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