/ 
bioperl-0.6
/ Bio::SeqFeatureI

NAME

Bio::SeqFeatureI - Abstract interface of a Sequence Feature

SYNOPSIS

    # get a seqfeature somehow, eg,

    foreach $feat ( $annseq->all_seqfeatures() ) {
            print "Feature from ", $feat->start, "to ", $feat->end, " Primary tag  " $feat->primary_tag, 
	    " From", $feat->source_tag() "\n";

            if( $feat->strand == 0 ) {
		print "Feature applicable to either strand\n";
            } else {
                print "Feature on strand ", $feat->strand,"\n"; # -1,1
            }

            foreach $tag ( $feat->all_tags() ) {
		print "Feature has tag ",$tag,"with value," $feat->has_tag($tag), "\n";
            }
	}

DESCRIPTION

This interface is the functions one can expect for any Sequence Feature, whatever its implemtation or whether it is a more complex type (eg, a Gene). This object doesn't actually provide any implemention, it just provides the definitions of what methods one can call. See Bio::SeqFeature::Generic for a good standard implementation of this object

CONTACT

Describe contact details here

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
Function: Returns the start coordinate of the feature
Returns : integer
Args    : none

end

Title   : end
Usage   : $end = $feat->end
Function: Returns the end coordinate of the feature
Returns : integer
Args    : none

strand

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

sub_SeqFeature

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

primary_tag

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

source_tag

Title   : source_tag
Usage   : $tag = $feat->source_tag()
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    :

all_tags

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

gff_string

Title   : gff_string
Usage   : $str = $feat->gff_string
Function: provides the feature information in GFF
          version 2 format.
Returns : A string
Args    : None

RangeI methods

These methods are inherited from RangeI and can be used directly from a SeqFeatureI interface. Remember that a SeqFeature is-a RangeI, and so wherever you see RangeI you can use a feature ($r in the below documentation).

overlaps

Title   : overlaps
Usage   : if($feat->overlaps($r)) { do stuff }
          if($feat->overlaps(200)) { do stuff }
Function: tests if $feat overlaps $r
Args    : a RangeI to test for overlap with, or a point
Returns : true if the Range overlaps with the feature, false otherwise

contains

Title   : contains
Usage   : if($feat->contains($r) { do stuff }
Function: tests whether $feat totally contains $r
Args    : a RangeI to test for being contained
Returns : true if the argument is totaly contained within this range

equals

Title   : equals
Usage   : if($feat->equals($r))
Function: test whether $feat has the same start, end, strand as $r
Args    : a RangeI to test for equality
Returns : true if they are describing the same range

Geometrical methods

These methods do things to the geometry of ranges, and return triplets (start, stop, strand) from which new ranges could be built.

Title   : intersection
Usage   : ($start, $stop, $strand) = $feat->intersection($r)
Function: gives the range that is contained by both ranges
Args    : a RangeI to compare this one to
Returns : nothing if they don't overlap, or the range that they do overlap

union

Title   : union
Usage   : ($start, $stop, $strand) = $feat->union($r);
        : ($start, $stop, $strand) = Bio::RangeI->union(@ranges);
Function: finds the minimal range that contains all of the ranges
Args    : a range or list of ranges to find the union of
Returns : the range containing all of the ranges