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                 util = new SharedUtil();
  28
  29                 int i;
  30
  31                 if (format == "list") {
  32                         for (i=0; i<globaldata->Estimators.size(); i++) {
  33                                 if (validCalculator->isValidCalculator("vennsingle", globaldata->Estimators[i]) == true) {
  34                                         if (globaldata->Estimators[i] == "sobs") {
  35                                                 vennCalculators.push_back(new Sobs());
  36                                         }else if (globaldata->Estimators[i] == "chao") {
  37                                                 vennCalculators.push_back(new Chao1());
  38                                         }else if (globaldata->Estimators[i] == "ace") {
  39                                                 convert(globaldata->getAbund(), abund);
  40                                                 if(abund < 5)
  41                                                         abund = 10;
  42                                                 vennCalculators.push_back(new Ace(abund));
  43                                         //}else if (globaldata->Estimators[i] == "jack") {
  44                                                 //vennCalculators.push_back(new Jackknife());
  45                                         }
  46                                 }
  47                         }
  48                 }else {
  49                         for (i=0; i<globaldata->Estimators.size(); i++) {
  50                                 if (validCalculator->isValidCalculator("vennshared", globaldata->Estimators[i]) == true) {
  51                                         if (globaldata->Estimators[i] == "sharedsobs") {
  52                                                 vennCalculators.push_back(new SharedSobsCS());
  53                                         }else if (globaldata->Estimators[i] == "sharedchao") {
  54                                                 vennCalculators.push_back(new SharedChao1());
  55                                         }else if (globaldata->Estimators[i] == "sharedace") {
  56                                                 vennCalculators.push_back(new SharedAce());
  57                                         }
  58                                 }
  59                         }
  60                 }
  61
  62                 venn = new Venn();
  63
  64                 //reset calc for next command
  65                 globaldata->setCalc("");
  66
  67
  68         }
  69         catch(exception& e) {
  70                 cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function VennCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  71                 exit(1);
  72         }
  73         catch(...) {
  74                 cout << "An unknown error has occurred in the VennCommand class function VennCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  75                 exit(1);
  76         }
  77 }
  78 //**********************************************************************************************************************
  79
  80 VennCommand::~VennCommand(){
  81         delete input;
  82         delete read;
  83         delete venn;
  84         delete util;
  85 }
  86
  87 //**********************************************************************************************************************
  88
  89 int VennCommand::execute(){
  90         try {
  91                 int count = 1;
  92
  93                 //if the users entered no valid calculators don't execute command
  94                 if (vennCalculators.size() == 0) { return 0; }
  95
  96                 if (format == "sharedfile") {
  97                         //you have groups
  98                         read = new ReadPhilFile(globaldata->inputFileName);
  99                         read->read(&*globaldata);
 100
 101                         input = globaldata->ginput;
 102                         order = input->getSharedOrderVector();
 103                 }else if (format == "shared") {
 104                         //you are using a list and a groupfile
 105                         read = new ReadPhilFile(globaldata->inputFileName);
 106                         read->read(&*globaldata);
 107
 108                         input = globaldata->ginput;
 109                         SharedList = globaldata->gSharedList;
 110                         order = SharedList->getSharedOrderVector();
 111                 }else if (format == "list") {
 112                         //you are using just a list file and have only one group
 113                         read = new ReadPhilFile(globaldata->inputFileName);
 114                         read->read(&*globaldata);
 115
 116                         ordersingle = globaldata->gorder;
 117                         input = globaldata->ginput;
 118                 }
 119
 120
 121                 if (format != "list") {
 122
 123                         util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "venn");
 124                         globaldata->setGroups("");
 125
 126                         while(order != NULL){
 127
 128                                 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
 129
 130                                         cout << order->getLabel() << '\t' << count << endl;
 131                                         venn->getPic(order, vennCalculators);
 132
 133                                 }
 134
 135                                 //get next line to process
 136                                 if (format == "sharedfile") {
 137                                         order = input->getSharedOrderVector();
 138                                 }else {
 139                                         //you are using a list and a groupfile
 140                                         SharedList = input->getSharedListVector(); //get new list vector to process
 141                                         if (SharedList != NULL) {
 142                                                 order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
 143                                         }else {
 144                                                 break;
 145                                         }
 146                                 }
 147                                 count++;
 148                         }
 149
 150                         //reset groups parameter
 151                         globaldata->Groups.clear();
 152
 153                 }else{
 154                         while(ordersingle != NULL){
 155
 156                                 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(ordersingle->getLabel()) == 1){
 157
 158                                         cout << ordersingle->getLabel() << '\t' << count << endl;
 159                                         venn->getPic(ordersingle, vennCalculators);
 160
 161                                 }
 162
 163                                 ordersingle = (input->getOrderVector());
 164                                 count++;
 165                         }
 166                 }
 167
 168                 return 0;
 169         }
 170         catch(exception& e) {
 171                 cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 172                 exit(1);
 173         }
 174         catch(...) {
 175                 cout << "An unknown error has occurred in the VennCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 176                 exit(1);
 177         }
 178 }
 179
 180 //**********************************************************************************************************************
 181