/ 
Prospect-0.92
River stage zero No dependents
/ Prospect::ThreadSummary

NAME

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

$Id: ThreadSummary.pm,v 1.14 2003/11/04 01:01:33 cavs 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 Prospect::Thread( $xml );
my $s = new Prospect::ThreadSummary( $t );
 
print "qname: "     . $s->qname() . "\n";
print "tname: "     . $s->tname() . "\n";
print "raw_score: " . $s->raw_score() . "\n";

DESCRIPTION

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