rarefactsharedcommand.cpp

   1 /*
   2  *  rarefactsharedcommand.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/6/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "rarefactsharedcommand.h"
  11 #include "sharedsobs.h"
  12 #include "sharednseqs.h"
  13
  14 //**********************************************************************************************************************
  15
  16 RareFactSharedCommand::RareFactSharedCommand(){
  17         try {
  18                 globaldata = GlobalData::getInstance();
  19                 string fileNameRoot;
  20                 fileNameRoot = getRootName(globaldata->inputFileName);
  21                 format = globaldata->getFormat();
  22                 validCalculator = new ValidCalculators();
  23                 util = new SharedUtil();
  24
  25                 int i;
  26                 for (i=0; i<globaldata->Estimators.size(); i++) {
  27                         if (validCalculator->isValidCalculator("sharedrarefaction", globaldata->Estimators[i]) == true) {
  28                                 if (globaldata->Estimators[i] == "sharedobserved") {
  29                                         rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
  30                                 }else if (globaldata->Estimators[i] == "sharednseqs") {
  31                                         rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", "")));
  32                                 }
  33
  34                         }
  35                 }
  36
  37                 //reset calc for next command
  38                 globaldata->setCalc("");
  39
  40         }
  41         catch(exception& e) {
  42                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  43                 exit(1);
  44         }
  45         catch(...) {
  46                 cout << "An unknown error has occurred in the RareFactSharedCommand class function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  47                 exit(1);
  48         }
  49
  50 }
  51
  52 //**********************************************************************************************************************
  53
  54 RareFactSharedCommand::~RareFactSharedCommand(){
  55         delete order;
  56         delete input;
  57         delete rCurve;
  58         delete read;
  59         delete util;
  60 }
  61
  62 //**********************************************************************************************************************
  63
  64 int RareFactSharedCommand::execute(){
  65         try {
  66                 int count = 1;
  67
  68                 //if the users entered no valid calculators don't execute command
  69                 if (rDisplays.size() == 0) { return 0; }
  70
  71                 if (format == "sharedfile") {
  72                         read = new ReadPhilFile(globaldata->inputFileName);
  73                         read->read(&*globaldata);
  74
  75                         input = globaldata->ginput;
  76                         order = input->getSharedOrderVector();
  77                 }else {
  78                         //you are using a list and a groupfile
  79                         read = new ReadPhilFile(globaldata->inputFileName);
  80                         read->read(&*globaldata);
  81
  82                         input = globaldata->ginput;
  83                         SharedList = globaldata->gSharedList;
  84                         order = SharedList->getSharedOrderVector();
  85                 }
  86
  87                 //set users groups
  88                 util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "rarefact");
  89
  90                 while(order != NULL){
  91
  92                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
  93                                 //create collectors curve
  94                                 rCurve = new Rarefact(order, rDisplays);
  95                                 convert(globaldata->getFreq(), freq);
  96                                 convert(globaldata->getIters(), nIters);
  97                                 rCurve->getSharedCurve(freq, nIters);
  98
  99                                 delete rCurve;
 100
 101                                 cout << order->getLabel() << '\t' << count << endl;
 102                         }
 103
 104                         //get next line to process
 105                         if (format == "sharedfile") {
 106                                 order = input->getSharedOrderVector();
 107                         }else {
 108                                 //you are using a list and a groupfile
 109                                 SharedList = input->getSharedListVector(); //get new list vector to process
 110                                 if (SharedList != NULL) {
 111                                         order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
 112                                 }else {
 113                                         break;
 114                                 }
 115                         }
 116
 117                         count++;
 118                 }
 119
 120                 for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
 121
 122                 //reset groups parameter
 123                 globaldata->Groups.clear();  globaldata->setGroups("");
 124
 125                 return 0;
 126         }
 127         catch(exception& e) {
 128                 cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 129                 exit(1);
 130         }
 131         catch(...) {
 132                 cout << "An unknown error has occurred in the RareFactSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 133                 exit(1);
 134         }
 135 }
 136
 137
 138 //**********************************************************************************************************************