matrixoutputcommand.cpp

   1 /*
   2  *  matrixoutputcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 5/20/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "matrixoutputcommand.h"
  11 #include "sharedjabund.h"
  12 #include "sharedsorabund.h"
  13 #include "sharedjclass.h"
  14 #include "sharedsorclass.h"
  15 #include "sharedjest.h"
  16 #include "sharedsorest.h"
  17 #include "sharedthetayc.h"
  18 #include "sharedthetan.h"
  19 #include "sharedmorisitahorn.h"
  20 #include "sharedbraycurtis.h"
  21
  22
  23 //**********************************************************************************************************************
  24
  25 MatrixOutputCommand::MatrixOutputCommand(){
  26         try {
  27                 globaldata = GlobalData::getInstance();
  28                 validCalculator = new ValidCalculators();
  29
  30                 int i;
  31                 for (i=0; i<globaldata->Estimators.size(); i++) {
  32                         if (validCalculator->isValidCalculator("matrix", globaldata->Estimators[i]) == true) {
  33                                 if (globaldata->Estimators[i] == "jabund") {
  34                                         matrixCalculators.push_back(new JAbund());
  35                                 }else if (globaldata->Estimators[i] == "sorabund") {
  36                                         matrixCalculators.push_back(new SorAbund());
  37                                 }else if (globaldata->Estimators[i] == "jclass") {
  38                                         matrixCalculators.push_back(new Jclass());
  39                                 }else if (globaldata->Estimators[i] == "sorclass") {
  40                                         matrixCalculators.push_back(new SorClass());
  41                                 }else if (globaldata->Estimators[i] == "jest") {
  42                                         matrixCalculators.push_back(new Jest());
  43                                 }else if (globaldata->Estimators[i] == "sorest") {
  44                                         matrixCalculators.push_back(new SorEst());
  45                                 }else if (globaldata->Estimators[i] == "thetayc") {
  46                                         matrixCalculators.push_back(new ThetaYC());
  47                                 }else if (globaldata->Estimators[i] == "thetan") {
  48                                         matrixCalculators.push_back(new ThetaN());
  49                                 }else if (globaldata->Estimators[i] == "morisitahorn") {
  50                                         matrixCalculators.push_back(new MorHorn());
  51                                 }else if (globaldata->Estimators[i] == "braycurtis") {
  52                                         matrixCalculators.push_back(new BrayCurtis());
  53                                 }
  54                         }
  55                 }
  56
  57                 //reset calc for next command
  58                 globaldata->setCalc("");
  59
  60         }
  61         catch(exception& e) {
  62                 cout << "Standard Error: " << e.what() << " has occurred in the MatrixOutputCommand class Function MatrixOutputCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  63                 exit(1);
  64         }
  65         catch(...) {
  66                 cout << "An unknown error has occurred in the MatrixOutputCommand class function MatrixOutputCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  67                 exit(1);
  68         }
  69 }
  70 //**********************************************************************************************************************
  71
  72 MatrixOutputCommand::~MatrixOutputCommand(){
  73         delete input;
  74         delete read;
  75 }
  76
  77 //**********************************************************************************************************************
  78
  79 int MatrixOutputCommand::execute(){
  80         try {
  81                 int count = 1;
  82
  83                 //if the users entered no valid calculators don't execute command
  84                 if (matrixCalculators.size() == 0) { cout << "No valid calculators." << endl; return 0; }
  85
  86                 //you have groups
  87                 read = new ReadOTUFile(globaldata->inputFileName);
  88                 read->read(&*globaldata);
  89
  90                 input = globaldata->ginput;
  91                 lookup = input->getSharedRAbundVectors();
  92                 vector<SharedRAbundVector*> lastLookup = lookup;
  93
  94                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
  95                 set<string> processedLabels;
  96                 set<string> userLabels = globaldata->labels;
  97                 set<int> userLines = globaldata->lines;
  98
  99                 if (lookup.size() < 2) { cout << "You have not provided enough valid groups.  I cannot run the command." << endl; return 0;}
 100
 101                 numGroups = globaldata->Groups.size();
 102
 103                 //as long as you are not at the end of the file or done wih the lines you want
 104                 while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 105
 106                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
 107                                 cout << lookup[0]->getLabel() << '\t' << count << endl;
 108                                 process(lookup);
 109
 110                                 processedLabels.insert(lookup[0]->getLabel());
 111                                 userLabels.erase(lookup[0]->getLabel());
 112                                 userLines.erase(count);
 113                         }
 114
 115                         if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
 116                                 cout << lastLookup[0]->getLabel() << '\t' << count << endl;
 117                                 process(lastLookup);
 118
 119                                 processedLabels.insert(lastLookup[0]->getLabel());
 120                                 userLabels.erase(lastLookup[0]->getLabel());
 121                         }
 122
 123                         //prevent memory leak
 124                         if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  } }
 125                         lastLookup = lookup;
 126
 127                         //get next line to process
 128                         lookup = input->getSharedRAbundVectors();
 129                         count++;
 130                 }
 131
 132                 //output error messages about any remaining user labels
 133                 set<string>::iterator it;
 134                 bool needToRun = false;
 135                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 136                         cout << "Your file does not include the label "<< *it;
 137                         if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
 138                                 cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
 139                                 needToRun = true;
 140                         }else {
 141                                 cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
 142                         }
 143                 }
 144
 145                 //run last line if you need to
 146                 if (needToRun == true)  {
 147                         cout << lastLookup[0]->getLabel() << '\t' << count << endl;
 148                         process(lastLookup);
 149                 }
 150
 151                 for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  }
 152
 153
 154                 //reset groups parameter
 155                 globaldata->Groups.clear();  globaldata->setGroups("");
 156
 157                 return 0;
 158         }
 159         catch(exception& e) {
 160                 cout << "Standard Error: " << e.what() << " has occurred in the MatrixOutputCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 161                 exit(1);
 162         }
 163         catch(...) {
 164                 cout << "An unknown error has occurred in the MatrixOutputCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 165                 exit(1);
 166         }
 167 }
 168 /***********************************************************/
 169 void MatrixOutputCommand::printSims(ostream& out) {
 170         try {
 171
 172                 //output column headers
 173                 out << simMatrix.size() << endl;
 174
 175                 for (int m = 0; m < simMatrix.size(); m++)      {
 176                         out << lookup[m]->getGroup() << '\t';
 177                         for (int n = 0; n < m; n++)     {
 178                                 out << simMatrix[m][n] << '\t';
 179                         }
 180                         out << endl;
 181                 }
 182
 183         }
 184         catch(exception& e) {
 185                 cout << "Standard Error: " << e.what() << " has occurred in the MatrixOutputCommand class Function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 186                 exit(1);
 187         }
 188         catch(...) {
 189                 cout << "An unknown error has occurred in the MatrixOutputCommand class function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 190                 exit(1);
 191         }
 192 }
 193 /***********************************************************/
 194 void MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
 195         try {
 196
 197                                 EstOutput data;
 198                                 vector<SharedRAbundVector*> subset;
 199
 200                                 //for each calculator
 201                                 for(int i = 0 ; i < matrixCalculators.size(); i++) {
 202
 203                                         //initialize simMatrix
 204                                         simMatrix.clear();
 205                                         simMatrix.resize(numGroups);
 206                                         for (int m = 0; m < simMatrix.size(); m++)      {
 207                                                 for (int j = 0; j < simMatrix.size(); j++)      {
 208                                                         simMatrix[m].push_back(0.0);
 209                                                 }
 210                                         }
 211
 212                                         for (int k = 0; k < thisLookup.size(); k++) {
 213                                                 for (int l = k; l < thisLookup.size(); l++) {
 214                                                         if (k != l) { //we dont need to similiarity of a groups to itself
 215                                                                 //get estimated similarity between 2 groups
 216
 217                                                                 subset.clear(); //clear out old pair of sharedrabunds
 218                                                                 //add new pair of sharedrabunds
 219                                                                 subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
 220
 221                                                                 data = matrixCalculators[i]->getValues(subset); //saves the calculator outputs
 222                                                                 //save values in similarity matrix
 223                                                                 simMatrix[k][l] = 1.0 - data[0];  //convert similiarity to distance
 224                                                                 simMatrix[l][k] = 1.0 - data[0];  //convert similiarity to distance
 225                                                         }
 226                                                 }
 227                                         }
 228
 229                                         exportFileName = getRootName(globaldata->inputFileName) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".dist";
 230                                         openOutputFile(exportFileName, out);
 231                                         printSims(out);
 232                                         out.close();
 233
 234                                 }
 235
 236
 237
 238         }
 239         catch(exception& e) {
 240                 cout << "Standard Error: " << e.what() << " has occurred in the MatrixOutputCommand class Function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 241                 exit(1);
 242         }
 243         catch(...) {
 244                 cout << "An unknown error has occurred in the MatrixOutputCommand class function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 245                 exit(1);
 246         }
 247 }
 248 /***********************************************************/
 249
 250
 251