NAME¶
Bio::Tools::EUtilities::EUtilDataI - eutil data object interface
SYNOPSIS¶
# say you had some data in a hash ref ($data) and wanted to create hierarchies
# of object using the same interface, starting with the topmost...
# $object is a Bio::Tools::EUtilities::EUtilDataI instance
$object->_add_data($data);
# in _add_data()... sort through keys and create subobjects as needed
if ($key eq 'foo') {
my $sub = Bio::Tools::EUtilities::FooData->new(-eutil => 'efoo',
-type => 'foo');
$sub->_add_data($subdata);
# store into parent object as needed...
...
}
# access stored data
while (my $sub = $parent->next_Foo) {...}
DESCRIPTION¶
This is a simple interface which allows creation of simple typed object
hierarchies. Single layers can be accessed via simple iterators (next_*
methods) or retrieved all at once (get_*) methods; nested data can be iterated
through nested iterators for each object, or retrieved using get_all_*
methods.
This interface defines common methods required for all eutil data-holding
objects:
_add_data(),
eutil(), and
type(). It also
specifies inheriting interface classes use at least one of three methods:
get_ids(),
get_term(), or
get_database(), which are the
three types of data that eutils mainly centers on.
Generally,
eutil() is the Bio::Tools::EUtilities parser used to set the
data. Similarly,
datatype() is the specific data type for the class.
Implementations which rely on subclasses to store data and have iterators should
also define a generalized
rewind() method that (by default) rewinds all
iterators to the start. Args passed can specify exactly which iterator to
rewind and (if possible) recursively rewind nested object iterators.
As the method implies,
_add_data() is a private method that adds data
chunks to the object and sets internal parameters for the various data
objects. Methods corresponding to the data type simply return the set data or
iterate through the data sets if the values are more complex. Data can
alternatively be passed through the object constructor.
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.
https://redmine.open-bio.org/projects/bioperl/
AUTHOR¶
Email cjfields at bioperl dot org
APPENDIX¶
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
eutil¶
Title : eutil
Usage : $eutil->$foo->eutil
Function : Get/Set eutil
Returns : string
Args : string (eutil)
Throws : on invalid eutil
datatype¶
Title : type
Usage : $type = $qd->datatype;
Function: retrieve simple data type object holds (linkset, docsum, item, etc)
Returns : string (eutil name)
Args : none
Note : this is probably more useful for devs than for users as a way to keep
track of the various types of modules used
rewind¶
Title : rewind
Usage : $esum->rewind
Function : rewinds the requested iterator
Returns : none
Args : [OPTIONAL] may include 'all', 'recursive', etc.
_add_data¶
Title : _add_data
Usage : $foo->_add_data($data)
Function : adds data to current object as a chunk
Returns : none
Args : hash ref containing relevant data
to_string¶
Title : to_string
Usage : $foo->to_string()
Function : converts current object to string
Returns : none
Args : (optional) simple data for text formatting
Note : Used generally for debugging and for the print_* methods
_text_wrap¶
Title : _text_wrap
Usage : $foo->_text_wrap($string)
Function : private internal wrapper for Text::Wrap::wrap
Returns : string
Args : string
Note : Internal use only. Simple wrapper method.