NAME

Bio::Prospect::ThreadSummary - Distilled version of a Bio::Prospect::Thread

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

SYNOPSIS

 my $in  = new IO::File  $ARGV[0]   or die( "can't open $ARGV[0] for reading" );
 my $xml = '';
 while(<$in>) { $xml .= $_; }
 close($in);
  
 my $t = new Bio::Prospect::Thread( $xml );
 my $s = new Bio::Prospect::ThreadSummary( $t );
  
 print "qname: "     . $s->qname() . "\n";
 print "tname: "     . $s->tname() . "\n";
 print "raw_score: " . $s->raw_score() . "\n";

DESCRIPTION

Bio::Prospect::ThreadSummary -- Distilled version of a Bio::Prospect::Thread. Only contains score and position information, no sequences or alignments.

TODO

Integrate exception handling

METHODS

new()

 Name:      new()
 Purpose:   return ThreadSummary object
 Arguments: Bio::Prospect::Thread
 Returns:   Bio::Prospect::ThreadSummary

qname()

 Name:      qname()
 Purpose:   return the name of the query sequence
 Arguments: none
 Returns:   string

qstart()

 Name:      qstart()
 Purpose:   return the start of the alignment on the query sequence
 Arguments: none
 Returns:   integer

qend()

 Name:      qend()
 Purpose:   return the end of the alignment on the query sequence
 Arguments: none
 Returns:   integer

target_start()

 Name:      target_start()
 Purpose:   return the start position of the query sequence
 Arguments: none
 Returns:   integer

target_end()

 Name:      target_end()
 Purpose:   return the end position of the query sequence
 Arguments: none
 Returns:   integer

tname()

 Name:      tname()
 Purpose:   return the name of the template sequence
 Arguments: none
 Returns:   string

tstart()

 Name:      tstart()
 Purpose:   return the start of the alignment on the template sequence
 Arguments: none
 Returns:   integer

tend()

 Name:      tend()
 Purpose:   return the end of the alignment on the template sequence
 Arguments: none
 Returns:   integer

template_start()

 Name:      template_start()
 Purpose:   return the start of the alignment on the template sequence.
 Arguments: none
 Returns:   integer

template_end()

 Name:      template_end()
 Purpose:   return the end of the alignment on the template sequence.
 Arguments: none
 Returns:   integer

align_len()

 Name:      align_len()
 Purpose:   length of the alignment
 Arguments: none
 Returns:   integer

identities()

 Name:      identities()
 Purpose:   number of identities
 Arguments: none
 Returns:   integer

svm_score()

 Name:      svm_score()
 Purpose:   return the svm score
 Arguments: none
 Returns:   float

raw_score()

 Name:      raw_score()
 Purpose:   return the raw score
 Arguments: none
 Returns:   float

gap_score()

 Name:      gap_score()
 Purpose:   return the gap score
 Arguments: none
 Returns:   float

mutation_score()

 Name:      mutation_score()
 Purpose:   return the mutation score
 Arguments: none
 Returns:   float

ssfit_score()

 Name:      ssfit_score()
 Purpose:   return the ssfit score
 Arguments: none
 Returns:   float

pair_score()

 Name:      pair_score()
 Purpose:   return the pairwise score
 Arguments: none
 Returns:   float

singleton_score()

 Name:      singleton_score()
 Purpose:   return the singletonwise score
 Arguments: none
 Returns:   float

rgyr()

 Name:      rgyr()
 Purpose:   return the radius of gyration
 Arguments: none
 Returns:   float

INTERNAL METHODS & ROUTINES

The following functions are documented for developers' benefit. THESE SHOULD NOT BE CALLED OUTSIDE OF THIS MODULE. YOU'VE BEEN WARNED.

_init()

 Name:      _init()
 Purpose:   build ThreadSummary object from Thread object
 Arguments: none
 Returns:   none

cpanm Bio::Prospect::File

perl -MCPAN -e shell
install Bio::Prospect::File