Bio::Prospect::File -- interface to Prospect Files

$Id: File.pm,v 1.15 2003/11/18 19:45:45 rkh Exp $

 use Bio::Prospect::File;

 my $pf = new Bio::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();
 }

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

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

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

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

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

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

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