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                                 if (parameter == "comparegroups") { //stores groups to be compared
 273                                         sharedGroups.clear(); //clears out old values
 274                                         globaldata->splitAtDash(value, sharedGroups);
 275                                 }
 276
 277                         }
 278
 279                         //gets the last parameter and value
 280                         if (errorFree)  { //gets the last parameter and value
 281                                 value = optionText;
 282                                 splitAtEquals(parameter, value);
 283                                 //is it a valid parameter
 284                                 if (validParameter->isValidParameter(parameter) != true) { return false; }
 285                                 if(!validCommandParameter(parameter,commandName)) {
 286                                         cout << "'" << parameter << "' is not a valid parameter for the " << commandName << " command.\n";
 287                                         return false;
 288                                 }
 289                                 if(!validParameterValue(value, parameter)) {
 290                                         if(parameter.compare("precision") == 0)
 291                                                 cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n";
 292                                         else {
 293                                         vector<double> bounds = intParams[parameter];
 294                                         double a = bounds.at(0);
 295                                         double b = bounds.at(1);
 296                                         double c = bounds.at(2);
 297                                         double d = bounds.at(3);
 298                                         double e = bounds.at(4);
 299                                         cout << "The '" << parameter << "' parameter needs to be ";
 300                                         if(c == 1)
 301                                                         cout << "either '" << a << "' or '" << b << "'.\n";
 302                                         else
 303                                         {
 304                                                 if(a != piSent)
 305                                                 {
 306                                                         cout << ">";
 307                                                         if(d != 0)
 308                                                                 cout << "=";
 309                                                         cout << " '" << a << "'";
 310                                                 }
 311                                                 if(b == piSent)
 312                                                         cout << ".\n";
 313                                                 else if(a != piSent)
 314                                                         cout << " and ";
 315                                                 if(b != piSent)
 316                                                 {
 317                                                         cout << "<";
 318                                                         if(e != 0)
 319                                                                 cout << "=";
 320                                                         cout << " '" << b << ".\n";
 321                                                 }
 322                                         }
 323                                         }
 324                                         return false;
 325                                 }
 326                                 if (parameter == "phylip" )             { phylipfile = value; }
 327                                 if (parameter == "column" )             { columnfile = value; }
 328                                 if (parameter == "list" )               { listfile = value; }
 329                                 if (parameter == "rabund" )             { rabundfile = value; }
 330                                 if (parameter == "sabund" )             { sabundfile = value; }
 331                                 if (parameter == "name" )               { namefile = value; }
 332                                 if (parameter == "order" )              { orderfile = value; }
 333                                 if (parameter == "group" )              { groupfile = value; }
 334                                 if (parameter == "shared" )             { sharedfile = value; }
 335                                 if (parameter == "fasta" )              { fastafile = value; }
 336                                 if (parameter == "tree" )               { treefile = value; }
 337                                 if (parameter == "cutoff" )                     { cutoff = value; }
 338                                 if (parameter == "precision" )          { precision = value; }
 339                                 if (parameter == "iters" )                      { iters = value; }
 340                                 if (parameter == "jumble" )                     { jumble = value; }
 341                                 if (parameter == "freq" )                       { freq = value; }
 342                                 if (parameter == "method" )                     { method = value; }
 343                                 if (parameter == "fileroot" )           { fileroot = value; }
 344                                 if (parameter == "line" )                       { line = value; }
 345                                 if (parameter == "label" )                      { label = value; }
 346                                 if (parameter == "random" )                     { randomtree = value;   }
 347                                 if (parameter == "abund" )          { abund = value; }
 348
 349                                 if (parameter == "comparegroups") { //stores groups to be compared
 350                                         sharedGroups.clear(); //clears out old values
 351                                         globaldata->splitAtDash(value, sharedGroups);
 352                                 }
 353                         }
 354                 }
 355
 356                 //make sure the user does not use both the line and label parameters
 357                 if ((line != "") && (label != "")) { cout << "You may use either the line or label parameters, but not both." << endl; return false; }
 358
 359                 if (commandName == "read.dist") {
 360                         validateReadFiles();
 361                         validateReadDist();
 362                 }else if (commandName == "read.otu") {
 363                         //you want to do shared commands
 364                         if ((listfile != "") && (groupfile != ""))      {
 365                                 validateParseFiles(); //checks the listfile and groupfile parameters
 366                         }else { //you want to do single commands
 367                                 validateReadFiles();
 368                                 validateReadPhil();
 369                         }
 370                 }else if (commandName == "read.shared") {
 371                         //you want to do shared commands with just the shared file
 372                         validateReadFiles();
 373                 }else if (commandName == "read.tree") {
 374                         validateTreeFiles(); //checks the treefile and groupfile parameters
 375                 }else if (commandName == "deconvolute") {
 376                         if (fastafile == "") { cout << "You must enter a fastafile with the deconvolute() command." << endl; return false; }
 377                         validateReadFiles();
 378                 }
 379
 380                 //are you trying to cluster before you have read something
 381                 if ((commandName == "cluster") && (globaldata->getSparseMatrix() == NULL) ||
 382                         (commandName == "cluster") && (globaldata->getListVector() == NULL)) {
 383                                 cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl;
 384                                 errorFree = false;
 385                 }
 386
 387                 if (commandName == "parsimony") {
 388                         //are you trying to use parsimony without reading a tree or saying you want random distribution
 389                         if (randomtree == "")  {
 390                                 if (globaldata->gTree.size() == 0) {
 391                                         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;  }
 392                         }
 393                 }
 394
 395                 if ((commandName == "unifrac.weighted") || (commandName == "unifrac.unweighted")) {
 396                         if (globaldata->gTree.size() == 0) {//no trees were read
 397                                 cout << "You must execute the read.tree command, before you may execute the unifrac.weighted or unifrac.unweighted command." << endl; return false;  }
 398                 }
 399
 400                 //check for valid method
 401                 if(commandName == "get.group") {
 402                         if ((globaldata->getGroupFile() == "")) { cout << "You must read a group before you can use the get.group command." << endl; return false; }
 403                 }
 404                 if (commandName == "get.label" || commandName == "get.line") {
 405                         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; }
 406                 }
 407                 if (commandName == "cluster") {
 408                         if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
 409                         else {cout << "Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average." << endl; return false; }
 410                 }
 411
 412                 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single") ){
 413                         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; }
 414                 }
 415
 416                 if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") ){
 417                         if (globaldata->getSharedFile() == "") {
 418                                 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; }
 419                                 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; }
 420                         }
 421                 }
 422
 423                 globaldata->clearAbund();
 424
 425                 return errorFree;
 426 }
 427
 428 /*******************************************************/
 429
 430 /******************************************************/
 431 //This function checks to make sure the user entered a file to
 432 // read and that the file exists and can be opened.
 433 void ErrorCheck::validateReadFiles() {
 434         try {
 435                 //Validating files for read
 436                 ifstream filehandle;
 437                 int ableToOpen;
 438
 439                 //are we reading a phylipfile
 440                 if (phylipfile != "") {
 441                         ableToOpen = openInputFile(phylipfile, filehandle);
 442                         filehandle.close();
 443                         //unable to open
 444                         if (ableToOpen == 1) { errorFree = false; }
 445                         else { globaldata->inputFileName = phylipfile; }
 446                 //are we reading a phylipfile
 447                 }else if (columnfile != "") {
 448                         ableToOpen = openInputFile(columnfile, filehandle);
 449                         filehandle.close();
 450                         //unable to open
 451                         if (ableToOpen == 1) { errorFree = false; }
 452                         else { globaldata->inputFileName = columnfile; }
 453                 //are we reading a listfile
 454                 }else if (listfile!= "") {
 455                         ableToOpen = openInputFile(listfile, filehandle);
 456                         filehandle.close();
 457                         //unable to open
 458                         if (ableToOpen == 1) {  errorFree = false; }
 459                         else { globaldata->inputFileName = listfile; }
 460                 //are we reading a rabundfile
 461                 }else if (rabundfile != "") {
 462                         ableToOpen = openInputFile(rabundfile, filehandle);
 463                         filehandle.close();
 464                         //unable to open
 465                         if (ableToOpen == 1) {  errorFree = false; }
 466                         else { globaldata->inputFileName = rabundfile; }
 467                 //are we reading a sabundfile
 468                 }else if (sabundfile != "") {
 469                         ableToOpen = openInputFile(sabundfile, filehandle);
 470                         filehandle.close();
 471                         //unable to open
 472                         if (ableToOpen == 1) {  errorFree = false; }
 473                         else { globaldata->inputFileName = sabundfile; }
 474                 }else if (fastafile != "") {
 475                         ableToOpen = openInputFile(fastafile, filehandle);
 476                         filehandle.close();
 477                         //unable to open
 478                         if (ableToOpen == 1) {  errorFree = false; }
 479                         else { globaldata->inputFileName = fastafile; }
 480                 }else if (sharedfile != "") {
 481                         ableToOpen = openInputFile(sharedfile, filehandle);
 482                         filehandle.close();
 483                         //unable to open
 484                         if (ableToOpen == 1) {  errorFree = false; }
 485                         else { globaldata->inputFileName = sharedfile; }
 486                 }else{ //no file given
 487                         errorFree = false;
 488                 }
 489         }
 490         catch(exception& e) {
 491                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 492                 exit(1);
 493         }
 494         catch(...) {
 495                 cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 496                 exit(1);
 497         }
 498
 499 }
 500 /*******************************************************/
 501
 502 /******************************************************/
 503 //This function checks to see if the given paramter
 504 //is a valid paramter for the given command.
 505 bool ErrorCheck::validCommandParameter(string parameter, string commandName) {
 506         try {
 507                 for(int i = 0; i < commandParameters[commandName].size(); i++)
 508                         if(parameter.compare(commandParameters[commandName][i]) == 0)
 509                                 return true;
 510                 return false;
 511         }
 512
 513         catch(exception& e) {
 514                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 515                 exit(1);
 516         }
 517         catch(...) {
 518                 cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 519                 exit(1);
 520         }
 521 }
 522 /*******************************************************/
 523
 524 /******************************************************/
 525 //This function checks to see if the given paramter value
 526 //is convertable into an int if that parameter requires it.
 527 bool ErrorCheck::validParameterValue(string value, string parameter) {
 528         try {
 529                 int pVal;
 530                 if(intParams.count(parameter) == 1)
 531                 {
 532                         vector<double> bounds = intParams[parameter];
 533                         bool valid = convertTest(value, pVal);
 534                         if(!valid)
 535                                 return false;
 536                         if(parameter.compare("precision") == 0)
 537                         {
 538                                 double logNum = log10((double)pVal);
 539                                 double diff = (double)((int)logNum - logNum);
 540                                 if(diff != 0)
 541                                         return false;
 542                         }
 543                         double a = bounds.at(0);
 544                         double b = bounds.at(1);
 545                         double c = bounds.at(2);
 546                         double d = bounds.at(3);
 547                         double e = bounds.at(4);
 548                         bool a0 = pVal > a;
 549                         bool a1 = pVal >= a;
 550                         bool b0 = pVal < b;
 551                         bool b1 = pVal <= b;
 552
 553                         if(c != 1)
 554                         {
 555                                 if(a == piSent && b == piSent)
 556                                         return true;
 557                                 if(a != piSent && b == piSent)
 558                                 {
 559                                         if(d == 0)
 560                                                 return a0;
 561                                         else
 562                                                 return a1;
 563                                 }
 564                                 else if(a == piSent && b != piSent)
 565                                 {
 566                                         if(e == 0)
 567                                                 return b0;
 568                                         else
 569                                                 return b1;
 570                                 }
 571                                 else
 572                                 {
 573                                         if(d == 0 && e == 0)
 574                                                 return (a0 && b0);
 575                                         else if(d == 0 && e == 1)
 576                                                 return (a0 && b1);
 577                                         else if(d == 1 && e == 0)
 578                                                 return (a1 && b0);
 579                                         else
 580                                                 return (a1 && b1);
 581                                 }
 582                         }
 583                         else
 584                         {
 585                                 if(a == piSent && b == piSent)
 586                                         return true;
 587                                 if(a != piSent && b == piSent)
 588                                         return (pVal == a);
 589                                 else if(a == piSent && b != piSent)
 590                                         return (pVal == b);
 591                                 else
 592                                         return (pVal == a || pVal == b);
 593                         }
 594                 }
 595                 return true;
 596         }
 597
 598         catch(exception& e) {
 599                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 600                 exit(1);
 601         }
 602         catch(...) {
 603                 cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 604                 exit(1);
 605         }
 606 }
 607 /*******************************************************/
 608
 609 /******************************************************/
 610 //This function checks to make sure the user entered appropriate
 611 // format parameters on a distfile read
 612 void ErrorCheck::validateReadDist() {
 613         try {
 614                 ifstream filehandle;
 615                 int ableToOpen;
 616
 617                 if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist you must enter a phylip or a column." << endl; errorFree = false; }
 618                 else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist you must enter ONLY ONE of the following: phylip or column." << endl; errorFree = false; }
 619
 620                 if (columnfile != "") {
 621                         if (namefile == "") {
 622                                 cout << "You need to provide a namefile if you are going to use the column format." << endl;
 623                                 errorFree = false;
 624                         }else {
 625                                 ableToOpen = openInputFile(namefile, filehandle);
 626                                 filehandle.close();
 627                                 //unable to open
 628                                 if (ableToOpen == 1) { errorFree = false; }
 629                         }
 630                 }
 631         }
 632         catch(exception& e) {
 633                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 634                 exit(1);
 635         }
 636         catch(...) {
 637                 cout << "An unknown error has occurred in the ErrorCheck class function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 638                 exit(1);
 639         }
 640 }
 641 /*******************************************************/
 642
 643 /******************************************************/
 644 //This function checks to make sure the user entered appropriate
 645 // format parameters on a parselistcommand
 646 void ErrorCheck::validateParseFiles() {
 647         try {
 648                 ifstream filehandle;
 649                 int ableToOpen;
 650
 651                 //checks for valid files
 652
 653                 if (listfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
 654                 else if (groupfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
 655
 656                 //checks parameters on the read command
 657                 if (listfile != "") {
 658                         ableToOpen = openInputFile(listfile, filehandle);
 659                         filehandle.close();
 660                         if (ableToOpen == 1) { //unable to open
 661                                 errorFree = false;
 662                         }
 663                         if (groupfile != "") {
 664                                 ableToOpen = openInputFile(groupfile, filehandle);
 665                                 filehandle.close();
 666                                 if (ableToOpen == 1) { //unable to open
 667                                         errorFree = false;;
 668                                 }
 669                         }
 670                 }
 671         }
 672         catch(exception& e) {
 673                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 674                 exit(1);
 675         }
 676         catch(...) {
 677                 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 678                 exit(1);
 679         }
 680 }
 681 /*******************************************************/
 682
 683 /******************************************************/
 684 //This function checks to make sure the user entered appropriate
 685 // format parameters on a parselistcommand
 686 void ErrorCheck::validateTreeFiles() {
 687         try {
 688                 ifstream filehandle;
 689                 int ableToOpen;
 690
 691                 //checks for valid files
 692
 693                 if (treefile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
 694                 else if (groupfile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
 695
 696                 //checks parameters on the read command
 697                 if (treefile != "") {
 698                         ableToOpen = openInputFile(treefile, filehandle);
 699                         filehandle.close();
 700                         if (ableToOpen == 1) { //unable to open
 701                                 errorFree = false;
 702                         }
 703                         if (groupfile != "") {
 704                                 ableToOpen = openInputFile(groupfile, filehandle);
 705                                 filehandle.close();
 706                                 if (ableToOpen == 1) { //unable to open
 707                                         errorFree = false;;
 708                                 }
 709                         }
 710                 }
 711         }
 712         catch(exception& e) {
 713                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 714                 exit(1);
 715         }
 716         catch(...) {
 717                 cout << "An unknown error has occurred in the ErrorCheck class function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 718                 exit(1);
 719         }
 720 }
 721
 722 /*******************************************************/
 723
 724 /******************************************************/
 725 //This function checks to make sure the user entered appropriate
 726 // format parameters on a distfile read
 727 void ErrorCheck::validateReadPhil() {
 728         try {
 729                 ifstream filehandle;
 730                 int ableToOpen;
 731
 732                 //checks to make sure only one file type is given
 733                 if (listfile != "") {
 734                         if ((rabundfile != "") || (sabundfile != "")) {
 735                                 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
 736                 }else if (rabundfile != "") {
 737                         if ((listfile != "") || (sabundfile != "")) {
 738                                 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
 739                 }else if (sabundfile != "") {
 740                         if ((listfile != "") || (rabundfile != "")) {
 741                                 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
 742                 }else if ((listfile == "") && (rabundfile == "") && (sabundfile == "")) {
 743                             cout << "When executing a read.otu you must enter one of the following: list, rabund or sabund." << endl; errorFree = false;
 744                 }
 745
 746                 //checks parameters on the read command
 747                 if (orderfile != "") {
 748                         ableToOpen = openInputFile(orderfile, filehandle);
 749                         filehandle.close();
 750                         if (ableToOpen == 1) { //unable to open
 751                                 errorFree = false;
 752                         }
 753                 }
 754         }
 755         catch(exception& e) {
 756                 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 757                 exit(1);
 758         }
 759         catch(...) {
 760                 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 761                 exit(1);
 762         }
 763 }
 764 /*******************************************************/
 765
 766 /******************************************************/
 767
 768 void ErrorCheck::clear() {
 769         //option definitions should go here...
 770         phylipfile              =       "";
 771         columnfile              =       "";
 772         listfile                =       "";
 773         rabundfile              =       "";
 774         sabundfile              =       "";
 775         namefile                =       "";
 776         groupfile               =       "";
 777         orderfile               =       "";
 778         sharedfile              =       "";
 779         line                    =       "";
 780         label                   =       "";
 781         method                  =   "furthest";
 782 }
 783 /*******************************************************/
 784
 785 /******************************************************/
 786