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 "sharedsobs.h"
  12 #include "sharedchao1.h"
  13 #include "sharedace.h"
  14 #include "sharedjabund.h"
  15 #include "sharedsorabund.h"
  16 #include "sharedjclass.h"
  17 #include "sharedsorclass.h"
  18 #include "sharedjest.h"
  19 #include "sharedsorest.h"
  20 #include "sharedthetayc.h"
  21 #include "sharedthetan.h"
  22
  23 //**********************************************************************************************************************
  24
  25 SummarySharedCommand::SummarySharedCommand(){
  26         try {
  27                 globaldata = GlobalData::getInstance();
  28
  29                 int i;
  30                 for (i=0; i<globaldata->sharedSummaryEstimators.size(); i++) {
  31                         if (globaldata->sharedSummaryEstimators[i] == "sharedSobs") {
  32                                 sumCalculators.push_back(new SharedSobs());
  33                         }else if (globaldata->sharedSummaryEstimators[i] == "sharedChao") {
  34                                 sumCalculators.push_back(new SharedChao1());
  35                         }else if (globaldata->sharedSummaryEstimators[i] == "sharedAce") {
  36                                 sumCalculators.push_back(new SharedAce());
  37                         }else if (globaldata->sharedSummaryEstimators[i] == "sharedJabund") {
  38                                 sumCalculators.push_back(new SharedJAbund());
  39                         }else if (globaldata->sharedSummaryEstimators[i] == "sharedSorensonAbund") {
  40                                 sumCalculators.push_back(new SharedSorAbund());
  41                         }else if (globaldata->sharedSummaryEstimators[i] == "sharedJclass") {
  42                                 sumCalculators.push_back(new SharedJclass());
  43                         }else if (globaldata->sharedSummaryEstimators[i] == "sharedSorClass") {
  44                                 sumCalculators.push_back(new SharedSorClass());
  45                         }else if (globaldata->sharedSummaryEstimators[i] == "sharedJest") {
  46                                 sumCalculators.push_back(new SharedJest());
  47                         }else if (globaldata->sharedSummaryEstimators[i] == "sharedSorEst") {
  48                                 sumCalculators.push_back(new SharedSorEst());
  49                         }else if (globaldata->sharedSummaryEstimators[i] == "SharedThetaYC") {
  50                                 sumCalculators.push_back(new SharedThetaYC());
  51                         }else if (globaldata->sharedSummaryEstimators[i] == "SharedThetaN") {
  52                                 sumCalculators.push_back(new SharedThetaN());
  53                         }
  54                 }
  55         }
  56         catch(exception& e) {
  57                 cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function SummarySharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  58                 exit(1);
  59         }
  60         catch(...) {
  61                 cout << "An unknown error has occurred in the SummarySharedCommand class function SummarySharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  62                 exit(1);
  63         }
  64 }
  65 //**********************************************************************************************************************
  66
  67 SummarySharedCommand::~SummarySharedCommand(){
  68         delete input;
  69         delete read;
  70 }
  71
  72 //**********************************************************************************************************************
  73
  74 int SummarySharedCommand::execute(){
  75         try {
  76                 outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary");
  77                 openOutputFile(outputFileName, outputFileHandle);
  78
  79                 read = new ReadPhilFile(globaldata->inputFileName);
  80                 read->read(&*globaldata);
  81
  82                 outputFileHandle << "label" <<'\t' << "comparison" << '\t';
  83                 for(int i=0;i<sumCalculators.size();i++){
  84                         outputFileHandle << '\t' << sumCalculators[i]->getName();
  85                 }
  86                 outputFileHandle << endl;
  87
  88                 SharedList = globaldata->gSharedList;
  89                 input = globaldata->ginput;
  90                 order = SharedList->getSharedOrderVector();
  91                 getGroupComb();
  92
  93                 int count = 1;
  94                 while(order != NULL){
  95
  96                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
  97
  98                                 cout << order->getLabel() << '\t' << count << endl;
  99                                 getSharedVectors();  //fills group vectors from order vector.
 100
 101                                 //randomize group order
 102                                 if (globaldata->getJumble() == "1") { random_shuffle(lookup.begin(), lookup.end()); }
 103
 104                                 int n = 1;
 105                                 for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
 106                                         for (int l = n; l < lookup.size(); l++) {
 107                                                 outputFileHandle << order->getLabel() << '\t' << groupComb[n-1] << '\t' << '\t'; //print out label and group
 108                                                 for(int i=0;i<sumCalculators.size();i++){
 109                                                         sumCalculators[i]->getValues(lookup[k], lookup[l]); //saves the calculator outputs
 110                                                         outputFileHandle << '\t';
 111                                                         sumCalculators[i]->print(outputFileHandle);
 112                                                 }
 113                                                 outputFileHandle << endl;
 114                                         }
 115                                         n++;
 116                                 }
 117                         }
 118
 119                         SharedList = input->getSharedListVector(); //get new list vector to process
 120                         if (SharedList != NULL) {
 121                                 order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
 122                                 count++;
 123                         }else {
 124                                 break;
 125                         }
 126                 }
 127
 128                 return 0;
 129         }
 130         catch(exception& e) {
 131                 cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 132                 exit(1);
 133         }
 134         catch(...) {
 135                 cout << "An unknown error has occurred in the SummarySharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 136                 exit(1);
 137         }
 138 }
 139
 140 //**********************************************************************************************************************
 141
 142 void SummarySharedCommand::getSharedVectors(){
 143 try {
 144                 lookup.clear();
 145                 //create and initialize vector of sharedvectors, one for each group
 146                 for (int i = 0; i < globaldata->gGroupmap->getNumGroups(); i++) {
 147                         SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
 148                         temp->setLabel(order->getLabel());
 149                         temp->setGroup(globaldata->gGroupmap->namesOfGroups[i]);
 150                         lookup.push_back(temp);
 151                 }
 152
 153                 int numSeqs = order->size();
 154                 //sample all the members
 155                 for(int i=0;i<numSeqs;i++){
 156                         //get first sample
 157                         individual chosen = order->get(i);
 158                         int abundance;
 159
 160                         //set info for sharedvector in chosens group
 161                         for (int j = 0; j < lookup.size(); j++) {
 162                                 if (chosen.group == lookup[j]->getGroup()) {
 163                                          abundance = lookup[j]->getAbundance(chosen.bin);
 164                                          lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
 165                                          break;
 166                                 }
 167                         }
 168
 169                 }
 170         }
 171         catch(exception& e) {
 172                 cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 173                 exit(1);
 174         }
 175         catch(...) {
 176                 cout << "An unknown error has occurred in the SummarySharedCommand class function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 177                 exit(1);
 178         }
 179
 180 }
 181
 182 /**************************************************************************************/
 183 void SummarySharedCommand::getGroupComb() {
 184         try {
 185                 string group;
 186
 187                 int n = 1;
 188                 for (int i = 0; i < (globaldata->gGroupmap->getNumGroups() - 1); i++) {
 189                         for (int l = n; l < globaldata->gGroupmap->getNumGroups(); l++) {
 190                                 group = globaldata->gGroupmap->namesOfGroups[i] + globaldata->gGroupmap->namesOfGroups[l];
 191                                 groupComb.push_back(group);
 192                         }
 193                         n++;
 194                 }
 195         }
 196         catch(exception& e) {
 197                 cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function getGroupComb. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 198                 exit(1);
 199         }
 200         catch(...) {
 201                 cout << "An unknown error has occurred in the SummarySharedCommand class function getGroupComb. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 202                 exit(1);
 203         }
 204
 205 }
 206