Provided by: libboulder-perl_1.30-6_all bug

NAME

       Boulder - An API for hierarchical tag/value structures

SYNOPSIS

          # Read a series of People records from STDIN.
          # Add an "Eligibility" attribute to all those whose
          # Age >= 35 and Friends list includes "Fred"

          use Boulder::Stream;

          my $stream = Boulder::Stream->newFh;

          while ( my $record = <$stream> ) {
             next unless $record->Age >= 35;
             my @friends = $record->Friends;
             next unless grep {$_ eq 'Fred'} @friends;

             $record->insert(Eligibility => 'yes');
             print $stream $record;
           }

       Related manual pages:

         basics
         ------
         Stone            hierarchical tag/value records
         Stone::Cursor    Traverse a hierarchy

         Boulder::Stream  stream-oriented storage for Stones
         Boulder::Store   record-oriented storage for Stones
         Boulder::XML     XML conversion for Stones
         Boulder::String  conversion to strings

         genome-related
         ---------------

         Boulder::Genbank   parse Genbank (DNA sequence) records
         Boulder::Blast     parse BLAST (basic local alignment search tool) reports
         Boulder::Medline   parse Medline (pubmed) records
         Boulder::Omim      parse OMIM (online Mendelian inheritance in man) records
         Boulder::Swissprot parse Swissprot records
         Boulder::Unigene   parse Unigene records

DESCRIPTION

   Boulder IO
       Boulder IO is a simple TAG=VALUE data format designed for sharing data between programs
       connected via a pipe.  It is also simple enough to use as a common data exchange format
       between databases, Web pages, and other data representations.

       The basic data format is very simple.  It consists of a series of TAG=VALUE pairs
       separated by newlines.  It is record-oriented.  The end of a record is indicated by an
       empty delimiter alone on a line.  The delimiter is "=" by default, but can be adjusted by
       the user.

       An example boulder stream looks like this:

               Name=Lincoln Stein
               Home=/u/bush202/lds32
               Organization=Cold Spring Harbor Laboratory
               Login=lds32
               Password_age=20
               Password_expires=60
               Alias=lstein
               Alias=steinl
               =
               Name=Leigh Deacon
               Home=/u/bush202/tanager
               Organization=Cold Spring Harbor Laboratory
               Login=tanager
               Password_age=2
               Password_expires=60
               =

       Notes:

       (1) There is no need for all tags to appear in all records, or indeed for all the records
           to be homogeneous.

       (2) Multiple values are allowed, as with the Alias tag in the second record.

       (3) Lines can be any length, as in a potential 40 Kbp DNA sequence entry.

       (4) Tags can be any alphanumeric character (upper or lower case) and may contain embedded
           spaces.  Conventionally we use the characters A-Z0-9_, because they can be used
           without single quoting as keys in Perl associative arrays, but this is merely
           stylistic.  Values can be any character at all except for the reserved characters {}=%
           and newline.  You can incorporate binary data into the data stream by escaping these
           characters in the URL manner, using a % sign followed by the (capitalized) hexadecimal
           code for the character.  The module makes this automatic.

   Hierarchical Records
       The simple boulder format can be extended to accommodate nested relations and other
       intresting structures.  Nested records can be created in this way:

        Name=Lincoln Stein
        Home=/u/bush202/lds32
        Organization=Cold Spring Harbor Laboratory
        Login=lds32
        Password_age=20
        Password_expires=60
        Privileges={
          ChangePasswd=yes
          CronJobs=yes
          Reboot=yes
          Shutdown=no
        }
        =
        Name=Leigh Deacon
        Home=/u/bush202/tanager
        Organization=Cold Spring Harbor Laboratory
        Login=tanager
        Password_age=2
        Password_expires=60
        Privileges={
          ChangePasswd=yes
          CronJobs=no
          Reboot=no
          Shutdown=no
        }
        =

       As in the original format, tags may be multivalued.  For example, there might be several
       Privilege record assigned to a login account.  Each subrecord may contain further
       subrecords.

       Within the program, a hierarchical record is encapsulated within a "Stone", an opaque
       structure that implements methods for fetching and settings its various tags.

   Using Boulder for I/O
       The Boulder API was designed to make reading and writing of complex hierarchical records
       almost as easy as reading and writing single lines of text.

       Boulder::Stream
           The main component of the Boulder modules is Boulder::Stream, which provides a stream-
           oriented view of the data.  You can read and write to Boulder::Streams via tied
           filehandles, or via method calls.  Data records are flattened into a simple format
           called "boulderio" format.

       Boulder::XML
           Boulder::XML acts like Boulder::Stream, but the serialization format is XML.  You need
           XML::Parser installed to use this module.

       Boulder::Store
           This is a simple persistent storage class which allows you to store several (thousand)
           Stone's into a DB_File database.  You must have libdb and the Perl DB_File extensions
           installed in order to take advantage of this class.

       Boulder::Genbank
       Boulder::Unigene
       Boulder::OMIM
       Boulder::Blast
       Boulder::Medline
       Boulder::SwissProt
           These are parsers and accessors for various biological data sources.  They act like
           Boulder::Stream, but return a set of Stone objects that have certain prescribed tags
           and values.  Many of these modules were written by Luca I.G. Toldo
           <luca.toldo@merck.de>.

   Stone Objects
       The Stone object encapsulates a set of tags and values.  Any tag can be single- or
       multivalued, and tags are allowed to contain subtags to any depth.  A simple set of
       methods named tags(), get(), put(), insert(), replace() and so forth, allows you to
       examine the tags that are available, get and set their values, and search for particular
       tags.  In addition, an autoload mechanism allows you to use method calls to access tags,
       for example:

          my @friends = $record->Friends;

       is equivalent to:

          my @friends = $record->get('Friends');

       A Stone::Cursor class allows you to traverse Stones systematically.

       A full explanation of the Stone class can be found in its manual page.

AUTHOR

       Lincoln D. Stein <lstein@cshl.org>, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
       This module can be used and distributed on the same terms as Perl itself.

SEE ALSO

       Boulder::Blast, Boulder::Genbank, Boulder::Medline, Boulder::Unigene, Boulder::Omim,
       Boulder::SwissProt