#
# BioPerl module for Bio::Seq::SeqBuilder
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Hilmar Lapp <hlapp at gmx.net>
#
# Copyright Hilmar Lapp
#
# You may distribute this module under the same terms as perl itself
#
# (c) Hilmar Lapp, hlapp at gmx.net, 2002.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# POD documentation - main docs before the code
=head1 NAME
Bio::Seq::SeqBuilder - Configurable object builder for sequence stream parsers
=head1 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
}
=head1 DESCRIPTION
This is an implementation of L<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.
=head1 FEEDBACK
=head2 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/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 Reporting Bugs
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://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Hilmar Lapp
Email hlapp at gmx.net
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Seq::SeqBuilder;
use strict;
# Object preamble - inherits from Bio::Root::Root
use base qw(Bio::Root::Root Bio::Factory::ObjectBuilderI);
my %slot_param_map = ("add_SeqFeature" => "features",
);
my %param_slot_map = ("features" => "add_SeqFeature",
);
=head2 new
Title : new
Usage : my $obj = Bio::Seq::SeqBuilder->new();
Function: Builds a new Bio::Seq::SeqBuilder object
Returns : an instance of Bio::Seq::SeqBuilder
Args :
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->{'wanted_slots'} = [];
$self->{'unwanted_slots'} = [];
$self->{'object_conds'} = [];
$self->{'_objhash'} = {};
$self->want_all(1);
return $self;
}
=head1 Methods for implementing L<Bio::Factory::ObjectBuilderI>
=cut
=head2 want_slot
Title : want_slot
Usage :
Function: Whether or not the object builder wants to populate the
specified slot of the object to be built.
The slot can be specified either as the name of the
respective method, or the initialization parameter that
would be otherwise passed to new() of the object to be
built.
Note that usually only the parser will call this
method. Use add_wanted_slots and add_unwanted_slots for
configuration.
Example :
Returns : TRUE if the object builder wants to populate the slot, and
FALSE otherwise.
Args : the name of the slot (a string)
=cut
sub want_slot{
my ($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 $ok;
}
=head2 add_slot_value
Title : add_slot_value
Usage :
Function: Adds one or more values to the specified slot of the object
to be built.
Naming the slot is the same as for want_slot().
The object builder may further filter the content to be
set, or even completely ignore the request.
If this method reports failure, the caller should not add
more values to the same slot. In addition, the caller may
find it appropriate to abandon the object being built
altogether.
This implementation will allow the caller to overwrite the
return value from want_slot(), because the slot is not
checked against want_slot().
Note that usually only the parser will call this method,
but you may call it from anywhere if you know what you are
doing. A derived class may be used to further manipulate
the value to be added.
Example :
Returns : TRUE on success, and FALSE otherwise
Args : the name of the slot (a string)
parameters determining the value to be set
OR
alternatively, a list of slotname/value pairs in the style
of named parameters as they would be passed to new(), where
each element at an even index is the parameter (slot) name
starting with a dash, and each element at an odd index is
the value of the preceding name.
=cut
sub add_slot_value{
my ($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;
}
=head2 want_object
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
=cut
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;
}
=head2 make_object
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
=cut
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;
}
=head1 Implementation specific methods
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.
=cut
=head2 get_wanted_slots
Title : get_wanted_slots
Usage : $obj->get_wanted_slots($newval)
Function: Get the list of wanted slots
Example :
Returns : a list of strings
Args :
=cut
sub get_wanted_slots{
my $self = shift;
return @{$self->{'wanted_slots'}};
}
=head2 add_wanted_slot
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)
=cut
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;
}
=head2 remove_wanted_slots
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
=cut
sub remove_wanted_slots{
my $self = shift;
my @slots = $self->get_wanted_slots();
$self->{'wanted_slots'} = [];
return @slots;
}
=head2 get_unwanted_slots
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
=cut
sub get_unwanted_slots{
my $self = shift;
return @{$self->{'unwanted_slots'}};
}
=head2 add_unwanted_slot
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)
=cut
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;
}
=head2 remove_unwanted_slots
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
=cut
sub remove_unwanted_slots{
my $self = shift;
my @slots = $self->get_unwanted_slots();
$self->{'unwanted_slots'} = [];
return @slots;
}
=head2 want_none
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
=cut
sub want_none{
my $self = shift;
$self->want_all(0);
$self->remove_wanted_slots();
$self->remove_unwanted_slots();
return 1;
}
=head2 want_all
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)
=cut
sub want_all{
my $self = shift;
return $self->{'want_all'} = shift if @_;
return $self->{'want_all'};
}
=head2 get_object_conditions
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
=cut
sub get_object_conditions{
my $self = shift;
return @{$self->{'object_conds'}};
}
=head2 add_object_condition
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
=cut
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;
}
=head2 remove_object_conditions
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
=cut
sub remove_object_conditions{
my $self = shift;
my @conds = $self->get_object_conditions();
$self->{'object_conds'} = [];
return @conds;
}
=head1 Methods to control what type of object is built
=cut
=head2 sequence_factory
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)
=cut
sub sequence_factory{
my $self = shift;
if(@_) {
delete $self->{'_objskel'};
return $self->{'sequence_factory'} = shift;
}
return $self->{'sequence_factory'};
}
1;