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bio::index::abstract(3pm) [debian man page]

Bio::Index::Abstract(3pm)				User Contributed Perl Documentation				 Bio::Index::Abstract(3pm)

NAME
Bio::Index::Abstract - Abstract interface for indexing a flat file SYNOPSIS
You should not be using this module directly USING DB_FILE To use DB_File and not SDBM for this index, pass the value: -dbm_package => 'DB_File' to new (see below). DESCRIPTION
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. 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 one of 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 - Ewan Birney, James Gilbert Email - birney@sanger.ac.uk, jgrg@sanger.ac.uk APPENDIX
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 pathtype Title : pathtype Usage : $index->pathtype($pathtype) Function: Set the type of the file path Only two values are supported, 'relative' or 'absolute'. If the user does not give any value, it is set to absolute by default. Thus it mimics the default behavior of Bio::Index::Abstract module. Example : my $index = Bio::Index::Abstract->(-pathtype => 'relative', -file => $file.inx, ); or $index->pathtype('relative'); Returns : Type of the path. Args : String (relative|absolute) _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 : $first_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 perl v5.14.2 2012-03-02 Bio::Index::Abstract(3pm)
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