Bio::Index::Abstract - Abstract interface for indexing a flat file You should not be using this module directly To use DB_File and not SDBM for this index, pass the value: -dbm_package => 'DB_File' to new (see below). This object provides the basic mechanism to associate positions in files with names. The position and filenames are stored in DBM which can then be accessed later on. It is the equivalent of flat file indexing (eg, SRS or efetch). This object is the guts to the mechanism, which will be used by the specific objects inheriting from it.

Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email - birney@sanger.ac.uk, jgrg@sanger.ac.uk The rest of the documentation details each of the object methods. Internal methods are usually preceded with an "_" (underscore).

new
Usage : $index = Bio::Index::Abstract->new( -filename => $dbm_file, -write_flag => 0, -dbm_package => 'DB_File', -verbose => 0); Function: Returns a new index object. If filename is specified, then open_dbm() is immediately called. Bio::Index::Abstract->new() will usually be called directly only when opening an existing index. Returns : A new index object Args : -filename The name of the dbm index file. -write_flag TRUE if write access to the dbm file is needed. -dbm_package The Perl dbm module to use for the index. -verbose Print debugging output to STDERR if TRUE.

filename
Title : filename Usage : $value = $self->filename(); $self->filename($value); Function: Gets or sets the name of the dbm index file. Returns : The current value of filename Args : Value of filename if setting, or none if getting the value.

write_flag
Title : write_flag Usage : $value = $self->write_flag(); $self->write_flag($value); Function: Gets or sets the value of write_flag, which is wether the dbm file should be opened with write access. Returns : The current value of write_flag (default 0) Args : Value of write_flag if setting, or none if getting the value.

dbm_package
Usage : $value = $self->dbm_package(); $self->dbm_package($value); Function: Gets or sets the name of the Perl dbm module used. If the value is unset, then it returns the value of the package variable $USE_DBM_TYPE or if that is unset, then it chooses the best available dbm type, choosing 'DB_File' in preference to 'SDBM_File'. Bio::Abstract::Index may work with other dbm file types. Returns : The current value of dbm_package Args : Value of dbm_package if setting, or none if getting the value.

db
Title : db Usage : $index->db Function: Returns a ref to the hash which is tied to the dbm file. Used internally when adding and retrieving data from the database. Example : $db = $index->db(); $db->{ $some_key } = $data $data = $index->db->{ $some_key }; Returns : ref to HASH Args : NONE

get_stream
Title : get_stream Usage : $stream = $index->get_stream( $id ); Function: Returns a file handle with the file pointer at the approprite place This provides for a way to get the actual file contents and not an object WARNING: you must parse the record deliminter *yourself*. Abstract wont do this for you So this code $fh = $index->get_stream($myid); while( <$fh> ) { # do something } will parse the entire file if you don't put in a last statement in, like while( <$fh> ) { /^\/\// && last; # end of record # do something } Returns : A filehandle object Args : string represents the accession number Notes : This method should not be used without forethought

cachesize
Usage : $index->cachesize(1000000) Function: Sets the dbm file cache size for the index. Needs to be set before the DBM file gets opened. Example : $index->cachesize(1000000) Returns : size of the curent cache

ffactor
Usage : $index->ffactor(1000000) Function: Sets the dbm file fill factor. Needs to be set before the DBM file gets opened. Example : $index->ffactor(1000000) Returns : size of the curent cache

open_dbm
Usage : $index->open_dbm() Function: Opens the dbm file associated with the index object. Write access is only given if explicitly asked for by calling new(-write => 1) or having set the write_flag(1) on the index object. The type of dbm file opened is that returned by dbm_package(). The name of the file to be is opened is obtained by calling the filename() method. Example : $index->_open_dbm() Returns : 1 on success

_version
Title : _version Usage : $type = $index->_version() Function: Returns a string which identifes the version of an index module. Used to permanently identify an index file as having been created by a particular version of the index module. Must be provided by the sub class Example : Returns : Args : none

_code_base
Title : _code_base Usage : $code = $db->_code_base(); Function: Example : Returns : Code package to be used with this Args :

_type_and_version
Title : _type_and_version Usage : Called by _initalize Function: Checks that the index opened is made by the same index module and version of that module that made it. If the index is empty, then it adds the information to the database. Example : Returns : 1 or exception Args : none

_check_file_sizes
Title : _check_file_sizes Usage : $index->_check_file_sizes() Function: Verifies that the files listed in the database are the same size as when the database was built, or throws an exception. Called by the new() function. Example : Returns : 1 or exception Args :

make_index
Title : make_index Usage : $index->make_index( FILE_LIST ) Function: Takes a list of file names, checks that they are all fully qualified, and then calls _filename() on each. It supplies _filename() with the name of the file, and an integer which is stored with each record created by _filename(). Can be called multiple times, and can be used to add to an existing index file. Example : $index->make_index( '/home/seqs1', '/home/seqs2', '/nfs/pub/big_db' ); Returns : Number of files indexed Args : LIST OF FILES

_filename
Title : _filename Usage : $index->_filename( FILE INT ) Function: Indexes the file Example : Returns : Args :

_file_handle
Title : _file_handle Usage : $fh = $index->_file_handle( INT ) Function: Returns an open filehandle for the file index INT. On opening a new filehandle it caches it in the @{$index->_filehandle} array. If the requested filehandle is already open, it simply returns it from the array. Example : $fist_file_indexed = $index->_file_handle( 0 ); Returns : ref to a filehandle Args : INT

_file_count
Title : _file_count Usage : $index->_file_count( INT ) Function: Used by the index building sub in a sub class to track the number of files indexed. Sets or gets the number of files indexed when called with or without an argument. Example : Returns : INT Args : INT

add_record
Title : add_record Usage : $index->add_record( $id, @stuff ); Function: Calls pack_record on @stuff, and adds the result of pack_record to the index database under key $id. If $id is a reference to an array, then a new entry is added under a key corresponding to each element of the array. Example : $index->add_record( $id, $fileNumber, $begin, $end ) Returns : TRUE on success or FALSE on failure Args : ID LIST

pack_record
Title : pack_record Usage : $packed_string = $index->pack_record( LIST ) Function: Packs an array of scalars into a single string joined by ASCII 034 (which is unlikely to be used in any of the strings), and returns it. Example : $packed_string = $index->pack_record( $fileNumber, $begin, $end ) Returns : STRING or undef Args : LIST

unpack_record
Title : unpack_record Usage : $index->unpack_record( STRING ) Function: Splits the sting provided into an array, splitting on ASCII 034. Example : ( $fileNumber, $begin, $end ) = $index->unpack_record( $self->db->{$id} ) Returns : A 3 element ARRAY Args : STRING containing ASCII 034

count_records
Title : count_records Usage : $recs = $seqdb->count_records() Function: return count of all recs in the index Example : Returns : a scalar Args : none

DESTROY
Title : DESTROY Usage : Called automatically when index goes out of scope Function: Closes connection to database and handles to sequence files Returns : NEVER Args : NONE