Provided by: libbio-perl-perl_1.7.2-2_all bug

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