BioMart
AttributeTable
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Summary
BioMart::AttributeTable
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
AttributeTables provide access to one or more rows of attribute values, each
containing one or more columns. They are used as placeholders for filters,
and BioMart::ResultTable objects inherit their functionality, and extend them.
Description
An AttributeTable object contains a table of data in rows and columns (the
minimal table being 1 X 1). It can be used in a variety of contexts within
the BioMart system.
It can be set as the value in a BioMart::Configuration::ValueFilter or
BioMart::Configuration::FilterList object to be used in a Query against a
dataset. BioMart::ResultTable objects inherit all functionality from
BioMart::AttributeTable, and extends it.
It basically presents a FIFO stack of array_ref objects. Adding a row pushes
this onto the stack, increasing its size by 1. Getting a row shifts an
array_ref from the stack, decreasing its size by 1. Thus, it is possible for
an AttributeTable to be exhausted, whereby the next call to getRow will return
null. This can be avoided by prefacing each call to next_row with a call to
hasMoreRows.
Methods
Methods description
Usage : my $attTable = BioMart::AttributeTable->new();
Description: creates a new AttributeTable object.
Returntype : BioMart::Configuration::AttributeTable
Exceptions : none
Caller : general |
Usage : $attTable->addRow($row);
Description: adds a row (array_ref) of data to the AttributeTable.
Note, values from array_ref are harvested to avoid
unintended reference operations.
Returntype : none
Exceptions : none
Caller : caller |
Usage : if ($table->hasMoreRows) { ... }
Descripton : Determine if an AttributeTable has rows remaining to be
processed.
Note that the return for this method is currently the number of
rows remaining, but this may change in the future.
Returntype : boolean, >1 (true) if there are more rows, 0 (false) otherwise
Exceptions : none
Caller : caller |
Usage : my $row = $attTable->nextRow; foreach my $col (@{$row}) { ... }
Description: returns a reference to the next row of data.
Returntype : array_ref. This returns null if the table is exhausted
Problems associated with this can be avoided by prefacing
each call to nextRow with a test of hasMoreRows.
Exceptions : none
Caller : caller |
Methods code
sub _hashCode
{ my $self = shift;
return $self->get('hc');
}
1;} | sub _new
{ my ($self, @param) = @_;
$self->SUPER::_new(@param);
$self->attr('columns', []);
$self->attr('hashedResults', undef);
my $digest = Digest::MD5->new;
$digest->add(scalar localtime);
$self->attr('hc', $digest->hexdigest);} | sub addRow
{ my ($self,$row) = @_;
my $columns = $self->get('columns');
push @{$columns}, [ @{ $row } ];
$self->set('columns',$columns);
} | sub addRows
{ my ($self,$rows) = @_;
my $columns = $self->get('columns');
push @{$columns}, @{ $rows };
$self->set('columns',$columns);
} | sub getRows
{
my $self = shift;
return $self->get('columns');} | sub hasMoreRows
{ my $self = shift;
my $columns = $self->get('columns');
my $ret = @{$columns};
return $ret;} | sub hashedResults
{ my ($self,$value) = @_;
if ($value){
$self->set('hashedResults',$value);
}
return $self->get('hashedResults');} | sub nextRow
{ my $self = shift;
if ($self->hasMoreRows) {
my $columns = $self->get('columns');
my $rowref = shift @{$columns};
$self->set('columns', $columns);
return $rowref;
}
return undef;
}
} | sub setRows
{ my ($self,$rows) = @_;
$self->set('columns',$rows);} | General documentation
| AUTHOR - Arek Kasprzyk, Syed Haider, Darin London, Damian Smedley | Top |