/ 
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/ DAS::GUS::Segment

NAME

DAS::GUS::Segment - DAS-style access to a GUS database

SYNOPSIS

  # Get a Bio::Das::SegmentI object from a DAS::GUS database
  
  $segment = $das->segment( -name  => 'Landmark',
   						    -start => $start,
							-stop  => $stop );

DESCRIPTION

AUTHOR

Name: Haiming Wang Email: hwang@uga.edu

new

Title	: new
Usage	: $segment = $db->segment(-name  => 'AAEL01000015',
								  -start => $start,
								  -stop  => $stop );
Function: Create a segment object 
Returns	: a new DAS::GUS::Segment object 
Args	: see below

This method creates a new DAS::GUS::Segment object accoring to a segment name, such as contig 'AAEL0100015'. Generally this is called automatically by the DAS::GUS module.

There are five positional arguments:

$factory		a DAS::GUS adaptor to use for database access
$start		start of the desired segment relative to source sequence
$stop			stop of the desired segment relative to source sequence
$srcfeature_id 	ID of the source sequence
$class		type of the sequence, i.e. chromosome, contig
$name  		name of the segment 
$atts			attributes of the segment

name

Title		: name
Usage		: $segname = $seg->name();
Function	: Return the name of the segment
Returns	: see avove
Args		: none
Status	: public

class

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

attributes

Title	: attributes
Usage	: $obj->attributes($newval)
Function: Return the segment attributes
Returns	: attributes string for gff3 dump
Args	:

seq_id

Title	: seq_id
Usage	: $ref = $s->seq_id
Function: return the ID of the landmark, aliased to name() for 
		  backward compatibility
Return	: a string
Args	: none
Status	: public

start

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

low

Title	: low
Usage	: $s->low
Function: start of segment; 
		  Alias of start for backward compatibility
Returns : integer
Args	: none
Status	: Public

end

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

high

Title	: high
Usage	: $s->high
Function: end of segment; 
		  Alias of end for backward compatibility.
Returns : integer
Args	: none
Status	: Public

stop

Title	: stop
Usage	: $s->stop
Function: end of segment; 
		  Alias of end for backward compatibility.
Returns : integer
Args	: none
Status	: Public

length

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

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 returns 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"	retunr features that completely contain the segment

Two types of argument lists are accepts. 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 feture 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.

_getUniqueTypes

Title   : _getUniqueTypes
Usage   : $segment->_getUniqueTypes()
Function: filter out the duplicate types and return an array of
          unique feature types in 'type_source' format
Returns : an array of feature types
Args    : array ref
Status  : Private

For example, in the config file

[Gene] feature = gene:Genbank

[BLASTX] feature = match:WU_BLASTX

_getUniqeTypes will subsitute ':' with '_' and return [ gene_Genbank, match_WU_BLASTX ], the latter can be used to find the corresponding element in SQL xml files.

get_all_SeqFeature, get_SeqFeatures, top_SeqFeatures, all_SeqFeatures

Title	: get_all_SeqFeature, get_SeqFeatures, top_SeqFeatures, 
		  all_SeqFeatures
Usage	: $s->get_all_SeqFeature()
Function: get the sequence string fro this segment
		  Several aliases of features() for backword compatibility
Returns	: a string
Args	: none
Status	: Public

seq

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

secondary_structure_encodings

Title	: secondary_structure_encodings
Usage	: $s->secondary_structure_encodings
Function: get the secondary structure prediction scores for segment
Returns	: hash ref { secondary_structure_type => string of 0-9 one digit per base }
Args	: none
Status	: Public

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 segments was originally generated.

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)

alphabet

Title	: alphabet
Usage	: $obj->alphabet($newval)
Function:
Returns	: scalar 'dna'
Args	: on set, new value ( a scalar or undef, optional )
Status	: Public

display_id, display_name, accession_number, desc

Title	: display_id, display_name, accession_number, desc
Usage	: $s->display_name()
Function: Alias of name()
		  Several aliases for name; it may be that these could do something
		  better than just giving back the name.
Returns	: string
Args	: none
Status	: Public

get_feature_stream

Title	: get_feature_stream
Usage	:
Function:
Returns	:
Args	:
Status	:

clone

Title	: clone
Usage	: $copy = $s->clone
Function: make a copy of this segment
Returns	: a Bio::DB::GFF::Segment object
Args	: none
Status	: Public

sourceseq

Title	: sourceseq
Usage	: $obj->sourceseq($newval)
Function: get feature name according to a feature_id
Returns	: value of sourceseq(a scalar)
Args	: on set, new value ( a scalar or undef, optional )
Status	: Public

abs_ref

Title	: abs_ref
Usage	: $obj->abs_ref()
Function: Alisas of sourceseq
		  Alias of sourceseq for backward compatibility
Returns	: value of sourceseq ( a scalar )
Args	: none
Status	: Public

abs_start

Title	: abs_start
Usage	: $obj->abs_start()
Function: Alias of start
Returns	: value of start ( a scalar )
Args	: none
Status	: Public

abs_end

Title	: abs_end
Usage	: $obj->abs_end()
Function: Alias of end
Returns	: value of end ( a scalar )
Args	: none
Status	: Public

asString

Title	: asString
Usage	: $s->asString
Function: human-readable string for segment
		  Returns a human-readable string representing this sequence. 
		  Format is: sourceseq:start,stop
Returns	: a string
Args	: none
Status	: Public