Christopher Fields > BioPerl-1.6.920 > Bio::Annotation::Comment

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Module Version: 1.006920   Source   Latest Release: BioPerl-1.6.924

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)
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