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 ReadPhilFile(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                         shared->getSharedVectors(i, SharedList); //fills sharedGroups with new info and updates sharedVector
  50                         SharedList = input->getSharedListVector(); //get new list vector to process
  51                         printSharedData(); //prints info to the .shared file
  52                         i++;
  53                 }
  54                 return 0;
  55         }
  56         catch(exception& e) {
  57                 cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  58                 exit(1);
  59         }
  60         catch(...) {
  61                 cout << "An unknown error has occurred in the SharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  62                 exit(1);
  63         }
  64
  65 }
  66 //**********************************************************************************************************************
  67 void SharedCommand::printSharedData() {
  68         try {
  69                 //prints out horizontally
  70                 for (it = shared->sharedGroups.begin(); it != shared->sharedGroups.end(); it++) {
  71                         out << it->second->getLabel() << "\t" << it->first << "\t"; //prints out label and groupname
  72                         it->second->print(out); // prints sharedrabundvector
  73                 }
  74         }
  75         catch(exception& e) {
  76                 cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function printSharedData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  77                 exit(1);
  78         }
  79         catch(...) {
  80                 cout << "An unknown error has occurred in the SharedCommand class function printSharedData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  81                 exit(1);
  82         }
  83
  84 }
  85
  86 //**********************************************************************************************************************
  87
  88 SharedCommand::~SharedCommand(){
  89         //delete list;
  90         delete read;
  91 }
  92
  93 //**********************************************************************************************************************