treegroupscommand.cpp

   1 /*
   2  *  treegroupscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 4/8/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "treegroupscommand.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 TreeGroupCommand::TreeGroupCommand(){
  26         try {
  27                 globaldata = GlobalData::getInstance();
  28                 format = globaldata->getFormat();
  29                 validCalculator = new ValidCalculators();
  30                 util = new SharedUtil();
  31
  32                 int i;
  33                 for (i=0; i<globaldata->Estimators.size(); i++) {
  34                         if (validCalculator->isValidCalculator("treegroup", globaldata->Estimators[i]) == true) {
  35                                 if (globaldata->Estimators[i] == "jabund") {
  36                                         treeCalculators.push_back(new JAbund());
  37                                 }else if (globaldata->Estimators[i] == "sorabund") {
  38                                         treeCalculators.push_back(new SorAbund());
  39                                 }else if (globaldata->Estimators[i] == "jclass") {
  40                                         treeCalculators.push_back(new Jclass());
  41                                 }else if (globaldata->Estimators[i] == "sorclass") {
  42                                         treeCalculators.push_back(new SorClass());
  43                                 }else if (globaldata->Estimators[i] == "jest") {
  44                                         treeCalculators.push_back(new Jest());
  45                                 }else if (globaldata->Estimators[i] == "sorest") {
  46                                         treeCalculators.push_back(new SorEst());
  47                                 }else if (globaldata->Estimators[i] == "thetayc") {
  48                                         treeCalculators.push_back(new ThetaYC());
  49                                 }else if (globaldata->Estimators[i] == "thetan") {
  50                                         treeCalculators.push_back(new ThetaN());
  51                                 }else if (globaldata->Estimators[i] == "morisitahorn") {
  52                                         treeCalculators.push_back(new MorHorn());
  53                                 }else if (globaldata->Estimators[i] == "braycurtis") {
  54                                         treeCalculators.push_back(new BrayCurtis());
  55                                 }
  56                         }
  57                 }
  58
  59                 //reset calc for next command
  60                 globaldata->setCalc("");
  61
  62         }
  63         catch(exception& e) {
  64                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function TreeGroupCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  65                 exit(1);
  66         }
  67         catch(...) {
  68                 cout << "An unknown error has occurred in the TreeGroupCommand class function TreeGroupCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  69                 exit(1);
  70         }
  71 }
  72 //**********************************************************************************************************************
  73
  74 TreeGroupCommand::~TreeGroupCommand(){
  75         delete input;
  76         delete read;
  77         delete util;
  78 }
  79
  80 //**********************************************************************************************************************
  81
  82 int TreeGroupCommand::execute(){
  83         try {
  84                 int count = 1;
  85                 EstOutput data;
  86                 vector<SharedRAbundVector*> subset;
  87
  88                 //if the users entered no valid calculators don't execute command
  89                 if (treeCalculators.size() == 0) { return 0; }
  90
  91                 //you have groups
  92                 read = new ReadOTUFile(globaldata->inputFileName);
  93                 read->read(&*globaldata);
  94
  95                 input = globaldata->ginput;
  96                 lookup = input->getSharedRAbundVectors();
  97
  98                 if (lookup.size() < 2) { cout << "You have not provided enough valid groups.  I cannot run the command." << endl; }
  99
 100                 numGroups = globaldata->Groups.size();
 101                 groupNames = "";
 102                 for (int i = 0; i < numGroups; i++) { groupNames += globaldata->Groups[i]; }
 103
 104                 //clear globaldatas old tree names if any
 105                 globaldata->Treenames.clear();
 106
 107                 //fills globaldatas tree names
 108                 globaldata->Treenames = globaldata->Groups;
 109
 110                 //create treemap class from groupmap for tree class to use
 111                 tmap = new TreeMap();
 112                 tmap->makeSim(globaldata->gGroupmap);
 113                 globaldata->gTreemap = tmap;
 114
 115                 while(lookup[0] != NULL){
 116
 117                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
 118
 119                                 cout << lookup[0]->getLabel() << '\t' << count << endl;
 120
 121                                 //for each calculator
 122                                 for(int i = 0 ; i < treeCalculators.size(); i++) {
 123
 124                                         //initialize simMatrix
 125                                         simMatrix.clear();
 126                                         simMatrix.resize(numGroups);
 127                                         for (int m = 0; m < simMatrix.size(); m++)      {
 128                                                 for (int j = 0; j < simMatrix.size(); j++)      {
 129                                                         simMatrix[m].push_back(0.0);
 130                                                 }
 131                                         }
 132
 133                                         //initialize index
 134                                         index.clear();
 135                                         for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
 136
 137                                         //create a new filename
 138                                         outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + lookup[0]->getLabel() + ".tre";
 139
 140                                         for (int k = 0; k < lookup.size(); k++) {
 141                                                 for (int l = k; l < lookup.size(); l++) {
 142                                                         if (k != l) { //we dont need to similiarity of a groups to itself
 143                                                                 //get estimated similarity between 2 groups
 144
 145                                                                 subset.clear(); //clear out old pair of sharedrabunds
 146                                                                 //add new pair of sharedrabunds
 147                                                                 subset.push_back(lookup[k]); subset.push_back(lookup[l]);
 148
 149                                                                 data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
 150                                                                 //save values in similarity matrix
 151                                                                 simMatrix[k][l] = data[0];
 152                                                                 simMatrix[l][k] = data[0];
 153                                                         }
 154                                                 }
 155                                         }
 156
 157                                         //creates tree from similarity matrix and write out file
 158                                         createTree();
 159                                 }
 160                         }
 161
 162                         //get next line to process
 163                         lookup = input->getSharedRAbundVectors();
 164                         count++;
 165                 }
 166
 167                 //reset groups parameter
 168                 globaldata->Groups.clear();  globaldata->setGroups("");
 169
 170                 return 0;
 171         }
 172         catch(exception& e) {
 173                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 174                 exit(1);
 175         }
 176         catch(...) {
 177                 cout << "An unknown error has occurred in the TreeGroupCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 178                 exit(1);
 179         }
 180 }
 181 //**********************************************************************************************************************
 182
 183 void TreeGroupCommand::createTree(){
 184         try {
 185                 //create tree
 186                 t = new Tree();
 187
 188                 //do merges and create tree structure by setting parents and children
 189                 //there are numGroups - 1 merges to do
 190                 for (int i = 0; i < (numGroups - 1); i++) {
 191
 192                         float largest = 0.0;
 193                         int row, column;
 194                         //find largest value in sims matrix by searching lower triangle
 195                         for (int j = 1; j < simMatrix.size(); j++) {
 196                                 for (int k = 0; k < j; k++) {
 197                                         if (simMatrix[j][k] > largest) {  largest = simMatrix[j][k]; row = j; column = k;  }
 198                                 }
 199                         }
 200
 201                         //set non-leaf node info and update leaves to know their parents
 202                         //non-leaf
 203                         t->tree[numGroups + i].setChildren(index[row], index[column]);
 204
 205                         //parents
 206                         t->tree[index[row]].setParent(numGroups + i);
 207                         t->tree[index[column]].setParent(numGroups + i);
 208
 209                         //blength = distance / 2;
 210                         float blength = ((1.0 - largest) / 2);
 211
 212                         //branchlengths
 213                         t->tree[index[row]].setBranchLength(blength - t->tree[index[row]].getLengthToLeaves());
 214                         t->tree[index[column]].setBranchLength(blength - t->tree[index[column]].getLengthToLeaves());
 215
 216                         //set your length to leaves to your childs length plus branchlength
 217                         t->tree[numGroups + i].setLengthToLeaves(t->tree[index[row]].getLengthToLeaves() + t->tree[index[row]].getBranchLength());
 218
 219
 220                         //update index
 221                         index[row] = numGroups+i;
 222                         index[column] = numGroups+i;
 223
 224                         //zero out highest value that caused the merge.
 225                         simMatrix[row][column] = 0.0;
 226                         simMatrix[column][row] = 0.0;
 227
 228                         //merge values in simsMatrix
 229                         for (int n = 0; n < simMatrix.size(); n++)      {
 230                                 //row becomes merge of 2 groups
 231                                 simMatrix[row][n] = (simMatrix[row][n] + simMatrix[column][n]) / 2;
 232                                 simMatrix[n][row] = simMatrix[row][n];
 233                                 //delete column
 234                                 simMatrix[column][n] = 0.0;
 235                                 simMatrix[n][column] = 0.0;
 236                         }
 237                 }
 238
 239                 //assemble tree
 240                 t->assembleTree();
 241
 242                 //print newick file
 243                 t->createNewickFile(outputFile);
 244
 245                 //delete tree
 246                 delete t;
 247
 248         }
 249         catch(exception& e) {
 250                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 251                 exit(1);
 252         }
 253         catch(...) {
 254                 cout << "An unknown error has occurred in the TreeGroupCommand class function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 255                 exit(1);
 256         }
 257 }
 258 /***********************************************************/
 259 void TreeGroupCommand::printSims() {
 260         try {
 261                 cout << "simsMatrix" << endl;
 262                 for (int m = 0; m < simMatrix.size(); m++)      {
 263                         for (int n = 0; n < simMatrix.size(); n++)      {
 264                                 cout << simMatrix[m][n] << '\t';
 265                         }
 266                         cout << endl;
 267                 }
 268
 269         }
 270         catch(exception& e) {
 271                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 272                 exit(1);
 273         }
 274         catch(...) {
 275                 cout << "An unknown error has occurred in the TreeGroupCommand class function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 276                 exit(1);
 277         }
 278 }
 279 /***********************************************************/
 280
 281