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Bio::Seq::QualI.3pm

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