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 #include <math.h>
  12
  13 /*******************************************************/
  14
  15 /******************************************************/
  16
  17 ErrorCheck::ErrorCheck() {
  18         globaldata = GlobalData::getInstance();
  19         validCommand = new ValidCommands();
  20         validParameter = new ValidParameters();
  21 }
  22 /*******************************************************/
  23
  24 /******************************************************/
  25
  26 void ErrorCheck::refresh() {
  27         columnfile = globaldata->getColumnFile();
  28         phylipfile = globaldata->getPhylipFile();
  29         listfile = globaldata->getListFile();
  30         rabundfile = globaldata->getRabundFile();
  31         sabundfile = globaldata->getSabundFile();
  32         namefile = globaldata->getNameFile();
  33         groupfile = globaldata->getGroupFile();
  34         orderfile = globaldata->getOrderFile();
  35         fastafile = globaldata->getFastaFile();
  36         treefile = globaldata->getTreeFile();
  37         cutoff = globaldata->getCutOff();
  38         format = globaldata->getFormat();
  39         method = globaldata->getMethod();
  40
  41
  42         string p[] = {
  43                 "phylip",              //0
  44                 "column",             //1
  45                 "list",               //2
  46                 "rabund",             //3
  47                 "sabund",             //4
  48                 "name",               //5
  49                 "order",              //6
  50                 "group",              //7
  51                 "fasta",              //8
  52                 "treefile",           //9
  53                 "cutoff",             //10
  54                 "precision",          //11
  55                 "iters",              //12
  56                 "jumble",             //13
  57                 "freq",               //14
  58                 "method",             //15
  59                 "fileroot",           //16
  60                 "line",               //17
  61                 "label",              //18
  62                 "single",             //19
  63                 "rarefaction",        //20
  64                 "shared",             //21
  65                 "summary",            //22
  66                 "sharedrarefaction",  //23
  67                 "sharedsummary",      //24
  68                 "comparegroups",      //25
  69                 "abund",              //26
  70                 };
  71
  72         string c0[] = {p[0],p[5],p[10],p[11]};
  73         string c1[] = {p[2],p[6],p[7]};
  74         string c2[] = {p[10],p[11],p[15]};
  75         string c3[] = {p[8]};
  76         string c4[] = {p[14],p[17],p[18],p[19],p[26]};
  77         string c5[] = {p[13],p[14],p[17],p[18],p[21],p[25]};
  78         string c6[] = {""};
  79         string c7[] = {""};
  80         string c8[] = {""};
  81         string c9[] = {p[12],p[14],p[17],p[18],p[20],p[26]};
  82         string c10[] = {p[12],p[13],p[17],p[18],p[23]};
  83         string c11[] = {p[17],p[18],p[22],p[26]};
  84         string c12[] =  {p[13],p[17],p[18],p[24]};
  85         string c13[] = {""};
  86
  87         vector<string> v0 (c0, c0+sizeof(c0)/sizeof(string));
  88         vector<string> v1 (c1, c1+sizeof(c1)/sizeof(string));
  89         vector<string> v2 (c2, c2+sizeof(c2)/sizeof(string));
  90         vector<string> v3 (c3, c3+sizeof(c3)/sizeof(string));
  91         vector<string> v4 (c4, c4+sizeof(c4)/sizeof(string));
  92         vector<string> v5 (c5, c5+sizeof(c5)/sizeof(string));
  93         vector<string> v6 (c6, c6+sizeof(c6)/sizeof(string));
  94         vector<string> v7 (c7, c7+sizeof(c7)/sizeof(string));
  95         vector<string> v8 (c8, c8+sizeof(c8)/sizeof(string));
  96         vector<string> v9 (c9, c9+sizeof(c9)/sizeof(string));
  97         vector<string> v10 (c10, c10+sizeof(c10)/sizeof(string));
  98         vector<string> v11 (c11, c11+sizeof(c11)/sizeof(string));
  99         vector<string> v12 (c12, c12+sizeof(c12)/sizeof(string));
 100         vector<string> v13 (c13, c13+sizeof(c13)/sizeof(string));
 101
 102         vector<vector<string> > allCommands;
 103         allCommands.push_back(v0);
 104         allCommands.push_back(v1);
 105         allCommands.push_back(v2);
 106         allCommands.push_back(v3);
 107         allCommands.push_back(v4);
 108         allCommands.push_back(v5);
 109         allCommands.push_back(v6);
 110         allCommands.push_back(v7);
 111         allCommands.push_back(v8);
 112         allCommands.push_back(v9);
 113         allCommands.push_back(v10);
 114         allCommands.push_back(v11);
 115         allCommands.push_back(v12);
 116         allCommands.push_back(v13);
 117
 118         string commands[] = {
 119         "read.dist",          //0
 120         "read.otu",           //1
 121         "cluster",            //2
 122         "deconvolute",        //3
 123         "collect.single",     //4
 124         "collect.shared",     //5
 125         "get.group",          //6
 126         "get.label",          //7
 127         "get.line",           //8
 128         "rarefaction.single", //9
 129         "rarefaction.shared", //10
 130         "summary.single",     //11
 131         "summary.shared",     //12
 132         "quit"                //13
 133         };
 134
 135         for(int i = 0; i < allCommands.size(); i++)
 136                 commandParameters[commands[i]] = allCommands.at(i);
 137
 138          //{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};
 139         piSent = 3.14159;
 140         double ip0[] = {10, piSent, 0, 1, 0};
 141         double ip1[] = {10, piSent, 0, 1, 0};
 142         double ip2[] = {0, 1, 1, 0, 0};
 143         double ip3[] =  {1, piSent, 0, 0, 0};
 144         double ip4[] = {1, piSent, 0, 1, 0};
 145         double ip5[] = {5, piSent, 0, 1, 0};
 146
 147         vector<double> ipv0 (ip0, ip0+sizeof(ip0)/sizeof(double));
 148         vector<double> ipv1 (ip1, ip1+sizeof(ip1)/sizeof(double));
 149         vector<double> ipv2 (ip2, ip2+sizeof(ip2)/sizeof(double));
 150         vector<double> ipv3 (ip3, ip3+sizeof(ip3)/sizeof(double));
 151         vector<double> ipv4 (ip4, ip4+sizeof(ip4)/sizeof(double));
 152         vector<double> ipv5 (ip5, ip5+sizeof(ip5)/sizeof(double));
 153
 154         intParams[p[11]] = ipv0;
 155         intParams[p[12]] = ipv1;
 156         intParams[p[13]] = ipv2;
 157         intParams[p[14]] = ipv3;
 158         intParams[p[17]] = ipv4;
 159         intParams[p[26]] = ipv5;
 160
 161         randomtree = globaldata->getRandomTree();
 162         sharedfile = globaldata->getSharedFile();
 163 }
 164
 165 /*******************************************************/
 166
 167 /******************************************************/
 168
 169 ErrorCheck::~ErrorCheck() {}
 170
 171 /*******************************************************/
 172
 173 /******************************************************/
 174
 175 bool ErrorCheck::checkInput(string input) {
 176                 errorFree = true;
 177                 clear();
 178
 179                 //refresh variable
 180                 refresh();
 181
 182                 //get command name and parameters
 183                 int openParen = input.find_first_of('(');
 184                 int closeParen = input.find_last_of(')');
 185
 186                 if(openParen != -1 && closeParen != -1){
 187                         commandName = input.substr(0, openParen);   //commandName contains everything before "("
 188                         optionText = input.substr(openParen+1, closeParen-openParen-1); //optionString contains everything between "(" and ")".
 189                 }else if (openParen == -1) { //there is no parenthesis
 190                         cout << input << " is not a valid command. You are missing the ()." << endl;
 191                         return false;
 192                 }
 193
 194                 //is it a valid command
 195                 if (validCommand->isValidCommand(commandName) != true) { return false; }
 196
 197                 string parameter, value;
 198
 199                 //reads in parameters and values
 200                 if((optionText != "") && (commandName != "help")){
 201                         while((optionText.find_first_of(',') != -1) && (errorFree)) {  //while there are parameters
 202                                 splitAtComma(value, optionText);
 203                                 splitAtEquals(parameter, value);
 204
 205                                 //is it a valid parameter
 206                                 if (validParameter->isValidParameter(parameter) != true) { return false; }
 207                                 if(!validCommandParameter(parameter,commandName)) {
 208                                         cout << "'" << parameter << "' is not a valid parameter for the " << commandName << " command.\n";
 209                                         return false;
 210                                 }
 211                                 if(!validParameterValue(value, parameter)) {
 212                                         if(parameter.compare("precision") == 0)
 213                                                 cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n";
 214                                         else {
 215                                         vector<double> bounds = intParams[parameter];
 216                                         double a = bounds.at(0);
 217                                         double b = bounds.at(1);
 218                                         double c = bounds.at(2);
 219                                         double d = bounds.at(3);
 220                                         double e = bounds.at(4);
 221                                         cout << "The '" << parameter << "' parameter needs to be ";
 222                                         if(c == 1)
 223                                                         cout << "either '" << a << "' or '" << b << "'.\n";
 224                                         else
 225                                         {
 226                                                 if(a != piSent)
 227                                                 {
 228                                                         cout << ">";
 229                                                         if(d != 0)
 230                                                                 cout << "=";
 231                                                         cout << " '" << a << "'";
 232                                                 }
 233                                                 if(b == piSent)
 234                                                         cout << ".\n";
 235                                                 else if(a != piSent)
 236                                                         cout << " and ";
 237                                                 if(b != piSent)
 238                                                 {
 239                                                         cout << "<";
 240                                                         if(e != 0)
 241                                                                 cout << "=";
 242                                                         cout << " '" << b << ".\n";
 243                                                 }
 244                                         }
 245                                         }
 246                                         return false;
 247                                 }
 248
 249                                 if (parameter == "phylip" )             { phylipfile = value; }
 250                                 if (parameter == "column" )             { columnfile = value; }
 251                                 if (parameter == "list" )               { listfile = value; }
 252                                 if (parameter == "rabund" )             { rabundfile = value; }
 253                                 if (parameter == "sabund" )             { sabundfile = value; }
 254                                 if (parameter == "name" )               { namefile = value; }
 255                                 if (parameter == "order" )              { orderfile = value; }
 256                                 if (parameter == "fasta" )              { fastafile = value; }
 257                                 if (parameter == "tree" )               { treefile = value; }
 258                                 if (parameter == "group" )              { groupfile = value; }
 259                                 if (parameter == "shared" )             { sharedfile = value; }
 260                                 if (parameter == "cutoff" )                     { cutoff = value; }
 261                                 if (parameter == "precision" )          { precision = value; }
 262                                 if (parameter == "iters" )                      { iters = value; }
 263                                 if (parameter == "jumble" )                     { jumble = value; }
 264                                 if (parameter == "freq" )                       { freq = value; }
 265                                 if (parameter == "method" )                     { method = value; }
 266                                 if (parameter == "fileroot" )           { fileroot = value; }
 267                                 if (parameter == "line" )                       { line = value; }
 268                                 if (parameter == "label" )                      { label = value; }
 269                                 if (parameter == "abund" )          { abund = value; }
 270                                 if (parameter == "random" )                     { randomtree = value;   }
 271                         }
 272
 273                         //gets the last parameter and value
 274                         if (errorFree)  { //gets the last parameter and value
 275                                 value = optionText;
 276                                 splitAtEquals(parameter, value);
 277                                 //is it a valid parameter
 278                                 if (validParameter->isValidParameter(parameter) != true) { return false; }
 279                                 if(!validCommandParameter(parameter,commandName)) {
 280                                         cout << "'" << parameter << "' is not a valid parameter for the " << commandName << " command.\n";
 281                                         return false;
 282                                 }
 283                                 if(!validParameterValue(value, parameter)) {
 284                                         if(parameter.compare("precision") == 0)
 285                                                 cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n";
 286                                         else {
 287                                         vector<double> bounds = intParams[parameter];
 288                                         double a = bounds.at(0);
 289                                         double b = bounds.at(1);
 290                                         double c = bounds.at(2);
 291                                         double d = bounds.at(3);
 292                                         double e = bounds.at(4);
 293                                         cout << "The '" << parameter << "' parameter needs to be ";
 294                                         if(c == 1)
 295                                                         cout << "either '" << a << "' or '" << b << "'.\n";
 296                                         else
 297                                         {
 298                                                 if(a != piSent)
 299                                                 {
 300                                                         cout << ">";
 301                                                         if(d != 0)
 302                                                                 cout << "=";
 303                                                         cout << " '" << a << "'";
 304                                                 }
 305                                                 if(b == piSent)
 306                                                         cout << ".\n";
 307                                                 else if(a != piSent)
 308                                                         cout << " and ";
 309                                                 if(b != piSent)
 310                                                 {
 311                                                         cout << "<";
 312                                                         if(e != 0)
 313                                                                 cout << "=";
 314                                                         cout << " '" << b << ".\n";
 315                                                 }
 316                                         }
 317                                         }
 318                                         return false;
 319                                 }
 320                                 if (parameter == "phylip" )             { phylipfile = value; }
 321                                 if (parameter == "column" )             { columnfile = value; }
 322                                 if (parameter == "list" )               { listfile = value; }
 323                                 if (parameter == "rabund" )             { rabundfile = value; }
 324                                 if (parameter == "sabund" )             { sabundfile = value; }
 325                                 if (parameter == "name" )               { namefile = value; }
 326                                 if (parameter == "order" )              { orderfile = value; }
 327                                 if (parameter == "group" )              { groupfile = value; }
 328                                 if (parameter == "shared" )             { sharedfile = value; }
 329                                 if (parameter == "fasta" )              { fastafile = value; }
 330                                 if (parameter == "tree" )               { treefile = value; }
 331                                 if (parameter == "cutoff" )                     { cutoff = value; }
 332                                 if (parameter == "precision" )          { precision = value; }
 333                                 if (parameter == "iters" )                      { iters = value; }
 334                                 if (parameter == "jumble" )                     { jumble = value; }
 335                                 if (parameter == "freq" )                       { freq = value; }
 336                                 if (parameter == "method" )                     { method = value; }
 337                                 if (parameter == "fileroot" )           { fileroot = value; }
 338                                 if (parameter == "line" )                       { line = value; }
 339                                 if (parameter == "label" )                      { label = value; }
 340                                 if (parameter == "random" )                     { randomtree = value;   }
 341                                 if (parameter == "abund" )          { abund = value; }
 342                         }
 343                 }
 344
 345                 //make sure the user does not use both the line and label parameters
 346                 if ((line != "") && (label != "")) { cout << "You may use either the line or label parameters, but not both." << endl; return false; }
 347
 348                 if (commandName == "read.dist") {
 349                         validateReadFiles();
 350                         validateReadDist();
 351                 }else if (commandName == "read.otu") {
 352                         //you want to do shared commands
 353                         if ((listfile != "") && (groupfile != ""))      {
 354                                 validateParseFiles(); //checks the listfile and groupfile parameters
 355                         }else { //you want to do single commands
 356                                 validateReadFiles();
 357                                 validateReadPhil();
 358                         }
 359                 }else if (commandName == "read.shared") {
 360                         //you want to do shared commands with just the shared file
 361                         validateReadFiles();
 362                 }else if (commandName == "read.tree") {
 363                         validateTreeFiles(); //checks the treefile and groupfile parameters
 364                 }else if (commandName == "deconvolute") {
 365                         if (fastafile == "") { cout << "You must enter a fastafile with the deconvolute() command." << endl; return false; }
 366                         validateReadFiles();
 367                 }
 368
 369                 //are you trying to cluster before you have read something
 370                 if ((commandName == "cluster") && (globaldata->getSparseMatrix() == NULL) ||
 371                         (commandName == "cluster") && (globaldata->getListVector() == NULL)) {
 372                                 cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl;
 373                                 errorFree = false;
 374                 }
 375
 376                 if (commandName == "parsimony") {
 377                         //are you trying to use parsimony without reading a tree or saying you want random distribution
 378                         if (randomtree == "")  {
 379                                 if (globaldata->gTree.size() == 0) {
 380                                         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;  }
 381                         }
 382                 }
 383
 384                 if ((commandName == "unifrac.weighted") || (commandName == "unifrac.unweighted")) {
 385                         if (globaldata->gTree.size() == 0) {//no trees were read
 386                                 cout << "You must execute the read.tree command, before you may execute the unifrac.weighted or unifrac.unweighted command." << endl; return false;  }
 387                 }
 388
 389                 //check for valid method
 390                 if(commandName == "get.group") {
 391                         if ((globaldata->getGroupFile() == "")) { cout << "You must read a group before you can use the get.group command." << endl; return false; }
 392                 }
 393                 if (commandName == "get.label" || commandName == "get.line") {
 394                         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; }
 395                 }
 396                 if (commandName == "cluster") {
 397                         if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
 398                         else {cout << "Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average." << endl; return false; }
 399                 }
 400
 401                 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single") ){
 402                         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; }
 403                 }
 404
 405                 if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") ){
 406                         if (globaldata->getSharedFile() == "") {
 407                                 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; }
 408                                 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; }
 409                         }
 410                 }
 411
 412                 return errorFree;
 413 }
 414
 415 /*******************************************************/
 416
 417 /******************************************************/
 418 //This function checks to make sure the user entered a file to
 419 // read and that the file exists and can be opened.
 420 void ErrorCheck::validateReadFiles() {
 421         try {
 422                 //Validating files for read
 423                 ifstream filehandle;
 424                 int ableToOpen;
 425
 426                 //are we reading a phylipfile
 427                 if (phylipfile != "") {
 428                         ableToOpen = openInputFile(phylipfile, filehandle);
 429                         filehandle.close();
 430                         //unable to open
 431                         if (ableToOpen == 1) { errorFree = false; }
 432                         else { globaldata->inputFileName = phylipfile; }
 433                 //are we reading a phylipfile
 434                 }else if (columnfile != "") {
 435                         ableToOpen = openInputFile(columnfile, filehandle);
 436                         filehandle.close();
 437                         //unable to open
 438                         if (ableToOpen == 1) { errorFree = false; }
 439                         else { globaldata->inputFileName = columnfile; }
 440                 //are we reading a listfile
 441                 }else if (listfile!= "") {
 442                         ableToOpen = openInputFile(listfile, filehandle);
 443                         filehandle.close();
 444                         //unable to open
 445                         if (ableToOpen == 1) {  errorFree = false; }
 446                         else { globaldata->inputFileName = listfile; }
 447                 //are we reading a rabundfile
 448                 }else if (rabundfile != "") {
 449                         ableToOpen = openInputFile(rabundfile, filehandle);
 450                         filehandle.close();
 451                         //unable to open
 452                         if (ableToOpen == 1) {  errorFree = false; }
 453                         else { globaldata->inputFileName = rabundfile; }
 454                 //are we reading a sabundfile
 455                 }else if (sabundfile != "") {
 456                         ableToOpen = openInputFile(sabundfile, filehandle);
 457                         filehandle.close();
 458                         //unable to open
 459                         if (ableToOpen == 1) {  errorFree = false; }
 460                         else { globaldata->inputFileName = sabundfile; }
 461                 }else if (fastafile != "") {
 462                         ableToOpen = openInputFile(fastafile, filehandle);
 463                         filehandle.close();
 464                         //unable to open
 465                         if (ableToOpen == 1) {  errorFree = false; }
 466                         else { globaldata->inputFileName = fastafile; }
 467                 }else if (sharedfile != "") {
 468                         ableToOpen = openInputFile(sharedfile, filehandle);
 469                         filehandle.close();
 470                         //unable to open
 471                         if (ableToOpen == 1) {  errorFree = false; }
 472                         else { globaldata->inputFileName = sharedfile; }
 473                 }else{ //no file given
 474                         errorFree = false;
 475                 }
 476         }
 477         catch(exception& e) {
 478                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 479                 exit(1);
 480         }
 481         catch(...) {
 482                 cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 483                 exit(1);
 484         }
 485
 486 }
 487 /*******************************************************/
 488
 489 /******************************************************/
 490 //This function checks to see if the given paramter
 491 //is a valid paramter for the given command.
 492 bool ErrorCheck::validCommandParameter(string parameter, string commandName) {
 493         try {
 494                 for(int i = 0; i < commandParameters[commandName].size(); i++)
 495                         if(parameter.compare(commandParameters[commandName][i]) == 0)
 496                                 return true;
 497                 return false;
 498         }
 499
 500         catch(exception& e) {
 501                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 502                 exit(1);
 503         }
 504         catch(...) {
 505                 cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 506                 exit(1);
 507         }
 508 }
 509 /*******************************************************/
 510
 511 /******************************************************/
 512 //This function checks to see if the given paramter value
 513 //is convertable into an int if that parameter requires it.
 514 bool ErrorCheck::validParameterValue(string value, string parameter) {
 515         try {
 516                 int pVal;
 517                 if(intParams.count(parameter) == 1)
 518                 {
 519                         vector<double> bounds = intParams[parameter];
 520                         bool valid = convertTest(value, pVal);
 521                         if(!valid)
 522                                 return false;
 523                         if(parameter.compare("precision") == 0)
 524                         {
 525                                 double logNum = log10((double)pVal);
 526                                 double diff = (double)((int)logNum - logNum);
 527                                 if(diff != 0)
 528                                         return false;
 529                         }
 530                         double a = bounds.at(0);
 531                         double b = bounds.at(1);
 532                         double c = bounds.at(2);
 533                         double d = bounds.at(3);
 534                         double e = bounds.at(4);
 535                         bool a0 = pVal > a;
 536                         bool a1 = pVal >= a;
 537                         bool b0 = pVal < b;
 538                         bool b1 = pVal <= b;
 539
 540                         if(c != 1)
 541                         {
 542                                 if(a == piSent && b == piSent)
 543                                         return true;
 544                                 if(a != piSent && b == piSent)
 545                                 {
 546                                         if(d == 0)
 547                                                 return a0;
 548                                         else
 549                                                 return a1;
 550                                 }
 551                                 else if(a == piSent && b != piSent)
 552                                 {
 553                                         if(e == 0)
 554                                                 return b0;
 555                                         else
 556                                                 return b1;
 557                                 }
 558                                 else
 559                                 {
 560                                         if(d == 0 && e == 0)
 561                                                 return (a0 && b0);
 562                                         else if(d == 0 && e == 1)
 563                                                 return (a0 && b1);
 564                                         else if(d == 1 && e == 0)
 565                                                 return (a1 && b0);
 566                                         else
 567                                                 return (a1 && b1);
 568                                 }
 569                         }
 570                         else
 571                         {
 572                                 if(a == piSent && b == piSent)
 573                                         return true;
 574                                 if(a != piSent && b == piSent)
 575                                         return (pVal == a);
 576                                 else if(a == piSent && b != piSent)
 577                                         return (pVal == b);
 578                                 else
 579                                         return (pVal == a || pVal == b);
 580                         }
 581                 }
 582                 return true;
 583         }
 584
 585         catch(exception& e) {
 586                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 587                 exit(1);
 588         }
 589         catch(...) {
 590                 cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 591                 exit(1);
 592         }
 593 }
 594 /*******************************************************/
 595
 596 /******************************************************/
 597 //This function checks to make sure the user entered appropriate
 598 // format parameters on a distfile read
 599 void ErrorCheck::validateReadDist() {
 600         try {
 601                 ifstream filehandle;
 602                 int ableToOpen;
 603
 604                 if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist you must enter a phylip or a column." << endl; errorFree = false; }
 605                 else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist you must enter ONLY ONE of the following: phylip or column." << endl; errorFree = false; }
 606
 607                 if (columnfile != "") {
 608                         if (namefile == "") {
 609                                 cout << "You need to provide a namefile if you are going to use the column format." << endl;
 610                                 errorFree = false;
 611                         }else {
 612                                 ableToOpen = openInputFile(namefile, filehandle);
 613                                 filehandle.close();
 614                                 //unable to open
 615                                 if (ableToOpen == 1) { errorFree = false; }
 616                         }
 617                 }
 618         }
 619         catch(exception& e) {
 620                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 621                 exit(1);
 622         }
 623         catch(...) {
 624                 cout << "An unknown error has occurred in the ErrorCheck class function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 625                 exit(1);
 626         }
 627 }
 628 /*******************************************************/
 629
 630 /******************************************************/
 631 //This function checks to make sure the user entered appropriate
 632 // format parameters on a parselistcommand
 633 void ErrorCheck::validateParseFiles() {
 634         try {
 635                 ifstream filehandle;
 636                 int ableToOpen;
 637
 638                 //checks for valid files
 639
 640                 if (listfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
 641                 else if (groupfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
 642
 643                 //checks parameters on the read command
 644                 if (listfile != "") {
 645                         ableToOpen = openInputFile(listfile, filehandle);
 646                         filehandle.close();
 647                         if (ableToOpen == 1) { //unable to open
 648                                 errorFree = false;
 649                         }
 650                         if (groupfile != "") {
 651                                 ableToOpen = openInputFile(groupfile, filehandle);
 652                                 filehandle.close();
 653                                 if (ableToOpen == 1) { //unable to open
 654                                         errorFree = false;;
 655                                 }
 656                         }
 657                 }
 658         }
 659         catch(exception& e) {
 660                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 661                 exit(1);
 662         }
 663         catch(...) {
 664                 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 665                 exit(1);
 666         }
 667 }
 668 /*******************************************************/
 669
 670 /******************************************************/
 671 //This function checks to make sure the user entered appropriate
 672 // format parameters on a parselistcommand
 673 void ErrorCheck::validateTreeFiles() {
 674         try {
 675                 ifstream filehandle;
 676                 int ableToOpen;
 677
 678                 //checks for valid files
 679
 680                 if (treefile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
 681                 else if (groupfile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
 682
 683                 //checks parameters on the read command
 684                 if (treefile != "") {
 685                         ableToOpen = openInputFile(treefile, filehandle);
 686                         filehandle.close();
 687                         if (ableToOpen == 1) { //unable to open
 688                                 errorFree = false;
 689                         }
 690                         if (groupfile != "") {
 691                                 ableToOpen = openInputFile(groupfile, filehandle);
 692                                 filehandle.close();
 693                                 if (ableToOpen == 1) { //unable to open
 694                                         errorFree = false;;
 695                                 }
 696                         }
 697                 }
 698         }
 699         catch(exception& e) {
 700                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 701                 exit(1);
 702         }
 703         catch(...) {
 704                 cout << "An unknown error has occurred in the ErrorCheck class function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 705                 exit(1);
 706         }
 707 }
 708
 709 /*******************************************************/
 710
 711 /******************************************************/
 712 //This function checks to make sure the user entered appropriate
 713 // format parameters on a distfile read
 714 void ErrorCheck::validateReadPhil() {
 715         try {
 716                 ifstream filehandle;
 717                 int ableToOpen;
 718
 719                 //checks to make sure only one file type is given
 720                 if (listfile != "") {
 721                         if ((rabundfile != "") || (sabundfile != "")) {
 722                                 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
 723                 }else if (rabundfile != "") {
 724                         if ((listfile != "") || (sabundfile != "")) {
 725                                 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
 726                 }else if (sabundfile != "") {
 727                         if ((listfile != "") || (rabundfile != "")) {
 728                                 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
 729                 }else if ((listfile == "") && (rabundfile == "") && (sabundfile == "")) {
 730                             cout << "When executing a read.otu you must enter one of the following: list, rabund or sabund." << endl; errorFree = false;
 731                 }
 732
 733                 //checks parameters on the read command
 734                 if (orderfile != "") {
 735                         ableToOpen = openInputFile(orderfile, filehandle);
 736                         filehandle.close();
 737                         if (ableToOpen == 1) { //unable to open
 738                                 errorFree = false;
 739                         }
 740                 }
 741         }
 742         catch(exception& e) {
 743                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 744                 exit(1);
 745         }
 746         catch(...) {
 747                 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 748                 exit(1);
 749         }
 750 }
 751 /*******************************************************/
 752
 753 /******************************************************/
 754
 755 void ErrorCheck::clear() {
 756         //option definitions should go here...
 757         phylipfile              =       "";
 758         columnfile              =       "";
 759         listfile                =       "";
 760         rabundfile              =       "";
 761         sabundfile              =       "";
 762         namefile                =       "";
 763         groupfile               =       "";
 764         orderfile               =       "";
 765         sharedfile              =       "";
 766         line                    =       "";
 767         label                   =       "";
 768         method                  =   "furthest";
 769 }
 770 /*******************************************************/
 771
 772 /******************************************************/
 773