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Summary

Bio::Search::Iteration::GenericIteration - A generic implementation of the Bio::Search::Iteration::IterationI interface.

Package variables

Inherit

Bio::Root::Root Bio::Search::Iteration::IterationI

Synopsis

    use Bio::Search::Iteration::GenericIteration;
    my $it = Bio::Search::GenericIteration->new(
                              -number => 1,
                              -converged => 0,
                              -newhits_unclassified => [@newhits_unclass],
                              -newhits_below => [@newhits_below_threshold],
                              -newhits_not_below => [@newhits_not_below_threshold],
                              -oldhits_below => [@oldhits_below_threshold],
                              -oldhits_newly_below => [@oldhits_newly_below_threshold],
                              -oldhits_not_below => [@oldhits_not_below_threshold],
                                        );

# TODO: Describe how to configure a SearchIO stream so that it generates
# GenericIteration objects.

Description

This module acts as a container for Bio::Search::Hit::HitI objects,
allowing a Search::Result::ResultI object to partition its hits based
on which iteration the hit occurred in (e.g., a PSI-BLAST round).
Unless you're writing a parser, you won't ever need to create a
GenericIteration or any other IterationI-implementing object. If you use
the SearchIO system, IterationI objects are created automatically from
a SearchIO stream which returns Bio::Search::Result::ResultI objects
and you get the IterationI objects via the ResultI API.
For documentation on what you can do with GenericIteration (and other IterationI
objects), please see the API documentation in
Bio::Search::Iteration::IterationI.
Bio::Search::Iteration::GenericIteration is similar in spirit to the deprecated
Bio::Tools::BPlite::Iteration modules in bioperl releases prior to 1.6, except
that Bio::Search::Iteration::GenericIteration is a pure container, without any
parsing functionality as is in Bio::Tools::BPlite::Iteration.

Methods

Methods description

 Title   : new
 Usage   : my $obj = Bio::Search::Iteration->new(%args);
 Function: Builds a new Bio::Search::Iteration object 
 Returns : Bio::Search::Iteration::GenericIteration object
 Args    : -number => integer for the number of this iteration (required)
           -converged => boolean value whether or not the iteration converged
           -newhits_unclassified => array reference to hits that were not found
                       in a previous iteration for the iteration and have not been 
                       classified with regard to the inclusion threshold

           # The following are only used for PSI-BLAST reports:

           -newhits_below => array reference to hits were not found in a 
                        previous iteration and are below the inclusion threshold.
           -newhits_not_below => array reference to hits that were not found in a 
                        previous iteration below threshold that and are not below 
                        the inclusion threshold threshold.
           -oldhits_below => array reference to hits that were found
                        in a previous iteration below inclusion threshold and are
                        still below threshold in the current iteration.
           -oldhits_newly_below => array reference to hits that were found
                        in a previous iteration above threshold but are below
                        threshold in the current iteration.
           -oldhits_not_below => array reference to hits that were found in a
                        previous iteration above threshold that and are still above
                        the inclusion threshold threshold.

           -hit_factory => Bio::Factory::ObjectFactoryI capable of making
                        Bio::Search::Hit::HitI objects

 Title   : hit_factory
 Usage   : $hit->hit_factory($hit_factory)
 Function: Get/set the factory used to build HitI objects if necessary.
 Returns : Bio::Factory::ObjectFactoryI
 Args    : Bio::Factory::ObjectFactoryI

 Title   : rewind
 Usage   : $iteration->rewind;
 Function: Allow one to reset the Hit iterators to the beginning
           Since this is an in-memory implementation
 Returns : none
 Args    : none

 Title   : newhits_unclassified
 Usage   : foreach( $iteration->hits_unclassified ) {...}
 Function: Gets all newhits that have not been partitioned into
           sets relative to the inclusion threshold.
 Returns : Array of Bio::Search::Hit::HitI objects.
 Args    : none

 Purpose : Frees up the memory used by the get_hit() functionality.
           For the memory-conscious.

Methods code

sub new {

  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  my ($number, $newhits_unclassified, $newhits_below, $newhits_not_below,
      $oldhits_below, $oldhits_newly_below, $oldhits_not_below, $converged,
      $h_f) =
      $self->_rearrange([qw(NUMBER
                            NEWHITS_UNCLASSIFIED
                            NEWHITS_BELOW
                            NEWHITS_NOT_BELOW
                            OLDHITS_BELOW
                            OLDHITS_NEWLY_BELOW
                            OLDHITS_NOT_BELOW
                            CONVERGED
                            HIT_FACTORY
                           )], @args);

  if( ! defined $number ) { 
      $self->throw(-class=>'Bio::Root::BadParameter',
                   -text=>"Iteration number not specified.");
  } else { 
      $self->number($number);
  }

  defined $converged && $self->converged($converged);

  # TODO: Performance optimization test calling add_hit() vs. simple assignment:
  #       push @{$self->{'_hits_new'}}, @{$newhits};
  #             vs.
  #       foreach(@{$newhits_below}) {$self->add_hit(-hit=>$_, -old=>0, -below=>1);}

  if(defined $newhits_unclassified ) {
    if( ref($newhits_unclassified) =~ /ARRAY/i) {
         push @{$self->{'_newhits_unclassified'}}, @{$newhits_unclassified};
    } else {
      $self->throw(-class=>'Bio::Root::BadParameter',
                   -text=>"Parameter NEWHITS is not an array ref: $newhits_unclassified");
    }
  } else {
      $self->{'_newhits_unclassified'} = [];
  }

  if(defined $newhits_below ) {
    if( ref($newhits_below) =~ /ARRAY/i) {
        push @{$self->{'_newhits_below_threshold'}}, @{$newhits_below};
    } else {
      $self->throw(-class=>'Bio::Root::BadParameter',
                   -text=>"Parameter NEWHITS_BELOW is not an array ref: $newhits_below");
    }
  } else {
      $self->{'_newhits_below_threshold'} = [];
  }

  if(defined $newhits_not_below ) {
    if( ref($newhits_not_below) =~ /ARRAY/i) {
         push @{$self->{'_newhits_not_below_threshold'}}, @{$newhits_not_below};
    } else {
      $self->throw(-class=>'Bio::Root::BadParameter',
                   -text=>"Parameter NEWHITS_NOT_BELOW is not an array ref: $newhits_not_below");
    }
  } else {
      $self->{'_newhits_not_below_threshold'} = [];
  }

  if(defined $oldhits_below ) {
    if( ref($oldhits_below) =~ /ARRAY/i) {
         push @{$self->{'_oldhits_below_threshold'}}, @{$oldhits_below};
    } else {
      $self->throw(-class=>'Bio::Root::BadParameter',
                   -text=>"Parameter OLDHITS_BELOW is not an array ref: $oldhits_below");
    }
  } else {
      $self->{'_oldhits_below_threshold'} = [];
  }

  if(defined $oldhits_newly_below ) {
    if( ref($oldhits_newly_below) =~ /ARRAY/i) {
         push @{$self->{'_oldhits_newly_below_threshold'}}, @{$oldhits_newly_below};
    } else {
      $self->throw(-class=>'Bio::Root::BadParameter',
                   -text=>"Parameter OLDHITS_NEWLY_BELOW is not an array ref: $oldhits_newly_below");
    }
  } else {
      $self->{'_oldhits_newly_below_threshold'} = [];
  }

  if(defined $oldhits_not_below ) {
    if( ref($oldhits_not_below) =~ /ARRAY/i) {
         push @{$self->{'_oldhits_not_below_threshold'}}, @{$oldhits_not_below};
    } else {
      $self->throw(-class=>'Bio::Root::BadParameter',
                   -text=>"Parameter OLDHITS_NOT_BELOW is not an array ref: $oldhits_not_below");
    }
  } else {
      $self->{'_oldhits_not_below_threshold'} = [];
  }
  
  $self->hit_factory($h_f) if $h_f;
  
  return $self;

}

sub number {

    my ($self,$value) = @_;
    my $previous = $self->{'_number'};
    if( defined $value || ! defined $previous ) {
        $value = $previous = '' unless defined $value;
        $self->{'_number'} = $value;
    } 
    return $previous;

}

sub converged {

    my ($self,$value) = @_;
    my $previous = $self->{'_converged'};
    if( defined $value || ! defined $previous ) {
        $value = $previous = '' unless defined $value;
        $self->{'_converged'} = $value;
    } 
    return $previous;

}

sub hit_factory {

    my $self = shift;
    if (@_) { $self->{_hit_factory} = shift }
    return $self->{_hit_factory} || return;

}

sub next_hit {

   my ($self) = @_;

   unless($self->{'_hit_queue_started'}) {
       $self->{'_hit_queue'} = ( [$self->oldhits(), $self->newhits()] );
       $self->{'_hit_queue_started'} = 1;
   }
   return shift @{$self->{'_hit_queue'}};

}

sub next_hit_new {

   my ($self) = @_;

   unless($self->{'_hit_queue_new_started'}) {
       $self->{'_hit_queue_new'} = [$self->newhits()];
       $self->{'_hit_queue_new_started'} = 1;
   }
   return shift @{$self->{'_hit_queue_new'}};

}

sub next_hit_old {

   my ($self,$found_again) = @_;

   unless($self->{'_hit_queue_old_started'}) {
       $self->{'_hit_queue_old'} = [$self->oldhits()];
       $self->{'_hit_queue_old_started'} = 1;
   }
   return shift @{$self->{'_hit_queue_old'}};

}

sub rewind {

   my $self = shift;
   $self->{'_hit_queue_started'} = 0;
   $self->{'_hit_queue_new_started'} = 0;
   $self->{'_hit_queue_old_started'} = 0;
   foreach ($self->hits) {
      $_->rewind;
   }

}

sub num_hits {

   my $self = shift;

   return $self->num_hits_old + $self->num_hits_new;

}

sub num_hits_new {

   my $self = shift;

    return scalar $self->newhits();

}

sub num_hits_old {

   my ($self,$found_again) = @_;

   return scalar $self->oldhits();

}

sub add_hit {

     my ($self,@args) = @_;
    my( $hit, $old, $below, $newly_below ) = 
        $self->_rearrange([qw(HIT
                              OLD
                              BELOW_THRESHOLD
                              NEWLY_BELOW
                             )], @args);
    my $count = 0;

    unless( ref($hit) eq 'HASH' || $hit->isa('Bio::Search::Hit::HitI') ) { 
        $self->throw(-class=>'Bio::Root::BadParameter',
                     -text=>"Passed in " .ref($hit). 
                    " as a Hit which is not a Bio::Search::Hit::HitI.");
    }

    if($old) {
        if ($newly_below) {
            push @{$self->{'_oldhits_newly_below_threshold'}}, $hit;
            $count = scalar @{$self->{'_oldhits_newly_below_threshold'}};
        } elsif ($below) {
            push @{$self->{'_oldhits_below_threshold'}}, $hit;
            $count = scalar @{$self->{'_oldhits_below_threshold'}};
        } else {
            push @{$self->{'_oldhits_not_below_threshold'}}, $hit;
            $count = scalar @{$self->{'_oldhits_not_below_threshold'}};
        }
    } elsif (defined $old) {
        # -old is defined but false, so this is a new PSI-BLAST hit
        if ($below) {
            push @{$self->{'_newhits_below_threshold'}}, $hit;
            $count = scalar @{$self->{'_newhits_below_threshold'}};
        } elsif (defined $below) {
            push @{$self->{'_newhits_not_below_threshold'}}, $hit;
            $count = scalar @{$self->{'_newhits_not_below_threshold'}};
        } else {
            # -below not defined, PSI-BLAST threshold may not be known
            push @{$self->{'_newhits_unclassified'}}, $hit;
            $count = scalar @{$self->{'_newhits_unclassified'}};
        }
    } else {
        # -old not defined, so it's non-PSI-BLAST
        push @{$self->{'_newhits_unclassified'}}, $hit;
        $count = scalar @{$self->{'_newhits_unclassified'}};
    }
    return $count;

}

sub hits {

     my $self = shift;
#    print STDERR "Called GenericIteration::hits()\n";
    my @new = $self->newhits;
    my @old = $self->oldhits;
    return ( @new, @old );

}

sub newhits {

     my $self = shift;
    my @hits = $self->newhits_below_threshold;
    push @hits, $self->newhits_not_below_threshold;
    push @hits, $self->newhits_unclassified;
    return @hits;

}

sub newhits_below_threshold {

     my $self = shift;
    if (ref $self->{'_newhits_below_threshold'} ) {
        my $factory = $self->hit_factory || return @{$self->{'_newhits_below_threshold'}};
        for (0..$#{$self->{'_newhits_below_threshold'}}) {
            ref(${$self->{'_newhits_below_threshold'}}[$_]) eq 'HASH' || next;
            ${$self->{'_newhits_below_threshold'}}[$_] = $factory->create_object(%{${$self->{'_newhits_below_threshold'}}[$_]});
        }
        return @{$self->{'_newhits_below_threshold'}};
    }
    return;

}

sub newhits_not_below_threshold {

     my $self = shift;
    if (ref $self->{'_newhits_not_below_threshold'} ) {
        my $factory = $self->hit_factory || return @{$self->{'_newhits_not_below_threshold'}};
        for (0..$#{$self->{'_newhits_not_below_threshold'}}) {
            ref(${$self->{'_newhits_not_below_threshold'}}[$_]) eq 'HASH' || next;
            ${$self->{'_newhits_not_below_threshold'}}[$_] = $factory->create_object(%{${$self->{'_newhits_not_below_threshold'}}[$_]});
        }
        return @{$self->{'_newhits_not_below_threshold'}};
    }
    return;

}

sub newhits_unclassified {

     my $self = shift;
    if (ref $self->{'_newhits_unclassified'} ) {
        my $factory = $self->hit_factory || return @{$self->{'_newhits_unclassified'}};
        for (0..$#{$self->{'_newhits_unclassified'}}) {
            ref(${$self->{'_newhits_unclassified'}}[$_]) eq 'HASH' || next;
            ${$self->{'_newhits_unclassified'}}[$_] = $factory->create_object(%{${$self->{'_newhits_unclassified'}}[$_]});
        }
        return @{$self->{'_newhits_unclassified'}};
    }
    return;

}

sub oldhits {

     my $self = shift;
    my @hits = $self->oldhits_below_threshold;
    push @hits, $self->oldhits_newly_below_threshold;
    push @hits, $self->oldhits_not_below_threshold;
    return @hits;

}

sub oldhits_below_threshold {

     my $self = shift;
    if (ref $self->{'_oldhits_below_threshold'} ) {
        my $factory = $self->hit_factory || return @{$self->{'_oldhits_below_threshold'}};
        for (0..$#{$self->{'_oldhits_below_threshold'}}) {
            ref(${$self->{'_oldhits_below_threshold'}}[$_]) eq 'HASH' || next;
            ${$self->{'_oldhits_below_threshold'}}[$_] = $factory->create_object(%{${$self->{'_oldhits_below_threshold'}}[$_]});
        }
        return @{$self->{'_oldhits_below_threshold'}};
    }
    return;

}

sub oldhits_newly_below_threshold {

     my $self = shift;
    if (ref $self->{'_oldhits_newly_below_threshold'} ) {
        my $factory = $self->hit_factory || return @{$self->{'_oldhits_newly_below_threshold'}};
        for (0..$#{$self->{'_oldhits_newly_below_threshold'}}) {
            ref(${$self->{'_oldhits_newly_below_threshold'}}[$_]) eq 'HASH' || next;
            ${$self->{'_oldhits_newly_below_threshold'}}[$_] = $factory->create_object(%{${$self->{'_oldhits_newly_below_threshold'}}[$_]});
        }
        return @{$self->{'_oldhits_newly_below_threshold'}};
    }
    return;

}

sub oldhits_not_below_threshold {

     my $self = shift;
    if (ref $self->{'_oldhits_not_below_threshold'} ) {
        my $factory = $self->hit_factory || return @{$self->{'_oldhits_not_below_threshold'}};
        for (0..$#{$self->{'_oldhits_not_below_threshold'}}) {
            ref(${$self->{'_oldhits_not_below_threshold'}}[$_]) eq 'HASH' || next;
            ${$self->{'_oldhits_not_below_threshold'}}[$_] = $factory->create_object(%{${$self->{'_oldhits_not_below_threshold'}}[$_]});
        }
        return @{$self->{'_oldhits_not_below_threshold'}};
    }
    return;

}

sub hits_below_threshold {

    my $self = shift;
    my @hits = $self->newhits_below_threshold;
    push @hits, $self->oldhits_newly_below_threshold;
    return @hits;

}

sub get_hit {

    my ($self,$name) = @_;
    $self->_create_hit_lookup() unless defined $self->{'_hit_lookup'};

    return $self->{'_hit_lookup'}->{"\U$name"};
}

# Internal method.

}

sub _create_hit_lookup {

    my $self = shift;
    foreach ($self->hits) {
        my $hname = $_->name;
        $self->{'_hit_lookup'}->{"\U$hname"} = $_;
    }

}

sub free_hit_lookup {

    my $self = shift;
    undef $self->{'_hit_lookup'};
}

1;

}

General documentation

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
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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.

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/

Email sac@bioperl.org

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