NAME

Prospect::File -- interface to Prospect Files

$Id: File.pm,v 1.14 2003/11/07 00:45:28 cavs Exp $

SYNOPSIS

            

              
              
use Prospect::File;
my $pf = new Prospect::File( $fn );
while( my $t = $pf->next_thread() ) {
  printf("%s->%s   raw=%d mut=%d pair=%d\n",
     $t->qname(), $t->tname(), $t->raw_score(), 
     $t->mutation_score(), $t->pair_score() );
  print $t->alignment();
}
            
          

DESCRIPTION

Prospect::File is a subclass of IO::File and is intended for use for parsing Prospect XML files. It is used by Prospect::LocalClient to return Thread objects from Prospect output.

METHODS

new()

            

              
              
Name:      new()
Purpose:   constructor
Arguments: 
Returns:   Prospect::File
            
          

fdopen()

            

              
              
Name:      fdopen()
Purpose:   overrides fdopen in IO::File
Arguments: same as IO::File::fdopen
Returns:   nothing
            
          

open()

            

              
              
Name:      open()
Purpose:   overrides open in IO::File
Arguments: same as IO::File::open
Returns:   nothing
            
          

next_thread()

            

              
              
Name:      next_thread()
Purpose:   return next Thread object
Arguments: none
Returns:   Prospect::Thread
            
          

next_thread_as_xml()

            

              
              
Name:      next_thread_as_xml()
Purpose:   return next threading xml tag
Arguments: none
Returns:   xml string
            
          

fdopen()

            

              
              
Name:      _advance()
Purpose:   INTERNAL METHOD: check if proper Prospect xml
Arguments: none
Returns:   1 - okay, 0 - bad xml