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Bio::Seq::QualI(3)    User Contributed Perl Documentation   Bio::Seq::QualI(3)

NAME
       Bio::Seq::QualI - Interface definition for a Bio::Seq::Qual

SYNOPSIS
	   # get a Bio::Seq::Qual compliant object somehow

	   # to test this is a seq object

	   $obj->isa("Bio::Seq::QualI")
	      || $obj->throw("$obj does not implement the Bio::Seq::QualI interface");

	   # accessors

	   $string    = $obj->qual();
	   $substring = $obj->subqual(12,50);
	   $display   = $obj->display_id(); # for human display
	   $id	      = $obj->primary_id(); # unique id for this object,
					    # implementation defined
	   $unique_key= $obj->accession_number();
			      # unique biological id

DESCRIPTION
       This object defines an abstract interface to basic quality information.
       PrimaryQual is an object just for the quality and its name(s), nothing
       more. There is a pure perl implementation of this in
       Bio::Seq::PrimaryQual. If you just want to use Bio::Seq::PrimaryQual
       objects, then please read that module first. This module defines the
       interface, and is of more interest to people who want to wrap their own
       Perl Objects/RDBs/FileSystems etc in way that they "are" bioperl
       quality objects, even though it is not using Perl to store the sequence
       etc.

       This interface defines what bioperl consideres necessary to "be" a
       sequence of qualities, without providing an implementation of this. (An
       implementation is provided in Bio::Seq::PrimaryQual). If you want to
       provide a Bio::Seq::PrimaryQual 'compliant' object which in fact wraps
       another object/database/out-of-perl experience, then this is the
       correct thing to wrap, generally by providing a wrapper class which
       would inherit from your object and this Bio::Seq::QualI interface. The
       wrapper class then would have methods lists in the "Implementation
       Specific Functions" which would provide these methods for your object.

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@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   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:

	 http://bugzilla.open-bio.org/

AUTHOR - Chad Matsalla
       This module is heavily based on Bio::Seq::PrimarySeq and is modeled
       after or outright copies sections of it. Thanks Ewan!

       Email bioinformatics@dieselwurks.com

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

Implementation Specific Functions
       These functions are the ones that a specific implementation must
       define.

   qual()
	Title	: qual()
	Usage	: @quality_values  = @{$obj->qual()};
	Function: Returns the quality as a reference to an array containing the
	       quality values. The individual elements of the quality array are
	       not validated and can be any numeric value.
	Returns : A reference to an array.
	Status	:

   subqual($start,$end)
	Title	: subqual($start,$end)
	Usage	: @subset_of_quality_values = @{$obj->subseq(10,40)};
	Function: returns the quality values from $start to $end, where the
	       first value is 1 and the number is inclusive, ie 1-2 are the first
	       two bases of the sequence. Start cannot be larger than end but can
	       be equal.
	Returns : A reference to an array.
	Args	: a start position and an end position

   display_id()
	Title	: display_id()
	Usage	: $id_string = $obj->display_id() _or_
		  $id_string = $obj->display_id($new_display_id);
	Function: Returns the display id, aka the common name of the Quality
	       object.
	       The semantics of this is that it is the most likely string to be
	       used as an identifier of the quality sequence, and likely to have
	       "human" readability.  The id is equivalent to the ID field of the
	       GenBank/EMBL databanks and the id field of the Swissprot/sptrembl
	       database. In fasta format, the >(\S+) is presumed to be the id,
	       though some people overload the id to embed other information.
	       Bioperl does not use any embedded information in the ID field,
	       and people are encouraged to use other mechanisms (accession field
	       for example, or extending the sequence object) to solve this.
	       Notice that $seq->id() maps to this function, mainly for
	       legacy/convience issues
	Returns : A string
	Args	: If an arg is provided, it will replace the existing display_id
	       in the object.

   accession_number()
	Title	: accession_number()
	Usage	: $unique_biological_key = $obj->accession_number(); _or_
		  $unique_biological_key = $obj->accession_number($new_acc_num);
	Function: Returns the unique biological id for a sequence, commonly
	       called the accession_number. For sequences from established
	       databases, the implementors should try to use the correct
	       accession number. Notice that primary_id() provides the unique id
	       for the implemetation, allowing multiple objects to have the same
	       accession number in a particular implementation. For sequences
	       with no accession number, this method should return "unknown".
	Returns : A string.
	Args	: If an arg is provided, it will replace the existing
	       accession_number in the object.

   primary_id()
	Title	: primary_id()
	Usage	: $unique_implementation_key = $obj->primary_id(); _or_
		  $unique_implementation_key = $obj->primary_id($new_prim_id);
	Function: Returns the unique id for this object in this implementation.
	       This allows implementations to manage their own object ids in a
	       way the implementaiton can control clients can expect one id to
	       map to one object. For sequences with no accession number, this
	       method should return a stringified memory location.
	Returns : A string
	Args	: If an arg is provided, it will replace the existing
	       primary_id in the object.

   can_call_new()
	Title	: can_call_new()
	Usage	: if( $obj->can_call_new ) {
		    $newobj = $obj->new( %param );
		}
	Function: can_call_new returns 1 or 0 depending on whether an
	       implementation allows new constructor to be called. If a new
	       constructor is allowed, then it should take the followed hashed
	       constructor list.
		  $myobject->new( -qual => $quality_as_string,
				  -display_id  => $id,
				  -accession_number => $accession,
				  );
	Example :
	Returns : 1 or 0
	Args	:

   qualat($position)
	Title	: qualat($position)
	Usage	: $quality = $obj->qualat(10);
	Function: Return the quality value at the given location, where the
	       first value is 1 and the number is inclusive, ie 1-2 are the first
	       two bases of the sequence. Start cannot be larger than end but can
	       be equal.
	Returns : A scalar.
	Args	: A position.

Optional Implementation Functions
       The following functions rely on the above functions. A implementing
       class does not need to provide these functions, as they will be
       provided by this class, but is free to override these functions.

       All of revcom(), trunc(), and translate() create new sequence objects.
       They will call new() on the class of the sequence object instance
       passed as argument, unless can_call_new() returns FALSE. In the latter
       case a Bio::PrimarySeq object will be created. Implementors which
       really want to control how objects are created (eg, for object
       persistence over a database, or objects in a CORBA framework), they are
       encouraged to override these methods

   revcom
	Title	: revcom
	Usage	: @rev = @{$qual->revcom()};
	Function: Produces a new Bio::Seq::QualI implementing object which
	       is reversed from the original quality array.
	       The id is the same id as the orginal sequence, and the accession number
	       is also indentical. If someone wants to track that this sequence has
	       been reversed, it needs to define its own extensions

	       To do an inplace edit of an object you can go:

	       $qual = $qual->revcom();

	       This of course, causes Perl to handle the garbage collection of the old
	       object, but it is roughly speaking as efficient as an inplace edit.
	Returns : A new (fresh) Bio::Seq::PrimaryQualI object
	Args	: none

   trunc()
	Title	: trunc
	Usage	: $subseq = $myseq->trunc(10,100);
	Function: Provides a truncation of a sequence,
	Returns : a fresh Bio::Seq::QualI implementing object
	Args	: Two integers denoting first and last base of the sub-sequence.

   translate()
	Title	: translate()
	Usage	: $protein_seq_obj = $dna_seq_obj->translate
		  #if full CDS expected:
		  $protein_seq_obj = $cds_seq_obj->translate(undef,undef,undef,undef,1);
	Function: Completely useless in this interface.
	Returns : Nothing.
	Args	: Nothing.

   id()
	Title	: id()
	Usage	: $id = $qual->id()
	Function: ID of the quality. This should normally be (and actually is in
		  the implementation provided here) just a synonym for display_id().
	Example :
	Returns : A string.
	Args	:

   length()
	Title	: length()
	Usage	: $length = $qual->length();
	Function: Return the length of the array holding the quality values.
	       Under most circumstances, this should match the number of quality
	       values but no validation is done when the PrimaryQual object is
	       constructed and non-digits could be put into this array. Is this a
	       bug? Just enough rope...
	Returns : A scalar (the number of elements in the quality array).
	Args	: None.

   desc()
	Title	: desc()
	Usage	: $qual->desc($newval);
		  $description = $seq->desc();
	Function: Get/set description text for a qual object
	Example :
	Returns : value of desc
	Args	: newvalue (optional)

Private functions
       These are some private functions for the PrimarySeqI interface. You do
       not need to implement these functions

   _attempt_to_load_Seq
	Title	: _attempt_to_load_Seq
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   qualtype()
	Title	: qualtype()
	Usage	: if( $obj->qualtype eq 'phd' ) { /Do Something/ }
	Function: At this time, this function is not used for
	       Bio::Seq::PrimaryQual objects. In fact, now it is a month later and
	       I just completed the Bio::Seq::SeqWithQuality object and this is
	       definitely deprecated.
	Returns : Nothing. (not implemented)
	Args	: none
	Status	: Virtual

perl v5.14.1			  2011-07-22		    Bio::Seq::QualI(3)
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