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Revision 1.9 - (download) (as text) (annotate)
Wed Jun 20 16:43:13 2007 UTC (12 years, 5 months ago) by arodri7
Branch: MAIN
Changes since 1.8: +169 -52 lines
added PCH and IDENTICAL classes

package Observation;

require Exporter;
@EXPORT_OK = qw(get_objects); 

use strict;
use warnings;
use HTML;

1;

# $Id: Observation.pm,v 1.9 2007/06/20 16:43:13 arodri7 Exp $

=head1 NAME

Observation -- A presentation layer for observations in SEED.

=head1 DESCRIPTION

The SEED environment contains various sources of information for sequence features. The purpose of this library is to provide a 
single interface to this data.

The data can be used to display information for a given sequence feature (protein or other, but primarily information is computed for proteins). 

Example:


use FIG;
use Observation;

my $fig = new FIG;
my $fid = "fig|83333.1.peg.3";

my $observations = Observation::get_objects($fid);
foreach my $observation (@$observations) {
    print "ID: " . $fid . "\n";
    print "Start: " . $observation->start() . "\n";
    ...
}

B<return an array of objects>


print "$Observation->acc\n" prints the Accession number if present for the Observation

=cut

=head1 BACKGROUND

=head2 Data incorporated in the Observations 

As the goal of this library is to provide an integrated view, we combine diverse sources of evidence.

=head3 SEED core evidence

The core SEED data structures provided by FIG.pm. These are Similarities, BBHs and PCHs.

=head3 Attribute based Evidence

We use the SEED attribute infrastructure to store information computed by a variety of computational procedures.

These are e.g. InterPro hits via InterProScan (ipr), NCBI Conserved Domain Database Hits via PSSM(cdd), 
PFAM hits via HMM(pfam), SignalP results(signalp), and various others.

=head1 METHODS

The public methods this package provides are listed below:

=head3 acc()

A valid accession or remote ID (in the style of a db_xref) or a valid local ID (FID) in case this is supported.

=cut

sub acc {
  my ($self) = @_;

  return $self->{acc};
}

=head3 description()

The description of the hit. Taken from the data or from the our Ontology database for some cases e.g. IPR or PFAM.

B<Please note:>
Either remoteid or description is required.

=cut

sub description {
  my ($self) = @_;

  return $self->{description};
}

=head3 class()

The class of evidence (required). This is usually simply the name of the tool or the name of the SEED data structure.
B<Please note> the connection of class and display_method and URL.
    
Current valid classes are:

=over 9

=item IDENTICAL (seq)

=item SIM (seq)

=item BBH (seq)

=item PCH (fc)

=item FIGFAM (seq)

=item IPR (dom)

=item CDD (dom)

=item PFAM (dom)

=item SIGNALP (dom)

=item  CELLO(loc)

=item TMHMM (loc)

=item HMMTOP (loc)

=back

=cut

sub class {
  my ($self) = @_;

  return $self->{class};
}

=head3 type()

The type of evidence (required).

Where type is one of the following:

=over 8

=item seq=Sequence similarity

=item dom=domain based match

=item loc=Localization of the feature

=item fc=Functional coupling.

=back

=cut

sub type {
  my ($self) = @_;

  return $self->{acc};
}

=head3 start()

Start of hit in query sequence.

=cut

sub start {
  my ($self) = @_;

  return $self->{start};
}

=head3 end()

End of the hit in query sequence.

=cut

sub stop {
  my ($self) = @_;

  return $self->{stop};
}

=head3 evalue()

E-value or P-Value if present.

=cut

sub evalue {
  my ($self) = @_;

  return $self->{evalue};
}

=head3 score()

Score if present. 

B<Please note: >
Either score or eval are required.

=cut

sub score {
  my ($self) = @_;
  return $self->{score};
}


=head3 display_method()

If available use the function specified here to display the "raw" observation.
In the case of a BLAST alignment of fid1 and fid2 a cgi script 
will be called to display the results of running the command "bl2seq fid1 fid2". 

B<Please note> that URL linked to in display_method() is an external component and needs to added to the code for every class of evidence.

=cut 

sub display {
  
  die "Abstract Method Called\n";

}


=head3 rank()

Returns an integer from 1 - 10 indicating the importance of this observations. 

Currently always returns 1.

=cut

sub rank {
  my ($self) = @_;

#  return $self->{rank};

  return 1;
}

=head3 supports_annotation()

Does a this observation support the annotation of its feature?

Returns

=over 3

=item 10, if feature annotation is identical to $self->description

=item 1, Feature annotation is similar to $self->annotation; this is computed using FIG::SameFunc() 

=item undef

=back 

=cut

sub supports_annotation {
  my ($self) = @_;

  # no code here so far

  return $self->{supports_annotation};
}

=head3 url()

URL describing the subject. In case of a BLAST hit against a sequence, this URL will lead to a page displaying the sequence record for the sequence. In case of an HMM hit, the URL will be to the URL description.

=cut

sub url {
  my ($self) = @_;

  my $url = get_url($self->type, $self->acc);

  return $url;
}

=head3 get_objects()

This is the B<REAL WORKHORSE> method of this Package.

It will probably have to:

- get all sims for the feature
- get all bbhs for the feature
- copy information from sim to bbh (bbh have no match location etc)
- get pchs (difficult)
- get attributes (there is code for this that in get_attribute_based_observations
- get_attributes_based_observations returns an array of arrays of hashes like this"    

  my $dataset
     [
       [ { name => 'acc', value => '1234' },
 	{ name => 'from', value => '4' },
 	{ name => 'to', value => '400' },
 	....
       ],
       [ { name => 'acc', value => '456' },
 	{ name => 'from', value => '1' },
 	{ name => 'to', value => '100' },
 	....
       ],
       ...
     ];
   return $datasets;
 }

It will invoke the required calls to the SEED API to retrieve the information required.

=cut

sub get_objects {
    my ($self,$fid,$classes) = @_;
    
    
    my $objects = [];
    my @matched_datasets=();

    # call function that fetches attribute based observations
    # returns an array of arrays of hashes
 
    if(scalar(@$classes) < 1){
	get_attribute_based_observations($fid,\@matched_datasets);
	get_sims_observations($fid,\@matched_datasets);
	get_identical_proteins($fid,\@matched_datasets);  
	get_functional_coupling($fid,\@matched_datasets);
    }
    else{
	#IPR,CDD,CELLO,PFAM,SIGNALP - attribute based
	my %domain_classes;
	my $identical_flag=0;
	my $pch_flag=0;
	foreach my $class (@$classes){
	    if($class =~ /(IPR|CDD|PFAM)/){
		$domain_classes{$class} = 1;
	    }
	    elsif ($class eq "IDENTICAL")
	    {
		$identical_flag = 1;
	    }
	    elsif ($class eq "PCH")
	    {
		$pch_flag = 1;
	    }
	}

	if ($identical_flag ==1)
	{
	    get_identical_proteins($fid,\@matched_datasets);
	}
	if ( (defined($domain_classes{IPR})) || (defined($domain_classes{CDD})) || (defined($domain_classes{PFAM})) ) {
	    get_attribute_based_domain_observations($fid,\%domain_classes,\@matched_datasets);
	}
	if ($pch_flag == 1)
        {
            get_functional_coupling($fid,\@matched_datasets);
        }

	#add CELLO and SignalP later
    }
 
    foreach my $dataset (@matched_datasets) {
	my $object;
	if($dataset->{'type'} eq "dom"){
	    $object = Observation::Domain->new($dataset);
	}
	if($dataset->{'class'} eq "PCH"){
            $object = Observation::FC->new($dataset);
        }
	if ($dataset->{'class'} eq "IDENTICAL"){
	    $object = Observation::Identical->new($dataset);
	}
	push (@$objects, $object);
    }
    
    return $objects;

}

=head1 Internal Methods 

These methods are not meant to be used outside of this package. 

B<Please do not use them outside of this package!>

=cut


=head3 get_url (internal)

get_url() return a valid URL or undef for any observation.

URLs are constructed by looking at the Accession acc()  and  name()

Info from both attributes is combined with a table of base URLs stored in this function.

=cut

sub get_url {

 my ($self) = @_;
 my $url='';

# a hash with a URL for each observation; identified by name() 
#my $URL             => { 'PFAM' => "http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?" ,\
#                       'IPR'    => "http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=" ,\
#                          'CDD' => "http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=",\
#                       'PIR'    => "http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=",\
#                       'FIGFAM' => '',\
#	                   'sim'=> "http://www.theseed.org/linkin.cgi?id=",\
#			   'bbh'=> "http://www.theseed.org/linkin.cgi?id="
#};

# if (defined $URL{$self->name}) {
#     $url = $URL{$self->name}.$self->acc;
#     return $url;
# }
# else 
     return undef;
}

=head3 get_display_method (internal)

get_display_method() return a valid URL or undef for any observation.

URLs are constructed by looking at the Accession acc()  and  name() 
and Info from both attributes is combined with a table of base URLs stored in this function.

=cut

sub get_display_method {

 my ($self) = @_;

# a hash with a URL for each observation; identified by name() 
#my $URL             => { 'sim'=> "http://www.theseed.org/featalign.cgi?id1=",\
#	                 'bbh'=> "http://www.theseed.org/featalign.cgi?id1="
# };

#if (defined $URL{$self->name}) {
#     $url = $URL{$self->name}.$self->feature_id."&id2=".$self->acc;
#     return $url;
# }
# else 
     return undef;
}


sub get_attribute_based_domain_observations{

    # we read a FIG ID and a reference to an array (of arrays of hashes, see above)
    my ($fid,$domain_classes,$datasets_ref) = (@_);

    my $fig = new FIG;
    
    foreach my $attr_ref ($fig->get_attributes($fid)) {
	my $key = @$attr_ref[1];
	my @parts = split("::",$key);
	my $class = $parts[0];
	
	if($domain_classes->{$parts[0]}){
	    my $val = @$attr_ref[2];
	    if($val =~/^(\d+\.\d+|0\.0);(\d+)-(\d+)/){
		my $raw_evalue = $1;
		my $from = $2;
		my $to = $3;
		my $evalue;
		if($raw_evalue =~/(\d+)\.(\d+)/){
		    my $part2 = 1000 - $1;
		    my $part1 = $2/100;
		    $evalue = $part1."e-".$part2;
		}
		else{
		    $evalue = "0.0";
		}

		my $dataset = {'class' => $class,
			       'acc' => $key,
			       'type' => "dom" ,
			       'evalue' => $evalue,
			       'start' => $from,
			       'stop' => $to
			       };
		
		push (@{$datasets_ref} ,$dataset);
	    }
	}
    }
}
    
=head3 get_attribute_based_evidence (internal)

This method retrieves evidence from the attribute server

=cut

sub get_attribute_based_observations{

    # we read a FIG ID and a reference to an array (of arrays of hashes, see above)
    my ($fid,$datasets_ref) = (@_);

    my $_myfig = new FIG;
    
    foreach my $attr_ref ($_myfig->get_attributes($fid)) {

        # convert the ref into a string for easier handling
        my ($string) = "@$attr_ref";

#	print "S:$string\n";
        my ($key,$val) = ( $string =~ /\S+\s(\S+)\s(\S+)/);

        # THIS SHOULD BE DONE ANOTHER WAY FM->TD
        # we need to do the right thing for each type, ie no evalue for CELLO and no coordinates, but a score, etc
        # as fas as possible this should be configured so that the type of observation and the regexp are
        # stored somewhere for easy expansion
        #

        if (($key =~ /PFAM::/) || ( $key =~ /IPR::/) || ( $key =~ /CDD::/) ) {

            # some keys are composite CDD::1233244 or PFAM:PF1233

            if ( $key =~ /::/ ) {
                my ($firstkey,$restkey) = ( $key =~ /([a-zA-Z0-9]+)::(.*)/);
                $val=$restkey.";".$val;
                $key=$firstkey;
            }

            my ($acc,$raw_evalue, $from,$to) = ($val =~ /(\S+);(\S+);(\d+)-(\d+)/ );

	    my $evalue= 255;
	    if (defined $raw_evalue) { # some of the tool do not give us an evalue

		my ($k,$expo) = ( $raw_evalue =~ /(\d+).(\d+)/);
		my ($new_k, $new_exp);
		
		#
		#  THIS DOES NOT WORK PROPERLY 
		# 
		if($raw_evalue =~/(\d+).(\d+)/){
		    
#		    $new_exp = (1000+$expo);
	#	    $new_k = $k / 100;
		    
		}
		$evalue = "0.01"#new_k."e-".$new_exp;
	    }

            # unroll it all into an array of hashes
            # this needs to be done differently for different types of observations
            my $dataset = [ { name => 'class', value => $key },
                            { name => 'acc' , value => $acc},
                            { name => 'type', value => "dom"} , # this clearly needs to be done properly FM->TD
			    { name => 'evalue', value => $evalue },
                            { name => 'start', value => $from},
                            { name => 'stop' , value => $to}
                            ];

            push (@{$datasets_ref} ,$dataset);
        }
    }
}

=head3 get_sims_observations() (internal)

This methods retrieves sims fills the internal data structures.

=cut

sub get_sims_observations{

    my ($fid,$datasets_ref) = (@_);
    my $fig = new FIG;
    my @sims= $fig->nsims($fid,100,1e-20,"fig");
    my ($dataset);
    foreach my $sim (@sims){
	my $hit = $sim->[1];
	my $evalue = $sim->[10];
	my $from = $sim->[8];
	my $to = $sim->[9];
	$dataset = [ { name => 'class', value => "SIM" },
			{ name => 'acc' , value => $hit},
			{ name => 'type', value => "seq"} ,
			{ name => 'evalue', value => $evalue },
			{ name => 'start', value => $from},
			{ name => 'stop' , value => $to}
			];
    push (@{$datasets_ref} ,$dataset);
    }
}

=head3 get_identical_proteins() (internal)

This methods retrieves sims fills the internal data structures.

=cut

sub get_identical_proteins{

    my ($fid,$datasets_ref) = (@_);
    my $fig = new FIG;
    my @funcs = ();

    my @maps_to = grep { $_ ne $fid and $_ !~ /^xxx/ } map { $_->[0] } $fig->mapped_prot_ids($fid);
    
    foreach my $id (@maps_to) {
        my ($tmp, $who);
        if (($id ne $fid) && ($tmp = $fig->function_of($id))) {
            if ($id =~ /^fig\|/)           { $who = "FIG" }
            elsif ($id =~ /^gi\|/)            { $who = "NCBI" }
            elsif ($id =~ /^^[NXYZA]P_/)      { $who = "RefSeq" }
            elsif ($id =~ /^sp\|/)            { $who = "SwissProt" }
            elsif ($id =~ /^uni\|/)           { $who = "UniProt" }
            elsif ($id =~ /^tigr\|/)          { $who = "TIGR" }
            elsif ($id =~ /^pir\|/)           { $who = "PIR" }
            elsif ($id =~ /^kegg\|/)          { $who = "KEGG" }
            elsif ($id =~ /^tr\|/)            { $who = "TrEMBL" }
            elsif ($id =~ /^eric\|/)          { $who = "ASAP" }

            push(@funcs, [$id,$who,$tmp]);
        }
    }

    my ($dataset);
    foreach my $row (@funcs){
        my $id = $row->[0];
        my $organism = $fig->org_of($fid);
        my $who = $row->[1];
        my $assignment = $row->[2];
	
	my $dataset = {'class' => 'IDENTICAL',
		       'id' => $id,
		       'organism' => $organism,
		       'type' => 'seq',
		       'database' => $who,
		       'function' => $assignment
		       };

        push (@{$datasets_ref} ,$dataset);
    }

}

=head3 get_functional_coupling() (internal)

This methods retrieves the functional coupling of a protein given a peg ID

=cut

sub get_functional_coupling{

    my ($fid,$datasets_ref) = (@_);
    my $fig = new FIG;
    my @funcs = ();

    # initialize some variables
    my($sc,$neigh);

    # set default parameters for coupling and evidence
    my ($bound,$sim_cutoff,$coupling_cutoff) = (5000, 1.0e-10, 4);

    # get the fc data
    my @fc_data = $fig->coupling_and_evidence($fid,$bound,$sim_cutoff,$coupling_cutoff,1);

    # retrieve data
    my @rows = map { ($sc,$neigh) = @$_;
		     [$sc,$neigh,scalar $fig->function_of($neigh)]
		  } @fc_data;
		     
    my ($dataset);
    foreach my $row (@rows){
        my $id = $row->[1];
        my $score = $row->[0];
        my $description = $row->[2];
	my $dataset = {'class' => 'PCH',
		       'score' => $score,
                       'id' => $id,
                       'type' => 'fc',
                       'function' => $description
                       };

        push (@{$datasets_ref} ,$dataset);
    }
}

=head3 get_sims_and_bbhs() (internal)

This methods retrieves sims and also BBHs and fills the internal data structures.

=cut

#     sub get_sims_and_bbhs{

# 	# blast m8 output format
# 	# id1, id2, %ident, align len, mismatches, gaps, q.start, q.stop, s. start, s.stop, eval, bit
	
# 	my $Sims=();
# 	@sims_src = $fig->sims($fid,80,500,"fig",0);
# 	print "found $#sims_src SIMs\n";
# 	foreach $sims (@sims_src) {
# 	    my ($sims_string) = "@$sims";
# #       print "$sims_string\n";
# 	    my ($rfid,$start,$stop,$eval) = ( $sims_string =~ /\S+\s+(\S+)\s+\S+\s\S+\s+(\S+)\s+(\S+)\s+
# 					      \S+\s+\S+\s+\S+\s+\S+\s+(\S+)+.*/);
# #       print "ID: $rfid, E:$eval, Start:$start stop:$stop\n";
# 	    $Sims{$rfid}{'eval'}=$eval;
# 	    $Sims{$rfid}{'start'}=$start;
# 	    $Sims{$rfid}{'stop'}=$stop;
# 	    print "$rfid $Sims{$rfid}{'eval'}\n";
# 	}
	
# 	# BBHs
# 	my $BBHs=();
	
# 	@bbhs_src = $fig->bbhs($fid,1.0e-10);
# 	print "found $#bbhs_src BBHs\n";
# 	foreach $bbh (@bbhs_src) {
# 	    #print "@$bbh\n";
# 	    my ($bbh_string) = "@$bbh";
# 	    my ($rfid,$eval,$score) = ( $bbh_string =~ /(\S+)\s(\S+)\s(\S+)/);
# 	    #print "ID: $rfid, E:$eval, S:$score\n";
# 	    $BBHs{$rfid}{'eval'}=$eval;
# 	    $BBHs{$rfid}{'score'}=$score;
# #print "$rfid $BBHs{$rfid}{'eval'}\n";
# 	}

#     }



=head3 new (internal)

Instantiate a new object.

=cut

sub new {
  my ($class,$dataset) = @_;
  

  #$self = { acc => '',
#	    description => '',
#	    class => '',
#	    type => '',
#	    start => '',
#	    stop => '',
#	    evalue => '',
#	    score => '',
#	    display_method => '',
#	    feature_id => '',
#	    rank => '',
#	    supports_annotation => '',
#	    id => '',
#            organism => '',
#            who => ''
#	  };
  
  my $self = { class => $dataset->{'class'},
	       type => $dataset->{'type'}
	    };
  
  bless($self,$class);
  
  return $self;
}

=head3 feature_id (internal)


=cut

sub feature_id {
  my ($self) = @_;

  return $self->{feature_id};
}

=head3 id (internal)

Returns the ID  of the identical sequence

=cut

sub id {
    my ($self) = @_;

    return $self->{id};
}

=head3 organism (internal)

Returns the organism  of the identical sequence

=cut

sub organism {
    my ($self) = @_;

    return $self->{organism};
}

=head3 function (internal)

Returns the function of the identical sequence

=cut

sub function {
    my ($self) = @_;

    return $self->{function};
}

=head3 database (internal)

Returns the database of the identical sequence

=cut

sub database {
    my ($self) = @_;

    return $self->{database};
}


############################################################
############################################################
package Observation::Identical;

use base qw(Observation);

sub new {
    
    my ($class,$dataset) = @_; 
    my $self = $class->SUPER::new($dataset);
    $self->{id} = $dataset->{'id'};
    $self->{organism} = $dataset->{'organism'};
    $self->{function} = $dataset->{'function'};
    $self->{database} = $dataset->{'database'};

    bless($self,$class);
    return $self;
}

=head3 display()

If available use the function specified here to display the "raw" observation.
This code will display a table for the identical protein


B<Please note> that URL linked to in display_method() is an external component and needs to added to the code for every class of evi
dence.

=cut

sub display{
    my ($self, $cgi, $dataset) = @_;

    my $all_domains = [];
    my $count_identical = 0;
    my $content;
    foreach my $thing (@$dataset) {
	next if ($thing->class ne "IDENTICAL");
        my $single_domain = [];
        push(@$single_domain,$thing->database);
        my $id = $thing->id;
        $count_identical++;
        push(@$single_domain,&HTML::set_prot_links($cgi,$id));
        push(@$single_domain,$thing->organism);
        #push(@$single_domain,$thing->type);
        push(@$single_domain,$thing->function);
        push(@$all_domains,$single_domain);
    }

    if ($count_identical >0){
        $content = $all_domains;
    }
    else{
        $content = "<p>This PEG does not have any essentially identical proteins</p>";
    }
    return ($content);
}

1;


#########################################
#########################################
package Observation::FC;
1;

use base qw(Observation);

sub new {
    
    my ($class,$dataset) = @_; 
    my $self = $class->SUPER::new($dataset);
    $self->{score} = $dataset->{'score'};
    $self->{id} = $dataset->{'id'};
    $self->{function} = $dataset->{'function'};
    
    bless($self,$class);
    return $self;
}

=head3 display()

If available use the function specified here to display the "raw" observation.
This code will display a table for the identical protein


B<Please note> that URL linked to in display_method() is an external component and needs to added to the code for every class of evi
dence.

=cut

sub display {
    my ($self,$cgi,$dataset, $fid) = @_;

    my $functional_data = [];
    my $count = 0;
    my $content;

    foreach my $thing (@$dataset) {
	my $single_domain = [];
	next if ($thing->class ne "PCH");
	$count++;

	# construct the score link
	my $score = $thing->score;
	my $toid = $thing->id;
	my $link = $cgi->url(-relative => 1) . "?user=master&request=show_coupling_evidence&prot=$fid&to=$toid&SPROUT=";
	my $sc_link = "<a href=$link>$score</a>";

	push(@$single_domain,$sc_link);
	push(@$single_domain,$thing->id);
	push(@$single_domain,$thing->function);
	push(@$functional_data,$single_domain);
    }

    if ($count >0){
	$content = $functional_data;
    }
    else
    {
	$content = "<p>This PEG does not have any functional coupling</p>";
    }
    return ($content);
}


#########################################
#########################################
package Observation::Domain;

use base qw(Observation);

sub new {
    
    my ($class,$dataset) = @_; 
    my $self = $class->SUPER::new($dataset);
    $self->{evalue} = $dataset->{'evalue'};
    $self->{acc} = $dataset->{'acc'};
    $self->{start} = $dataset->{'start'};
    $self->{stop} = $dataset->{'stop'};
    
    bless($self,$class);
    return $self;
}

sub display {
    my ($thing,$gd) = @_;
    my $lines = [];
    my $line_config = { 'title' => $thing->acc,
			'short_title' => $thing->type,
			'basepair_offset' => '1' };
    my $color = "4";
    
    my $line_data = [];
    my $links_list = [];
    my $descriptions = [];
    
    my $description_function;
    $description_function = {"title" => $thing->class,
			     "value" => $thing->acc};
    
    push(@$descriptions,$description_function);
    
    my $score;
    $score = {"title" => "score",
	      "value" => $thing->evalue};
    push(@$descriptions,$score);
    
    my $link_id;
    if ($thing->acc =~/CDD::(\d+)/){
	$link_id = $1;
    }
    
    my $link;
    $link = {"link_title" => $thing->acc,
	     "link" => "http://0-www.ncbi.nlm.nih.gov.library.vu.edu.au:80/Structure/cdd/cddsrv.cgi?uid=$link_id"};
    push(@$links_list,$link);
    
    my $element_hash = {
	"title" => $thing->type,
	"start" => $thing->start,
	"end" =>  $thing->stop,
	"color"=> $color,
	"zlayer" => '2',
	"links_list" => $links_list,
	"description" => $descriptions};
    
    push(@$line_data,$element_hash);
    $gd->add_line($line_data, $line_config);
    
    return $gd;

}
 

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