readclustal.cpp

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