NAME

       Bio::OntologyIO::simplehierarchy - a base class parser for simple hierarchy-by-indentation
                         type formats

SYNOPSIS

         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();

DESCRIPTION

       Needs Graph.pm from CPAN.  This class is nearly identical to OntologyIO::dagflat, see
       Bio::OntologyIO::dagflat for details.

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 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 the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR

       Allen Day

       Email: allenday@ucla.edu

   CONTRIBUTOR
       Christian Zmasek

APPENDIX

       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 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 one to parse multiple input
                                    files into the same ontology and still have
                                    separately rooted.
                  -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.

       See Bio::OntologyIO.

   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 one 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)