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