tag fourth (and hopefully last) alpha

[bioperl-live.git] / branch-1-6 / Bio / Seq / PrimaryQual.pm

# $Id$
#
# bioperl module for Bio::PrimaryQual
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Chad Matsalla <bioinformatics@dieselwurks.com>
#
# Copyright Chad Matsalla
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

Bio::Seq::PrimaryQual - Bioperl lightweight Quality Object

=head1 SYNOPSIS

 use Bio::Seq::PrimaryQual;

 # you can use either a space-delimited string for quality

 my $string_quals = "10 20 30 40 50 40 30 20 10";
 my $qualobj = Bio::Seq::PrimaryQual->new
              ( '-qual' => $string_quals,
                '-id'  => 'QualityFragment-12',
                '-accession_number' => 'X78121',
                );

 # _or_ you can use an array of quality values

 my @q2 = split/ /,$string_quals;
 $qualobj = Bio::Seq::PrimaryQual->new( '-qual' => \@q2,
       '-primary_id'     =>      'chads primary_id',
       '-desc'           =>      'chads desc',
       '-accession_number' => 'chads accession_number',
      '-id'             =>      'chads id'
      );

 # to get the quality values out:

 my @quals = @{$qualobj->qual()};

 # to give _new_ quality values

 my $newqualstring = "50 90 1000 20 12 0 0";
 $qualobj->qual($newqualstring);


=head1 DESCRIPTION

This module provides a mechanism for storing quality
values. Much more useful as part of
Bio::Seq::SeqWithQuality where these quality values
are associated with the sequence information.

=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 one
of the Bioperl mailing lists.  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
the bugs and their resolution.  Bug reports can be submitted via the
web:

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

=head1 AUTHOR - Chad Matsalla

Email bioinformatics@dieselwurks.com

=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::PrimaryQual;
use vars qw(%valid_type);
use strict;


use base qw(Bio::Root::Root Bio::Seq::QualI);


=head2 new()

 Title   : new()
 Usage   : $qual = Bio::Seq::PrimaryQual->new
        ( -qual => '10 20 30 40 50 50 20 10',
          -id  => 'human_id',
          -accession_number => 'AL000012',
        );

 Function: Returns a new Bio::Seq::PrimaryQual object from basic 
        constructors, being a string _or_ a reference to an array for the
        sequence and strings for id and accession_number. Note that you
        can provide an empty quality string.
 Returns : a new Bio::Seq::PrimaryQual object

=cut




sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);

    # default: turn ON the warnings (duh)
    my($qual,$id,$acc,$pid,$desc,$given_id,$header) =
        $self->_rearrange([qw(QUAL
                              DISPLAY_ID
                              ACCESSION_NUMBER
                              PRIMARY_ID
                              DESC
                              ID
                              HEADER
                              )],
                          @args);
    if( defined $id && defined $given_id ) {
        if( $id ne $given_id ) {
            $self->throw("Provided both id and display_id constructor functions. [$id] [$given_id]");   
        }
    }
    if( defined $given_id ) { $id = $given_id; }
    
    # note: the sequence string may be empty
    $self->qual(defined($qual) ? $qual : []);
     $header && $self->header($header);
    $id      && $self->display_id($id);
    $acc     && $self->accession_number($acc);
    $pid     && $self->primary_id($pid);
    $desc    && $self->desc($desc);

    return $self;
}

=head2 qual()

 Title   : qual()
 Usage   : @quality_values  = @{$obj->qual()};
 Function: Returns the quality as a reference to an array containing the
           quality values. The individual elements of the quality array are
           not validated and can be any numeric value.
 Returns : A reference to an array.

=cut

sub qual {
    my ($self,$value) = @_;

    if( ! defined $value || length($value) == 0 ) { 
        $self->{'qual'} ||= [];
    } elsif( ref($value) =~ /ARRAY/i ) {
        # if the user passed in a reference to an array
        $self->{'qual'} = $value;
    } elsif(! $self->validate_qual($value)){
        $self->throw("Attempting to set the quality to [$value] which does not look healthy");      
    } else {
        $value =~ s/^\s+//;
        $self->{'qual'} = [split(/\s+/,$value)];
    }
    
    return $self->{'qual'};
}

=head2 validate_qual($qualstring)

 Title   : validate_qual($qualstring)
 Usage   : print("Valid.") if { &validate_qual($self,$qualities); }
 Function: Make sure that the quality, if it has length > 0, contains at
        least one digit. Note that quality strings are parsed into arrays
        using split/\d+/,$quality_string, so make sure that your quality
        scalar looks like this if you want it to be parsed properly.
 Returns : 1 for a valid sequence (WHY? Shouldn\'t it return 0? <boggle>)
 Args    : a scalar (any scalar, why PrimarySeq author?) and a scalar
        containing the string to validate.

=cut

sub validate_qual {
    # how do I validate quality values?
    # \d+\s+\d+..., I suppose
    my ($self,$qualstr) = @_;
    # why the CORE?? -- (Because Bio::PrimarySeqI namespace has a 
    #                    length method, you have to qualify 
    #                    which length to use)
    return 0 if (!defined $qualstr || CORE::length($qualstr) <= 0);   
    return 1 if( $qualstr =~ /\d/);
    
    return 0;
}

=head2 subqual($start,$end)

 Title   : subqual($start,$end)
 Usage   : @subset_of_quality_values = @{$obj->subqual(10,40)};
 Function: returns the quality values from $start to $end, where the
        first value is 1 and the number is inclusive, ie 1-2 are the
        first two bases of the sequence. Start cannot be larger than
        end but can be equal.
 Returns : A reference to an array.
 Args    : a start position and an end position

=cut


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

   if( $start > $end ){
       $self->throw("in subqual, start [$start] has to be greater than end [$end]");
   }

   if( $start <= 0 || $end > $self->length ) {
       $self->throw("You have to have start positive and length less than the total length of sequence [$start:$end] Total ".$self->length."");
   }

   # remove one from start, and then length is end-start

   $start--;
        $end--;
        my @sub_qual_array = @{$self->{qual}}[$start..$end];

        #   return substr $self->seq(), $start, ($end-$start);
        return \@sub_qual_array;

}

=head2 display_id()

 Title   : display_id()
 Usage   : $id_string = $obj->display_id();
 Function: returns the display id, aka the common name of the Quality
        object.
        The semantics of this is that it is the most likely string to be
        used as an identifier of the quality sequence, and likely to have
        "human" readability.  The id is equivalent to the ID field of the
        GenBank/EMBL databanks and the id field of the Swissprot/sptrembl
        database. In fasta format, the >(\S+) is presumed to be the id,
        though some people overload the id to embed other information.
        Bioperl does not use any embedded information in the ID field,
        and people are encouraged to use other mechanisms (accession
        field for example, or extending the sequence object) to solve
        this. Notice that $seq->id() maps to this function, mainly for
        legacy/convience issues
 Returns : A string
 Args    : None

=cut

sub display_id {
   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'display_id'} = $value;
    }
    return $obj->{'display_id'};

}

=head2 header()

 Title   : header()
 Usage   : $header = $obj->header();
 Function: Get/set the header that the user wants printed for this
     quality object.
 Returns : A string
 Args    : None

=cut

sub header {
   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'header'} = $value;
    }
    return $obj->{'header'};

}

=head2 accession_number()

 Title   : accession_number()
 Usage   : $unique_biological_key = $obj->accession_number();
 Function: Returns the unique biological id for a sequence, commonly
        called the accession_number. For sequences from established
        databases, the implementors should try to use the correct
        accession number. Notice that primary_id() provides the unique id
        for the implemetation, allowing multiple objects to have the same
        accession number in a particular implementation. For sequences
        with no accession number, this method should return "unknown".
 Returns : A string
 Args    : None

=cut

sub accession_number {
    my( $obj, $acc ) = @_;

    if (defined $acc) {
        $obj->{'accession_number'} = $acc;
    } else {
        $acc = $obj->{'accession_number'};
        $acc = 'unknown' unless defined $acc;
    }
    return $acc;
}

=head2 primary_id()

 Title   : primary_id()
 Usage   : $unique_implementation_key = $obj->primary_id();
 Function: Returns the unique id for this object in this implementation.
        This allows implementations to manage their own object ids in a
        way the implementaiton can control clients can expect one id to
        map to one object. For sequences with no accession number, this
        method should return a stringified memory location.
 Returns : A string
 Args    : None

=cut

sub primary_id {
   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'primary_id'} = $value;
    }
   return $obj->{'primary_id'};

}

=head2 desc()

 Title   : desc()
 Usage   : $qual->desc($newval);
           $description = $qual->desc();
 Function: Get/set description text for a qual object
 Example :
 Returns : Value of desc
 Args    : newvalue (optional)

=cut

sub desc {
   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'desc'} = $value;
    }
    return $obj->{'desc'};

}

=head2 id()

 Title   : id()
 Usage   : $id = $qual->id();
 Function: Return the ID of the quality. This should normally be (and
        actually is in the implementation provided here) just a synonym
        for display_id().
 Returns : A string.
 Args    : None.

=cut

sub id {
   my ($self,$value) = @_;
   if( defined $value ) {
        return $self->display_id($value);
   }
   return $self->display_id();
}

=head2 length()

 Title   : length()
 Usage   : $length = $qual->length();
 Function: Return the length of the array holding the quality values.
        Under most circumstances, this should match the number of quality
        values but no validation is done when the PrimaryQual object is
        constructed and non-digits could be put into this array. Is this
        a bug? Just enough rope...
 Returns : A scalar (the number of elements in the quality array).
 Args    : None.

=cut

sub length {
    my $self = shift;
    if (ref($self->{qual}) ne "ARRAY") {
        $self->warn("{qual} is not an array here. Why? It appears to be ".ref($self->{qual})."(".$self->{qual}."). Good thing this can _never_ happen.");
    }
    return scalar(@{$self->{qual}});
}

=head2 qualat($position)

 Title   : qualat($position)
 Usage   : $quality = $obj->qualat(10);
 Function: Return the quality value at the given location, where the
        first value is 1 and the number is inclusive, ie 1-2 are the first
        two bases of the sequence. Start cannot be larger than end but can
        be equal.
 Returns : A scalar.
 Args    : A position.

=cut

sub qualat {
    my ($self,$val) = @_;
    my @qualat = @{$self->subqual($val,$val)};
    if (scalar(@qualat) == 1) {
        return $qualat[0];
    }
    else {
        $self->throw("AAAH! qualat provided more then one quality.");
    }
} 

=head2 to_string()

 Title   : to_string()
 Usage   : $quality = $obj->to_string();
 Function: Return a textual representation of what the object contains.
        For this module, this function will return:
                qual
                display_id
                accession_number
                primary_id
                desc
                id
                length
 Returns : A scalar.
 Args    : None.

=cut

sub to_string {
    my ($self,$out,$result) = shift;
    $out = "qual: ".join(',',@{$self->qual()});
    foreach (qw(display_id accession_number primary_id desc id)) {
        $result = $self->$_();
        if (!$result) { $result = "<unset>"; }
        $out .= "$_: $result\n";
    }
    return $out;
}


sub to_string_automatic {
    my ($self,$sub_result,$out) = shift;
    foreach (sort keys %$self) {
        print("Working on $_\n");
        eval { $self->$_(); };
        if ($@) { $sub_result = ref($_); }
        elsif (!($sub_result = $self->$_())) {
            $sub_result = "<unset>";
        }
        if (ref($sub_result) eq "ARRAY") {
            print("This thing ($_) is an array!\n");
            $sub_result = join(',',@$sub_result);       
        }
        $out .= "$_: ".$sub_result."\n";
    }
    return $out;
} 

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