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Bio::DB::Map::SQL::MarkerAdaptor
Adaptor Object for Markers

Bio::DB::Map::SQL::MarkerAdaptor - Adaptor Object for Markers


NAME

Bio::DB::Map::SQL::MarkerAdaptor - Adaptor Object for Markers


SYNOPSIS

Give standard usage here


DESCRIPTION

Describe the object here


FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.


  bioperl-l@bioperl.org             - General discussion

  http://bioperl.org/MailList.shtml - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:


  bioperl-bugs@bioperl.org

  http://bioperl.org/bioperl-bugs/


AUTHOR - Jason Stajich

Email jason@chg.mc.duke.edu

Describe contact details here


APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

get


 Title   : get

 Usage   : my @markers = $markeradaptor->get(-ids => \@ids );

 Function: gets a list of Bio::DB::Map::Marker objects based on

           the list of queries

 Returns : list of Bio::DB::Map::Marker objects

 Args    : -id   => markerid

           -ids  => array ref of marker ids

           -name => marker name

           -names=> array ref of marker names

           -pcrprimers => array ref of pcrprimers to use to search for marker  

=cut

sub get { my ($self, @args) = @_; my ($id, $ids, $name, $names, $pcrprimers ) = $self->_rearrange( [qw(ID IDS NAME NAMES PCRPRIMERS )], @args );


    my (@n, @i);

    

    # for now we will ignore bad users who specify > 1 argument

    # by just handling input in a precedence order.    

    

    if( defined $pcrprimers ) {

        # pcr primers trump all for now

        if( ref($pcrprimers) !~ /array/i || 

            scalar @$pcrprimers != 2 ) {

            $self->warn("Did not supply a 2-entry array ref or paramer -pcrprimers");

            return undef;

        }

        return $self->_get_marker_by_primers(@$pcrprimers);

    }

    

    

    if( defined $names ) {

        if( ref($names) !~ /array/i ) {

            $self->warn("Must specify an array ref for the parameter -names");

            return undef;

        }

        @n = @$names;       

    } elsif( defined $name ) {

        @n = ($name);   

    }

    if( defined $ids ) {

        if( ref($ids ) !~ /array/i ) {

            $self->warn("Must specify an array ref for the parameter - ids");

            return undef;

        }       

        @i = @$ids;

    } elsif( defined $id ) {

        @i = ($id);

    } 

    if( ! @i && ! @n ) {

        $self->warn("did not pass in appropriate arguments to get!");

        return ();

    }

    # should we try and be sure that the lists produce a unique list?    

    return ( $self->_get_markers_by_ids(@i),

             $self->_get_markers_by_names(@n) );

}

write


 Title   : write

 Usage   : $marker_adaptor->write($marker);

 Function: Store a new Marker or update an existing one 

 Returns : Bio::DB::Map::MarkerI object (id updated if necessary)

           or undef if not properly updated 

 Args    : Bio::DB::Map::MarkerI object

delete


 Title   : delete

 Usage   : $markeradaptor->delete($marker);

 Function: Removes a marker from the database

 Returns : none

 Args    : Bio::DB::Map::MarkerI object

add_duplicate_marker


 Title   : add_marker_duplicate_marker

 Usage   : boolean $adaptor->add_duplicate_marker($marker ); 

 Function: Tries to find a duplicate marker for a marker and 

           updates it to contain merge of the two information srcs

 Returns : boolean if marker was added

 Args    : Bio::DB::Map::MarkerI object
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