summarysharedcommand.cpp

   1 /*
   2  *  summarysharedcommand.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/2/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "summarysharedcommand.h"
  11 #include "sharedchao1.h"
  12 #include "sharedace.h"
  13 #include "sharedjabund.h"
  14 #include "sharedsorabund.h"
  15 #include "sharedjclass.h"
  16 #include "sharedsorclass.h"
  17 #include "sharedjest.h"
  18 #include "sharedsorest.h"
  19 #include "sharedthetayc.h"
  20 #include "sharedthetan.h"
  21
  22 //**********************************************************************************************************************
  23
  24 SummarySharedCommand::SummarySharedCommand(){
  25         try {
  26                 globaldata = GlobalData::getInstance();
  27
  28                 int i;
  29                 for (i=0; i<globaldata->sharedSummaryEstimators.size(); i++) {
  30                         if (globaldata->sharedSummaryEstimators[i] == "sharedChao") {
  31                                 sumCalculators.push_back(new SharedChao1());
  32                         }else if (globaldata->sharedSummaryEstimators[i] == "sharedAce") {
  33                                 sumCalculators.push_back(new SharedAce());
  34                         }else if (globaldata->sharedSummaryEstimators[i] == "sharedJabund") {
  35                                 sumCalculators.push_back(new SharedJAbund());
  36                         }else if (globaldata->sharedSummaryEstimators[i] == "sharedSorensonAbund") {
  37                                 sumCalculators.push_back(new SharedSorAbund());
  38                         }else if (globaldata->sharedSummaryEstimators[i] == "sharedJclass") {
  39                                 sumCalculators.push_back(new SharedJclass());
  40                         }else if (globaldata->sharedSummaryEstimators[i] == "sharedSorClass") {
  41                                 sumCalculators.push_back(new SharedSorClass());
  42                         }else if (globaldata->sharedSummaryEstimators[i] == "sharedJest") {
  43                                 sumCalculators.push_back(new SharedJest());
  44                         }else if (globaldata->sharedSummaryEstimators[i] == "sharedSorEst") {
  45                                 sumCalculators.push_back(new SharedSorEst());
  46                         }else if (globaldata->sharedSummaryEstimators[i] == "SharedThetaYC") {
  47                                 sumCalculators.push_back(new SharedThetaYC());
  48                         }else if (globaldata->sharedSummaryEstimators[i] == "SharedThetaN") {
  49                                 sumCalculators.push_back(new SharedThetaN());
  50                         }
  51                 }
  52         }
  53         catch(exception& e) {
  54                 cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function SummarySharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  55                 exit(1);
  56         }
  57         catch(...) {
  58                 cout << "An unknown error has occurred in the SummarySharedCommand class function SummarySharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  59                 exit(1);
  60         }
  61 }
  62 //**********************************************************************************************************************
  63
  64 SummarySharedCommand::~SummarySharedCommand(){
  65         delete input;
  66         delete read;
  67 }
  68
  69 //**********************************************************************************************************************
  70
  71 int SummarySharedCommand::execute(){
  72         try {
  73                 outputFileName = ((getRootName(globaldata->inputFileName)) + "sharedSummary");
  74                 openOutputFile(outputFileName, outputFileHandle);
  75
  76                 read = new ReadPhilFile(globaldata->inputFileName);
  77                 read->read(&*globaldata);
  78
  79                 outputFileHandle << '\t' << '\t' << '\t' << '\t'; //pads file for labels and groupnames
  80                 for(int i=0;i<sumCalculators.size();i++){
  81                         outputFileHandle << '\t' << sumCalculators[i]->getName();
  82                 }
  83                 outputFileHandle << endl;
  84
  85                 list = globaldata->glist;
  86                 input = globaldata->ginput;
  87                 order = list->getSharedOrderVector();
  88                 getGroupComb();
  89
  90                 int count = 1;
  91                 while(order != NULL){
  92
  93                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
  94
  95                                 cout << order->getLabel() << '\t' << count << endl;
  96                                 getSharedVectors();  //fills group vectors from order vector.
  97
  98                                 //randomize group order
  99                                 if (globaldata->getJumble() == "1") { random_shuffle(lookup.begin(), lookup.end()); }
 100
 101                                 int n = 1;
 102                                 for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
 103                                         for (int l = n; l < lookup.size(); l++) {
 104                                                 outputFileHandle << order->getLabel() << '\t' << groupComb[n-1] << '\t'; //print out label and group
 105                                                 for(int i=0;i<sumCalculators.size();i++){
 106                                                         sumCalculators[i]->getValues(lookup[k], lookup[l]); //saves the calculator outputs
 107                                                         outputFileHandle << '\t';
 108                                                         sumCalculators[i]->print(outputFileHandle);
 109                                                 }
 110                                                 outputFileHandle << endl;
 111                                         }
 112                                         n++;
 113                                 }
 114                         }
 115
 116                         list = input->getListVector(); //get new list vector to process
 117                         if (list != NULL) {
 118                                 order = list->getSharedOrderVector(); //gets new order vector with group info.
 119                                 count++;
 120                         }else {
 121                                 break;
 122                         }
 123                 }
 124
 125                 return 0;
 126         }
 127         catch(exception& e) {
 128                 cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 129                 exit(1);
 130         }
 131         catch(...) {
 132                 cout << "An unknown error has occurred in the SummarySharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 133                 exit(1);
 134         }
 135 }
 136
 137 //**********************************************************************************************************************
 138
 139 void SummarySharedCommand::getSharedVectors(){
 140 try {
 141                 lookup.clear();
 142                 //create and initialize vector of sharedvectors, one for each group
 143                 for (int i = 0; i < globaldata->gGroupmap->getNumGroups(); i++) {
 144                         SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
 145                         temp->setLabel(order->getLabel());
 146                         temp->setGroup(globaldata->gGroupmap->namesOfGroups[i]);
 147                         lookup.push_back(temp);
 148                 }
 149
 150                 int numSeqs = order->size();
 151                 //sample all the members
 152                 for(int i=0;i<numSeqs;i++){
 153                         //get first sample
 154                         individual chosen = order->get(i);
 155                         int abundance;
 156
 157                         //set info for sharedvector in chosens group
 158                         for (int j = 0; j < lookup.size(); j++) {
 159                                 if (chosen.group == lookup[j]->getGroup()) {
 160                                          abundance = lookup[j]->getAbundance(chosen.bin);
 161                                          lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
 162                                          break;
 163                                 }
 164                         }
 165
 166                 }
 167         }
 168         catch(exception& e) {
 169                 cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 170                 exit(1);
 171         }
 172         catch(...) {
 173                 cout << "An unknown error has occurred in the SummarySharedCommand class function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 174                 exit(1);
 175         }
 176
 177 }
 178
 179 /**************************************************************************************/
 180 void SummarySharedCommand::getGroupComb() {
 181         try {
 182                 string group;
 183
 184                 int n = 1;
 185                 for (int i = 0; i < (globaldata->gGroupmap->getNumGroups() - 1); i++) {
 186                         for (int l = n; l < globaldata->gGroupmap->getNumGroups(); l++) {
 187                                 group = globaldata->gGroupmap->namesOfGroups[i] + globaldata->gGroupmap->namesOfGroups[l];
 188                                 groupComb.push_back(group);
 189                         }
 190                         n++;
 191                 }
 192         }
 193         catch(exception& e) {
 194                 cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function getGroupComb. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 195                 exit(1);
 196         }
 197         catch(...) {
 198                 cout << "An unknown error has occurred in the SummarySharedCommand class function getGroupComb. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 199                 exit(1);
 200         }
 201
 202 }
 203