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 "sharedsobscollectsummary.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                 outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary");
  29                 openOutputFile(outputFileName, outputFileHandle);
  30                 format = globaldata->getFormat();
  31                 validCalculator = new ValidCalculators();
  32
  33                 int i;
  34                 for (i=0; i<globaldata->Estimators.size(); i++) {
  35                         if (validCalculator->isValidCalculator("sharedsummary", globaldata->Estimators[i]) == true) {
  36                                 if (globaldata->Estimators[i] == "sharedsobs") {
  37                                         sumCalculators.push_back(new SharedSobsCS());
  38                                 }else if (globaldata->Estimators[i] == "sharedchao") {
  39                                         sumCalculators.push_back(new SharedChao1());
  40                                 }else if (globaldata->Estimators[i] == "sharedace") {
  41                                         sumCalculators.push_back(new SharedAce());
  42                                 }else if (globaldata->Estimators[i] == "sharedjabund") {
  43                                         sumCalculators.push_back(new SharedJAbund());
  44                                 }else if (globaldata->Estimators[i] == "sharedsorensonabund") {
  45                                         sumCalculators.push_back(new SharedSorAbund());
  46                                 }else if (globaldata->Estimators[i] == "sharedjclass") {
  47                                         sumCalculators.push_back(new SharedJclass());
  48                                 }else if (globaldata->Estimators[i] == "sharedsorclass") {
  49                                         sumCalculators.push_back(new SharedSorClass());
  50                                 }else if (globaldata->Estimators[i] == "sharedjest") {
  51                                         sumCalculators.push_back(new SharedJest());
  52                                 }else if (globaldata->Estimators[i] == "sharedsorest") {
  53                                         sumCalculators.push_back(new SharedSorEst());
  54                                 }else if (globaldata->Estimators[i] == "sharedthetayc") {
  55                                         sumCalculators.push_back(new SharedThetaYC());
  56                                 }else if (globaldata->Estimators[i] == "sharedthetan") {
  57                                         sumCalculators.push_back(new SharedThetaN());
  58                                 }
  59                         }
  60                 }
  61
  62                 //reset calc for next command
  63                 globaldata->setCalc("");
  64
  65         }
  66         catch(exception& e) {
  67                 cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function SummarySharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  68                 exit(1);
  69         }
  70         catch(...) {
  71                 cout << "An unknown error has occurred in the SummarySharedCommand class function SummarySharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  72                 exit(1);
  73         }
  74 }
  75 //**********************************************************************************************************************
  76
  77 SummarySharedCommand::~SummarySharedCommand(){
  78         delete input;
  79         delete read;
  80 }
  81
  82 //**********************************************************************************************************************
  83
  84 int SummarySharedCommand::execute(){
  85         try {
  86                 int count = 1;
  87
  88                 //if the users entered no valid calculators don't execute command
  89                 if (sumCalculators.size() == 0) { return 0; }
  90
  91                 if (format == "sharedfile") {
  92                         read = new ReadPhilFile(globaldata->inputFileName);
  93                         read->read(&*globaldata);
  94
  95                         input = globaldata->ginput;
  96                         order = input->getSharedOrderVector();
  97                 }else {
  98                         //you are using a list and a groupfile
  99                         read = new ReadPhilFile(globaldata->inputFileName);
 100                         read->read(&*globaldata);
 101
 102                         input = globaldata->ginput;
 103                         SharedList = globaldata->gSharedList;
 104                         order = SharedList->getSharedOrderVector();
 105                 }
 106
 107                 //output estimator names as column headers
 108                 outputFileHandle << "label" <<'\t' << "comparison" << '\t';
 109                 for(int i=0;i<sumCalculators.size();i++){
 110                         outputFileHandle << '\t' << sumCalculators[i]->getName();
 111                 }
 112                 outputFileHandle << endl;
 113
 114                 while(order != NULL){
 115
 116                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
 117
 118                                 cout << order->getLabel() << '\t' << count << endl;
 119                                 getSharedVectors();  //fills group vectors from order vector.
 120
 121                                 //randomize group order
 122                                 if (globaldata->getJumble() == "1") { random_shuffle(lookup.begin(), lookup.end()); }
 123
 124                                 int n = 1;
 125                                 for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
 126                                         for (int l = n; l < lookup.size(); l++) {
 127                                                 outputFileHandle << order->getLabel() << '\t' << (lookup[k]->getGroup() + lookup[l]->getGroup()) << '\t' << '\t'; //print out label and group
 128                                                 for(int i=0;i<sumCalculators.size();i++){
 129                                                         sumCalculators[i]->getValues(lookup[k], lookup[l]); //saves the calculator outputs
 130                                                         outputFileHandle << '\t';
 131                                                         sumCalculators[i]->print(outputFileHandle);
 132                                                 }
 133                                                 outputFileHandle << endl;
 134                                         }
 135                                         n++;
 136                                 }
 137                         }
 138
 139                         //get next line to process
 140                         if (format == "sharedfile") {
 141                                 order = input->getSharedOrderVector();
 142                         }else {
 143                                 //you are using a list and a groupfile
 144                                 SharedList = input->getSharedListVector(); //get new list vector to process
 145                                 if (SharedList != NULL) {
 146                                         order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
 147                                 }else {
 148                                         break;
 149                                 }
 150                         }
 151                         count++;
 152                 }
 153
 154                 return 0;
 155         }
 156         catch(exception& e) {
 157                 cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 158                 exit(1);
 159         }
 160         catch(...) {
 161                 cout << "An unknown error has occurred in the SummarySharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 162                 exit(1);
 163         }
 164 }
 165
 166 //**********************************************************************************************************************
 167
 168 void SummarySharedCommand::getSharedVectors(){
 169 try {
 170                 lookup.clear();
 171                 //create and initialize vector of sharedvectors, one for each group
 172                 for (int i = 0; i < globaldata->gGroupmap->getNumGroups(); i++) {
 173                         SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
 174                         temp->setLabel(order->getLabel());
 175                         temp->setGroup(globaldata->gGroupmap->namesOfGroups[i]);
 176                         lookup.push_back(temp);
 177                 }
 178
 179                 int numSeqs = order->size();
 180                 //sample all the members
 181                 for(int i=0;i<numSeqs;i++){
 182                         //get first sample
 183                         individual chosen = order->get(i);
 184                         int abundance;
 185
 186                         //set info for sharedvector in chosens group
 187                         for (int j = 0; j < lookup.size(); j++) {
 188                                 if (chosen.group == lookup[j]->getGroup()) {
 189                                          abundance = lookup[j]->getAbundance(chosen.bin);
 190                                          lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
 191                                          break;
 192                                 }
 193                         }
 194
 195                 }
 196         }
 197         catch(exception& e) {
 198                 cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 199                 exit(1);
 200         }
 201         catch(...) {
 202                 cout << "An unknown error has occurred in the SummarySharedCommand class function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 203                 exit(1);
 204         }
 205
 206 }
 207
 208 //**********************************************************************************************************************