/ 
bioperl-1.0.2
/ 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, 
	          ", produced by ", $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 ", $tag, "with values, ",
		      join(' ',$feat->each_tag_value($tag)), "\n";
            }
	    print "new feature\n" if $feat->has_tag('new');
	    # features can have sub features
	    my @subfeat = $feat->sub_SeqFeature();
	}

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

FEEDBACK

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://bio.perl.org/MailList.html             - About the mailing lists

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 email or the web:

bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/

APPENDIX

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

Bio::RangeI methods

List of interfaces inherited from Bio::RangeI.

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

SeqFeatureI specific methods

New method interfaces.

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   : $tag_exists = $self->has_tag('some_tag')
Function: 
Returns : TRUE if the specified tag exists, and FALSE otherwise
Args    :

each_tag_value

Title   : each_tag_value
Usage   : @values = $self->each_tag_value('some_tag')
Function: 
Returns : An array comprising the values of the specified tag.
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;
          $str = $feat->gff_string($gff_formatter);
Function: Provides the feature information in GFF format.

          The implementation provided here returns GFF2 by default. If you
          want a different version, supply an object implementing a method
          gff_string() accepting a SeqFeatureI object as argument. E.g., to
          obtain GFF1 format, do the following:

               my $gffio = Bio::Tools::GFF->new(-gff_version => 1);
               $gff1str = $feat->gff_string($gff1io);

Returns : A string
Args    : Optionally, an object implementing gff_string().

_static_gff_formatter

Title   : _static_gff_formatter
Usage   :
Function:
Example :
Returns : 
Args    :

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.

intersection

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 do not 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

location

 Title   : location
 Usage   : my $location = $seqfeature->location()
 Function: returns a location object suitable for identifying location 
	   of feature on sequence or parent feature  
 Returns : Bio::LocationI object
 Args    : none