Bio::Seq SeqBuilder
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::Seq::SeqBuilder - Configurable object builder for sequence stream parsers
Package variables
Privates (from "my" definitions)
%slot_param_map = ("add_SeqFeature" => "features", )
%param_slot_map = ("features" => "add_SeqFeature", )
Inherit
Bio::Factory::ObjectBuilderI Bio::Root::Root
Synopsis
   use Bio::SeqIO;
# usually you won't instantiate this yourself - a SeqIO object - # you will have one already my $seqin = Bio::SeqIO->new(-fh => \*STDIN, -format => "genbank"); my $builder = $seqin->sequence_builder(); # if you need only sequence, id, and description (e.g. for # conversion to FASTA format): $builder->want_none(); $builder->add_wanted_slot('display_id','desc','seq'); # if you want everything except the sequence and features $builder->want_all(1); # this is the default if it's untouched $builder->add_unwanted_slot('seq','features'); # if you want only human sequences shorter than 5kb and skip all # others $builder->add_object_condition(sub { my $h = shift; return 0 if $h->{'-length'} > 5000; return 0 if exists($h->{'-species'}) && ($h->{'-species'}->binomial() ne "Homo sapiens"); return 1; }); # when you are finished with configuring the builder, just use # the SeqIO API as you would normally while(my $seq = $seqin->next_seq()) { # do something }
Description
This is an implementation of Bio::Factory::ObjectBuilderI used by
parsers of rich sequence streams. It provides for a relatively
easy-to-use configurator of the parsing flow.
Configuring the parsing process may be for you if you need much less
information, or much less sequence, than the stream actually
contains. Configuration can in both cases speed up the parsing time
considerably, because unwanted sections or the rest of unwanted
sequences are skipped over by the parser. This configuration could
also conserve memory if you're running out of available RAM.
See the methods of the class-specific implementation section for
further documentation of what can be configured.
Methods
newDescriptionCode
want_slotDescriptionCode
add_slot_valueDescriptionCode
want_objectDescriptionCode
make_objectDescriptionCode
get_wanted_slotsDescriptionCode
add_wanted_slotDescriptionCode
remove_wanted_slotsDescriptionCode
get_unwanted_slotsDescriptionCode
add_unwanted_slotDescriptionCode
remove_unwanted_slotsDescriptionCode
want_noneDescriptionCode
want_allDescriptionCode
get_object_conditionsDescriptionCode
add_object_conditionDescriptionCode
remove_object_conditionsDescriptionCode
sequence_factoryDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Seq::SeqBuilder->new();
Function: Builds a new Bio::Seq::SeqBuilder object
Returns : an instance of Bio::Seq::SeqBuilder
Args :
want_slotcodeprevnextTop
 Title   : want_slot
Usage :
Function: Whether or not the object builder wants to populate the
specified slot of the object to be built.
The slot can be specified either as the name of the respective method, or the initialization parameter that would be otherwise passed to new() of the object to be built. Note that usually only the parser will call this method. Use add_wanted_slots and add_unwanted_slots for configuration. Example : Returns : TRUE if the object builder wants to populate the slot, and FALSE otherwise. Args : the name of the slot (a string)
add_slot_valuecodeprevnextTop
 Title   : add_slot_value
Usage :
Function: Adds one or more values to the specified slot of the object
to be built.
Naming the slot is the same as for want_slot(). The object builder may further filter the content to be set, or even completely ignore the request. If this method reports failure, the caller should not add more values to the same slot. In addition, the caller may find it appropriate to abandon the object being built altogether. This implementation will allow the caller to overwrite the return value from want_slot(), because the slot is not checked against want_slot(). Note that usually only the parser will call this method, but you may call it from anywhere if you know what you are doing. A derived class may be used to further manipulate the value to be added. Example : Returns : TRUE on success, and FALSE otherwise Args : the name of the slot (a string) parameters determining the value to be set OR alternatively, a list of slotname/value pairs in the style of named parameters as they would be passed to new(), where each element at an even index is the parameter (slot) name starting with a dash, and each element at an odd index is the value of the preceding name.
want_objectcodeprevnextTop
 Title   : want_object
Usage :
Function: Whether or not the object builder is still interested in
continuing with the object being built.
If this method returns FALSE, the caller should not add any more values to slots, or otherwise risks that the builder throws an exception. In addition, make_object() is likely to return undef after this method returned FALSE. Note that usually only the parser will call this method. Use add_object_condition for configuration. Example : Returns : TRUE if the object builder wants to continue building the present object, and FALSE otherwise. Args : none
make_objectcodeprevnextTop
 Title   : make_object
Usage :
Function: Get the built object.
This method is allowed to return undef if no value has ever been added since the last call to make_object(), or if want_object() returned FALSE (or would have returned FALSE) before calling this method. For an implementation that allows consecutive building of objects, a caller must call this method once, and only once, between subsequent objects to be built. I.e., a call to make_object implies 'end_object.' Example : Returns : the object that was built Args : none
get_wanted_slotscodeprevnextTop
 Title   : get_wanted_slots
Usage : $obj->get_wanted_slots($newval)
Function: Get the list of wanted slots
Example :
Returns : a list of strings
Args :
add_wanted_slotcodeprevnextTop
 Title   : add_wanted_slot
Usage :
Function: Adds the specified slots to the list of wanted slots.
Example :
Returns : TRUE
Args : an array of slot names (strings)
remove_wanted_slotscodeprevnextTop
 Title   : remove_wanted_slots
Usage :
Function: Removes all wanted slots added previously through
add_wanted_slots().
Example :
Returns : the previous list of wanted slot names
Args : none
get_unwanted_slotscodeprevnextTop
 Title   : get_unwanted_slots
Usage : $obj->get_unwanted_slots($newval)
Function: Get the list of unwanted slots.
Example :
Returns : a list of strings
Args : none
add_unwanted_slotcodeprevnextTop
 Title   : add_unwanted_slot
Usage :
Function: Adds the specified slots to the list of unwanted slots.
Example :
Returns : TRUE
Args : an array of slot names (strings)
remove_unwanted_slotscodeprevnextTop
 Title   : remove_unwanted_slots
Usage :
Function: Removes the list of unwanted slots added previously through
add_unwanted_slots().
Example :
Returns : the previous list of unwanted slot names
Args : none
want_nonecodeprevnextTop
 Title   : want_none
Usage :
Function: Disables all slots. After calling this method, want_slot()
will return FALSE regardless of slot name.
This is different from removed_wanted_slots() in that it also sets want_all() to FALSE. Note that it also resets the list of unwanted slots in order to avoid slots being in both lists. Example : Returns : TRUE Args : none
want_allcodeprevnextTop
 Title   : want_all
Usage : $obj->want_all($newval)
Function: Whether or not this sequence object builder wants to
populate all slots that the object has. Whether an object
supports a slot is generally determined by what can()
returns. You can add additional 'virtual' slots by calling
add_wanted_slot.
This will be ON by default. Call $obj->want_none() to disable all slots. Example : Returns : TRUE if this builder wants to populate all slots, and FALSE otherwise. Args : on set, new value (a scalar or undef, optional)
get_object_conditionscodeprevnextTop
 Title   : get_object_conditions
Usage :
Function: Get the list of conditions an object must meet in order to
be 'wanted.' See want_object() for where this is used.
Conditions in this implementation are closures (anonymous functions) which are passed one parameter, a hash reference the keys of which are equal to initialization paramaters. The closure must return TRUE to make the object 'wanted.' Conditions will be implicitly ANDed. Example : Returns : a list of closures Args : none
add_object_conditioncodeprevnextTop
 Title   : add_object_condition
Usage :
Function: Adds a condition an object must meet in order to be 'wanted.'
See want_object() for where this is used.
Conditions in this implementation must be closures (anonymous functions). These will be passed one parameter, which is a hash reference with the sequence object initialization parameters being the keys. Conditions are implicitly ANDed. If you want other operators, perform those tests inside of one closure instead of multiple. This will also be more efficient. Example : Returns : TRUE Args : the list of conditions
remove_object_conditionscodeprevnextTop
 Title   : remove_object_conditions
Usage :
Function: Removes the conditions an object must meet in order to be
'wanted.'
Example :
Returns : The list of previously set conditions (an array of closures)
Args : none
sequence_factorycodeprevnextTop
 Title   : sequence_factory
Usage : $obj->sequence_factory($newval)
Function: Get/set the sequence factory to be used by this object
builder.
Example :
Returns : the Bio::Factory::SequenceFactoryI implementing object to use
Args : on set, new value (a Bio::Factory::SequenceFactoryI
implementing object or undef, optional)
Methods code
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;

    my $self = $class->SUPER::new(@args);

    $self->{'wanted_slots'} = [];
    $self->{'unwanted_slots'} = [];
    $self->{'object_conds'} = [];
    $self->{'_objhash'} = {};
    $self->want_all(1);

    return $self;
}
want_slotdescriptionprevnextTop
sub want_slot {
	my ($self,$slot) = @_;
	my $ok = 0;

	$slot = substr($slot,1) if substr($slot,0,1) eq '-';
	if($self->want_all()) {
	foreach ($self->get_unwanted_slots()) {
		# this always overrides in want-all mode
return 0 if($slot eq $_); } if(! exists($self->{'_objskel'})) { $self->{'_objskel'} = $self->sequence_factory->create_object(); } if(exists($param_slot_map{$slot})) { $ok = $self->{'_objskel'}->can($param_slot_map{$slot}); } else { $ok = $self->{'_objskel'}->can($slot); } return $ok if $ok; # even if the object 'cannot' do this slot, it might have been
# added to the list of wanted slot, so carry on
} foreach ($self->get_wanted_slots()) { if($slot eq $_) { $ok = 1; last; } } return $ok;
}
add_slot_valuedescriptionprevnextTop
sub add_slot_value {
	my ($self,$slot,@args) = @_;

	my $h = $self->{'_objhash'};
	return unless $h;
	# multiple named parameter variant of calling?
if((@args > 1) && (@args % 2) && (substr($slot,0,1) eq '-')) { unshift(@args, $slot); while(@args) { my $key = shift(@args); $h->{$key} = shift(@args); } } else { if($slot eq 'add_SeqFeature') { $slot = '-'.$slot_param_map{$slot}; $h->{$slot} = [] unless $h->{$slot}; push(@{$h->{$slot}}, @args); } else { $slot = '-'.$slot unless substr($slot,0,1) eq '-'; $h->{$slot} = $args[0]; } } return 1;
}
want_objectdescriptionprevnextTop
sub want_object {
	my $self = shift;

	my $ok = 1;
	foreach my $cond ($self->get_object_conditions()) {
		$ok = &$cond($self->{'_objhash'});
		last unless $ok;
	}
	delete $self->{'_objhash'} unless $ok;
	return $ok;
}
make_objectdescriptionprevnextTop
sub make_object {
	my $self = shift;

	my $obj;
	if(exists($self->{'_objhash'}) && %{$self->{'_objhash'}}) {
		$obj = $self->sequence_factory->create_object(%{$self->{'_objhash'}});
	}
	$self->{'_objhash'} = {}; # reset
return $obj;
}
get_wanted_slotsdescriptionprevnextTop
sub get_wanted_slots {
	my $self = shift;

	return @{$self->{'wanted_slots'}};
}
add_wanted_slotdescriptionprevnextTop
sub add_wanted_slot {
	my ($self,@slots) = @_;

	my $myslots = $self->{'wanted_slots'};
	foreach my $slot (@slots) {
		if(! grep { $slot eq $_; } @$myslots) {
			push(@$myslots, $slot);
		}
	}
	return 1;
}
remove_wanted_slotsdescriptionprevnextTop
sub remove_wanted_slots {
	my $self = shift;
	my @slots = $self->get_wanted_slots();
	$self->{'wanted_slots'} = [];
	return @slots;
}
get_unwanted_slotsdescriptionprevnextTop
sub get_unwanted_slots {
	my $self = shift;

	return @{$self->{'unwanted_slots'}};
}
add_unwanted_slotdescriptionprevnextTop
sub add_unwanted_slot {
	my ($self,@slots) = @_;

	my $myslots = $self->{'unwanted_slots'};
	foreach my $slot (@slots) {
		if(! grep { $slot eq $_; } @$myslots) {
			push(@$myslots, $slot);
		}
	}
	return 1;
}
remove_unwanted_slotsdescriptionprevnextTop
sub remove_unwanted_slots {
	my $self = shift;
	my @slots = $self->get_unwanted_slots();
	$self->{'unwanted_slots'} = [];
	return @slots;
}
want_nonedescriptionprevnextTop
sub want_none {
	my $self = shift;

	$self->want_all(0);
	$self->remove_wanted_slots();
	$self->remove_unwanted_slots();
	return 1;
}
want_alldescriptionprevnextTop
sub want_all {
	my $self = shift;

	return $self->{'want_all'} = shift if @_;
	return $self->{'want_all'};
}
get_object_conditionsdescriptionprevnextTop
sub get_object_conditions {
	my $self = shift;

	return @{$self->{'object_conds'}};
}
add_object_conditiondescriptionprevnextTop
sub add_object_condition {
	my ($self,@conds) = @_;

	if(grep { ref($_) ne 'CODE'; } @conds) {
		$self->throw("conditions against which to validate an object ".
						 "must be anonymous code blocks");
	}
	push(@{$self->{'object_conds'}}, @conds);
	return 1;
}
remove_object_conditionsdescriptionprevnextTop
sub remove_object_conditions {
	my $self = shift;
	my @conds = $self->get_object_conditions();
	$self->{'object_conds'} = [];
	return @conds;
}
sequence_factorydescriptionprevnextTop
sub sequence_factory {
	my $self = shift;

	if(@_) {
		delete $self->{'_objskel'};
		return $self->{'sequence_factory'} = shift;
	}
	return $self->{'sequence_factory'};
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Hilmar LappTop
Email hlapp at gmx.net
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Methods for implementing Bio::Factory::ObjectBuilderITop
Implementation specific methodsTop
These methods allow to conveniently configure this sequence object
builder as to which slots are desired, and under which circumstances a
sequence object should be abandoned altogether. The default mode is
want_all(1), which means the builder will report all slots as wanted
that the object created by the sequence factory supports.
You can add specific slots you want through add_wanted_slots(). In
most cases, you will want to call want_none() before in order to relax
zero acceptance through a list of wanted slots.
Alternatively, you can add specific unwanted slots through
add_unwanted_slots(). In this case, you will usually want to call
want_all(1) before (which is the default if you never touched the
builder) to restrict unrestricted acceptance.
I.e., want_all(1) means want all slots except for the unwanted, and
want_none() means only those explicitly wanted.
If a slot is in both the unwanted and the wanted list, the following
rules hold. In want-all mode, the unwanted list overrules. In
want-none mode, the wanted list overrides the unwanted list. If this
is confusing to you, just try to avoid having slots at the same time
in the wanted and the unwanted lists.
Methods to control what type of object is builtTop