Bio::Index Abstract
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Bio::Index::Abstract - Abstract interface for indexing a flat file
Package variables
Globals (from "use vars" definitions)
Included modules
You should not be using this module directly
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.
No description
Methods description
DESTROYcode    nextTop
 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
  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()
Example :
Returns : 1 or exception
Args :
 Title   : _code_base
Usage : $code = $db->_code_base();
Example :
Returns : Code package to be used with this
Args :
  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
  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
  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
Example :
Returns : 1 or exception
Args : none
  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
  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
  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
 Title   : count_records
Usage : $recs = $seqdb->count_records()
Function: return count of all recs in the index
Example :
Returns : a scalar
Args : none
  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
 Usage   : $value = $self->dbm_package();
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.
  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
 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
  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
  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
-dbm_package The Perl dbm module to use for the
-verbose Print debugging output to STDERR if
  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
  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
  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
Methods code
    foreach my $func (qw(filename write_flag)) {
        no strict 'refs';
        my $field = "_$func";

        *$func = sub {
            my( $self, $value ) = @_;
            if (defined $value) {
                $self->{$field} = $value;
            return $self->{$field};
    my $self = shift;

sub _check_file_sizes {
    my $self = shift;
    my $num  = $self->_file_count() || 0;
    for (my $i = 0; $i < $num; $i++) {
        my( $file, $stored_size ) = $self->unpack_record( $self->db->{"__FILE_$i"} );
        my $size = -s $file;
        unless ($size == $stored_size) {
            $self->throw("file $i [ $file ] has changed size $stored_size -> $size. This probably means you need to rebuild the index.");
    return 1;
sub _code_base {
   my ($self) = @_;
   my $code_key    = '__TYPE_AND_VERSION';
   my $record;

   $record = $self->db->{$code_key};

   my($code,$version) = $self->unpack_record($record);
   if( wantarray ) {
       return ($code,$version);
   } else {
       return $code;
sub _file_count {
    my $self = shift;
    if (@_) {
        $self->db->{'__FILE_COUNT'} = shift;
    return $self->db->{'__FILE_COUNT'};
sub _file_handle {
    my( $self, $i ) = @_;
    unless ($self->{'_filehandle'}[$i]) {
        my $fh = Symbol::gensym();
        my @rec = $self->unpack_record($self->db->{"__FILE_$i"})
            or $self->throw("Can't get filename for index : $i");
        my $file = $rec[0];
        open $fh, $file or $self->throw("Can't read file '$file' : $!");
        $self->{'_filehandle'}[$i] = $fh; # Cache filehandle
} return $self->{'_filehandle'}[$i];
sub _index_file {
    my $self = shift;
    my $pkg = ref($self);
    $self->throw("Error: '$pkg' does not provide the _index_file() method");
sub _type_and_version {
    my $self    = shift;
    my $key     = '__TYPE_AND_VERSION';
    my $version = $self->_version();
    my $type    = ref $self;
    # Run check or add type and version key if missing
if (my $rec = $self->db->{ $key }) { my( $db_type, $db_version ) = $self->unpack_record($rec); $self->throw("This index file is from version [$db_version] - You need to rebuild it to use module version [$version]") unless $db_version == $version; $self->throw("This index file is type [$db_type] - Can't access it with module for [$type]") unless $db_type eq $type; } else { $self->add_record( $key, $type, $version ) or $self->throw("Can't add Type and Version record"); } return 1;
sub _version {
    my $self = shift;
    $self->throw("In Bio::Index::Abstract, no _version method in sub class");
sub add_record {
    my( $self, $id, @rec ) = @_;
    $self->debug( "Adding key $id\n") if( $self->verbose > 0 );
    $self->db->{$id} = $self->pack_record( @rec );
    return 1;
sub cachesize {
    my( $self, $size ) = @_;

	if(defined $size){
		$self->{'_cachesize'} = $size;
	return ( $self->{'_cachesize'} );
sub count_records {
   my ($self,@args) = @_;
   my $db = $self->db;
   my $c = 0;
   while (my($id, $rec) = each %$db) {
       if( $id =~ /^__/ ) {
           # internal info
next; } $c++; } return ($c);
sub db {
    return $_[0]->{'_DB'};
sub dbm_package {
    my( $self, $value ) = @_;
    my $to_require = 0;
    if( $value || ! $self->{'_dbm_package'} ) {
	my $type = $value || $USE_DBM_TYPE || 'DB_File';	
	if( $type =~ /DB_File/i ) {
	    eval { 
		require DB_File;
	    $type = ( $@ ) ? 'SDBM_File' : 'DB_File';
	if( $type ne 'DB_File' ) {
	    eval { require "$"; };
	    $self->throw($@) if( $@ );
	$self->{'_dbm_package'} = $type;
	if( ! defined $USE_DBM_TYPE ) {
	    $USE_DBM_TYPE = $self->{'_dbm_package'};
    return $self->{'_dbm_package'};
sub ffactor {
    my( $self, $size ) = @_;

	if(defined $size){
		$self->{'_ffactor'} = $size;
	return ( $self->{'_ffactor'} );
sub get_stream {
   my ($self,$id) = @_;

   my ($desc,$acc,$out);
   my $db = $self->db();

   if (my $rec = $db->{ $id }) {
       my( @record );
       my ($file, $begin, $end) = $self->unpack_record( $rec );
       # Get the (possibly cached) filehandle
my $fh = $self->_file_handle( $file ); # move to start
seek($fh, $begin, 0); return $fh; } else { $self->throw("Unable to find a record for $id in the flat file index"); }
sub make_index {
    my($self, @files) = @_;
    my $count = 0;
	my $recs = 0;
    # blow up if write flag is not set. EB fix
if( !defined $self->write_flag ) { $self->throw("Attempting to make an index on a read-only database. What about a WRITE flag on opening the index?"); } # We're really fussy/lazy, expecting all file names to be fully qualified
$self->throw("No files to index provided") unless @files; for(my $i=0;$i<scalar @files; $i++) { if( $Bio::Root::IO::FILESPECLOADED && File::Spec->can('rel2abs') ) { if( ! File::Spec->file_name_is_absolute($files[$i]) ) { $files[$i] = File::Spec->rel2abs($files[$i]); } } else { if( $^O =~ /MSWin/i ) { ($files[$i] =~ m|^[A-Za-z]:/|) ||
$self->throw("Not an absolute file path '$files[$i]'");
} else { ($files[$i] =~ m|^/|) ||
$self->throw("Not an absolute file path '$files[$i]'");
} } $self->throw("File does not exist '$files[$i]'") unless -e $files[$i]; } # Add each file to the index
FILE : foreach my $file (@files) { my $i; # index for this file
# Get new index for this file and increment file count
if ( defined(my $count = $self->_file_count) ) { $i = $count; } else { $i = 0; $self->_file_count(0); } # see whether this file has been already indexed
my ($record,$number,$size); if( ($record = $self->db->{"__FILENAME_$file"}) ) { ($number,$size) = $self->unpack_record($record); # if it is the same size - fine. Otherwise die
if( -s $file == $size ) { warn "File $file already indexed. Skipping...\n"; next FILE; } else { $self->throw("In index, $file has changed size ($size). Indicates that the index is out of date"); } } # index this file
warn "Indexing file $file\n" if( $self->verbose > 0); # this is supplied by the subclass and does the serious work
$recs += $self->_index_file( $file, $i ); # Specific method for each type of index
# Save file name and size for this index
$self->add_record("__FILE_$i", $file, -s $file) or $self->throw("Can't add data to file: $file"); $self->add_record("__FILENAME_$file", $i, -s $file) or $self->throw("Can't add data to file: $file"); # increment file lines
$i++; $self->_file_count($i); my $temp; $temp = $self->_file_count(); } return ($count, $recs);
sub new {
    my($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    my( $filename, $write_flag, $dbm_package, $cachesize, $ffactor ) =
			      )], @args);
    # Store any parameters passed
$self->filename($filename) if $filename; $self->cachesize($cachesize) if $cachesize; $self->ffactor($ffactor) if $ffactor; $self->write_flag($write_flag) if $write_flag; $self->dbm_package($dbm_package) if $dbm_package; $self->{'_filehandle'} = []; # Array in which to cache SeqIO objects
$self->{'_DB'} = {}; # Gets tied to the DBM file
# Open database
$self->open_dbm() if $filename; return $self;
sub open_dbm {
    my( $self ) = @_;
    my $filename = $self->filename()
        or $self->throw("filename() not set");

    my $db = $self->db();
    # Close the dbm file if already open (maybe we're getting
# or dropping write access
if (ref($db) ne 'HASH') { untie($db); } # What kind of DBM file are we going to open?
my $dbm_type = $self->dbm_package; # Choose mode for opening dbm file (read/write+create or read-only).
my $mode_flags = $self->write_flag ? O_RDWR|O_CREAT : O_RDONLY; # Open the dbm file
if ($dbm_type eq 'DB_File') { my $hash_inf = DB_File::HASHINFO->new(); my $cache = $self->cachesize(); my $ffactor = $self->ffactor(); if ($cache){ $hash_inf->{'cachesize'} = $cache; } if ($ffactor){ $hash_inf->{'ffactor'} = $ffactor; } tie( %$db, $dbm_type, $filename, $mode_flags, 0644, $hash_inf ) or $self->throw("Can't open '$dbm_type' dbm file '$filename' : $!"); } else { tie( %$db, $dbm_type, $filename, $mode_flags, 0644 ) or $self->throw("Can't open '$dbm_type' dbm file '$filename' : $!"); } # The following methods access data in the dbm file:
# Now, if we're a Bio::Index::Abstract caterpillar, then we
# transform ourselves into a Bio::Index::<something> butterfly!
if( ref($self) eq "Bio::Index::Abstract" ) { my $pkg = $self->_code_base(); bless $self, $pkg; } # Check or set this is the right kind and version of index
$self->_type_and_version(); # Check files haven't changed size since they were indexed
$self->_check_file_sizes(); return 1;
sub pack_record {
    my( $self, @args ) = @_;
    return join "\034", @args;
sub unpack_record {
    my( $self, @args ) = @_;
    return split /\034/, $args[0];
General documentation
To use DB_File and not SDBM for this index, pass the value:
    -dbm_package => 'DB_File'
to new (see below).
Mailing ListsTop
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.             - General discussion - About the mailing lists
Reporting BugsTop
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:
AUTHOR - Ewan Birney, James GilbertTop
Email -,
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with an "_" (underscore).
 Title   : filename
Usage : $value = $self->filename();
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.
 Title   : write_flag
Usage : $value = $self->write_flag();
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.
  Title   : _filename
Usage : $index->_filename( FILE INT )
Function: Indexes the file
Example :
Returns :
Args :