Summary

Bio::SearchIO::IteratedSearchResultEventBuilder - Event Handler for
SearchIO events.

Package variables

Included modules

Inherit

Bio::SearchIO::SearchResultEventBuilder

Synopsis

# Do not use this object directly, this object is part of the SearchIO
# event based parsing system.

Description

This object handles Search Events generated by the SearchIO classes
and build appropriate Bio::Search::* objects from them.

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::SearchIO::IteratedSearchResultEventBuilder();
 Function: Builds a new Bio::SearchIO::IteratedSearchResultEventBuilder object 
 Returns : Bio::SearchIO::IteratedSearchResultEventBuilder
 Args    : -hsp_factory    => Bio::Factory::ObjectFactoryI
           -hit_factory    => Bio::Factory::ObjectFactoryI
           -result_factory => Bio::Factory::ObjectFactoryI
           -iteration_factory => Bio::Factory::ObjectFactoryI
           -inclusion_threshold => e-value threshold for inclusion in the
                                   PSI-BLAST score matrix model (blastpgp)
           -signif      => float or scientific notation number to be used
                           as a P- or Expect value cutoff
           -score       => integer or scientific notation number to be used
                           as a blast score value cutoff
           -bits        => integer or scientific notation number to be used
                           as a bit score value cutoff
           -hit_filter  => reference to a function to be used for
                           filtering hits based on arbitrary criteria.

 Title   : will_handle
 Usage   : if( $handler->will_handle($event_type) ) { ... }
 Function: Tests if this event builder knows how to process a specific event
 Returns : boolean
 Args    : event type name

 Title   : start_result
 Usage   : $handler->start_result($resulttype)
 Function: Begins a result event cycle
 Returns : none 
 Args    : Type of Report

 Title   : end_result
 Usage   : my @results = $parser->end_result
 Function: Finishes a result handler cycle 
 Returns : A Bio::Search::Result::ResultI
 Args    : none

 Title   : start_iteration
 Usage   : $handler->start_iteration()
 Function: Starts an Iteration event cycle
 Returns : none
 Args    : type of event and associated hashref

 Title   : end_iteration
 Usage   : $handler->end_iteration()
 Function: Ends an Iteration event cycle
 Returns : Bio::Search::Iteration object
 Args    : type of event and associated hashref

 Usage     : $obj->max_significance();
 Purpose   : Set/Get the P or Expect value used as significance screening cutoff.
             This is the value of the -signif parameter supplied to new().
             Hits with P or E-value above this are skipped.
 Returns   : Scientific notation number with this format: 1.0e-05.
 Argument  : Number (sci notation, float, integer) (when setting)
 Throws    : Bio::Root::BadParameter exception if the supplied argument is
           : not a valid number.
 Comments  : Screening of significant hits uses the data provided on the
           : description line. For NCBI BLAST1 and WU-BLAST, this data 
           : is P-value. for NCBI BLAST2 it is an Expect value.

 Usage     : $obj->min_score();
 Purpose   : Gets the Blast score used as screening cutoff.
             This is the value of the -score parameter supplied to new().
             Hits with scores below this are skipped.
 Returns   : Integer (or undef if not set)
 Argument  : Integer (when setting)
 Throws    : Bio::Root::BadParameter exception if the supplied argument is
           : not a valid number.
 Comments  : Screening of significant hits uses the data provided on the
           : description line.

 Usage     : $obj->min_bits();
 Purpose   : Gets the Blast bit score used as screening cutoff.
             This is the value of the -bits parameter supplied to new().
             Hits with bits score below this are skipped.
 Returns   : Integer (or undef if not set)
 Argument  : Integer (when setting)
 Throws    : Bio::Root::BadParameter exception if the supplied argument is
           : not a valid number.
 Comments  : Screening of significant hits uses the data provided on the
           : description line.

 Usage     : $obj->hit_filter();
 Purpose   : Set/Get a function reference used for filtering out hits.
             This is the value of the -hit_filter parameter supplied to new().
             Hits that fail to pass the filter are skipped.
 Returns   : Function ref (or undef if not set)
 Argument  : Function ref (when setting)
 Throws    : Bio::Root::BadParameter exception if the supplied argument is
           : not a function reference.

Methods code

sub new {

     my ($class,@args) = @_;
    my $self = $class->SUPER::new(@args);
    my ($hitF, $resultF, $hspF, $iterationF) =
        $self->_rearrange([qw(
                              HIT_FACTORY
                              RESULT_FACTORY
			      HSP_FACTORY
                              ITERATION_FACTORY
                             )],@args);

    $self->_init_parse_params(@args);

    # Note that we need to override the setting of result and factories here
    # so that we can set different default factories than are set by the super class.
    $self->register_factory('result', $resultF || 
                            Bio::Factory::ObjectFactory->new(
                                 -type      => 'Bio::Search::Result::BlastResult',
                                 -interface => 'Bio::Search::Result::ResultI'));

    $self->register_factory('hit', $hitF || 
                            Bio::Factory::ObjectFactory->new(
                                 -type      => 'Bio::Search::Hit::BlastHit',
                                 -interface => 'Bio::Search::Hit::HitI'));

    $self->register_factory('hsp', $hspF || 
                            Bio::Factory::ObjectFactory->new(
                                 -type      => 'Bio::Search::HSP::GenericHSP',
                                 -interface => 'Bio::Search::HSP::HSPI'));

    # TODO: Change this to BlastIteration (maybe)
    $self->register_factory('iteration', $iterationF || 
                            Bio::Factory::ObjectFactory->new(
                                 -type      => 'Bio::Search::Iteration::GenericIteration',
                                 -interface => 'Bio::Search::Iteration::IterationI'));
    return $self;

}

sub _init_parse_params {

    my ($self, @args) = @_;
    # -FILT_FUNC has been replaced by -HIT_FILTER.
    # Leaving -FILT_FUNC in place for backward compatibility
    my($ithresh, $signif, $score, $bits, $hit_filter, $filt_func) =
           $self->_rearrange([qw(INCLUSION_THRESHOLD
                                 SIGNIF SCORE BITS HIT_FILTER FILT_FUNC
                                )], @args);

    $self->inclusion_threshold( defined($ithresh) ? $ithresh : $DEFAULT_INCLUSION_THRESHOLD);
    my $hit_filt = $hit_filter || $filt_func;
    defined $hit_filter && $self->hit_filter($hit_filt);
    defined $signif     && $self->max_significance($signif);
    defined $score      && $self->min_score($score);
    defined $bits       && $self->min_bits($bits);

}

sub will_handle {

   my ($self,$type) = @_;
   # these are the events we recognize
   return ( $type eq 'hsp' || $type eq 'hit' || $type eq 'result' || $type eq 'iteration' ||
            $type eq 'newhits' || $type eq 'oldhits' );

}

sub start_result {

   my $self = shift;
   #print STDERR "ISREB: start_result()\n";
   $self->SUPER::start_result(@_);
   $self->{'_iterations'} = [];
   $self->{'_iteration_count'} = 0;
   $self->{'_old_hit_names'} = undef;
   $self->{'_hit_names_below'} = undef;
   return;

}

sub end_result {

    my ($self,$type,$data) = @_;
    #print STDERR "ISREB: end_result\n";
    ## How is runid getting set? Purpose?
    if( defined $data->{'runid'} &&
        $data->{'runid'} !~ /^\s+$/ ) {        

        if( $data->{'runid'} !~ /^lcl\|/) { 
            $data->{"RESULT-query_name"}= $data->{'runid'};
        } else { 
            ($data->{"RESULT-query_name"},$data->{"RESULT-query_description"}) = 
                split(/\s+/,$data->{"RESULT-query_description"},2);
        }
        
        if( my @a = split(/\|/,$data->{'RESULT-query_name'}) ) {
            my $acc = pop @a ; # this is for accession |1234|gb|AAABB1.1|AAABB1
            # this is for |123|gb|ABC1.1|
            $acc = pop @a if( ! defined $acc || $acc =~ /^\s+$/);
            $data->{"RESULT-query_accession"}= $acc;
        }
        delete $data->{'runid'};
    }
    my %args = map { my $v = $data->{$_}; s/RESULT//; ($_ => $v); } 
               grep { /^RESULT/ } keys %{$data};
    
    $args{'-algorithm'} =  uc( $args{'-algorithm_name'} || 
                               $data->{'RESULT-algorithm_name'} || $type);

    $args{'-iterations'} = $self->{'_iterations'};

    my $result = $self->factory('result')->create_object(%args);
    $result->hit_factory($self->factory('hit'));
    $self->{'_iterations'} = [];
    return $result;

}

sub _add_hit {

    my ($self, $hit) = @_;
	
    my $hit_name = uc($hit->{-name});
    my $hit_signif = $hit->{-significance};
    my $ithresh = $self->{'_inclusion_threshold'};
	
    # Test significance using custom function (if supplied)
    my $add_hit = 1;
	
    my $hit_filter = $self->{'_hit_filter'};
	
    if($hit_filter) {
        # since &hit_filter is out of our control and would expect a HitI object,
        # we're forced to make one for it
        $hit = $self->factory('hit')->create_object(%{$hit});
        $add_hit = 0 unless &$hit_filter($hit);
    } else {
        if($self->{'_confirm_significance'}) {
            $add_hit = 0 unless $hit_signif <= $self->{'_max_significance'};
        }
        if($self->{'_confirm_score'}) {
            my $hit_score = $hit->{-score} || $hit->{-hsps}->[0]->{-score};
            $add_hit = 0 unless $hit_score >= $self->{'_min_score'};
        }
        if($self->{'_confirm_bits'}) {
            my $hit_bits = $hit->{-bits} || $hit->{-hsps}->[0]->{-bits};
            $add_hit = 0 unless $hit_bits >= $self->{'_min_bits'};
        }
    }
	
    $add_hit && $self->_store_hit($hit, $hit_name, $hit_signif);
    # Building hit lookup hashes for determining if the hit is old/new and 
    # above/below threshold.
    $self->{'_old_hit_names'}->{$hit_name}++;
    $self->{'_hit_names_below'}->{$hit_name}++ if $hit_signif <= $ithresh;

}

sub _store_hit {

    my ($self, $hit, $hit_name, $hit_signif) = @_;

    my $ithresh = $self->{'_inclusion_threshold'};

    if (exists $self->{'_old_hit_names'}->{$hit_name}) {
        if (exists $self->{'_hit_names_below'}->{$hit_name}) {
            push @{$self->{'_oldhits_below'}}, $hit;
        } elsif ($hit_signif <= $ithresh) {
            push @{$self->{'_oldhits_newly_below'}}, $hit;
        } else {
            push @{$self->{'_oldhits_not_below'}}, $hit;
        }
    } else {
        if ($hit_signif <= $ithresh) {
            push @{$self->{'_newhits_below'}}, $hit;
        } else {
            push @{$self->{'_newhits_not_below'}}, $hit;
        }
    }
    $self->{'_hitcount'}++;

}

sub start_iteration {

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

    #print STDERR "ISREB: start_iteration()\n";
    $self->{'_iteration_count'}++;

    # Reset arrays for the various classes of hits.
#    $self->{'_newhits_unclassified'}     = [];
    $self->{'_newhits_below'}        = [];
    $self->{'_newhits_not_below'}    = [];
    $self->{'_oldhits_below'}        = [];
    $self->{'_oldhits_newly_below'}  = [];
    $self->{'_oldhits_not_below'}    = [];
    $self->{'_hitcount'} = 0;
    return;

}

sub end_iteration {

    my ($self,$type,$data) = @_;   

    # print STDERR "ISREB: end_iteration()\n";

    my %args = map { my $v = $data->{$_}; s/ITERATION//; ($_ => $v); } 
    grep { /^ITERATION/ } keys %{$data};

    $args{'-number'} = $self->{'_iteration_count'};
    $args{'-oldhits_below'} = $self->{'_oldhits_below'};
    $args{'-oldhits_newly_below'} = $self->{'_oldhits_newly_below'};
    $args{'-oldhits_not_below'} = $self->{'_oldhits_not_below'};
    $args{'-newhits_below'} = $self->{'_newhits_below'};
    $args{'-newhits_not_below'} = $self->{'_newhits_not_below'};
    $args{'-hit_factory'} = $self->factory('hit');

    my $it = $self->factory('iteration')->create_object(%args);
    push @{$self->{'_iterations'}}, $it;
    return $it;

}

sub max_significance {

    my $self = shift;
    if (@_) {
        my $sig = shift;
        if( $sig =~ /[^\d.e-]/ or $sig <= 0) {
            $self->throw(-class => 'Bio::Root::BadParameter',
                         -text => "Invalid significance value: $sig\n".
                         "Must be a number greater than zero.",
                         -value=>$sig);
        }
        $self->{'_confirm_significance'} = 1;
        $self->{'_max_significance'} = $sig;
    }
    sprintf "%.1e", $self->{'_max_significance'};

}

sub signif {

 shift->max_significance

}

sub min_score {

    my $self = shift;
    if (@_) {
        my $score = shift;
        if( $score =~ /[^\de+]/ or $score <= 0) {
            $self->throw(-class => 'Bio::Root::BadParameter',
                         -text => "Invalid score value: $score\n".
                                  "Must be an integer greater than zero.",
                        -value => $score);
        }
        $self->{'_confirm_score'} = 1;
        $self->{'_min_score'} = $score;
    }
    return $self->{'_min_score'};

}

sub min_bits {

    my $self = shift;
    if (@_) {
        my $bits = shift;
        if( $bits =~ /[^\de+]/ or $bits <= 0) {
            $self->throw(-class => 'Bio::Root::BadParameter',
                         -text => "Invalid bits value: $bits\n".
                                  "Must be an integer greater than zero.",
                        -value => $bits);
        }
        $self->{'_confirm_bits'} = 1;
        $self->{'_min_bits'} = $bits;
    }
    return $self->{'_min_bits'};

}

sub hit_filter {

    my $self = shift;
    if (@_) {
        my $func = shift;
        if(not ref $func eq 'CODE') {
            $self->throw(-class=>'Bio::Root::BadParameter',
                         -text=>"Not a function reference: $func\n".
                                "The -hit_filter parameter must be function reference.",
                         -value=> $func);
        }
        $self->{'_hit_filter'} = $func;
    }
    return $self->{'_hit_filter'};

}

sub inclusion_threshold {

    my $self = shift;
    return $self->{'_inclusion_threshold'} = shift if @_;
    return $self->{'_inclusion_threshold'};

}

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
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

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:

  http://bugzilla.open-bio.org/

Email sac-at-bioperl.org

Parts of code based on SearchResultEventBuilder by Jason Stajich jason@bioperl.org
Sendu Bala, bix@sendu.me.uk

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