readclustal.cpp

   1 /*
   2  *  readclustal.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 4/24/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "readclustal.h"
  11 #include <iostream>
  12 #include <fstream>
  13
  14 /*******************************************************************************/
  15 ReadClustal::ReadClustal(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 ReadClustal::~ReadClustal(){
  29 //      for(int i = 0; i < sequencedb.getNumSeqs(); i++)
  30 //              delete sequencedb.get(i);
  31 }
  32 /*******************************************************************************/
  33 void ReadClustal::read() {
  34         string temp;
  35         string name;
  36         string sequence;
  37         string firstName = "";
  38         for(int i = 0; i < 6; i++)
  39                 filehandle >> temp;
  40
  41         int count = 0;
  42         int numSeqs = 0;
  43         int lastSeqLength = 0;
  44         bool firstDone = false;
  45
  46         while(!filehandle.eof()) {
  47                 filehandle >> name;
  48                 if(numSeqs != 0) {
  49                         if(count == numSeqs)
  50                                 count = 0;
  51                 }
  52                 else if(!firstDone && firstName.compare("") == 0)
  53                         firstName = name;
  54                 else if(!firstDone && firstName.compare(name) == 0) {
  55                         numSeqs = count;
  56                         firstDone = true;
  57                         count = 0;
  58                 }
  59
  60                 if(name.find_first_of("*") == -1) {
  61                         filehandle >> sequence;
  62                         lastSeqLength = sequence.length();
  63                         if(!firstDone) {
  64                                 Sequence newSeq(name, sequence);
  65                                 sequencedb.add(newSeq);
  66                         }
  67                         else
  68                                 sequencedb.set(count, sequencedb.get(count).getUnaligned() + sequence);
  69
  70                         count++;
  71                 }
  72         }
  73         if(count == 1)
  74                 sequencedb.set(0, sequencedb.get(0).getUnaligned().substr(0, sequencedb.get(0).getUnaligned().length() - lastSeqLength));
  75
  76         filehandle.close();
  77 }
  78
  79 /*********************************************************************************/
  80 SequenceDB* ReadClustal::getDB() {
  81         return &sequencedb;
  82 }