 if (commandName == "read.dist") {
 348                         validateReadFiles();
 349                         validateReadDist();
 350                 }else if (commandName == "read.otu") {
 351                         //you want to do shared commands
 352                         if ((listfile != "") && (groupfile != ""))      {
 353                                 validateParseFiles(); //checks the listfile and groupfile parameters
 354                         }else { //you want to do single commands
 355                                 validateReadFiles();
 356                                 validateReadPhil();
 357                         }
 358                 }else if (commandName == "read.shared") {
 359                         //you want to do shared commands with just the shared file
 360                         validateReadFiles();
 361                 }else if (commandName == "read.tree") {
 362                         validateTreeFiles(); //checks the treefile and groupfile parameters
 363                 }else if (commandName == "deconvolute") {
 364                         if (fastafile == "") { cout << "You must enter a fastafile with the deconvolute() command." << endl; return false; }
 365                         validateReadFiles();
 366                 }
 367
 368                 //are you trying to cluster before you have read something
 369                 if ((commandName == "cluster") && (globaldata->getSparseMatrix() == NULL) ||
 370                         (commandName == "cluster") && (globaldata->getListVector() == NULL)) {
 371                                 cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl;
 372                                 errorFree = false;
 373                 }
 374
 375                 if (commandName == "parsimony") {
 376                         //are you trying to use parsimony without reading a tree or saying you want random distribution
 377                         if (randomtree == "")  {
 378                                 if (globaldata->gTree.size() == 0) {
 379                                         cout << "You must read a treefile and a groupfile or set the randomtree parameter to the output filename you wish, before you may execute the parsimony command." << endl; return false;  }
 380                         }
 381                 }
 382
 383                 if ((commandName == "unifrac.weighted") || (commandName == "unifrac.unweighted")) {
 384                         if (globaldata->gTree.size() == 0) {//no trees were read
 385                                 cout << "You must execute the read.tree command, before you may execute the unifrac.weighted or unifrac.unweighted command." << endl; return false;  }
 386                 }
 387
 388                 //check for valid method
 389                 if(commandName == "get.group") {
 390                         if ((globaldata->getGroupFile() == "")) { cout << "You must read a group before you can use the get.group command." << endl; return false; }
 391                 }
 392                 if (commandName == "get.label" || commandName == "get.line") {
 393                         if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the get.label or get.line command." << endl; return false; }
 394                 }
 395                 if (commandName == "cluster") {
 396                         if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
 397                         else {cout << "Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average." << endl; return false; }
 398                 }
 399
 400                 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single") ){
 401                         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; }
 402                 }
 403
 404                 if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") ){
 405                         if (globaldata->getSharedFile() == "") {
 406                                 if (globaldata->getListFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; }
 407                                 else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; }
 408                         }
 409                 }
 410
 411                 return errorFree;
 412 }
 413
 414 /*******************************************************/
 415
 416 /******************************************************/
 417 //This function checks to make sure the user entered a file to
 418 // read and that the file exists and can be opened.
 419 void ErrorCheck::validateReadFiles() {
 420         try {
 421                 //Validating files for read
 422                 ifstream filehandle;
 423                 int ableToOpen;
 424
 425                 //are we reading a phylipfile
 426                 if (phylipfile != "") {
 427                         ableToOpen = openInputFile(phylipfile, filehandle);
 428                         filehandle.close();
 429                         //unable to open
 430                         if (ableToOpen == 1) { errorFree = false; }
 431                         else { globaldata->inputFileName = phylipfile; }
 432                 //are we reading a phylipfile
 433                 }else if (columnfile != "") {
 434                         ableToOpen = openInputFile(columnfile, filehandle);
 435                         filehandle.close();
 436                         //unable to open
 437                         if (ableToOpen == 1) { errorFree = false; }
 438                         else { globaldata->inputFileName = columnfile; }
 439                 //are we reading a listfile
 440                 }else if (listfile!= "") {
 441                         ableToOpen = openInputFile(listfile, filehandle);
 442                         filehandle.close();
 443                         //unable to open
 444                         if (ableToOpen == 1) {  errorFree = false; }
 445                         else { globaldata->inputFileName = listfile; }
 446                 //are we reading a rabundfile
 447                 }else if (rabundfile != "") {
 448                         ableToOpen = openInputFile(rabundfile, filehandle);
 449                         filehandle.close();
 450                         //unable to open
 451                         if (ableToOpen == 1) {  errorFree = false; }
 452                         else { globaldata->inputFileName = rabundfile; }
 453                 //are we reading a sabundfile
 454                 }else if (sabundfile != "") {
 455                         ableToOpen = openInputFile(sabundfile, filehandle);
 456                         filehandle.close();
 457                         //unable to open
 458                         if (ableToOpen == 1) {  errorFree = false; }
 459                         else { globaldata->inputFileName = sabundfile; }
 460                 }else if (fastafile != "") {
 461                         ableToOpen = openInputFile(fastafile, filehandle);
 462                         filehandle.close();
 463                         //unable to open
 464                         if (ableToOpen == 1) {  errorFree = false; }
 465                         else { globaldata->inputFileName = fastafile; }
 466                 }else if (sharedfile != "") {
 467                         ableToOpen = openInputFile(sharedfile, filehandle);
 468                         filehandle.close();
 469                         //unable to open
 470                         if (ableToOpen == 1) {  errorFree = false; }
 471                         else { globaldata->inputFileName = sharedfile; }
 472                 }else{ //no file given
 473                         errorFree = false;
 474                 }
 475         }
 476         catch(exception& e) {
 477                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 478                 exit(1);
 479         }
 480         catch(...) {
 481                 cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 482                 exit(1);
 483         }
 484
 485 }
 486 /*******************************************************/
 487
 488 /******************************************************/
 489 //This function checks to see if the given paramter
 490 //is a valid paramter for the given command.
 491 bool ErrorCheck::validCommandParameter(string parameter, string commandName) {
 492         try {
 493                 for(int i = 0; i < commandParameters[commandName].size(); i++)
 494                         if(parameter.compare(commandParameters[commandName][i]) == 0)
 495                                 return true;
 496                 return false;
 497         }
 498
 499         catch(exception& e) {
 500                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 501                 exit(1);
 502         }
 503         catch(...) {
 504                 cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 505                 exit(1);
 506         }
 507 }
 508 /*******************************************************/
 509
 510 /******************************************************/
 511 //This function checks to see if the given paramter value
 512 //is convertable into an int if that parameter requires it.
 513 bool ErrorCheck::validParameterValue(string value, string parameter) {
 514         try {
 515                 int pVal;
 516                 if(intParams.count(parameter) == 1)
 517                 {
 518                         vector<double> bounds = intParams[parameter];
 519                         bool valid = convertTest(value, pVal);
 520                         if(!valid)
 521                                 return false;
 522                         if(parameter.compare("precision") == 0)
 523                         {
 524                                 double logNum = log10((double)pVal);
 525                                 double diff = (double)((int)logNum - logNum);
 526                                 if(diff != 0)
 527                                         return false;
 528                         }
 529                         double a = bounds.at(0);
 530                         double b = bounds.at(1);
 531                         double c = bounds.at(2);
 532                         double d = bounds.at(3);
 533                         double e = bounds.at(4);
 534                         bool a0 = pVal > a;
 535                         bool a1 = pVal >= a;
 536                         bool b0 = pVal < b;
 537                         bool b1 = pVal <= b;
 538
 539                         if(c != 1)
 540                         {
 541                                 if(a == piSent && b == piSent)
 542                                         return true;
 543                                 if(a != piSent && b == piSent)
 544                                 {
 545                                         if(d == 0)
 546                                                 return a0;
 547                                         else
 548                                                 return a1;
 549                                 }
 550                                 else if(a == piSent && b != piSent)
 551                                 {
 552                                         if(e == 0)
 553                                                 return b0;
 554                                         else
 555                                                 return b1;
 556                                 }
 557                                 else
 558                                 {
 559                                         if(d == 0 && e == 0)
 560                                                 return (a0 && b0);
 561                                         else if(d == 0 && e == 1)
 562                                                 return (a0 && b1);
 563                                         else if(d == 1 && e == 0)
 564                                                 return (a1 && b0);
 565                                         else
 566                                                 return (a1 && b1);
 567                                 }
 568                         }
 569                         else
 570                         {
 571                                 if(a == piSent && b == piSent)
 572                                         return true;
 573                                 if(a != piSent && b == piSent)
 574                                         return (pVal == a);
 575                                 else if(a == piSent && b != piSent)
 576                                         return (pVal == b);
 577                                 else
 578                                         return (pVal == a || pVal == b);
 579                         }
 580                 }
 581                 return true;
 582         }
 583
 584         catch(exception& e) {
 585                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 586                 exit(1);
 587         }
 588         catch(...) {
 589                 cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 590                 exit(1);
 591         }
 592 }
 593 /*******************************************************/
 594
 595 /******************************************************/
 596 //This function checks to make sure the user entered appropriate
 597 // format parameters on a distfile read
 598 void ErrorCheck::validateReadDist() {
 599         try {
 600                 ifstream filehandle;
 601                 int ableToOpen;
 602
 603                 if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist you must enter a phylip or a column." << endl; errorFree = false; }
 604                 else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist you must enter ONLY ONE of the following: phylip or column." << endl; errorFree = false; }
 605
 606                 if (columnfile != "") {
 607                         if (namefile == "") {
 608                                 cout << "You need to provide a namefile if you are going to use the column format." << endl;
 609                                 errorFree = false;
 610                         }else {
 611                                 ableToOpen = openInputFile(namefile, filehandle);
 612                                 filehandle.close();
 613                                 //unable to open
 614                                 if (ableToOpen == 1) { errorFree = false; }
 615                         }
 616                 }
 617         }
 618         catch(exception& e) {
 619                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 620                 exit(1);
 621         }
 622         catch(...) {
 623                 cout << "An unknown error has occurred in the ErrorCheck class function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 624                 exit(1);
 625         }
 626 }
 627 /*******************************************************/
 628
 629 /******************************************************/
 630 //This function checks to make sure the user entered appropriate
 631 // format parameters on a parselistcommand
 632 void ErrorCheck::validateParseFiles() {
 633         try {
 634                 ifstream filehandle;
 635                 int ableToOpen;
 636
 637                 //checks for valid files
 638
 639                 if (listfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
 640                 else if (groupfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
 641
 642                 //checks parameters on the read command
 643                 if (listfile != "") {
 644                         ableToOpen = openInputFile(listfile, filehandle);
 645                         filehandle.close();
 646                         if (ableToOpen == 1) { //unable to open
 647                                 errorFree = false;
 648                         }
 649                         if (groupfile != "") {
 650                                 ableToOpen = openInputFile(groupfile, filehandle);
 651                                 filehandle.close();
 652                                 if (ableToOpen == 1) { //unable to open
 653                                         errorFree = false;;
 654                                 }
 655                         }
 656                 }
 657         }
 658         catch(exception& e) {
 659                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 660                 exit(1);
 661         }
 662         catch(...) {
 663                 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 664                 exit(1);
 665         }
 666 }
 667 /*******************************************************/
 668
 669 /******************************************************/
 670 //This function checks to make sure the user entered appropriate
 671 // format parameters on a parselistcommand
 672 void ErrorCheck::validateTreeFiles() {
 673         try {
 674                 ifstream filehandle;
 675                 int ableToOpen;
 676
 677                 //checks for valid files
 678
 679                 if (treefile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
 680                 else if (groupfile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
 681
 682                 //checks parameters on the read command
 683                 if (treefile != "") {
 684                         ableToOpen = openInputFile(treefile, filehandle);
 685                         filehandle.close();
 686                         if (ableToOpen == 1) { //unable to open
 687                                 errorFree = false;
 688                         }
 689                         if (groupfile != "") {
 690                                 ableToOpen = openInputFile(groupfile, filehandle);
 691                                 filehandle.close();
 692                                 if (ableToOpen == 1) { //unable to open
 693                                         errorFree = false;;
 694                                 }
 695                         }
 696                 }
 697         }
 698         catch(exception& e) {
 699                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 700                 exit(1);
 701         }
 702         catch(...) {
 703                 cout << "An unknown error has occurred in the ErrorCheck class function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 704                 exit(1);
 705         }
 706 }
 707
 708 /*******************************************************/
 709
 710 /******************************************************/
 711 //This function checks to make sure the user entered appropriate
 712 // format parameters on a distfile read
 713 void ErrorCheck::validateReadPhil() {
 714         try {
 715                 ifstream filehandle;
 716                 int ableToOpen;
 717
 718                 //checks to make sure only one file type is given
 719                 if (listfile != "") {
 720                         if ((rabundfile != "") || (sabundfile != "")) {
 721                                 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
 722                 }else if (rabundfile != "") {
 723                         if ((listfile != "") || (sabundfile != "")) {
 724                                 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
 725                 }else if (sabundfile != "") {
 726                         if ((listfile != "") || (rabundfile != "")) {
 727                                 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
 728                 }else if ((listfile == "") && (rabundfile == "") && (sabundfile == "")) {
 729                             cout << "When executing a read.otu you must enter one of the following: list, rabund or sabund." << endl; errorFree = false;
 730                 }
 731
 732                 //checks parameters on the read command
 733                 if (orderfile != "") {
 734                         ableToOpen = openInputFile(orderfile, filehandle);
 735                         filehandle.close();
 736                         if (ableToOpen == 1) { //unable to open
 737                                 errorFree = false;
 738                         }
 739                 }
 740         }
 741         catch(exception& e) {
 742                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 743                 exit(1);
 744         }
 745         catch(...) {
 746                 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 747                 exit(1);
 748         }
 749 }
 750 /*******************************************************/
 751
 752 /******************************************************/
 753
 754 void ErrorCheck::clear() {
 755         //option definitions should go here...
 756         phylipfile              =       "";
 757         columnfile              =       "";
 758         listfile                =       "";
 759         rabundfile              =       "";
 760         sabundfile              =       "";
 761         namefile                =       "";
 762         groupfile               =       "";
 763         orderfile               =       "";
 764         sharedfile              =       "";
 765         line                    =       "";
 766         label                   =       "";
 767         method                  =   "furthest";
 768 }
 769 /*******************************************************/
 770
 771 /******************************************************/
 772