/ 
bioperl-0.6
/ Bio::SeqFeature::Generic

NAME

Bio::SeqFeature::Generic - Generic SeqFeature

SYNOPSIS

   $feat = new Bio::SeqFeature::Generic ( -start => 10, -end => 100,
				-strand => -1, -primary => 'repeat',
				-source => 'repeatmasker',
				-score  => 1000,
				-tag    => { 
				    new => 1,
				    author => 'someone',
				    sillytag => 'this is silly!' } );

   $feat = new Bio::SeqFeature::Generic ( -gff_string => $string );

   # add it to an annotated sequence

   $annseq->add_SeqFeature($feat);

DESCRIPTION

Bio::SeqFeature::Generic is a generic implementation for the Bio::SeqFeatureI interface, providing a simple object to provide all the information for a feature on a sequence.

For many Features, this is all you will need to use (for example, this is fine for Repeats in DNA sequence or Domains in protein sequence). For other features, which have more structure, this is a good base class to extend using inheritence to have new things: this is what is done in the Bio::SeqFeature::Gene, Bio::SeqFeature::Transcript and Bio::SeqFeature::Exon, which provide well coordinated classes to represent genes on DNA sequence (for example, you can get the protein sequence out from a transcript class).

For many Features, you want to add some piece of information, for example a common one is that this feature is 'new' whereas other features are 'old'. The tag system, which here is implemented using a hash can be used here. You can use the tag system to extend the SeqFeature::Generic programmatically: that is, you know that you have read in more information into the tag 'mytag' which you can the retrieve. This means you do not need to know how to write inherieted Perl to provide more complex information on a feature, and/or, if you do know but you donot want to write a new class every time you need some extra piece of information, you can use the tag system to easily store and then retrieve information.

The tag system can be written in/out of GFF format, and also into EMBL format via AnnSeqIO::EMBL.

CONTACT

Ewan Birney <birney@sanger.ac.uk>

DEVELOPERS

This class has been written with an eye out of inheritence. The fields the actual object hash are:

_gsf_tag_hash  = reference to a hash for the tags
_gsf_sub_array = reference to an array for sub arrays
_gsf_start     = scalar of the start point
_gsf_end       = scalar of the end point
_gsf_strand    = scalar of the strand

APPENDIX

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

start

Title   : start
Usage   : $start = $feat->start
          $feat->start(20)
Function: Get/set on the start coordinate of the feature
Returns : integer
Args    : none

end

Title   : end
Usage   : $end = $feat->end
          $feat->end($end)
Function: get/set on the end coordinate of the feature
Returns : integer
Args    : none

length

Title   : length
Usage   :
Function:
Example :
Returns : 
Args    :

strand

Title   : strand
Usage   : $strand = $feat->strand()
          $feat->strand($strand)
Function: get/set on strand information, being 1,-1 or 0
Returns : -1,1 or 0
Args    : none

score

Title   : score
Usage   : $score = $feat->score()
          $feat->score($score)
Function: get/set on score information
Returns : float
Args    : none if get, the new value if set

frame

Title   : frame
Usage   : $frame = $feat->frame()
          $feat->frame($frame)
Function: get/set on frame information
Returns : 0,1,2
Args    : none if get, the new value if set

sub_SeqFeature

Title   : sub_SeqFeature
Usage   : @feats = $feat->sub_SeqFeature();
Function: Returns an array of sub Sequence Features
Returns : An array
Args    : none

add_sub_SeqFeature

Title   : add_sub_SeqFeature
Usage   : $feat->add_sub_SeqFeature($subfeat);
          $feat->add_sub_SeqFeature($subfeat,'EXPAND')
Function: adds a SeqFeature into the subSeqFeature array.
          with no 'EXPAND' qualifer, subfeat will be tested
          as to whether it lies inside the parent, and throw
          an exception if not.

          If EXPAND is used, the parent's start/end/strand will
          be adjusted so that it grows to accommodate the new
          subFeature
Returns : nothing
Args    : An object which has the SeqFeatureI interface

flush_sub_SeqFeature

 Title   : flush_sub_SeqFeature
 Usage   : $sf->flush_sub_SeqFeature
 Function: Removes all sub SeqFeature
           (if you want to remove only a subset, take
	    an array of them all, flush them, and add
            back only the guys you want)
 Example :
 Returns : none
 Args    : none

primary_tag

Title   : primary_tag
Usage   : $tag = $feat->primary_tag()
          $feat->primary_tag('exon')
Function: get/set on the primary tag for a feature,
          eg 'exon'
Returns : a string 
Args    : none

source_tag

Title   : source_tag
Usage   : $tag = $feat->source_tag()
          $feat->source_tag('genscan');
Function: Returns the source tag for a feature,
          eg, 'genscan' 
Returns : a string 
Args    : none

has_tag

Title   : has_tag
Usage   : $value = $self->has_tag('some_tag')
Function: Returns the value of the tag (undef if 
          none)
Returns : 
Args    :

add_tag_value

Title   : add_tag_value
Usage   : $self->add_tag_value('note',"this is a note");
Returns : nothing
Args    : tag (string) and value (any scalar)

each_tag_value

Title   : each_tag_value
Usage   :
Function:
Example :
Returns : 
Args    :

all_tags

Title   : all_tags
Usage   : @tags = $feat->all_tags()
Function: gives all tags for this feature
Returns : an array of strings
Args    : none

attach_seq

Title   : attach_seq
Usage   : $sf->attach_seq($seq)
Function: Attaches a Bio::Seq object to this feature. This
          Bio::Seq object is for the *entire* sequence: ie
          from 1 to 10000
Example :
Returns : 
Args    :

seq

Title   : seq
Usage   : $tseq = $sf->seq()
Function: returns the truncated sequence (if there) for this
Example :
Returns : 
Args    :

entire_seq

Title   : entire_seq
Usage   : $whole_seq = $sf->entire_seq()
Function: gives the entire sequence that this seqfeature is attached to
Example :
Returns : 
Args    :

seqname

Title   : seqname
Usage   : $obj->seqname($newval)
Function: There are many cases when you make a feature that you
          do know the sequence name, but do not know its actual
          sequence. This is an attribute such that you can store 
          the seqname.

          This attribute should *not* be used in GFF dumping, as
          that should come from the collection in which the seq
          feature was found.
Returns : value of seqname
Args    : newvalue (optional)

slurp_gff_file

Title   : slurp_file
Usage   : @features = Bio::SeqFeature::Generic::slurp_gff_file(\*FILE);
Function: Sneaky function to load an entire file as in memory objects.
          Beware big files
Example :
Returns : 
Args    :

_from_gff_string

Title   : _from_gff_string
Usage   :
Function:
Example :
Returns : 
Args    :

_parse

Title   : _parse
Usage   :
Function: Parsing hints
Example :
Returns : 
Args    :