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 "sharednseqs.h"
  15 #include "sharedjabund.h"
  16 #include "sharedsorabund.h"
  17 #include "sharedjclass.h"
  18 #include "sharedsorclass.h"
  19 #include "sharedjest.h"
  20 #include "sharedsorest.h"
  21 #include "sharedthetayc.h"
  22 #include "sharedthetan.h"
  23 #include "sharedkstest.h"
  24 #include "whittaker.h"
  25 #include "sharedochiai.h"
  26 #include "sharedanderbergs.h"
  27 #include "sharedkulczynski.h"
  28 #include "sharedkulczynskicody.h"
  29 #include "sharedlennon.h"
  30 #include "sharedmorisitahorn.h"
  31 #include "sharedbraycurtis.h"
  32 #include "sharedjackknife.h"
  33 #include "sharedwhittaker.h"
  34
  35
  36 //**********************************************************************************************************************
  37
  38 SummarySharedCommand::SummarySharedCommand(){
  39         try {
  40                 globaldata = GlobalData::getInstance();
  41                 outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary");
  42                 openOutputFile(outputFileName, outputFileHandle);
  43                 format = globaldata->getFormat();
  44                 validCalculator = new ValidCalculators();
  45                 util = new SharedUtil();
  46                 mult = false;
  47
  48                 int i;
  49                 for (i=0; i<globaldata->Estimators.size(); i++) {
  50                         if (validCalculator->isValidCalculator("sharedsummary", globaldata->Estimators[i]) == true) {
  51                                 if (globaldata->Estimators[i] == "sharedsobs") {
  52                                         sumCalculators.push_back(new SharedSobsCS());
  53                                 }else if (globaldata->Estimators[i] == "sharedchao") {
  54                                         sumCalculators.push_back(new SharedChao1());
  55                                 }else if (globaldata->Estimators[i] == "sharedace") {
  56                                         sumCalculators.push_back(new SharedAce());
  57                                 }else if (globaldata->Estimators[i] == "jabund") {
  58                                         sumCalculators.push_back(new JAbund());
  59                                 }else if (globaldata->Estimators[i] == "sorabund") {
  60                                         sumCalculators.push_back(new SorAbund());
  61                                 }else if (globaldata->Estimators[i] == "jclass") {
  62                                         sumCalculators.push_back(new Jclass());
  63                                 }else if (globaldata->Estimators[i] == "sorclass") {
  64                                         sumCalculators.push_back(new SorClass());
  65                                 }else if (globaldata->Estimators[i] == "jest") {
  66                                         sumCalculators.push_back(new Jest());
  67                                 }else if (globaldata->Estimators[i] == "sorest") {
  68                                         sumCalculators.push_back(new SorEst());
  69                                 }else if (globaldata->Estimators[i] == "thetayc") {
  70                                         sumCalculators.push_back(new ThetaYC());
  71                                 }else if (globaldata->Estimators[i] == "thetan") {
  72                                         sumCalculators.push_back(new ThetaN());
  73                                 }else if (globaldata->Estimators[i] == "kstest") {
  74                                         sumCalculators.push_back(new KSTest());
  75                                 }else if (globaldata->Estimators[i] == "sharednseqs") {
  76                                         sumCalculators.push_back(new SharedNSeqs());
  77                                 }else if (globaldata->Estimators[i] == "ochiai") {
  78                                         sumCalculators.push_back(new Ochiai());
  79                                 }else if (globaldata->Estimators[i] == "anderberg") {
  80                                         sumCalculators.push_back(new Anderberg());
  81                                 }else if (globaldata->Estimators[i] == "kulczynski") {
  82                                         sumCalculators.push_back(new Kulczynski());
  83                                 }else if (globaldata->Estimators[i] == "kulczynskicody") {
  84                                         sumCalculators.push_back(new KulczynskiCody());
  85                                 }else if (globaldata->Estimators[i] == "lennon") {
  86                                         sumCalculators.push_back(new Lennon());
  87                                 }else if (globaldata->Estimators[i] == "morisitahorn") {
  88                                         sumCalculators.push_back(new MorHorn());
  89                                 }else if (globaldata->Estimators[i] == "braycurtis") {
  90                                         sumCalculators.push_back(new BrayCurtis());
  91                                 }else if (globaldata->Estimators[i] == "whittaker") {
  92                                         sumCalculators.push_back(new Whittaker());
  93                                 }
  94                         }
  95                 }
  96                 //reset calc for next command
  97                 globaldata->setCalc("");
  98
  99         }
 100         catch(exception& e) {
 101                 cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function SummarySharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 102                 exit(1);
 103         }
 104         catch(...) {
 105                 cout << "An unknown error has occurred in the SummarySharedCommand class function SummarySharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 106                 exit(1);
 107         }
 108 }
 109 //**********************************************************************************************************************
 110
 111 SummarySharedCommand::~SummarySharedCommand(){
 112         delete input;
 113         delete read;
 114         delete util;
 115 }
 116
 117 //**********************************************************************************************************************
 118
 119 int SummarySharedCommand::execute(){
 120         try {
 121                 int count = 1;
 122
 123                 //if the users entered no valid calculators don't execute command
 124                 if (sumCalculators.size() == 0) { return 0; }
 125                 //check if any calcs can do multiples
 126                 else{
 127                         for (int i = 0; i < sumCalculators.size(); i++) {
 128                                 if (sumCalculators[i]->getMultiple() == true) { mult = true; }
 129                         }
 130                 }
 131
 132                 if (format == "sharedfile") {
 133                         read = new ReadOTUFile(globaldata->inputFileName);
 134                         read->read(&*globaldata);
 135
 136                         input = globaldata->ginput;
 137                         order = input->getSharedOrderVector();
 138                 }else {
 139                         //you are using a list and a groupfile
 140                         read = new ReadOTUFile(globaldata->inputFileName);
 141                         read->read(&*globaldata);
 142
 143                         input = globaldata->ginput;
 144                         SharedList = globaldata->gSharedList;
 145                         order = SharedList->getSharedOrderVector();
 146                 }
 147
 148                 //set users groups
 149                 util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "summary");
 150
 151                 //output estimator names as column headers
 152                 outputFileHandle << "label" <<'\t' << "comparison" << '\t';
 153                 for(int i=0;i<sumCalculators.size();i++){
 154                         outputFileHandle << '\t' << sumCalculators[i]->getName();
 155                 }
 156                 outputFileHandle << endl;
 157
 158                 //create file and put column headers for multiple groups file
 159                 if (mult = true) {
 160                         outAllFileName = ((getRootName(globaldata->inputFileName)) + "sharedmultiple.summary");
 161                         openOutputFile(outAllFileName, outAll);
 162
 163                         outAll << "label" <<'\t' << "comparison" << '\t';
 164                         for(int i=0;i<sumCalculators.size();i++){
 165                                 if (sumCalculators[i]->getMultiple() == true) {
 166                                         outAll << '\t' << sumCalculators[i]->getName();
 167                                 }
 168                         }
 169                         outAll << endl;
 170                 }
 171
 172                 while(order != NULL){
 173
 174                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
 175
 176                                 cout << order->getLabel() << '\t' << count << endl;
 177                                 util->getSharedVectors(globaldata->Groups, lookup, order);  //fills group vectors from order vector.  //fills group vectors from order vector.
 178
 179                                 //loop through calculators and add to file all for all calcs that can do mutiple groups
 180                                 if (mult = true) {
 181                                         //output label
 182                                         outAll << order->getLabel() << '\t';
 183
 184                                         //output groups names
 185                                         string outNames = "";
 186                                         for (int j = 0; j < lookup.size(); j++) {
 187                                                 outNames += lookup[j]->getGroup() +  "-";
 188                                         }
 189                                         outNames = outNames.substr(0, outNames.length()-1); //rip off extra '-';
 190                                         outAll << outNames << '\t';
 191
 192                                         for(int i=0;i<sumCalculators.size();i++){
 193                                                 if (sumCalculators[i]->getMultiple() == true) {
 194                                                         sumCalculators[i]->getValues(lookup);
 195                                                         outAll << '\t';
 196                                                         sumCalculators[i]->print(outAll);
 197                                                 }
 198                                         }
 199                                         outAll << endl;
 200                                 }
 201
 202                                 int n = 1;
 203                                 vector<SharedRAbundVector*> subset;
 204                                 for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
 205                                         for (int l = n; l < lookup.size(); l++) {
 206
 207                                                 outputFileHandle << order->getLabel() << '\t';
 208
 209                                                 subset.clear(); //clear out old pair of sharedrabunds
 210                                                 //add new pair of sharedrabunds
 211                                                 subset.push_back(lookup[k]); subset.push_back(lookup[l]);
 212
 213                                                 //sort groups to be alphanumeric
 214                                                 if (lookup[k]->getGroup() > lookup[l]->getGroup()) {
 215                                                         outputFileHandle << (lookup[l]->getGroup() +'\t' + lookup[k]->getGroup()) << '\t'; //print out groups
 216                                                 }else{
 217                                                         outputFileHandle << (lookup[k]->getGroup() +'\t' + lookup[l]->getGroup()) << '\t'; //print out groups
 218                                                 }
 219
 220                                                 for(int i=0;i<sumCalculators.size();i++) {
 221                                                         sumCalculators[i]->getValues(subset); //saves the calculator outputs
 222                                                         outputFileHandle << '\t';
 223                                                         sumCalculators[i]->print(outputFileHandle);
 224                                                 }
 225                                                 outputFileHandle << endl;
 226                                         }
 227                                         n++;
 228                                 }
 229                         }
 230
 231                         //get next line to process
 232                         if (format == "sharedfile") {
 233                                 order = input->getSharedOrderVector();
 234                         }else {
 235                                 //you are using a list and a groupfile
 236                                 SharedList = input->getSharedListVector(); //get new list vector to process
 237                                 if (SharedList != NULL) {
 238                                         order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
 239                                 }else {
 240                                         break;
 241                                 }
 242                         }
 243                         count++;
 244                 }
 245
 246                 //reset groups parameter
 247                 globaldata->Groups.clear();  globaldata->setGroups("");
 248
 249                 return 0;
 250         }
 251         catch(exception& e) {
 252                 cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 253                 exit(1);
 254         }
 255         catch(...) {
 256                 cout << "An unknown error has occurred in the SummarySharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 257                 exit(1);
 258         }
 259 }
 260
 261 /***********************************************************/