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revision 1.71, Sun Jun 25 00:07:22 2006 UTC revision 1.74, Sun Jun 25 07:34:46 2006 UTC
# Line 1804  Line 1804 
1804      my ($self, $peg1, $peg2) = @_;      my ($self, $peg1, $peg2) = @_;
1805      # Declare the return values. We'll start with the coupling ID and undefine the      # Declare the return values. We'll start with the coupling ID and undefine the
1806      # flag and score until we have more information.      # flag and score until we have more information.
1807      my ($retVal, $inverted, $score) = (CouplingID($peg1, $peg2), undef, undef);      my ($retVal, $inverted, $score) = ($self->CouplingID($peg1, $peg2), undef, undef);
1808      # Find the coupling data.      # Find the coupling data.
1809      my @pegs = $self->GetAll(['Coupling', 'ParticipatesInCoupling'],      my @pegs = $self->GetAll(['Coupling', 'ParticipatesInCoupling'],
1810                                   "Coupling(id) = ? ORDER BY ParticipatesInCoupling(pos)",                                   "Coupling(id) = ? ORDER BY ParticipatesInCoupling(pos)",
# Line 1825  Line 1825 
1825      return ($retVal, $inverted, $score);      return ($retVal, $inverted, $score);
1826  }  }
1827    
1828    =head3 GetSynonymGroup
1829    
1830    C<< my $id = $sprout->GetSynonymGroup($fid); >>
1831    
1832    Return the synonym group name for the specified feature.
1833    
1834    =over 4
1835    
1836    =item fid
1837    
1838    ID of the feature whose synonym group is desired.
1839    
1840    =item RETURN
1841    
1842    The name of the synonym group to which the feature belongs. If the feature does
1843    not belong to a synonym group, the feature ID itself is returned.
1844    
1845    =back
1846    
1847    =cut
1848    
1849    sub GetSynonymGroup {
1850        # Get the parameters.
1851        my ($self, $fid) = @_;
1852        # Declare the return variable.
1853        my $retVal;
1854        # Find the synonym group.
1855        my @groups = $self->GetFlat(['IsSynonymGroupFor'], "IsSynonymGroupFor(to-link) = ?",
1856                                       [$fid], 'IsSynonymGroupFor(from-link)');
1857        # Check to see if we found anything.
1858        if (@groups) {
1859            $retVal = $groups[0];
1860        } else {
1861            $retVal = $fid;
1862        }
1863        # Return the result.
1864        return $retVal;
1865    }
1866    
1867  =head3 CouplingID  =head3 CouplingID
1868    
1869  C<< my $couplingID = Sprout::CouplingID($peg1, $peg2); >>  C<< my $couplingID = $sprout->CouplingID($peg1, $peg2); >>
1870    
1871  Return the coupling ID for a pair of feature IDs.  Return the coupling ID for a pair of feature IDs.
1872    
# Line 1860  Line 1899 
1899  =cut  =cut
1900  #: Return Type $;  #: Return Type $;
1901  sub CouplingID {  sub CouplingID {
1902      return join " ", sort @_;      my ($self, @pegs) = @_;
1903        return $self->DigestKey(join " ", sort @pegs);
1904  }  }
1905    
1906  =head3 ReadFasta  =head3 ReadFasta

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