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
  21
  22 //**********************************************************************************************************************
  23
  24 TreeGroupCommand::TreeGroupCommand(){
  25         try {
  26                 globaldata = GlobalData::getInstance();
  27                 format = globaldata->getFormat();
  28                 validCalculator = new ValidCalculators();
  29                 util = new SharedUtil();
  30
  31                 int i;
  32                 for (i=0; i<globaldata->Estimators.size(); i++) {
  33                         if (validCalculator->isValidCalculator("treegroup", globaldata->Estimators[i]) == true) {
  34                                 if (globaldata->Estimators[i] == "sharedjabund") {
  35                                         treeCalculators.push_back(new SharedJAbund());
  36                                 }else if (globaldata->Estimators[i] == "sharedsorensonabund") {
  37                                         treeCalculators.push_back(new SharedSorAbund());
  38                                 }else if (globaldata->Estimators[i] == "sharedjclass") {
  39                                         treeCalculators.push_back(new SharedJclass());
  40                                 }else if (globaldata->Estimators[i] == "sharedsorclass") {
  41                                         treeCalculators.push_back(new SharedSorClass());
  42                                 }else if (globaldata->Estimators[i] == "sharedjest") {
  43                                         treeCalculators.push_back(new SharedJest());
  44                                 }else if (globaldata->Estimators[i] == "sharedsorest") {
  45                                         treeCalculators.push_back(new SharedSorEst());
  46                                 }else if (globaldata->Estimators[i] == "sharedthetayc") {
  47                                         treeCalculators.push_back(new SharedThetaYC());
  48                                 }else if (globaldata->Estimators[i] == "sharedthetan") {
  49                                         treeCalculators.push_back(new SharedThetaN());
  50                                 }else if (globaldata->Estimators[i] == "sharedmorisitahorn") {
  51                                         treeCalculators.push_back(new SharedMorHorn());
  52                                 }
  53                         }
  54                 }
  55
  56                 //reset calc for next command
  57                 globaldata->setCalc("");
  58
  59         }
  60         catch(exception& e) {
  61                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function TreeGroupCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  62                 exit(1);
  63         }
  64         catch(...) {
  65                 cout << "An unknown error has occurred in the TreeGroupCommand class function TreeGroupCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  66                 exit(1);
  67         }
  68 }
  69 //**********************************************************************************************************************
  70
  71 TreeGroupCommand::~TreeGroupCommand(){
  72         delete input;
  73         delete read;
  74         delete util;
  75 }
  76
  77 //**********************************************************************************************************************
  78
  79 int TreeGroupCommand::execute(){
  80         try {
  81                 int count = 1;
  82                 EstOutput data;
  83
  84                 //if the users entered no valid calculators don't execute command
  85                 if (treeCalculators.size() == 0) { return 0; }
  86
  87                 if (format == "sharedfile") {
  88                         read = new ReadPhilFile(globaldata->inputFileName);
  89                         read->read(&*globaldata);
  90
  91                         input = globaldata->ginput;
  92                         order = input->getSharedOrderVector();
  93                 }else {
  94                         //you are using a list and a groupfile
  95                         read = new ReadPhilFile(globaldata->inputFileName);
  96                         read->read(&*globaldata);
  97
  98                         input = globaldata->ginput;
  99                         SharedList = globaldata->gSharedList;
 100                         order = SharedList->getSharedOrderVector();
 101                 }
 102
 103                 //set users groups
 104                 util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "treegroup");
 105                 numGroups = globaldata->Groups.size();
 106                 groupNames = "";
 107                 for (int i = 0; i < numGroups; i++) { groupNames += globaldata->Groups[i]; }
 108
 109                 //clear globaldatas old tree names if any
 110                 globaldata->Treenames.clear();
 111
 112                 //fills globaldatas tree names
 113                 globaldata->Treenames = globaldata->Groups;
 114
 115                 //create treemap class from groupmap for tree class to use
 116                 tmap = new TreeMap();
 117                 tmap->makeSim(globaldata->gGroupmap);
 118                 globaldata->gTreemap = tmap;
 119
 120                 while(order != NULL){
 121
 122                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
 123
 124                                 cout << order->getLabel() << '\t' << count << endl;
 125                                 util->getSharedVectors(globaldata->Groups, lookup, order);  //fills group vectors from order vector.
 126
 127                                 //for each calculator
 128                                 for(int i = 0 ; i < treeCalculators.size(); i++) {
 129
 130                                         //initialize simMatrix
 131                                         simMatrix.clear();
 132                                         simMatrix.resize(numGroups);
 133                                         for (int m = 0; m < simMatrix.size(); m++)      {
 134                                                 for (int j = 0; j < simMatrix.size(); j++)      {
 135                                                         simMatrix[m].push_back(0.0);
 136                                                 }
 137                                         }
 138
 139                                         //initialize index
 140                                         index.clear();
 141                                         for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
 142
 143                                         //create a new filename
 144                                         outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + order->getLabel() + groupNames + ".tre";
 145
 146                                         for (int k = 0; k < lookup.size(); k++) { // pass cdd each set of groups to commpare
 147                                                 for (int l = k; l < lookup.size(); l++) {
 148                                                         if (k != l) { //we dont need to similiarity of a groups to itself
 149                                                                 //get estimated similarity between 2 groups
 150                                                                 data = treeCalculators[i]->getValues(lookup[k], lookup[l]); //saves the calculator outputs
 151                                                                 //save values in similarity matrix
 152                                                                 simMatrix[k][l] = data[0];
 153                                                                 simMatrix[l][k] = data[0];
 154                                                         }
 155                                                 }
 156                                         }
 157
 158                                         //creates tree from similarity matrix and write out file
 159                                         createTree();
 160                                 }
 161                         }
 162
 163                         //get next line to process
 164                         if (format == "sharedfile") {
 165                                 order = input->getSharedOrderVector();
 166                         }else {
 167                                 //you are using a list and a groupfile
 168                                 SharedList = input->getSharedListVector(); //get new list vector to process
 169                                 if (SharedList != NULL) {
 170                                         order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
 171                                 }else {
 172                                         break;
 173                                 }
 174                         }
 175                         count++;
 176                 }
 177
 178                 //reset groups parameter
 179                 globaldata->Groups.clear();  globaldata->setGroups("");
 180
 181                 return 0;
 182         }
 183         catch(exception& e) {
 184                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 185                 exit(1);
 186         }
 187         catch(...) {
 188                 cout << "An unknown error has occurred in the TreeGroupCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 189                 exit(1);
 190         }
 191 }
 192 //**********************************************************************************************************************
 193
 194 void TreeGroupCommand::createTree(){
 195         try {
 196                 //create tree
 197                 t = new Tree();
 198
 199                 //do merges and create tree structure by setting parents and children
 200                 //there are numGroups - 1 merges to do
 201                 for (int i = 0; i < (numGroups - 1); i++) {
 202
 203                         float largest = 0.0;
 204                         int row, column;
 205                         //find largest value in sims matrix by searching lower triangle
 206                         for (int j = 1; j < simMatrix.size(); j++) {
 207                                 for (int k = 0; k < j; k++) {
 208                                         if (simMatrix[j][k] > largest) {  largest = simMatrix[j][k]; row = j; column = k;  }
 209                                 }
 210                         }
 211
 212                         //set non-leaf node info and update leaves to know their parents
 213                         //non-leaf
 214                         t->tree[numGroups + i].setChildren(index[row], index[column]);
 215
 216                         //parents
 217                         t->tree[index[row]].setParent(numGroups + i);
 218                         t->tree[index[column]].setParent(numGroups + i);
 219
 220                         //blength = distance / 2;
 221                         float blength = ((1.0 - largest) / 2);
 222
 223                         //branchlengths
 224                         t->tree[index[row]].setBranchLength(blength - t->tree[index[row]].getLengthToLeaves());
 225                         t->tree[index[column]].setBranchLength(blength - t->tree[index[column]].getLengthToLeaves());
 226
 227                         //set your length to leaves to your childs length plus branchlength
 228                         t->tree[numGroups + i].setLengthToLeaves(t->tree[index[row]].getLengthToLeaves() + t->tree[index[row]].getBranchLength());
 229
 230
 231                         //update index
 232                         index[row] = numGroups+i;
 233                         index[column] = numGroups+i;
 234
 235                         //zero out highest value that caused the merge.
 236                         simMatrix[row][column] = 0.0;
 237                         simMatrix[column][row] = 0.0;
 238
 239                         //merge values in simsMatrix
 240                         for (int n = 0; n < simMatrix.size(); n++)      {
 241                                 //row becomes merge of 2 groups
 242                                 simMatrix[row][n] = (simMatrix[row][n] + simMatrix[column][n]) / 2;
 243                                 simMatrix[n][row] = simMatrix[row][n];
 244                                 //delete column
 245                                 simMatrix[column][n] = 0.0;
 246                                 simMatrix[n][column] = 0.0;
 247                         }
 248                 }
 249
 250                 //assemble tree
 251                 t->assembleTree();
 252
 253                 //print newick file
 254                 t->createNewickFile(outputFile);
 255
 256                 //delete tree
 257                 delete t;
 258
 259         }
 260         catch(exception& e) {
 261                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 262                 exit(1);
 263         }
 264         catch(...) {
 265                 cout << "An unknown error has occurred in the TreeGroupCommand class function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 266                 exit(1);
 267         }
 268 }
 269 /***********************************************************/
 270 void TreeGroupCommand::printSims() {
 271         try {
 272                 cout << "simsMatrix" << endl;
 273                 for (int m = 0; m < simMatrix.size(); m++)      {
 274                         for (int n = 0; n < simMatrix.size(); n++)      {
 275                                 cout << simMatrix[m][n] << '\t';
 276                         }
 277                         cout << endl;
 278                 }
 279
 280         }
 281         catch(exception& e) {
 282                 cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 283                 exit(1);
 284         }
 285         catch(...) {
 286                 cout << "An unknown error has occurred in the TreeGroupCommand class function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 287                 exit(1);
 288         }
 289 }
 290 /***********************************************************/
 291
 292