Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::Das::SegmentI - DAS-style access to a feature database

SYNOPSIS

         # Get a Bio::Das::SegmentI object from a Bio::DasI database...

         $segment = $das->segment(-name=>'Landmark',
                                  -start=>$start,
                                  -end => $end);

         @features = $segment->overlapping_features(-type=>['type1','type2']);
         # each feature is a Bio::SeqFeatureI-compliant object

         @features = $segment->contained_features(-type=>['type1','type2']);

         @features = $segment->contained_in(-type=>['type1','type2']);

         $stream = $segment->get_feature_stream(-type=>['type1','type2','type3'];
         while (my $feature = $stream->next_seq) {
            # do something with feature
         }

         $count = $segment->features_callback(-type=>['type1','type2','type3'],
                                              -callback => sub { ... { }
                                              );

DESCRIPTION

       Bio::Das::SegmentI is a simplified alternative interface to sequence annotation databases
       used by the distributed annotation system. In this scheme, the genome is represented as a
       series of landmarks.  Each Bio::Das::SegmentI object ("segment") corresponds to a genomic
       region defined by a landmark and a start and end position relative to that landmark.  A
       segment is created using the Bio::DasI segment() method.

       Features can be filtered by the following attributes:

         1) their location relative to the segment (whether overlapping,
                 contained within, or completely containing)

         2) their type

         3) other attributes using tag/value semantics

       Access to the feature list uses three distinct APIs:

         1) fetching entire list of features at a time

         2) fetching an iterator across features

         3) a callback

FEEDBACK

   Mailing Lists
       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@bio.perl.org

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   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 the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Lincoln Stein

       Email lstein@cshl.org

APPENDIX

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

   seq_id
        Title   : seq_id
        Usage   : $ref = $s->seq_id
        Function: return the ID of the landmark
        Returns : a string
        Args    : none
        Status  : Public

   display_name
        Title   : seq_name
        Usage   : $ref = $s->seq_name
        Function: return the human-readable name for the landmark
        Returns : a string
        Args    : none
        Status  : Public

       This defaults to the same as seq_id.

   start
        Title   : start
        Usage   : $s->start
        Function: start of segment
        Returns : integer
        Args    : none
        Status  : Public

       This is a read-only accessor for the start of the segment.  Alias to low() for Gadfly
       compatibility.

   end
        Title   : end
        Usage   : $s->end
        Function: end of segment
        Returns : integer
        Args    : none
        Status  : Public

       This is a read-only accessor for the end of the segment. Alias to high() for Gadfly
       compatibility.

   length
        Title   : length
        Usage   : $s->length
        Function: length of segment
        Returns : integer
        Args    : none
        Status  : Public

       Returns the length of the segment.  Always a positive number.

   seq
        Title   : seq
        Usage   : $s->seq
        Function: get the sequence string for this segment
        Returns : a string
        Args    : none
        Status  : Public

       Returns the sequence for this segment as a simple string.

   ref
        Title   : ref
        Usage   : $ref = $s->ref([$newlandmark])
        Function: get/set the reference landmark for addressing
        Returns : a string
        Args    : none
        Status  : Public

       This method is used to examine/change the reference landmark used to establish the
       coordinate system.  By default, the landmark cannot be changed and therefore this has the
       same effect as seq_id().  The new landmark might be an ID, or another Das::SegmentI
       object.

   absolute
        Title   : absolute
        Usage   : $s->absolute([$new_value])
        Function: get/set absolute addressing mode
        Returns : flag
        Args    : new flag (optional)
        Status  : Public

       Turn on and off absolute-addressing mode.  In absolute addressing mode, coordinates are
       relative to some underlying "top level" coordinate system (such as a chromosome). ref()
       returns the identity of the top level landmark, and start() and end() return locations
       relative to that landmark.  In relative addressing mode, coordinates are relative to the
       landmark sequence specified at the time of segment creation or later modified by the ref()
       method.

       The default is to return false and to do nothing in response to attempts to set absolute
       addressing mode.

   features
        Title   : features
        Usage   : @features = $s->features(@args)
        Function: get features that overlap this segment
        Returns : a list of Bio::SeqFeatureI objects
        Args    : see below
        Status  : Public

       This method will find all features that intersect the segment in a variety of ways and
       return a list of Bio::SeqFeatureI objects.  The feature locations will use coordinates
       relative to the reference sequence in effect at the time that features() was called.

       The returned list can be limited to certain types, attributes or range intersection modes.
       Types of range intersection are one of:

          "overlaps"      the default
          "contains"      return features completely contained within the segment
          "contained_in"  return features that completely contain the segment

       Two types of argument lists are accepted.  In the positional argument form, the arguments
       are treated as a list of feature types.  In the named parameter form, the arguments are a
       series of -name=>value pairs.

         Argument    Description
         --------   ------------

         -types      An array reference to type names in the format
                     "method:source"

         -attributes A hashref containing a set of attributes to match

         -rangetype  One of "overlaps", "contains", or "contained_in".

         -iterator   Return an iterator across the features.

         -callback   A callback to invoke on each feature

       The -attributes argument is a hashref containing one or more attributes to match against:

         -attributes => { Gene => 'abc-1',
                          Note => 'confirmed' }

       Attribute matching is simple string matching, and multiple attributes are ANDed together.
       More complex filtering can be performed using the -callback option (see below).

       If -iterator is true, then the method returns an object reference that implements the
       next_seq() method.  Each call to next_seq() returns a new Bio::SeqFeatureI object.

       If -callback is passed a code reference, the code reference will be invoked on each
       feature returned.  The code will be passed two arguments consisting of the current feature
       and the segment object itself, and must return a true value. If the code returns a false
       value, feature retrieval will be aborted.

       -callback and -iterator are mutually exclusive options.  If -iterator is defined, then
       -callback is ignored.

       NOTE: the following methods all build on top of features(), and do not need to be
       explicitly implemented.

           overlapping_features()
           contained_features()
           contained_in()
           get_feature_stream()

   overlapping_features
        Title   : overlapping_features
        Usage   : @features = $s->overlapping_features(@args)
        Function: get features that overlap this segment
        Returns : a list of Bio::SeqFeatureI objects
        Args    : see below
        Status  : Public

       This method is identical to features() except that it defaults to finding overlapping
       features.

   contained_features
        Title   : contained_features
        Usage   : @features = $s->contained_features(@args)
        Function: get features that are contained in this segment
        Returns : a list of Bio::SeqFeatureI objects
        Args    : see below
        Status  : Public

       This method is identical to features() except that it defaults to a range type of
       'contained'.

   contained_in
        Title   : contained_in
        Usage   : @features = $s->contained_in(@args)
        Function: get features that contain this segment
        Returns : a list of Bio::SeqFeatureI objects
        Args    : see below
        Status  : Public

       This method is identical to features() except that it defaults to a range type of
       'contained_in'.

   get_feature_stream
        Title   : get_feature_stream
        Usage   : $iterator = $s->get_feature_stream(@args)
        Function: get an iterator across the segment
        Returns : an object that implements next_seq()
        Args    : see below
        Status  : Public

       This method is identical to features() except that it always generates an iterator.

       NOTE: This is defined in the interface in terms of features().  You do not have to
       implement it.

   factory
        Title   : factory
        Usage   : $factory = $s->factory
        Function: return the segment factory
        Returns : a Bio::DasI object
        Args    : see below
        Status  : Public

       This method returns a Bio::DasI object that can be used to fetch more segments.  This is
       typically the Bio::DasI object from which the segment was originally generated.

   primary_tag
        Title   : primary_tag
        Usage   : $tag = $s->primary_tag
        Function: identifies the segment as type "DasSegment"
        Returns : a string named "DasSegment"
        Args    : none
        Status  : Public, but see below

       This method provides Bio::Das::Segment objects with a primary_tag() field that identifies
       them as being of type "DasSegment".  This allows the Bio::Graphics engine to render
       segments just like a feature in order nis way useful.

       This does not need to be implemented.  It is defined by the interface.

   strand
        Title   : strand
        Usage   : $strand = $s->strand
        Function: identifies the segment strand as 0
        Returns : the number 0
        Args    : none
        Status  : Public, but see below

       This method provides Bio::Das::Segment objects with a strand() field that identifies it as
       being strandless.  This allows the Bio::Graphics engine to render segments just like a
       feature in order nis way useful.

       This does not need to be implemented.  It is defined by the interface.