Bio::OntologyIO::simplehierarchy.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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 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 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)