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
  45                 int i;
  46                 for (i=0; i<globaldata->Estimators.size(); i++) {
  47                         if (validCalculator->isValidCalculator("sharedsummary", globaldata->Estimators[i]) == true) {
  48                                 if (globaldata->Estimators[i] == "sharedsobs") {
  49                                         sumCalculators.push_back(new SharedSobsCS());
  50                                 }else if (globaldata->Estimators[i] == "sharedchao") {
  51                                         sumCalculators.push_back(new SharedChao1());
  52                                 }else if (globaldata->Estimators[i] == "sharedace") {
  53                                         sumCalculators.push_back(new SharedAce());
  54                                 }else if (globaldata->Estimators[i] == "jabund") {
  55                                         sumCalculators.push_back(new JAbund());
  56                                 }else if (globaldata->Estimators[i] == "sorabund") {
  57                                         sumCalculators.push_back(new SorAbund());
  58                                 }else if (globaldata->Estimators[i] == "jclass") {
  59                                         sumCalculators.push_back(new Jclass());
  60                                 }else if (globaldata->Estimators[i] == "sorclass") {
  61                                         sumCalculators.push_back(new SorClass());
  62                                 }else if (globaldata->Estimators[i] == "jest") {
  63                                         sumCalculators.push_back(new Jest());
  64                                 }else if (globaldata->Estimators[i] == "sorest") {
  65                                         sumCalculators.push_back(new SorEst());
  66                                 }else if (globaldata->Estimators[i] == "thetayc") {
  67                                         sumCalculators.push_back(new ThetaYC());
  68                                 }else if (globaldata->Estimators[i] == "thetan") {
  69                                         sumCalculators.push_back(new ThetaN());
  70                                 }else if (globaldata->Estimators[i] == "kstest") {
  71                                         sumCalculators.push_back(new KSTest());
  72                                 }else if (globaldata->Estimators[i] == "sharednseqs") {
  73                                         sumCalculators.push_back(new SharedNSeqs());
  74                                 }else if (globaldata->Estimators[i] == "ochiai") {
  75                                         sumCalculators.push_back(new Ochiai());
  76                                 }else if (globaldata->Estimators[i] == "anderberg") {
  77                                         sumCalculators.push_back(new Anderberg());
  78                                 }else if (globaldata->Estimators[i] == "kulczynski") {
  79                                         sumCalculators.push_back(new Kulczynski());
  80                                 }else if (globaldata->Estimators[i] == "kulczynskicody") {
  81                                         sumCalculators.push_back(new KulczynskiCody());
  82                                 }else if (globaldata->Estimators[i] == "lennon") {
  83                                         sumCalculators.push_back(new Lennon());
  84                                 }else if (globaldata->Estimators[i] == "morisitahorn") {
  85                                         sumCalculators.push_back(new MorHorn());
  86                                 }else if (globaldata->Estimators[i] == "braycurtis") {
  87                                         sumCalculators.push_back(new BrayCurtis());
  88                                 }else if (globaldata->Estimators[i] == "whittaker") {
  89                                         sumCalculators.push_back(new Whittaker());
  90                                 }
  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
 124                 if (format == "sharedfile") {
 125                         read = new ReadOTUFile(globaldata->inputFileName);
 126                         read->read(&*globaldata);
 127
 128                         input = globaldata->ginput;
 129                         order = input->getSharedOrderVector();
 130                 }else {
 131                         //you are using a list and a groupfile
 132                         read = new ReadOTUFile(globaldata->inputFileName);
 133                         read->read(&*globaldata);
 134
 135                         input = globaldata->ginput;
 136                         SharedList = globaldata->gSharedList;
 137                         order = SharedList->getSharedOrderVector();
 138                 }
 139
 140                 //set users groups
 141                 util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "summary");
 142
 143                 //output estimator names as column headers
 144                 outputFileHandle << "label" <<'\t' << "comparison" << '\t';
 145                 for(int i=0;i<sumCalculators.size();i++){
 146                         outputFileHandle << '\t' << sumCalculators[i]->getName();
 147                 }
 148                 outputFileHandle << endl;
 149
 150                 while(order != NULL){
 151
 152                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
 153
 154                                 cout << order->getLabel() << '\t' << count << endl;
 155                                 util->getSharedVectors(globaldata->Groups, lookup, order);  //fills group vectors from order vector.  //fills group vectors from order vector.
 156
 157                                 //randomize group order
 158                                 if (globaldata->getJumble() == "1") { random_shuffle(lookup.begin(), lookup.end()); }
 159
 160                                 int n = 1;
 161                                 for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
 162                                         for (int l = n; l < lookup.size(); l++) {
 163
 164                                                 outputFileHandle << order->getLabel() << '\t';
 165
 166                                                 //sort groups to be alphanumeric
 167                                                 if (lookup[k]->getGroup() > lookup[l]->getGroup()) {
 168                                                         outputFileHandle << (lookup[l]->getGroup() +'\t' + lookup[k]->getGroup()) << '\t'; //print out groups
 169                                                 }else{
 170                                                         outputFileHandle << (lookup[k]->getGroup() +'\t' + lookup[l]->getGroup()) << '\t'; //print out groups
 171                                                 }
 172
 173                                                 for(int i=0;i<sumCalculators.size();i++){
 174                                                         sumCalculators[i]->getValues(lookup[k], lookup[l]); //saves the calculator outputs
 175                                                         outputFileHandle << '\t';
 176                                                         sumCalculators[i]->print(outputFileHandle);
 177                                                 }
 178                                                 outputFileHandle << endl;
 179                                         }
 180                                         n++;
 181                                 }
 182                         }
 183
 184                         //get next line to process
 185                         if (format == "sharedfile") {
 186                                 order = input->getSharedOrderVector();
 187                         }else {
 188                                 //you are using a list and a groupfile
 189                                 SharedList = input->getSharedListVector(); //get new list vector to process
 190                                 if (SharedList != NULL) {
 191                                         order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
 192                                 }else {
 193                                         break;
 194                                 }
 195                         }
 196                         count++;
 197                 }
 198
 199                 //reset groups parameter
 200                 globaldata->Groups.clear();  globaldata->setGroups("");
 201
 202                 return 0;
 203         }
 204         catch(exception& e) {
 205                 cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 206                 exit(1);
 207         }
 208         catch(...) {
 209                 cout << "An unknown error has occurred in the SummarySharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 210                 exit(1);
 211         }
 212 }
 213
 214 /***********************************************************/