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 "sharedsobscollectsummary.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                 format = globaldata->getFormat();
  32                 validCalculator = new ValidCalculators();
  33
  34                 int i;
  35                 for (i=0; i<globaldata->Estimators.size(); i++) {
  36                         if (validCalculator->isValidCalculator("shared", globaldata->Estimators[i]) == true) {
  37                                 if (globaldata->Estimators[i] == "sharedchao") {
  38                                         cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao")));
  39                                 }else if (globaldata->Estimators[i] == "sharedsobs") {
  40                                         cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+"shared.sobs")));
  41                                 }else if (globaldata->Estimators[i] == "sharedace") {
  42                                         cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace")));
  43                                 }else if (globaldata->Estimators[i] == "sharedjabund") {
  44                                         cDisplays.push_back(new CollectDisplay(new SharedJAbund(), new SharedOneColumnFile(fileNameRoot+"shared.jabund")));
  45                                 }else if (globaldata->Estimators[i] == "sharedsorensonabund") {
  46                                         cDisplays.push_back(new CollectDisplay(new SharedSorAbund(), new SharedOneColumnFile(fileNameRoot+"shared.sorabund")));
  47                                 }else if (globaldata->Estimators[i] == "sharedjclass") {
  48                                         cDisplays.push_back(new CollectDisplay(new SharedJclass(), new SharedOneColumnFile(fileNameRoot+"shared.jclass")));
  49                                 }else if (globaldata->Estimators[i] == "sharedsorclass") {
  50                                         cDisplays.push_back(new CollectDisplay(new SharedSorClass(), new SharedOneColumnFile(fileNameRoot+"shared.sorclass")));
  51                                 }else if (globaldata->Estimators[i] == "sharedjest") {
  52                                         cDisplays.push_back(new CollectDisplay(new SharedJest(), new SharedOneColumnFile(fileNameRoot+"shared.jest")));
  53                                 }else if (globaldata->Estimators[i] == "sharedsorest") {
  54                                         cDisplays.push_back(new CollectDisplay(new SharedSorEst(), new SharedOneColumnFile(fileNameRoot+"shared.sorest")));
  55                                 }else if (globaldata->Estimators[i] == "sharedthetayc") {
  56                                         cDisplays.push_back(new CollectDisplay(new SharedThetaYC(), new SharedOneColumnFile(fileNameRoot+"shared.thetayc")));
  57                                 }else if (globaldata->Estimators[i] == "sharedthetan") {
  58                                         cDisplays.push_back(new CollectDisplay(new SharedThetaN(), new SharedOneColumnFile(fileNameRoot+"shared.thetan")));
  59                                 }
  60                         }
  61                 }
  62
  63                 //reset calc for next command
  64                 globaldata->setCalc("");
  65
  66         }
  67         catch(exception& e) {
  68                 cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  69                 exit(1);
  70         }
  71         catch(...) {
  72                 cout << "An unknown error has occurred in the CollectSharedCommand class function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  73                 exit(1);
  74         }
  75
  76 }
  77
  78 //**********************************************************************************************************************
  79
  80 CollectSharedCommand::~CollectSharedCommand(){
  81         delete order;
  82         delete input;
  83         delete cCurve;
  84         delete read;
  85 }
  86
  87 //**********************************************************************************************************************
  88
  89 int CollectSharedCommand::execute(){
  90         try {
  91                 int count = 1;
  92
  93                 //if the users entered no valid calculators don't execute command
  94                 if (cDisplays.size() == 0) { return 0; }
  95
  96                 if (format == "sharedfile") {
  97                         read = new ReadPhilFile(globaldata->inputFileName);
  98                         read->read(&*globaldata);
  99
 100                         input = globaldata->ginput;
 101                         order = input->getSharedOrderVector();
 102                 }else {
 103                         //you are using a list and a groupfile
 104                         read = new ReadPhilFile(globaldata->inputFileName);
 105                         read->read(&*globaldata);
 106
 107                         input = globaldata->ginput;
 108                         SharedList = globaldata->gSharedList;
 109                         order = SharedList->getSharedOrderVector();
 110                 }
 111                 set<string> orderList;
 112
 113                 while(order != NULL){
 114                         orderList.insert(order->getLabel());
 115                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
 116                                 //create collectors curve
 117                                 cCurve = new Collect(order, cDisplays);
 118                                 convert(globaldata->getFreq(), freq);
 119                                 cCurve->getSharedCurve(freq);
 120
 121                                 delete cCurve;
 122
 123                                 cout << order->getLabel() << '\t' << count << endl;
 124                         }
 125
 126                         //get next line to process
 127                         if (format == "sharedfile") {
 128                                 order = input->getSharedOrderVector();
 129                         }else {
 130                                 //you are using a list and a groupfile
 131                                 SharedList = input->getSharedListVector(); //get new list vector to process
 132                                 if (SharedList != NULL) {
 133                                         order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
 134                                 }else {
 135                                         break;
 136                                 }
 137                         }
 138
 139                         count++;
 140                 }
 141                 set<string>::iterator i;
 142                 for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
 143                         if(orderList.count(*i) == 0)
 144                                 cout << "'" << *i << "'" << " is not a valid label.\n";
 145                 globaldata->clearLabels();
 146                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 147                 return 0;
 148         }
 149         catch(exception& e) {
 150                 cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 151                 exit(1);
 152         }
 153         catch(...) {
 154                 cout << "An unknown error has occurred in the CollectSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 155                 exit(1);
 156         }
 157 }
 158
 159
 160 //**********************************************************************************************************************