Scott Cain > Bio-DB-Das-Chado-0.34 > Bio::DB::Das::Chado::Segment::Feature

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NAME ^

Bio::DB::Das::Chado::Segment::Feature

SYNOPSIS ^

See Bio::DB::Das::Chado.

DESCRIPTION ^

Not yet written

API ^

new

 Title   : new
 Usage   : $f = Bio::DB::Das::Chado::Segment::Feature->new(@args);
 Function: create a new feature object
 Returns : new Bio::DB::Das::Chado::Segment::Feature object
 Args    : see below
 Status  : Internal

This method is called by Bio::DB::Das::Chado::Segment to create a new feature using information obtained from the chado database.

The 11 arguments are positional:

  $factory      a Bio::DB::Das::Chado adaptor object (or descendent)
  $parent       the parent feature object (if it exists)
  $srcseq       the source sequence
  $start        start of this feature
  $stop         stop of this feature
  $type         a Bio::DB::GFF::Typename (containing a method and source)
  $score        the feature's score
  $strand       this feature's strand (relative to the source
                sequence, which has its own strandedness!)
  $phase        this feature's phase (often with respect to the 
                previous feature in a group of related features)
  $group        this feature's featureloc.locgroup (NOT a GFF holdover)
  $uniquename   this feature's internal unique database
                     name (feature.uniquename)
  $feature_id   the feature's feature_id

This is called when creating a feature from scratch. It does not have an inherited coordinate system.

feature and featureloc accessors ^

Methods below are accessors for data that is drawn directly from the Chado database and can be considered "primary" accessors for this class.

feature_id()

  Title   : feature_id
  Usage   : $obj->feature_id($newval)
  Function: holds feature.feature_id
  Returns : value of feature_id (a scalar)
  Args    : on set, new value (a scalar or undef, optional)

Implemented in Bio::DB::Das::Chado::Segment

organism

Usage
  $obj->organism()        #get existing value
  $obj->organism($newval) #set new value
Function
Returns

value of organism (a scalar)

Arguments

new value of organism (to set)

group()

  Title   : group
  Usage   : $group = $f->group([$new_group]);
  Function: Returns a feature name--this is here to maintain backward 
            compatibility with GFF and gbrowse.
  Returns : value of group (a scalar)
  Args    : on set, new value (a scalar or undef, optional)

srcfeature_id()

  Title   : srcfeature_id
  Usage   : $obj->srcfeature_id($newval)
  Function: ???
  Returns : value of srcfeature_id (a scalar)
  Args    : on set, new value (a scalar or undef, optional)

strand()

  Title   : strand
  Usage   : $obj->strand()
  Function: Returns the strand of the feature.  Unlike the other
            methods, the strand cannot be changed once the object is
            created (due to coordinate considerations).
            corresponds to featureloc.strand
  Returns : -1, 0, or 1
  Args    : on set, new value (a scalar or undef, optional)

phase

Usage
  $obj->phase()        #get existing value
  $obj->phase($newval) #set new value
Function
Returns

value of phase (a scalar)

Arguments

new value of phase (to set)

type()

  Title   : type
  Usage   : $obj->type($newval)
  Function: holds a Bio::DB::GFF::Typename object
  Returns : returns a Bio::DB::GFF::Typename object
  Args    : on set, new value

uniquename()

  Title   : uniquename
  Usage   : $obj->uniquename($newval)
  Function: holds feature.uniquename
  Returns : value of uniquename (a scalar)
  Args    : on set, new value (a scalar or undef, optional)

is_analysis()

  Title   : is_analysis
  Usage   : $obj->is_analysis($newval)
  Function: holds feature.is_analysis
  Returns : value of is_analysis (a scalar)
  Args    : on set, new value (a scalar or undef, optional)

SeqFeatureI methods ^

Bio::DB::Das::Chado::Segment::Feature implements the Bio::SeqFeatureI interface. Methods described below, see Bio:SeqFeatureI for more details.

attach_seq()

 Title   : attach_seq
 Usage   : $sf->attach_seq($seq)
 Function: Attaches a Bio::Seq object to this feature. This
           Bio::Seq object is for the *entire* sequence: ie
           from 1 to 10000
 Example :
 Returns : TRUE on success
 Args    : a Bio::PrimarySeqI compliant object

display_name()

  Title   : display_name
  Function: aliased to uniquename() for Bio::SeqFeatureI compatibility

entire_seq()

 Title   : entire_seq
 Usage   : $whole_seq = $sf->entire_seq()
 Function: gives the entire sequence that this seqfeature is attached to
 Example :
 Returns : a Bio::PrimarySeqI compliant object, or undef if there is no
           sequence attached
 Args    : none

get_all_tags()

  Title   : get_all_tags
  Function: aliased to all_tags() for Bio::SeqFeatureI compatibility

get_SeqFeatures()

  Title   : get_SeqFeatures
  Function: aliased to sub_SeqFeature() for Bio::SeqFeatureI compatibility

get_tag_values()

  Title   : get_tag_values
  Usage   : $feature->get_tag_values
  Function: Returns values associated with a particular tag
  Returns : A list of values
  Args    : A string (the name of the tag)

get_tagset_values()

  Title   : get_tagset_values
  Usage   :
  Function: ???
  Returns :
  Args    :

gff_string()

  Title   : gff_string
  Usage   :
  Function: ???
  Returns :
  Args    :

has_tag()

  Title   : has_tag
  Usage   :
  Function: ???
  Returns :
  Args    :

primary_tag()

  Title   : primary_tag
  Function: aliased to type() for Bio::SeqFeatureI compatibility

seq()

  Title   : seq
  Usage   :
  Function: ???
  Returns :
  Args    :

seq_id()

  Title   : seq_id
  Usage   : $obj->seq_id($newval)
  Function: Set or get the name of the reference sequence that the feature 
            resides on.
  Returns : value of seq_id (a scalar)
  Args    : on set, new value (a scalar or undef, optional)

Bio::RangeI methods ^

Bio::SeqFeatureI in turn ISA Bio::RangeI. Bio::RangeI interface methods described below, Bio::RangeI for details.

end()

  Title   : end
  Function: inherited, L<Bio::DB::Das::Chado::Segment>

start()

  Title   : start
  Function: inherited, L<Bio::DB::Das::Chado::Segment>

strand()

  Title   : strand
  Function: inherited, L<Bio::DB::Das::Chado::Segment>

other get/setters ^

abs_strand()

  Title   : abs_strand
  Usage   : $obj->abs_strand($newval)
  Function: aliased to strand() for backward compatibility

db_id()

  Title   : db_id
  Function: aliased to uniquename() for backward compatibility

factory()

  Title   : factory
  Usage   : $obj->factory($newval)
  Function: ???
  Returns : value of factory (a scalar)
  Args    : on set, new value (a scalar or undef, optional)

id()

  Title   : id
  Function: aliased to uniquename() for backward compatibility

info()

  Title   : info
  Function: aliased to uniquename() for backward compatibility
            with broken generic glyphs primarily

length()

  Title   : length
  Usage   : $obj->length()
  Function: convenience for end - start + 1
  Returns : length of feature in basepairs
  Args    : none

method()

 Title   : method
 Usage   : $obj->method
 Function: returns a Feature's method (SOFA type)
 Returns : the Features SOFA type
 Args    : none

name()

  Title   : name
  Function: aliased to group for backward compatibility

parent()

  Title   : parent
  Usage   : $obj->parent($newval)
  Function: ???
  Returns : value of parent (a scalar)
  Args    : on set, new value (a scalar or undef, optional)

score()

  Title   : score
  Usage   : $obj->score($newval)
  Function: holds the (alignment?) feature's score
  Returns : value of score (a scalar)
  Args    : on set, new value (a scalar or undef, optional)

target()

  Title   : target
  Usage   : $feature->target
  Function: returns a Bio::DB::Das::Chado::Segment that corresponds
            to the target of a similarity pair
  Returns : a Bio::DB::Das::Chado::Segment object
  Args    : none

Other methods ^

all_tags()

  Title   : all_tags
  Usage   :
  Function: ???
  Returns :
  Args    :

source()

  Title   : source
  Usage   : $f->source();
  Function: caches and returns the source from a GFF file, this is stored
            in dbxref with a db of 'GFF_Source'
  Returns : See above
  Args    : none

segments()

  Title   : segments
  Function: aliased to sub_SeqFeature() for compatibility

subfeatures

  Title   : subfeatures
  Usage   : $obj->subfeatures($newval)
  Function: returns a list of subfeatures
  Returns : value of subfeatures (a scalar)
FIXME THIS SHOULD RETURN A LIST OR AN ARRAY AND BE DOCUMENTED AS SUCH
NOT RETURN AN ARRAYREF OR HASHREF.  FOR ADDING/SETTING ELEMENTS WE
NEED ADD_ AND SET_ METHODS
  Args    : on set, new value (a scalar or undef, optional)

sub_SeqFeature()

 Title   : sub_SeqFeature
 Usage   : @feat = $feature->sub_SeqFeature([$type])
 Function: This method returns a list of any subfeatures
           that belong to the main feature.  For those
           features that contain heterogeneous subfeatures,
           you can retrieve a subset of the subfeatures by
           providing an array of types to filter on.

           For AcePerl compatibility, this method may also
           be called as segments().
 Returns : a list of Bio::DB::Das::Chado::Segment::Feature objects
 Args    : a feature method (optional)
 Status  : Public
Argh...! DONT DROP THE PROTEIN FEATURE
  dgg: polypeptide or protein is a most important feature, don't drop it!
  
  This is the part of a gene that has lots of attached critical info:
  protein ID, translation, GO terms, Dbxrefs to other proteins)
  While this exclusion fixes a display bug, e.g. Glyph/processed_transcript 
  it is much less problematic to patch the glyph displayers.
  
  elsif ( 0 && $inferCDS) {
    #just remove polypeptide features
    my @ok_feats = grep {$_->type->method ne 'polypeptide'} @features;
    warn @ok_feats if DEBUG;
    return @ok_feats;
  }

_do_the_inferring

Usage
  $obj->_do_the_inferring(@features)
Function

Takes a list of polypeptide and exon features and infers CDS and UTR features from them.

Returns

A list of CDS and UTR features

Arguments

A list of polypeptide and exon features

Caveats

This function will break with polycistronic genes, as there will be more than one polypeptide per set of exons, and this function assumes that there is only one.

_calc_phases

 Title   : _calc_phases
 Usage   : $feature->_calc_phases(@exons)
 Function: calculstes phases for exons without phases 
 Returns : a list of exon feature objects with phases
 Args    : a list of sorted (by transcription order) exons
 Status  : private

notes

 Title   : notes
 Usage   : @notes = $feature->notes
 Function: get the "notes" on a particular feature
 Returns : an array of string
 Args    : feature ID
 Status  : public

add_subfeature()

 Title   : add_subfeature
 Usage   : $feature->add_subfeature($feature)
 Function: This method adds a new subfeature to the object.
           It is used internally by aggregators, but is
           available for public use as well.
 Returns : nothing
 Args    : a Bio::DB::Das::Chado::Segment::Feature object
 Status  : Public

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

clone()

 Title   : clone
 Usage   : $feature = $f->clone
 Function: make a copy of the feature
 Returns : a new Bio::DB::Das::Chado::Segment::Feature object
 Args    : none
 Status  : Public

This method returns a copy of the feature.

sub_types()

 Title   : sub_types
 Usage   : @methods = $feature->sub_types
 Function: get methods of all sub-seqfeatures
 Returns : a list of method names
 Args    : none
 Status  : Public

For those features that contain subfeatures, this method will return a unique list of method names of those subfeatures, suitable for use with sub_SeqFeature().

Autogenerated Methods

 Title   : AUTOLOAD
 Usage   : @subfeat = $feature->Method
 Function: Return subfeatures using autogenerated methods
 Returns : a list of Bio::DB::Das::Chado::Segment::Feature objects
 Args    : none
 Status  : Public

Any method that begins with an initial capital letter will be passed to AUTOLOAD and treated as a call to sub_SeqFeature with the method name used as the method argument. For instance, this call:

  @exons = $feature->Exon;

is equivalent to this call:

  @exons = $feature->sub_SeqFeature('exon');

adjust_bounds()

 Title   : adjust_bounds
 Usage   : $feature->adjust_bounds
 Function: adjust the bounds of a feature
 Returns : ($start,$stop,$strand)
 Args    : none
 Status  : Public

This method adjusts the boundaries of the feature to enclose all its subfeatures. It returns the new start, stop and strand of the enclosing feature.

sort_features()

 Title   : sort_features
 Usage   : $feature->sort_features
 Function: sort features
 Returns : nothing
 Args    : none
 Status  : Public

This method sorts subfeatures in ascending order by their start position. For reverse strand features, it sorts subfeatures in descending order. After this is called sub_SeqFeature will return the features in order.

This method is called internally by merged_segments().

asString()

 Title   : asString
 Usage   : $string = $feature->asString
 Function: return human-readabled representation of feature
 Returns : a string
 Args    : none
 Status  : Public

This method returns a human-readable representation of the feature and is called by the overloaded "" operator.

synonyms()

 Title   : synonyms
 Usage   : @synonyms = $feature->synonyms
 Function: return a list of synonyms for a feature
 Returns : a list of strings
 Args    : none
 Status  : Public

Looks in the synonym table to collect all synonyms of a feature.

cmap_link()

 Title   : cmap_link
 Usage   : $link = $feature->cmap_link
 Function: returns a URL link to the corresponding feature in cmap
 Returns : a string
 Args    : none
 Status  : Public

Returns a link to a cmap installation (which is assumed to be on the same host as gbrowse). In addition to the cmap tables being present in chado, this method also assumes the presence of a link table called feature_to_cmap. See the cmap documentation for more information.

This function is intended primarily to be used in gbrowse conf files. For example:

  link       = sub {my $self = shift; return $self->cmap_link();}
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