bio::annotation::comment(3pm) [debian man page]
Bio::Annotation::Comment(3pm) User Contributed Perl Documentation 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) perl v5.14.2 2012-03-02 Bio::Annotation::Comment(3pm)
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Bio::Annotation::StructuredValue(3pm) User Contributed Perl Documentation Bio::Annotation::StructuredValue(3pm) NAME
Bio::Annotation::StructuredValue - A scalar with embedded structured information SYNOPSIS
use Bio::Annotation::StructuredValue; use Bio::Annotation::Collection; my $col = Bio::Annotation::Collection->new(); my $sv = Bio::Annotation::StructuredValue->new(-value => 'someval'); $col->add_Annotation('tagname', $sv); DESCRIPTION
Scalar value annotation 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 or the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Hilmar Lapp Email hlapp-at-gmx.net APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : my $sv = Bio::Annotation::StructuredValue->new(); Function: Instantiate a new StructuredValue object Returns : Bio::Annotation::StructuredValue object Args : -value => $value to initialize the object data field [optional] -tagname => $tag to initialize the tagname [optional] AnnotationI implementing functions as_text Title : as_text Usage : my $text = $obj->as_text Function: return the string "Value: $v" where $v is the value Returns : string Args : none 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 : my $hashtree = $value->hash_tree Function: For supporting the AnnotationI interface just returns the value as a hashref with the key 'value' pointing to the value Returns : hashrf Args : none 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 AnnotationCollection when adding this object. Example : Returns : value of tagname (a scalar) Args : new value (a scalar, optional) Specific accessors for StructuredValue value Title : value Usage : $obj->value($newval) Function: Get/set the value for this annotation. Set mode is here only to retain compatibility with SimpleValue. It is equivalent to calling add_value([0], $newval). In get mode, this implementation allows one to pass additional parameters that control how the structured annotation components will be joined together to form a string. Recognized are presently -joins a reference to an array of join strings, the elements at index i applying to joining annotations at dimension i. The last element will be re-used for dimensions higher than i. Defaults to ['; ']. -brackets a reference to an array of two strings denoting the opening and closing brackets for the elements of one dimension, if there is more than one element in the dimension. Defaults to ['(',')']. Returns : value of value Args : newvalue (optional) get_values Title : get_values Usage : Function: Get the top-level array of values. Each of the elements will recursively be a reference to an array or a scalar, depending on the depth of this structured value annotation. Example : Returns : an array Args : none get_all_values Title : get_all_values Usage : Function: Flattens all values in this structured annotation and returns them as an array. Example : Returns : the (flat) array of values Args : none add_value Title : add_value Usage : Function: Adds the given value to the structured annotation at the given index. The index is multi-dimensional, with the first dimension applying to the first level, and so forth. If a particular dimension or a particular index does not exist yet, it will be created. If it does exist and adding the value would mean replacing a scalar with an array reference, we throw an exception to prevent unintended damage. An index of -1 at any dimension means append. If an array of values is to be added, it will create an additional dimension at the index specified, unless the last index value is -1, in which case they will all be appended to the last dimension. Example : Returns : none Args : the index at which to add (a reference to an array) the value(s) to add perl v5.14.2 2012-03-02 Bio::Annotation::StructuredValue(3pm)