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Bio::Annotation::Comment.3pm

NAME

Bio::Annotation::Comment - A comment object, holding text

SYNOPSIS

     $comment = Bio::Annotation::Comment->new();
     $comment->text("This is the text of this comment");
     $annotation->add_Annotation('comment', $comment);
 
 

DESCRIPTION

A holder for comments in annotations, just plain text. This is a very simple object, and justifiably so.

AUTHOR - Ewan Birney

Email birney@ebi.ac.uk

APPENDIX

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

new

  Title   : new
  Usage   : $comment = Bio::Annotation::Comment->new( '-text' => 'some text for this comment');
  Function: This returns a new comment object, optionally with
            text filed
  Example :
  Returns : a Bio::Annotation::Comment object
  Args    : a hash with -text optionally set
 
 

AnnotationI implementing functions

as_text

  Title   : as_text
  Usage   :
  Function:
  Example :
  Returns : 
  Args    :
 
 

display_text

  Title   : display_text
  Usage   : my $str = $ann->display_text();
  Function: returns a string. Unlike as_text(), this method returns a string
            formatted as would be expected for te specific implementation.
 
            One can pass a callback as an argument which allows custom text
            generation; the callback is passed the current instance and any text
            returned
  Example :
  Returns : a string
  Args    : [optional] callback
 
 

hash_tree

  Title   : hash_tree
  Usage   :
  Function:
  Example :
  Returns : 
  Args    :
 
 

tagname

  Title   : tagname
  Usage   : $obj->tagname($newval)
  Function: Get/set the tagname for this annotation value.
 
            Setting this is optional. If set, it obviates the need to
            provide a tag to Bio::AnnotationCollectionI when adding
            this object. When obtaining an AnnotationI object from the
            collection, the collection will set the value to the tag
            under which it was stored unless the object has a tag
            stored already.
 
  Example : 
  Returns : value of tagname (a scalar)
  Args    : new value (a scalar, optional)
 
 

Specific accessors for Comments

text

  Title   : text
  Usage   : $value = $self->text($newval)
  Function: get/set for the text field. A comment object
            just holds a single string which is accessible through
            this method
  Example : 
  Returns : value of text
  Args    : newvalue (optional)
 
 

value

  Title   : value
  Usage   : $value = $self->value($newval)
  Function: Alias of the 'text' method
  Example :
  Returns : value of text
  Args    : newvalue (optional)
 
 

type

  Title   : type
  Usage   : $value = $self->type($newval)
  Function: get/set for the comment type field.  The comment type
            is normally found as a subfield within comment sections
            in some files, such as SwissProt
  Example : 
  Returns : value of text
  Args    : newvalue (optional)