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) : ReadSeqs(file) {
  16         try {
  17         }
  18         catch(exception& e) {
  19                 cout << "Standard Error: " << e.what() << " has occurred in the ReadTree class Function ReadTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  20                 exit(1);
  21         }
  22         catch(...) {
  23                 cout << "An unknown error has occurred in the ReadTree class function ReadTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  24                 exit(1);
  25         }
  26 }
  27 /*******************************************************************************/
  28 ReadNexus::~ReadNexus(){
  29 //      for(int i = 0; i < sequencedb.getNumSeqs(); i++)
  30 //              delete sequencedb.get(i);
  31 }
  32 /*******************************************************************************/
  33 void ReadNexus::read() {
  34         string temp;
  35         string name;
  36         string sequence;
  37         for(int i = 0; i < 5; i++)
  38                 filehandle >> temp;
  39
  40         int numSeqs = atoi(temp.substr(temp.find_first_of("=")+1, temp.length() - temp.find_first_of("=") - 1).c_str());
  41
  42         for(int i = 0; i < 9; i++)
  43                 filehandle >> temp;
  44
  45         int count = 0;
  46         bool firstDone = false;
  47         while(!filehandle.eof()){
  48                 filehandle >> name;
  49                 filehandle >> sequence;
  50                 if(name.compare(";") != 0) {
  51                         if(!firstDone) {
  52                                 Sequence newSeq(name, sequence);
  53                                 sequencedb.add(newSeq);
  54                         }
  55                         else
  56                                 sequencedb.set(count, sequencedb.get(count).getUnaligned() + sequence);
  57
  58                         count++;
  59                         if(count == numSeqs) {
  60                                 if(!firstDone)
  61                                         firstDone = true;
  62                                 count = 0;
  63                         }
  64                 }
  65         }
  66         filehandle.close();
  67 }
  68
  69 /*********************************************************************************/
  70 SequenceDB* ReadNexus::getDB() {
  71         return &sequencedb;
  72 }