venncommand.cpp

   1 /*
   2  *  venncommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 3/30/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "venncommand.h"
  11 #include "ace.h"
  12 #include "sobs.h"
  13 #include "chao1.h"
  14 //#include "jackknife.h"
  15 #include "sharedsobscollectsummary.h"
  16 #include "sharedchao1.h"
  17 #include "sharedace.h"
  18
  19
  20 //**********************************************************************************************************************
  21
  22 VennCommand::VennCommand(){
  23         try {
  24                 globaldata = GlobalData::getInstance();
  25                 format = globaldata->getFormat();
  26                 validCalculator = new ValidCalculators();
  27
  28                 int i;
  29
  30                 if (format == "list") {
  31                         for (i=0; i<globaldata->Estimators.size(); i++) {
  32                                 if (validCalculator->isValidCalculator("vennsingle", globaldata->Estimators[i]) == true) {
  33                                         if (globaldata->Estimators[i] == "sobs") {
  34                                                 vennCalculators.push_back(new Sobs());
  35                                         }else if (globaldata->Estimators[i] == "chao") {
  36                                                 vennCalculators.push_back(new Chao1());
  37                                         }else if (globaldata->Estimators[i] == "ace") {
  38                                                 convert(globaldata->getAbund(), abund);
  39                                                 if(abund < 5)
  40                                                         abund = 10;
  41                                                 vennCalculators.push_back(new Ace(abund));
  42                                         //}else if (globaldata->Estimators[i] == "jack") {
  43                                                 //vennCalculators.push_back(new Jackknife());
  44                                         }
  45                                 }
  46                         }
  47                 }else {
  48                         for (i=0; i<globaldata->Estimators.size(); i++) {
  49                                 if (validCalculator->isValidCalculator("vennshared", globaldata->Estimators[i]) == true) {
  50                                         if (globaldata->Estimators[i] == "sharedsobs") {
  51                                                 vennCalculators.push_back(new SharedSobsCS());
  52                                         }else if (globaldata->Estimators[i] == "sharedchao") {
  53                                                 vennCalculators.push_back(new SharedChao1());
  54                                         }else if (globaldata->Estimators[i] == "sharedace") {
  55                                                 vennCalculators.push_back(new SharedAce());
  56                                         }
  57                                 }
  58                         }
  59                 }
  60
  61                 venn = new Venn();
  62
  63                 //reset calc for next command
  64                 globaldata->setCalc("");
  65
  66
  67         }
  68         catch(exception& e) {
  69                 cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function VennCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  70                 exit(1);
  71         }
  72         catch(...) {
  73                 cout << "An unknown error has occurred in the VennCommand class function VennCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  74                 exit(1);
  75         }
  76 }
  77 //**********************************************************************************************************************
  78
  79 VennCommand::~VennCommand(){
  80         delete input;
  81         delete read;
  82         delete venn;
  83 }
  84
  85 //**********************************************************************************************************************
  86
  87 int VennCommand::execute(){
  88         try {
  89                 int count = 1;
  90
  91                 //if the users entered no valid calculators don't execute command
  92                 if (vennCalculators.size() == 0) { return 0; }
  93
  94                 if (format == "sharedfile") {
  95                         //you have groups
  96                         read = new ReadOTUFile(globaldata->inputFileName);
  97                         read->read(&*globaldata);
  98
  99                         input = globaldata->ginput;
 100                         lookup = input->getSharedRAbundVectors();
 101                 }else if (format == "shared") {
 102                         //you are using a list and a groupfile
 103                         read = new ReadOTUFile(globaldata->inputFileName);
 104                         read->read(&*globaldata);
 105
 106                         input = globaldata->ginput;
 107                         SharedList = globaldata->gSharedList;
 108                         lookup = SharedList->getSharedRAbundVector();
 109                 }else if (format == "list") {
 110                         //you are using just a list file and have only one group
 111                         read = new ReadOTUFile(globaldata->inputFileName);
 112                         read->read(&*globaldata);
 113
 114                         sabund = globaldata->sabund;
 115                         input = globaldata->ginput;
 116                 }
 117
 118
 119                 if (format != "list") {
 120
 121                         while(lookup[0] != NULL){
 122
 123                                 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
 124
 125                                         cout << lookup[0]->getLabel() << '\t' << count << endl;
 126
 127                                         if (lookup.size() > 4) {
 128                                                 cout << "Error: Too many groups chosen.  You may use up to 4 groups with the venn command.  I will use the first four groups in your groupfile." << endl;
 129                                                 for (int i = lookup.size(); i > 3; i--) { delete lookup[i]; lookup.pop_back(); }
 130                                         }
 131
 132                                         //util->getSharedVectors(globaldata->Groups, lookup, order);  //fills group vectors from order vector.
 133                                         venn->getPic(lookup, vennCalculators);
 134                                 }
 135
 136                                 //get next line to process
 137                                 lookup = input->getSharedRAbundVectors();
 138                                 count++;
 139                         }
 140
 141                         //reset groups parameter
 142                         globaldata->Groups.clear();
 143
 144                 }else{
 145
 146                         while(sabund != NULL){
 147
 148                                 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){
 149
 150                                         cout << sabund->getLabel() << '\t' << count << endl;
 151                                         venn->getPic(sabund, vennCalculators);
 152                                 }
 153
 154                                 sabund = input->getSAbundVector();
 155                                 count++;
 156                         }
 157                 }
 158
 159                 globaldata->setGroups("");
 160                 return 0;
 161         }
 162         catch(exception& e) {
 163                 cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 164                 exit(1);
 165         }
 166         catch(...) {
 167                 cout << "An unknown error has occurred in the VennCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 168                 exit(1);
 169         }
 170 }
 171
 172 //**********************************************************************************************************************