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                 EstOutput data;
  83                 vector<SharedRAbundVector*> subset;
  84
  85                 //if the users entered no valid calculators don't execute command
  86                 if (matrixCalculators.size() == 0) { cout << "No valid calculators." << endl; return 0; }
  87
  88                 //you have groups
  89                 read = new ReadOTUFile(globaldata->inputFileName);
  90                 read->read(&*globaldata);
  91
  92                 input = globaldata->ginput;
  93                 lookup = input->getSharedRAbundVectors();
  94
  95                 if (lookup.size() < 2) { cout << "You have not provided enough valid groups.  I cannot run the command." << endl; return 0;}
  96
  97                 numGroups = globaldata->Groups.size();
  98
  99                 while(lookup[0] != NULL){
 100
 101                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
 102
 103                                 cout << lookup[0]->getLabel() << '\t' << count << endl;
 104
 105                                 //for each calculator
 106                                 for(int i = 0 ; i < matrixCalculators.size(); i++) {
 107
 108                                         //initialize simMatrix
 109                                         simMatrix.clear();
 110                                         simMatrix.resize(numGroups);
 111                                         for (int m = 0; m < simMatrix.size(); m++)      {
 112                                                 for (int j = 0; j < simMatrix.size(); j++)      {
 113                                                         simMatrix[m].push_back(0.0);
 114                                                 }
 115                                         }
 116
 117                                         for (int k = 0; k < lookup.size(); k++) {
 118                                                 for (int l = k; l < lookup.size(); l++) {
 119                                                         if (k != l) { //we dont need to similiarity of a groups to itself
 120                                                                 //get estimated similarity between 2 groups
 121
 122                                                                 subset.clear(); //clear out old pair of sharedrabunds
 123                                                                 //add new pair of sharedrabunds
 124                                                                 subset.push_back(lookup[k]); subset.push_back(lookup[l]);
 125
 126                                                                 data = matrixCalculators[i]->getValues(subset); //saves the calculator outputs
 127                                                                 //save values in similarity matrix
 128                                                                 simMatrix[k][l] = 1.0 - data[0];  //convert similiarity to distance
 129                                                                 simMatrix[l][k] = 1.0 - data[0];  //convert similiarity to distance
 130                                                         }
 131                                                 }
 132                                         }
 133
 134                                         exportFileName = getRootName(globaldata->inputFileName) + matrixCalculators[i]->getName() + "." + lookup[0]->getLabel() + ".dist";
 135                                         openOutputFile(exportFileName, out);
 136                                         printSims(out);
 137                                         out.close();
 138
 139                                 }
 140                         }
 141
 142                         //prevent memory leak
 143                         for (int i = 0; i < lookup.size(); i++) {       delete lookup[i];       }
 144
 145                         //get next line to process
 146                         lookup = input->getSharedRAbundVectors();
 147                         count++;
 148                 }
 149
 150                 //reset groups parameter
 151                 globaldata->Groups.clear();  globaldata->setGroups("");
 152
 153                 return 0;
 154         }
 155         catch(exception& e) {
 156                 cout << "Standard Error: " << e.what() << " has occurred in the MatrixOutputCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 157                 exit(1);
 158         }
 159         catch(...) {
 160                 cout << "An unknown error has occurred in the MatrixOutputCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 161                 exit(1);
 162         }
 163 }
 164 /***********************************************************/
 165 void MatrixOutputCommand::printSims(ostream& out) {
 166         try {
 167
 168                 //output column headers
 169                 out << simMatrix.size() << endl;
 170
 171                 for (int m = 0; m < simMatrix.size(); m++)      {
 172                         out << lookup[m]->getGroup() << '\t';
 173                         for (int n = 0; n < m; n++)     {
 174                                 out << simMatrix[m][n] << '\t';
 175                         }
 176                         out << endl;
 177                 }
 178
 179         }
 180         catch(exception& e) {
 181                 cout << "Standard Error: " << e.what() << " has occurred in the MatrixOutputCommand class Function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 182                 exit(1);
 183         }
 184         catch(...) {
 185                 cout << "An unknown error has occurred in the MatrixOutputCommand class function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 186                 exit(1);
 187         }
 188 }
 189 /***********************************************************/
 190
 191