sharedcommand.cpp

   1 /*
   2  *  sharedcommand.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 "sharedcommand.h"
  11
  12 //**********************************************************************************************************************
  13
  14 SharedCommand::SharedCommand(){
  15         try {
  16                 globaldata = GlobalData::getInstance();
  17
  18                 //getting output filename
  19                 filename = globaldata->inputFileName;
  20                 filename = getRootName(filename);
  21                 filename = filename + "shared";
  22                 openOutputFile(filename, out);
  23         }
  24         catch(exception& e) {
  25                 cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function SharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  26                 exit(1);
  27         }
  28         catch(...) {
  29                 cout << "An unknown error has occurred in the SharedCommand class function SharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  30                 exit(1);
  31         }
  32
  33 }
  34 //**********************************************************************************************************************
  35
  36 int SharedCommand::execute(){
  37         try {
  38                 globaldata = GlobalData::getInstance();
  39
  40                 //read in listfile
  41                 read = new ReadOTUFile(globaldata->inputFileName);
  42                 read->read(&*globaldata);
  43                 input = globaldata->ginput;
  44                 SharedList = globaldata->gSharedList;
  45
  46                 shared = new Shared();
  47                 int i = 0;
  48                 while(SharedList != NULL){
  49
  50                         if(globaldata->allLines == 1 || globaldata->lines.count(i+1) == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
  51
  52                                 shared->getSharedVectors(i, SharedList); //fills sharedGroups with new info and updates sharedVector
  53                                 printSharedData(); //prints info to the .shared file
  54                         }
  55
  56                         SharedList = input->getSharedListVector(); //get new list vector to process
  57                         i++;
  58                 }
  59                 return 0;
  60         }
  61         catch(exception& e) {
  62                 cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  63                 exit(1);
  64         }
  65         catch(...) {
  66                 cout << "An unknown error has occurred in the SharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  67                 exit(1);
  68         }
  69
  70 }
  71 //**********************************************************************************************************************
  72 void SharedCommand::printSharedData() {
  73         try {
  74                 //prints out horizontally
  75                 for (it = shared->sharedGroups.begin(); it != shared->sharedGroups.end(); it++) {
  76                         out << it->second->getLabel() << "\t" << it->first << "\t"; //prints out label and groupname
  77                         it->second->print(out); // prints sharedrabundvector
  78                 }
  79         }
  80         catch(exception& e) {
  81                 cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function printSharedData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  82                 exit(1);
  83         }
  84         catch(...) {
  85                 cout << "An unknown error has occurred in the SharedCommand class function printSharedData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  86                 exit(1);
  87         }
  88
  89 }
  90
  91 //**********************************************************************************************************************
  92
  93 SharedCommand::~SharedCommand(){
  94         //delete list;
  95         delete read;
  96 }
  97
  98 //**********************************************************************************************************************