readnexus.cpp

   1 /*
   2  *  readnexusaln.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 4/22/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "readnexus.h"
  11 #include <iostream>
  12 #include <fstream>
  13
  14 /*******************************************************************************/
  15 ReadNexus::ReadNexus(string file) {
  16         try {
  17                 openInputFile(file, filehandle);
  18                 nexusFile = file;
  19                 globaldata = GlobalData::getInstance();
  20         }
  21         catch(exception& e) {
  22                 cout << "Standard Error: " << e.what() << " has occurred in the ReadTree class Function ReadTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  23                 exit(1);
  24         }
  25         catch(...) {
  26                 cout << "An unknown error has occurred in the ReadTree class function ReadTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  27                 exit(1);
  28         }
  29 }
  30 /*******************************************************************************/
  31 ReadNexus::~ReadNexus(){
  32 //      for(int i = 0; i < sequencedb.getNumSeqs(); i++)
  33 //              delete sequencedb.get(i);
  34 }
  35 /*******************************************************************************/
  36 void ReadNexus::read() {
  37         string temp;
  38         string name;
  39         string sequence;
  40         for(int i = 0; i < 5; i++)
  41                 filehandle >> temp;
  42
  43         int numSeqs = atoi(temp.substr(temp.find_first_of("=")+1, temp.length() - temp.find_first_of("=") - 1).c_str());
  44
  45         for(int i = 0; i < 9; i++)
  46                 filehandle >> temp;
  47
  48         int count = 0;
  49         bool firstDone = false;
  50         while(!filehandle.eof()){
  51                 filehandle >> name;
  52                 filehandle >> sequence;
  53                 if(name.compare(";") != 0) {
  54                         if(!firstDone) {
  55                                 Sequence newSeq(name, sequence);
  56                                 sequencedb.add(newSeq);
  57                         }
  58                         else
  59                                 sequencedb.set(count, sequencedb.get(count).getAligned() + sequence);
  60
  61                         count++;
  62                         if(count == numSeqs) {
  63                                 if(!firstDone)
  64                                         firstDone = true;
  65                                 count = 0;
  66                         }
  67                 }
  68         }
  69         filehandle.close();
  70 }
  71
  72 /*********************************************************************************/
  73 SequenceDB* ReadNexus::getDB() {
  74         return &sequencedb;
  75 }