Bio::SeqFeature::FeaturePair(3pm)			User Contributed Perl Documentation			 Bio::SeqFeature::FeaturePair(3pm)

NAME

       Bio::SeqFeature::FeaturePair - hold pair feature information e.g. blast hits

SYNOPSIS

	   my $feat  = Bio::SeqFeature::FeaturePair->new(-feature1 => $f1,
							-feature2 => $f2,
						     );

	   # Bio::SeqFeatureI methods can be used

	   my $start = $feat->start;
	   my $end   = $feat->end;

	   # Bio::FeaturePair methods can be used
	   my $hstart = $feat->hstart;
	   my $hend   = $feat->hend;

	  my $feature1 = $feat->feature1;  # returns feature1 object

DESCRIPTION

       A sequence feature object where the feature is itself a feature on another sequence - e.g. a blast hit where residues 1-40 of a protein
       sequence SW:HBA_HUMAN has hit to bases 100 - 220 on a genomic sequence HS120G22.  The genomic sequence coordinates are used to create one
       sequence feature $f1 and the protein coordinates are used to create feature $f2.  A FeaturePair object can then be made

	   my $fp = Bio::SeqFeature::FeaturePair->new(-feature1 => $f1,   # genomic
						     -feature2 => $f2,	 # protein
						     );

       This object can be used as a standard Bio::SeqFeatureI in which case

	   my $gstart = $fp->start  # returns start coord on feature1 - genomic seq.
	   my $gend   = $fp->end    # returns end coord on feature1.

       In general standard Bio::SeqFeatureI method calls return information in feature1.

       Data in the feature 2 object are generally obtained using the standard methods prefixed by h (for hit!)

	   my $pstart = $fp->hstart # returns start coord on feature2 = protein seq.
	   my $pend   = $fp->hend   # returns end coord on feature2.

       If you wish to swap feature1 and feature2 around :

	   $feat->invert

       so...

	   $feat->start # etc. returns data in $feature2 object

       No sub_SeqFeatures or tags can be stored in this object directly.  Any features or tags are expected to be stored in the contained objects
       feature1, and feature2.

CONTACT

       Ewan Birney <birney@sanger.ac.uk>

APPENDIX

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

   new
	Title	: new
	Usage	:
	Function: Constructor for this module. Accepts the following parameters:

		    -feature1	Bio::SeqFeatureI-compliant object
		    -feature2	Bio::SeqFeatureI-compliant object
		    -feature_factory  Bio::Factory::ObjectFactoryI compliant
				object to be used when feature1 and/or feature2
				are accessed without explicitly set before. This
				is mostly useful for derived classes who want to
				set their preferred class for feature objects.

	Example :
	Returns :
	Args	: see above

   feature1
	Title	: feature1
	Usage	: $f = $featpair->feature1
		  $featpair->feature1($feature)
	Function: Get/set for the query feature
	Returns : Bio::SeqFeatureI
	Args	: Bio::SeqFeatureI

   feature2
	Title	: feature2
	Usage	: $f = $featpair->feature2
		  $featpair->feature2($feature)
	Function: Get/set for the hit feature
	Returns : Bio::SeqFeatureI
	Args	: Bio::SeqFeatureI

   start
	Title	: start
	Usage	: $start = $featpair->start
		  $featpair->start(20)
	Function: Get/set on the start coordinate of feature1
	Returns : integer
	Args	: [optional] beginning of feature

   end
	Title	: end
	Usage	: $end = $featpair->end
		  $featpair->end($end)
	Function: get/set on the end coordinate of feature1
	Returns : integer
	Args	: [optional] ending point of feature

   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	: [optional] strand information to set

   location
	Title	: location
	Usage	: $location = $featpair->location
		  $featpair->location($location)
	Function: Get/set location object (using feature1)
	Returns : Bio::LocationI object
	Args	: [optional] LocationI to store

   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

   primary_tag
	Title	: primary_tag
	Usage	: $ptag = $featpair->primary_tag
	Function: get/set on the primary_tag of feature1
	Returns : 0,1,2
	Args	: none if get, the new value if set

   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

   seqname
	Title	: seqname
	Usage	: $obj->seq_id($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)

   hseqname
	Title	: hseqname
	Usage	: $featpair->hseqname($newval)
	Function: Get/set method for the name of
		  feature2.
	Returns : value of $feature2->seq_id
	Args	: newvalue (optional)

   hstart
	Title	: hstart
	Usage	: $start = $featpair->hstart
		  $featpair->hstart(20)
	Function: Get/set on the start coordinate of feature2
	Returns : integer
	Args	: none

   hend
	Title	: hend
	Usage	: $end = $featpair->hend
		  $featpair->hend($end)
	Function: get/set on the end coordinate of feature2
	Returns : integer
	Args	: none

   hstrand
	Title	: hstrand
	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

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

   hframe
	Title	: hframe
	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

   hprimary_tag
	Title	: hprimary_tag
	Usage	: $ptag = $featpair->hprimary_tag
	Function: Get/set on the primary_tag of feature2
	Returns : 0,1,2
	Args	: none if get, the new value if set

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

   invert
	Title	: invert
	Usage	: $tag = $feat->invert
	Function: Swaps feature1 and feature2 around
	Returns : Nothing
	Args	: none

   feature_factory
	Title	: feature_factory
	Usage	: $obj->feature_factory($newval)
	Function: Get/set the feature object factory for this feature pair.

		  The feature object factory will be used to create a feature
		  object if feature1() or feature2() is called in get mode
		  without having been set before.

		  The default is an instance of Bio::Factory::ObjectFactory
		  and hence allows the type to be changed dynamically at any
		  time.

	Example :
	Returns : The feature object factory in use (a
		  Bio::Factory::ObjectFactoryI compliant object)
	Args	: on set, a Bio::Factory::ObjectFactoryI compliant object

perl v5.14.2							    2012-03-02					 Bio::SeqFeature::FeaturePair(3pm)