simplehierarchy - a base class parser for simple hierarchy-by-indentation type formats use Bio::OntologyIO; # do not use directly -- use via Bio::OntologyIO my $parser = Bio::OntologyIO->new ( -format => "simplehierarchy", -file => "pathology_terms.csv", -indent_string => ",", -ontology_name => "eVOC", -term_factory => $fact, ); my $ontology = $parser->next_ontology(); Needs Graph.pm from CPAN. This class is nearly identical to OntologyIO::dagflat, see Bio::OntologyIO::dagflat for details.

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report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Allen Day Email: allenday@ucla.edu

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

new
Title : new Usage : see SYNOPSIS Function: Creates a new simplehierarchy parser. Returns : A new simplehierarchy parser object, implementing L<Bio::OntologyIO>. Args : -files => a single ontology flat file holding the term relationships, or an array ref holding the file names -file => if there is only a single flat file, it may also be specified via the -file parameter -ontology_name => the name of the ontology, defaults to "Gene Ontology" -file_is_root => Boolean indicating whether a virtual root term is to be added, the name of which will be derived from the file name. Default is false. Enabling this allows to parse multiple input files into the same ontology and still have separately rooted. -id_prefix => The prefix for the term identifiers. Terms in this format often come without identifiers, in which case -engine => the L<Bio::Ontology::OntologyEngineI> object to be reused (will be created otherwise); note that every L<Bio::Ontology::OntologyI> will qualify as well since that one inherits from the former. -indent_string => the string used to indent hierarchical levels in the file. For a file like this: term0 subterm1A subterm2A subterm1B subterm1C indent_string would be " ". Defaults to one space (" "). -comment_char => Allows specification of a regular expression string to indicate a comment line. Currently defaults to "[\|\-]". Note: this is not yet implemented.

ontology_name
Title : ontology_name Usage : $obj->ontology_name($newval) Function: Get/set the name of the ontology parsed by this module. Example : Returns : value of ontology_name (a scalar) Args : on set, new value (a scalar or undef, optional)

parse
Title : parse() Usage : $parser->parse(); Function: Parses the files set with "new" or with methods defs_file and _flat_files. Normally you should not need to call this method as it will be called automatically upon the first call to next_ontology(). Returns : [Bio::Ontology::OntologyEngineI] Args :

next_ontology
Title : next_ontology Usage : Function: Get the next available ontology from the parser. This is the method prescribed by Bio::OntologyIO. Example : Returns : An object implementing Bio::Ontology::OntologyI, and undef if there is no more ontology in the input. Args :

_flat_files
Title : _flat_files Usage : $files_to_parse = $parser->_flat_files(); Function: Get the array of ontology flat files that need to be parsed. Note that this array will decrease in elements over the parsing process. Therefore, it\'s value outside of this module will be limited. Also, be careful not to alter the array unless you know what you are doing. Returns : a reference to an array of zero or more strings Args : none

_defs_io
Title : _defs_io Usage : $obj->_defs_io($newval) Function: Get/set the Bio::Root::IO instance representing the definition file, if provided (see defs_file()). Example : Returns : value of _defs_io (a Bio::Root::IO object) Args : on set, new value (a Bio::Root::IO object or undef, optional)

indent_string
Title : indent_string Usage : $obj->indent_string($newval) Function: Example : Returns : value of indent_string (a scalar) Args : on set, new value (a scalar or undef, optional)

file_is_root
Title : file_is_root Usage : $obj->file_is_root($newval) Function: Boolean indicating whether a virtual root term is to be added, the name of which will be derived from the file name. Enabling this allows to parse multiple input files into the same ontology and still have separately rooted. Example : Returns : value of file_is_root (a scalar) Args : on set, new value (a scalar or undef, optional)

_virtual_root
Title : _virtual_root Usage : $obj->_virtual_root($newval) Function: Example : Returns : value of _virtual_root (a scalar) Args : on set, new value (a scalar or undef, optional)