collectsharedcommand.cpp

   1 /*
   2  *  collectsharedcommand.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 "collectsharedcommand.h"
  11 #include "sharedsobs.h"
  12 #include "sharedchao1.h"
  13 #include "sharedace.h"
  14 #include "sharedjabund.h"
  15 #include "sharedsorabund.h"
  16 #include "sharedjclass.h"
  17 #include "sharedsorclass.h"
  18 #include "sharedjest.h"
  19 #include "sharedsorest.h"
  20 #include "sharedthetayc.h"
  21 #include "sharedthetan.h"
  22
  23
  24 //**********************************************************************************************************************
  25
  26 CollectSharedCommand::CollectSharedCommand(){
  27         try {
  28                 globaldata = GlobalData::getInstance();
  29                 string fileNameRoot;
  30                 fileNameRoot = getRootName(globaldata->inputFileName);
  31                 groupmap = globaldata->gGroupmap;
  32
  33                 int i;
  34                 for (i=0; i<globaldata->sharedEstimators.size(); i++) {
  35                         if (globaldata->sharedEstimators[i] == "sharedChao") {
  36                                 cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao", groupmap->namesOfGroups)));
  37                         }else if (globaldata->sharedEstimators[i] == "sharedSobs") {
  38                                 cDisplays.push_back(new CollectDisplay(new SharedSobs(), new SharedOneColumnFile(fileNameRoot+"shared.sobs", groupmap->namesOfGroups)));
  39                         }else if (globaldata->sharedEstimators[i] == "sharedAce") {
  40                                 cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace", groupmap->namesOfGroups)));
  41                         }else if (globaldata->sharedEstimators[i] == "sharedJabund") {
  42                                 cDisplays.push_back(new CollectDisplay(new SharedJAbund(), new SharedOneColumnFile(fileNameRoot+"shared.jabund", groupmap->namesOfGroups)));
  43                         }else if (globaldata->sharedEstimators[i] == "sharedSorensonAbund") {
  44                                 cDisplays.push_back(new CollectDisplay(new SharedSorAbund(), new SharedOneColumnFile(fileNameRoot+"shared.sorabund", groupmap->namesOfGroups)));
  45                         }else if (globaldata->sharedEstimators[i] == "sharedJclass") {
  46                                 cDisplays.push_back(new CollectDisplay(new SharedJclass(), new SharedOneColumnFile(fileNameRoot+"shared.jclass", groupmap->namesOfGroups)));
  47                         }else if (globaldata->sharedEstimators[i] == "sharedSorClass") {
  48                                 cDisplays.push_back(new CollectDisplay(new SharedSorClass(), new SharedOneColumnFile(fileNameRoot+"shared.sorclass", groupmap->namesOfGroups)));
  49                         }else if (globaldata->sharedEstimators[i] == "sharedJest") {
  50                                 cDisplays.push_back(new CollectDisplay(new SharedJest(), new SharedOneColumnFile(fileNameRoot+"shared.jest", groupmap->namesOfGroups)));
  51                         }else if (globaldata->sharedEstimators[i] == "sharedSorEst") {
  52                                 cDisplays.push_back(new CollectDisplay(new SharedSorEst(), new SharedOneColumnFile(fileNameRoot+"shared.sorest", groupmap->namesOfGroups)));
  53                         }else if (globaldata->sharedEstimators[i] == "SharedThetaYC") {
  54                                 cDisplays.push_back(new CollectDisplay(new SharedThetaYC(), new SharedOneColumnFile(fileNameRoot+"shared.thetayc", groupmap->namesOfGroups)));
  55                         }else if (globaldata->sharedEstimators[i] == "SharedThetaN") {
  56                                 cDisplays.push_back(new CollectDisplay(new SharedThetaN(), new SharedOneColumnFile(fileNameRoot+"shared.thetan", groupmap->namesOfGroups)));
  57                         }
  58                 }
  59         }
  60         catch(exception& e) {
  61                 cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  62                 exit(1);
  63         }
  64         catch(...) {
  65                 cout << "An unknown error has occurred in the CollectSharedCommand class function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  66                 exit(1);
  67         }
  68
  69 }
  70
  71 //**********************************************************************************************************************
  72
  73 CollectSharedCommand::~CollectSharedCommand(){
  74         delete order;
  75         delete input;
  76         delete cCurve;
  77         delete read;
  78 }
  79
  80 //**********************************************************************************************************************
  81
  82 int CollectSharedCommand::execute(){
  83         try {
  84                 int count = 1;
  85                 read = new ReadPhilFile(globaldata->inputFileName);
  86                 read->read(&*globaldata);
  87
  88                 input = globaldata->ginput;
  89                 SharedList = globaldata->gSharedList;
  90                 order = SharedList->getSharedOrderVector();
  91
  92                 while(order != NULL){
  93
  94                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
  95                                 //create collectors curve
  96                                 cCurve = new Collect(order, cDisplays);
  97                                 convert(globaldata->getFreq(), freq);
  98                                 cCurve->getSharedCurve(freq);
  99
 100                                 delete cCurve;
 101
 102                                 cout << order->getLabel() << '\t' << count << endl;
 103                         }
 104
 105                         SharedList = input->getSharedListVector(); //get new list vector to process
 106                         if (SharedList != NULL) {
 107                                 order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
 108                                 count++;
 109                         }else {
 110                                 break;
 111                         }
 112
 113                 }
 114
 115                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 116                 return 0;
 117         }
 118         catch(exception& e) {
 119                 cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 120                 exit(1);
 121         }
 122         catch(...) {
 123                 cout << "An unknown error has occurred in the CollectSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 124                 exit(1);
 125         }
 126 }
 127
 128
 129 //**********************************************************************************************************************