Prospect::ThreadSummary - Distilled version of a Prospect::Thread
$Id: ThreadSummary.pm,v 1.14 2003/11/04 01:01:33 cavs Exp $
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";
Prospect::ThreadSummary -- Distilled version of a Prospect::Thread. Only contains score and position information, no sequences or alignments.
Integrate exception handling
Name: new() Purpose: return ThreadSummary object Arguments: Prospect::Thread Returns: Prospect::ThreadSummary
Name: qname() Purpose: return the name of the query sequence Arguments: none Returns: string
Name: qstart() Purpose: return the start of the alignment on the query sequence Arguments: none Returns: integer
Name: qend() Purpose: return the end of the alignment on the query sequence Arguments: none Returns: integer
Name: target_start() Purpose: return the start position of the query sequence Arguments: none Returns: integer
Name: target_end() Purpose: return the end position of the query sequence Arguments: none Returns: integer
Name: tname() Purpose: return the name of the template sequence Arguments: none Returns: string
Name: tstart() Purpose: return the start of the alignment on the template sequence Arguments: none Returns: integer
Name: tend() Purpose: return the end of the alignment on the template sequence Arguments: none Returns: integer
Name: template_start() Purpose: return the start of the alignment on the template sequence. Arguments: none Returns: integer
Name: template_end() Purpose: return the end of the alignment on the template sequence. Arguments: none Returns: integer
Name: align_len() Purpose: length of the alignment Arguments: none Returns: integer
Name: identities() Purpose: number of identities Arguments: none Returns: integer
Name: svm_score() Purpose: return the svm score Arguments: none Returns: float
Name: raw_score() Purpose: return the raw score Arguments: none Returns: float
Name: gap_score() Purpose: return the gap score Arguments: none Returns: float
Name: mutation_score() Purpose: return the mutation score Arguments: none Returns: float
Name: ssfit_score() Purpose: return the ssfit score Arguments: none Returns: float
Name: pair_score() Purpose: return the pairwise score Arguments: none Returns: float
Name: singleton_score() Purpose: return the singletonwise score Arguments: none Returns: float
Name: rgyr() Purpose: return the radius of gyration Arguments: none Returns: float
The following functions are documented for developers' benefit. THESE SHOULD NOT BE CALLED OUTSIDE OF THIS MODULE. YOU'VE BEEN WARNED.
Name: _init() Purpose: build ThreadSummary object from Thread object Arguments: none Returns: none
To install Prospect::File, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Prospect::File
CPAN shell
perl -MCPAN -e shell install Prospect::File
For more information on module installation, please visit the detailed CPAN module installation guide.