sensspeccommand.cpp

   1 /*
   2  *  sensspeccommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 7/6/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "sensspeccommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> SensSpecCommand::setParameters(){
  14         try {
  15                 CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
  16                 CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip);
  17                 //CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
  18                 CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pcolumn);
  19                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  20                 CommandParameter pcutoff("cutoff", "Number", "", "-1.00", "", "", "",false,false); parameters.push_back(pcutoff);
  21                 CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
  22                 CommandParameter phard("hard", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phard);
  23                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  24                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  25
  26                 vector<string> myArray;
  27                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  28                 return myArray;
  29         }
  30         catch(exception& e) {
  31                 m->errorOut(e, "SensSpecCommand", "setParameters");
  32                 exit(1);
  33         }
  34 }
  35 //**********************************************************************************************************************
  36 string SensSpecCommand::getHelpString(){
  37         try {
  38                 string helpString = "";
  39                 helpString += "The sens.spec command....\n";
  40                 return helpString;
  41         }
  42         catch(exception& e) {
  43                 m->errorOut(e, "SensSpecCommand", "getHelpString");
  44                 exit(1);
  45         }
  46 }
  47 //**********************************************************************************************************************
  48 SensSpecCommand::SensSpecCommand(){
  49         try {
  50                 abort = true; calledHelp = true;
  51                 setParameters();
  52                 vector<string> tempOutNames;
  53                 outputTypes["sensspec"] = tempOutNames;
  54         }
  55         catch(exception& e) {
  56                 m->errorOut(e, "SensSpecCommand", "SensSpecCommand");
  57                 exit(1);
  58         }
  59 }
  60 //***************************************************************************************************************
  61
  62 SensSpecCommand::SensSpecCommand(string option)  {
  63         try {
  64
  65                 abort = false; calledHelp = false;
  66                 allLines = 1;
  67
  68                 //allow user to run help
  69                 if(option == "help") { help(); abort = true; calledHelp = true; }
  70                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  71
  72                 else {
  73                         string temp;
  74
  75                         vector<string> myArray = setParameters();
  76
  77                         OptionParser parser(option);
  78                         map<string,string> parameters = parser.getParameters();
  79
  80                         ValidParameters validParameter;
  81                         map<string,string>::iterator it;
  82
  83                         //check to make sure all parameters are valid for command
  84                         for (it = parameters.begin(); it != parameters.end(); it++) {
  85                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  86                         }
  87
  88                         //initialize outputTypes
  89                         vector<string> tempOutNames;
  90                         outputTypes["sensspec"] = tempOutNames;
  91
  92                         //if the user changes the input directory command factory will send this info to us in the output parameter
  93                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  94                         if (inputDir == "not found"){   inputDir = "";          }
  95                         else {
  96                                 string path;
  97                                 it = parameters.find("list");
  98                                 //user has given a template file
  99                                 if(it != parameters.end()){
 100                                         path = m->hasPath(it->second);
 101                                         //if the user has not given a path then, add inputdir. else leave path alone.
 102                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 103                                 }
 104
 105                                 it = parameters.find("phylip");
 106                                 //user has given a template file
 107                                 if(it != parameters.end()){
 108                                         path = m->hasPath(it->second);
 109                                         //if the user has not given a path then, add inputdir. else leave path alone.
 110                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
 111                                 }
 112
 113                                 it = parameters.find("column");
 114                                 //user has given a template file
 115                                 if(it != parameters.end()){
 116                                         path = m->hasPath(it->second);
 117                                         //if the user has not given a path then, add inputdir. else leave path alone.
 118                                         if (path == "") {       parameters["column"] = inputDir + it->second;           }
 119                                 }
 120
 121                                 //it = parameters.find("name");
 122                                 //user has given a template file
 123                                 //if(it != parameters.end()){
 124                                         //path = m->hasPath(it->second);
 125                                         //if the user has not given a path then, add inputdir. else leave path alone.
 126                                         //if (path == "") {     parameters["name"] = inputDir + it->second;             }
 127                                 //}
 128
 129                         }
 130                         //check for required parameters
 131                         listFile = validParameter.validFile(parameters, "list", true);
 132                         if (listFile == "not found") {
 133                                 listFile = m->getListFile();
 134                                 if (listFile != "") { m->mothurOut("Using " + listFile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 135                                 else {  m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
 136                         }
 137                         else if (listFile == "not open") { abort = true; }
 138                         else { m->setListFile(listFile); }
 139
 140                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 141                         if (phylipfile == "not found") { phylipfile = "";  }
 142                         else if (phylipfile == "not open") { abort = true; }
 143                         else { distFile = phylipfile; format = "phylip"; m->setPhylipFile(phylipfile);  }
 144
 145                         columnfile = validParameter.validFile(parameters, "column", true);
 146                         if (columnfile == "not found") { columnfile = ""; }
 147                         else if (columnfile == "not open") { abort = true; }
 148                         else { distFile = columnfile; format = "column";   m->setColumnFile(columnfile); }
 149
 150                         if ((phylipfile == "") && (columnfile == "")) { //is there are current file available for either of these?
 151                                 //give priority to column, then phylip
 152                                 columnfile = m->getColumnFile();
 153                                 if (columnfile != "") {  distFile = columnfile; format = "column";  m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
 154                                 else {
 155                                         phylipfile = m->getPhylipFile();
 156                                         if (phylipfile != "") {  distFile = phylipfile; format = "phylip"; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 157                                         else {
 158                                                 m->mothurOut("No valid current files. You must provide a phylip or column file."); m->mothurOutEndLine();
 159                                                 abort = true;
 160                                         }
 161                                 }
 162                         }else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When executing a sens.spec command you must enter ONLY ONE of the following: phylip or column."); m->mothurOutEndLine(); abort = true; }
 163
 164
 165                         //if the user changes the output directory command factory will send this info to us in the output parameter
 166                         outputDir = validParameter.validFile(parameters, "outputdir", false);
 167                         if (outputDir == "not found"){
 168                                 outputDir = "";
 169                                 outputDir += m->hasPath(listFile); //if user entered a file with a path then preserve it
 170                         }
 171
 172                         //check for optional parameter and set defaults
 173                         // ...at some point should added some additional type checking...
 174                         temp = validParameter.validFile(parameters, "hard", false);
 175                         if (temp == "not found"){       hard = 0;       }
 176                         else if(!m->isTrue(temp))       {       hard = 0;       }
 177                         else if(m->isTrue(temp))        {       hard = 1;       }
 178
 179 //                      temp = validParameter.validFile(parameters, "name", true);
 180 //                      if (temp == "not found")        {       nameFile = "";          }
 181 //                      else if(temp == "not open")     {       abort = true;           }
 182 //                      else                                            {       nameFile = temp;        }
 183 //                      cout << "name:\t" << nameFile << endl;
 184
 185                         temp = validParameter.validFile(parameters, "cutoff", false);           if (temp == "not found") { temp = "-1.00"; }
 186                         m->mothurConvert(temp, cutoff);
 187 //                      cout << cutoff << endl;
 188
 189                         temp = validParameter.validFile(parameters, "precision", false);        if (temp == "not found") { temp = "100"; }
 190                         m->mothurConvert(temp, precision);
 191 //                      cout << precision << endl;
 192
 193                         string label = validParameter.validFile(parameters, "label", false);
 194                         if (label == "not found") { label = ""; }
 195                         else {
 196                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 197                                 else { allLines = 1;  }
 198                         }
 199
 200                         sensSpecFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + "sensspec";
 201                 }
 202         }
 203         catch(exception& e) {
 204                 m->errorOut(e, "SensSpecCommand", "SensSpecCommand");
 205                 exit(1);
 206         }
 207 }
 208 //***************************************************************************************************************
 209
 210 int SensSpecCommand::execute(){
 211         try{
 212                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 213
 214                 setUpOutput();
 215                 outputNames.push_back(sensSpecFileName); outputTypes["sensspec"].push_back(sensSpecFileName);
 216                 if(format == "phylip")          {       processPhylip();        }
 217                 else if(format == "column")     {       processColumn();        }
 218
 219                 if (m->control_pressed) { m->mothurRemove(sensSpecFileName); return 0; }
 220
 221                 m->mothurOutEndLine();
 222                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 223                 m->mothurOut(sensSpecFileName); m->mothurOutEndLine();
 224                 m->mothurOutEndLine();
 225
 226
 227                 return 0;
 228         }
 229         catch(exception& e) {
 230                 m->errorOut(e, "SensSpecCommand", "execute");
 231                 exit(1);
 232         }
 233 }
 234
 235 //***************************************************************************************************************
 236
 237 int SensSpecCommand::processPhylip(){
 238         try{
 239                 //probably need some checking to confirm that the names in the distance matrix are the same as those in the list file
 240                 string origCutoff = "";
 241                 bool getCutoff = 0;
 242                 if(cutoff == -1.00)     {       getCutoff = 1;                                                                                                                  }
 243                 else                            {       origCutoff = toString(cutoff);  cutoff += (0.49 / double(precision));   }
 244
 245                 map<string, int> seqMap;
 246                 string seqList;
 247
 248                 InputData input(listFile, "list");
 249                 ListVector* list = input.getListVector();
 250                 string lastLabel = list->getLabel();
 251
 252                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 253                 set<string> processedLabels;
 254                 set<string> userLabels = labels;
 255
 256
 257                 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 258
 259                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  }  delete list;  return 0;  }
 260
 261                         if(allLines == 1 || labels.count(list->getLabel()) == 1){
 262
 263                                 processedLabels.insert(list->getLabel());
 264                                 userLabels.erase(list->getLabel());
 265
 266                                 //process
 267                                 fillSeqMap(seqMap, list);
 268                                 process(seqMap, list->getLabel(), getCutoff, origCutoff);
 269                         }
 270
 271                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 272                                 string saveLabel = list->getLabel();
 273
 274                                 delete list;
 275                                 list = input.getListVector(lastLabel);
 276
 277                                 processedLabels.insert(list->getLabel());
 278                                 userLabels.erase(list->getLabel());
 279
 280                                 //process
 281                                 fillSeqMap(seqMap, list);
 282                                 process(seqMap, list->getLabel(), getCutoff, origCutoff);
 283
 284                                 //restore real lastlabel to save below
 285                                 list->setLabel(saveLabel);
 286                         }
 287
 288                         lastLabel = list->getLabel();
 289
 290                         delete list;
 291                         list = input.getListVector();
 292                 }
 293
 294
 295                 //output error messages about any remaining user labels
 296                 set<string>::iterator it;
 297                 bool needToRun = false;
 298                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 299                         m->mothurOut("Your file does not include the label " + *it);
 300                         if (processedLabels.count(lastLabel) != 1) {
 301                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 302                                 needToRun = true;
 303                         }else {
 304                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 305                         }
 306                 }
 307
 308                 //run last label if you need to
 309                 if (needToRun == true)  {
 310                         if (list != NULL) {     delete list;    }
 311                         list = input.getListVector(lastLabel);
 312
 313                         //process
 314                         fillSeqMap(seqMap, list);
 315                         process(seqMap, list->getLabel(), getCutoff, origCutoff);
 316
 317                         delete list;
 318                 }
 319
 320                 return 0;
 321         }
 322         catch(exception& e) {
 323                 m->errorOut(e, "SensSpecCommand", "processPhylip");
 324                 exit(1);
 325         }
 326 }
 327 //***************************************************************************************************************
 328 int SensSpecCommand::fillSeqMap(map<string, int>& seqMap, ListVector*& list){
 329         try {
 330                 //for each otu
 331                 for(int i=0;i<list->getNumBins();i++){
 332
 333                         if (m->control_pressed) { return 0; }
 334
 335                         string seqList = list->get(i);
 336                         int seqListLength = seqList.length();
 337                         string seqName = "";
 338
 339                         //parse bin by name, mapping each name to its otu number
 340                         for(int j=0;j<seqListLength;j++){
 341
 342                                 if(seqList[j] == ','){
 343                                         seqMap[seqName] = i;
 344                                         seqName = "";
 345                                 }
 346                                 else{
 347                                         seqName += seqList[j];
 348                                 }
 349
 350                         }
 351                         seqMap[seqName] = i;
 352                 }
 353
 354                 return 0;
 355         }
 356         catch(exception& e) {
 357                 m->errorOut(e, "SensSpecCommand", "fillSeqMap");
 358                 exit(1);
 359         }
 360 }
 361 //***************************************************************************************************************
 362 int SensSpecCommand::fillSeqPairSet(set<string>& seqPairSet, ListVector*& list){
 363         try {
 364                 int numSeqs = 0;
 365
 366                 //for each otu
 367                 for(int i=0;i<list->getNumBins();i++){
 368
 369                         if (m->control_pressed) { return 0; }
 370
 371                         vector<string> seqNameVector;
 372                         string bin = list->get(i);
 373                         m->splitAtComma(bin, seqNameVector);
 374
 375                         numSeqs += seqNameVector.size();
 376
 377                         for(int j=0;j<seqNameVector.size();j++){
 378                                 string seqPairString = "";
 379                                 for(int k=0;k<j;k++){
 380                                         if(seqNameVector[j] < seqNameVector[k]) {       seqPairString = seqNameVector[j] + '\t' + seqNameVector[k];     }
 381                                         else                                                                    {       seqPairString = seqNameVector[k] + '\t' + seqNameVector[j];     }
 382                                         seqPairSet.insert(seqPairString);
 383                                 }
 384                         }
 385                 }
 386
 387                 return numSeqs;
 388         }
 389         catch(exception& e) {
 390                 m->errorOut(e, "SensSpecCommand", "fillSeqMap");
 391                 exit(1);
 392         }
 393 }
 394 //***************************************************************************************************************
 395 int SensSpecCommand::process(map<string, int>& seqMap, string label, bool& getCutoff, string& origCutoff){
 396         try {
 397
 398                 int lNumSeqs = seqMap.size();
 399                 int pNumSeqs = 0;
 400
 401                 ifstream phylipFile;
 402                 m->openInputFile(distFile, phylipFile);
 403                 phylipFile >> pNumSeqs;
 404                 if(pNumSeqs != lNumSeqs){       m->mothurOut("numSeq mismatch!\n"); m->control_pressed = true; }
 405
 406                 string seqName;
 407                 double distance;
 408                 vector<int> otuIndices(lNumSeqs, -1);
 409
 410                 truePositives = 0;
 411                 falsePositives = 0;
 412                 trueNegatives = 0;
 413                 falseNegatives = 0;
 414
 415                 if(getCutoff == 1){
 416                         if(label != "unique"){
 417                                 origCutoff = label;
 418                                 convert(label, cutoff);
 419                                 if(hard == 0){  cutoff += (0.49 / double(precision));   }
 420                         }
 421                         else{
 422                                 origCutoff = "unique";
 423                                 cutoff = 0.0000;
 424                         }
 425                 }
 426
 427                 m->mothurOut(label); m->mothurOutEndLine();
 428
 429                 for(int i=0;i<lNumSeqs;i++){
 430
 431                         if (m->control_pressed) { return 0; }
 432
 433                         phylipFile >> seqName;
 434                         otuIndices[i] = seqMap[seqName];
 435
 436                         for(int j=0;j<i;j++){
 437                                 phylipFile >> distance;
 438
 439                                 if(distance <= cutoff){
 440                                         if(otuIndices[i] == otuIndices[j])      {       truePositives++;        }
 441                                         else                                                            {       falseNegatives++;       }
 442                                 }
 443                                 else{
 444                                         if(otuIndices[i] == otuIndices[j])      {       falsePositives++;       }
 445                                         else                                                            {       trueNegatives++;        }
 446                                 }
 447                         }
 448                 }
 449                 phylipFile.close();
 450
 451                 outputStatistics(label, origCutoff);
 452
 453                 return 0;
 454         }
 455         catch(exception& e) {
 456                 m->errorOut(e, "SensSpecCommand", "process");
 457                 exit(1);
 458         }
 459 }
 460 //***************************************************************************************************************
 461 int SensSpecCommand::process(set<string>& seqPairSet, string label, bool& getCutoff, string& origCutoff, int numSeqs){
 462         try {
 463                 int numDists = (numSeqs * (numSeqs-1) / 2);
 464
 465                 ifstream columnFile;
 466                 m->openInputFile(distFile, columnFile);
 467                 string seqNameA, seqNameB, seqPairString;
 468                 double distance;
 469
 470                 truePositives = 0;
 471                 falsePositives = 0;
 472                 trueNegatives = numDists;
 473                 falseNegatives = 0;
 474
 475                 if(getCutoff == 1){
 476                         if(label != "unique"){
 477                                 origCutoff = label;
 478                                 convert(label, cutoff);
 479                                 if(hard == 0){  cutoff += (0.49 / double(precision));   }
 480                         }
 481                         else{
 482                                 origCutoff = "unique";
 483                                 cutoff = 0.0000;
 484                         }
 485                 }
 486
 487                 m->mothurOut(label); m->mothurOutEndLine();
 488
 489                 while(columnFile){
 490                         columnFile >> seqNameA >> seqNameB >> distance;
 491                         if(seqNameA < seqNameB) {       seqPairString = seqNameA + '\t' + seqNameB;     }
 492                         else                                    {       seqPairString = seqNameB + '\t' + seqNameA;     }
 493
 494                         set<string>::iterator it = seqPairSet.find(seqPairString);
 495
 496                         if(distance <= cutoff){
 497                                 if(it != seqPairSet.end()){
 498                                         truePositives++;
 499                                         seqPairSet.erase(it);
 500                                 }
 501                                 else{
 502                                         falseNegatives++;
 503                                 }
 504                                 trueNegatives--;
 505                         }
 506                         else if(it != seqPairSet.end()){
 507                                 falsePositives++;
 508                                 trueNegatives--;
 509                                 seqPairSet.erase(it);
 510                         }
 511
 512                         m->gobble(columnFile);
 513                 }
 514                 falsePositives += seqPairSet.size();
 515
 516                 outputStatistics(label, origCutoff);
 517
 518
 519                 return 0;
 520         }
 521         catch(exception& e) {
 522                 m->errorOut(e, "SensSpecCommand", "process");
 523                 exit(1);
 524         }
 525 }
 526 //***************************************************************************************************************
 527
 528 int SensSpecCommand::processColumn(){
 529         try{
 530                 string origCutoff = "";
 531                 bool getCutoff = 0;
 532                 if(cutoff == -1.00)     {       getCutoff = 1;                                                                                                                  }
 533                 else                            {       origCutoff = toString(cutoff);  cutoff += (0.49 / double(precision));   }
 534
 535                 set<string> seqPairSet;
 536                 int numSeqs = 0;
 537
 538                 InputData input(listFile, "list");
 539                 ListVector* list = input.getListVector();
 540                 string lastLabel = list->getLabel();
 541
 542                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 543                 set<string> processedLabels;
 544                 set<string> userLabels = labels;
 545
 546
 547                 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 548
 549                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  }  delete list;  return 0;  }
 550
 551                         if(allLines == 1 || labels.count(list->getLabel()) == 1){
 552
 553                                 processedLabels.insert(list->getLabel());
 554                                 userLabels.erase(list->getLabel());
 555
 556                                 //process
 557                                 numSeqs = fillSeqPairSet(seqPairSet, list);
 558                                 process(seqPairSet, list->getLabel(), getCutoff, origCutoff, numSeqs);
 559                         }
 560
 561                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 562                                 string saveLabel = list->getLabel();
 563
 564                                 delete list;
 565                                 list = input.getListVector(lastLabel);
 566
 567                                 processedLabels.insert(list->getLabel());
 568                                 userLabels.erase(list->getLabel());
 569
 570                                 //process
 571                                 numSeqs = fillSeqPairSet(seqPairSet, list);
 572                                 process(seqPairSet, list->getLabel(), getCutoff, origCutoff, numSeqs);
 573
 574                                 //restore real lastlabel to save below
 575                                 list->setLabel(saveLabel);
 576                         }
 577
 578                         lastLabel = list->getLabel();
 579
 580                         delete list;
 581                         list = input.getListVector();
 582                 }
 583
 584
 585                 //output error messages about any remaining user labels
 586                 set<string>::iterator it;
 587                 bool needToRun = false;
 588                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 589                         m->mothurOut("Your file does not include the label " + *it);
 590                         if (processedLabels.count(lastLabel) != 1) {
 591                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 592                                 needToRun = true;
 593                         }else {
 594                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 595                         }
 596                 }
 597
 598                 //run last label if you need to
 599                 if (needToRun == true)  {
 600                         if (list != NULL) {     delete list;    }
 601                         list = input.getListVector(lastLabel);
 602
 603                         //process
 604                         numSeqs = fillSeqPairSet(seqPairSet, list);
 605                         delete list;
 606                         process(seqPairSet, list->getLabel(), getCutoff, origCutoff, numSeqs);
 607                 }
 608
 609                 return 0;
 610         }
 611         catch(exception& e) {
 612                 m->errorOut(e, "SensSpecCommand", "processColumn");
 613                 exit(1);
 614         }
 615 }
 616
 617 //***************************************************************************************************************
 618
 619 void SensSpecCommand::setUpOutput(){
 620         try{
 621                 ofstream sensSpecFile;
 622                 m->openOutputFile(sensSpecFileName, sensSpecFile);
 623
 624                 sensSpecFile << "label\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n";
 625
 626                 sensSpecFile.close();
 627         }
 628         catch(exception& e) {
 629                 m->errorOut(e, "SensSpecCommand", "setUpOutput");
 630                 exit(1);
 631         }
 632 }
 633
 634 //***************************************************************************************************************
 635
 636 void SensSpecCommand::outputStatistics(string label, string cutoff){
 637         try{
 638                 double tp = (double) truePositives;
 639                 double fp = (double) falsePositives;
 640                 double tn = (double) trueNegatives;
 641                 double fn = (double) falseNegatives;
 642
 643                 double p = tp + fn;
 644                 double n = fp + tn;
 645                 double pPrime = tp + fp;
 646                 double nPrime = tn + fn;
 647
 648                 double sensitivity = tp / p;
 649                 double specificity = tn / n;
 650                 double positivePredictiveValue = tp / pPrime;
 651                 double negativePredictiveValue = tn / nPrime;
 652                 double falseDiscoveryRate = fp / pPrime;
 653
 654                 double accuracy = (tp + tn) / (p + n);
 655                 double matthewsCorrCoef = (tp * tn - fp * fn) / sqrt(p * n * pPrime * nPrime);  if(p == 0 || n == 0){   matthewsCorrCoef = 0;   }
 656                 double f1Score = 2.0 * tp / (p + pPrime);
 657
 658
 659                 if(p == 0)                      {       sensitivity = 0;        matthewsCorrCoef = 0;   }
 660                 if(n == 0)                      {       specificity = 0;        matthewsCorrCoef = 0;   }
 661                 if(p + n == 0)          {       accuracy = 0;                                                           }
 662                 if(p + pPrime == 0)     {       f1Score = 0;                                                            }
 663                 if(pPrime == 0)         {       positivePredictiveValue = 0;    falseDiscoveryRate = 0; matthewsCorrCoef = 0;   }
 664                 if(nPrime == 0)         {       negativePredictiveValue = 0;    matthewsCorrCoef = 0;                                                   }
 665
 666                 ofstream sensSpecFile;
 667                 m->openOutputFileAppend(sensSpecFileName, sensSpecFile);
 668
 669                 sensSpecFile << label << '\t' << cutoff << '\t';
 670                 sensSpecFile << truePositives << '\t' << trueNegatives << '\t' << falsePositives << '\t' << falseNegatives << '\t';
 671                 sensSpecFile << setprecision(4);
 672                 sensSpecFile << sensitivity << '\t' << specificity << '\t' << positivePredictiveValue << '\t' << negativePredictiveValue << '\t';
 673                 sensSpecFile << falseDiscoveryRate << '\t' << accuracy << '\t' << matthewsCorrCoef << '\t' << f1Score << endl;
 674
 675                 sensSpecFile.close();
 676         }
 677         catch(exception& e) {
 678                 m->errorOut(e, "SensSpecCommand", "outputStatistics");
 679                 exit(1);
 680         }
 681 }
 682
 683 //***************************************************************************************************************
 684
 685
 686