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 "sharedbdiversity.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] == "sharedjabund") {
  55                                         sumCalculators.push_back(new SharedJAbund());
  56                                 }else if (globaldata->Estimators[i] == "sharedsorensonabund") {
  57                                         sumCalculators.push_back(new SharedSorAbund());
  58                                 }else if (globaldata->Estimators[i] == "sharedjclass") {
  59                                         sumCalculators.push_back(new SharedJclass());
  60                                 }else if (globaldata->Estimators[i] == "sharedsorclass") {
  61                                         sumCalculators.push_back(new SharedSorClass());
  62                                 }else if (globaldata->Estimators[i] == "sharedjest") {
  63                                         sumCalculators.push_back(new SharedJest());
  64                                 }else if (globaldata->Estimators[i] == "sharedsorest") {
  65                                         sumCalculators.push_back(new SharedSorEst());
  66                                 }else if (globaldata->Estimators[i] == "sharedthetayc") {
  67                                         sumCalculators.push_back(new SharedThetaYC());
  68                                 }else if (globaldata->Estimators[i] == "sharedthetan") {
  69                                         sumCalculators.push_back(new SharedThetaN());
  70                                 }else if (globaldata->Estimators[i] == "sharedkstest") {
  71                                         sumCalculators.push_back(new SharedKSTest());
  72                                 }else if (globaldata->Estimators[i] == "sharednseqs") {
  73                                         sumCalculators.push_back(new SharedNSeqs());
  74                                 }else if (globaldata->Estimators[i] == "sharedochiai") {
  75                                         sumCalculators.push_back(new SharedOchiai());
  76                                 }else if (globaldata->Estimators[i] == "sharedanderberg") {
  77                                         sumCalculators.push_back(new SharedAnderberg());
  78                                 }else if (globaldata->Estimators[i] == "sharedkulczynski") {
  79                                         sumCalculators.push_back(new SharedKulczynski());
  80                                 }else if (globaldata->Estimators[i] == "sharedkulczynskicody") {
  81                                         sumCalculators.push_back(new SharedKulczynskiCody());
  82                                 }else if (globaldata->Estimators[i] == "sharedlennon") {
  83                                         sumCalculators.push_back(new SharedLennon());
  84                                 }else if (globaldata->Estimators[i] == "sharedmorisitahorn") {
  85                                         sumCalculators.push_back(new SharedMorHorn());
  86                                 }else if (globaldata->Estimators[i] == "sharedbraycurtis") {
  87                                         sumCalculators.push_back(new SharedBrayCurtis());
  88                                 }
  89                                 else if (globaldata->Estimators[i] == "sharedbdiversity") {
  90                                         sumCalculators.push_back(new SharedBDiversity());
  91                                 }
  92
  93                         }
  94                 }
  95                 //reset calc for next command
  96                 globaldata->setCalc("");
  97
  98         }
  99         catch(exception& e) {
 100                 cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function SummarySharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 101                 exit(1);
 102         }
 103         catch(...) {
 104                 cout << "An unknown error has occurred in the SummarySharedCommand class function SummarySharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 105                 exit(1);
 106         }
 107 }
 108 //**********************************************************************************************************************
 109
 110 SummarySharedCommand::~SummarySharedCommand(){
 111         delete input;
 112         delete read;
 113         delete util;
 114 }
 115
 116 //**********************************************************************************************************************
 117
 118 int SummarySharedCommand::execute(){
 119         try {
 120                 int count = 1;
 121
 122                 //if the users entered no valid calculators don't execute command
 123                 if (sumCalculators.size() == 0) { return 0; }
 124
 125                 if (format == "sharedfile") {
 126                         read = new ReadPhilFile(globaldata->inputFileName);
 127                         read->read(&*globaldata);
 128
 129                         input = globaldata->ginput;
 130                         order = input->getSharedOrderVector();
 131                 }else {
 132                         //you are using a list and a groupfile
 133                         read = new ReadPhilFile(globaldata->inputFileName);
 134                         read->read(&*globaldata);
 135
 136                         input = globaldata->ginput;
 137                         SharedList = globaldata->gSharedList;
 138                         order = SharedList->getSharedOrderVector();
 139                 }
 140
 141                 //set users groups
 142                 util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "summary");
 143
 144                 //output estimator names as column headers
 145                 outputFileHandle << "label" <<'\t' << "comparison" << '\t';
 146                 for(int i=0;i<sumCalculators.size();i++){
 147                         outputFileHandle << '\t' << sumCalculators[i]->getName();
 148                 }
 149                 outputFileHandle << endl;
 150
 151                 while(order != NULL){
 152
 153                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
 154
 155                                 cout << order->getLabel() << '\t' << count << endl;
 156                                 util->getSharedVectors(globaldata->Groups, lookup, order);  //fills group vectors from order vector.  //fills group vectors from order vector.
 157
 158                                 //randomize group order
 159                                 if (globaldata->getJumble() == "1") { random_shuffle(lookup.begin(), lookup.end()); }
 160
 161                                 int n = 1;
 162                                 for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
 163                                         for (int l = n; l < lookup.size(); l++) {
 164
 165                                                 outputFileHandle << order->getLabel() << '\t';
 166
 167                                                 //sort groups to be alphanumeric
 168                                                 if (lookup[k]->getGroup() > lookup[l]->getGroup()) {
 169                                                         outputFileHandle << (lookup[l]->getGroup() +'\t' + lookup[k]->getGroup()) << '\t'; //print out groups
 170                                                 }else{
 171                                                         outputFileHandle << (lookup[k]->getGroup() +'\t' + lookup[l]->getGroup()) << '\t'; //print out groups
 172                                                 }
 173
 174                                                 for(int i=0;i<sumCalculators.size();i++){
 175                                                         sumCalculators[i]->getValues(lookup[k], lookup[l]); //saves the calculator outputs
 176                                                         outputFileHandle << '\t';
 177                                                         sumCalculators[i]->print(outputFileHandle);
 178                                                 }
 179                                                 outputFileHandle << endl;
 180                                         }
 181                                         n++;
 182                                 }
 183                         }
 184
 185                         //get next line to process
 186                         if (format == "sharedfile") {
 187                                 order = input->getSharedOrderVector();
 188                         }else {
 189                                 //you are using a list and a groupfile
 190                                 SharedList = input->getSharedListVector(); //get new list vector to process
 191                                 if (SharedList != NULL) {
 192                                         order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
 193                                 }else {
 194                                         break;
 195                                 }
 196                         }
 197                         count++;
 198                 }
 199
 200                 //reset groups parameter
 201                 globaldata->Groups.clear();  globaldata->setGroups("");
 202
 203                 return 0;
 204         }
 205         catch(exception& e) {
 206                 cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 207                 exit(1);
 208         }
 209         catch(...) {
 210                 cout << "An unknown error has occurred in the SummarySharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 211                 exit(1);
 212         }
 213 }
 214
 215 /***********************************************************/