Summary

Bio::DB::Flat::BinarySearch - BinarySearch search indexing system for
sequence files

Package variables

Included modules

Inherit

Bio::DB::RandomAccessI

Synopsis

  # See below

Description

This module can be used both to index sequence files and also to
retrieve sequences from existing sequence files.
This object allows indexing of sequence files both by a primary key
(say accession) and multiple secondary keys (say ids). This is
different from the Bio::Index::Abstract (see Bio::Index::Abstract)
which uses DBM files as storage. This module uses a binary search to
retrieve sequences which is more efficient for large datasets.

    my $sequencefile;  # Some fasta sequence file

Patterns have to be entered to define where the keys are to be indexed
and also where the start of each record. E.g. for fasta

    my $start_pattern   = "^>";
    my $primary_pattern = "^>(\\S+)";

So the start of a record is a line starting with a > and the
primary key is all characters up to the first space after the >
A string also has to be entered to defined what the primary key
(primary_namespace) is called.
The index can now be created using

    my $index = new Bio::DB::Flat::BinarySearch(
	     -start_pattern   => $start_pattern,
	     -primary_pattern => $primary_pattern,
             -primary_namespace => "ID",
					     );

To actually write it out to disk we need to enter a directory where
the indices will live, a database name and an array of sequence files
to index.

    my @files = ("file1","file2","file3");

    $index->build_index("/Users/michele/indices","mydatabase",@files);

The index is now ready to use. For large sequence files the perl way
of indexing takes a *long* time and a *huge* amount of memory. For
indexing things like dbEST I recommend using the C indexer. Sometimes just indexing files with one id per entry is not enough. For
instance you may want to retrieve sequences from swissprot using
their accessions as well as their ids.
To be able to do this when creating your index you need to pass in
a hash of secondary_patterns which have their namespaces as the keys
to the hash.
e.g. For Indexing something like
ID 1433_CAEEL STANDARD; PRT; 248 AA.
AC P41932;
DT 01-NOV-1995 (Rel. 32, Created)
DT 01-NOV-1995 (Rel. 32, Last sequence update)
DT 15-DEC-1998 (Rel. 37, Last annotation update)
DE 14-3-3-LIKE PROTEIN 1.
GN FTT-1 OR M117.2.
OS Caenorhabditis elegans.
OC Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea;
OC Rhabditidae; Peloderinae; Caenorhabditis.
OX NCBI_TaxID=6239;
RN [1]
where we want to index the accession (P41932) as the primary key and the
id (1433_CAEEL) as the secondary id. The index is created as follows

    my %secondary_patterns;

    my $start_pattern   = "^ID   (\\S+)";
    my $primary_pattern = "^AC   (\\S+)\;";

    $secondary_patterns{"ID"} = "^ID   (\\S+)";

    my $index = new Bio::DB::Flat::BinarySearch(
                -start_pattern     => $start_pattern,
                -primary_pattern   => $primary_pattern,
                -primary_namespace  => 'ID',
                -secondary_patterns => \%secondary_patterns);

    $index->build_index("/Users/michele/indices","mydb",($seqfile));

Of course having secondary indices makes indexing slower and more
of a memory hog. To fetch sequences using an existing index first of all create your sequence
object

    my $index = new Bio::DB::Flat::BinarySearch(-directory => $index_directory);

Now you can happily fetch sequences either by the primary key or
by the secondary keys.

    my $entry = $index->get_entry_by_id('HBA_HUMAN');

This returns just a string containing the whole entry. This is
useful is you just want to print the sequence to screen or write it to a file.
Other ways of getting sequences are

    my $fh = $index->get_stream_by_id('HBA_HUMAN');

This can then be passed to a seqio object for output or converting
into objects.

    my $seq = new Bio::SeqIO(-fh     => $fh,
			     -format => 'fasta');

The last way is to retrieve a sequence directly. This is the
slowest way of extracting as the sequence objects need to be made.

    my $seq = $index->get_Seq_by_id('HBA_HUMAN');

To access the secondary indices the secondary namespace needs to be known

    $index->secondary_namespaces("ID");

Then the following calls can be used

    my $seq   = $index->get_Seq_by_secondary('ID','1433_CAEEL');
    my $fh    = $index->get_stream_by_secondary('ID','1433_CAEEL');
    my $entry = $index->get_entry_by_secondary('ID','1433_CAEEL');

Methods

Methods description

 Title   : new
 Usage   : For reading 
             my $index = new Bio::DB::Flat::BinarySearch(
                     -directory => '/Users/michele/indices/dbest',
		     -dbname    => 'mydb',
                     -format    => 'fasta');

           For writing 

             my %secondary_patterns = {"ACC" => "^>\\S+ +(\\S+)"}
             my $index = new Bio::DB::Flat::BinarySearch(
		     -directory          => '/Users/michele/indices',
                     -dbname             => 'mydb',
		     -primary_pattern    => "^>(\\S+)",
                     -secondary_patterns => \%secondary_patterns,
		     -primary_namespace  => "ID");

             my @files = ('file1','file2','file3');

             $index->build_index(@files);

 Function: create a new Bio::DB::Flat::BinarySearch object
 Returns : new Bio::DB::Flat::BinarySearch
 Args    : -directory          Root directory for index files
           -dbname             Name of subdirectory containing indices for named database
           -write_flag         Allow building index
           -primary_pattern    Regexp defining the primary id
           -secondary_patterns A hash ref containing the secondary
                               patterns with the namespaces as keys
           -primary_namespace  A string defining what the primary key
                               is

 Status  : Public

 Title   : get_Seq_by_id
 Usage   : $obj->get_Seq_by_id($newval)
 Function: 
 Example : 
 Returns : value of get_Seq_by_id
 Args    : newvalue (optional)

 Title   : get_entry_by_id
 Usage   : $obj->get_entry_by_id($newval)
 Function: Get a Bio::SeqI object for a unique ID
 Returns : Bio::SeqI
 Args    : string

 Title   : get_stream_by_id
 Usage   : $obj->get_stream_by_id($id)
 Function: Gets a Sequence stream for an id
 Returns : Bio::SeqIO stream
 Args    : Id to lookup by

 Title   : get_Seq_by_acc
 Usage   : $obj->get_Seq_by_acc($acc)
 Function: Gets a Bio::SeqI object by accession number
 Returns : Bio::SeqI object
 Args    : string representing accession number

 Title   : get_Seq_by_secondary
 Usage   : $obj->get_Seq_by_secondary($acc)
 Function: Gets a Bio::SeqI object looking up secondary accessions
 Returns : Bio::SeqI object
 Args    : namespace name to check secondary namespace for

 Title   : read_header
 Usage   : $obj->read_header($fhl)
 Function: Reads the header from the db file
 Returns : width of a record
 Args    : filehandle

 Title   : read_record
 Usage   : $obj->read_record($fh,$pos,$len)
 Function: Reads a record from a filehandle
 Returns : String
 Args    : filehandle, offset, and length

 Title   : get_all_primary_ids
 Usage   : @ids = $seqdb->get_all_primary_ids()
 Function: gives an array of all the primary_ids of the
           sequence objects in the database.
 Returns : an array of strings
 Args    : none

 Title   : find_entry
 Usage   : $obj->find_entry($fh,$start,$end,$id,$recsize)
 Function: Extract an entry based on the start,end,id and record size
 Returns : string
 Args    : filehandle, start, end, id, recordsize

 Title   : build_index
 Usage   : $obj->build_index(@files)
 Function: Build the index based on a set of files
 Returns : count of the number of entries
 Args    : List of filenames

 Title   : _index_file
 Usage   : $obj->_index_file($newval)
 Function: 
 Example : 
 Returns : value of _index_file
 Args    : newvalue (optional)

 Title   : write_primary_index
 Usage   : $obj->write_primary_index($newval)
 Function: 
 Example : 
 Returns : value of write_primary_index
 Args    : newvalue (optional)

 Title   : write_secondary_indices
 Usage   : $obj->write_secondary_indices($newval)
 Function: 
 Example : 
 Returns : value of write_secondary_indices
 Args    : newvalue (optional)

 Title   : new_secondary_filehandle
 Usage   : $obj->new_secondary_filehandle($newval)
 Function: 
 Example : 
 Returns : value of new_secondary_filehandle
 Args    : newvalue (optional)

 Title   : open_secondary_index
 Usage   : $obj->open_secondary_index($newval)
 Function: 
 Example : 
 Returns : value of open_secondary_index
 Args    : newvalue (optional)

 Title   : _add_id_position
 Usage   : $obj->_add_id_position($newval)
 Function: 
 Example : 
 Returns : value of _add_id_position
 Args    : newvalue (optional)

 Title   : make_config_file
 Usage   : $obj->make_config_file($newval)
 Function: 
 Example : 
 Returns : value of make_config_file
 Args    : newvalue (optional)

 Title   : read_config_file
 Usage   : $obj->read_config_file($newval)
 Function: 
 Example : 
 Returns : value of read_config_file
 Args    : newvalue (optional)

 Title   : get_fileid_by_filename
 Usage   : $obj->get_fileid_by_filename($newval)
 Function: 
 Example : 
 Returns : value of get_fileid_by_filename
 Args    : newvalue (optional)

 Title   : get_filehandle_by_fileid
 Usage   : $obj->get_filehandle_by_fileid($newval)
 Function: 
 Example : 
 Returns : value of get_filehandle_by_fileid
 Args    : newvalue (optional)

 Title   : primary_index_file
 Usage   : $obj->primary_index_file($newval)
 Function: 
 Example : 
 Returns : value of primary_index_file
 Args    : newvalue (optional)

 Title   : primary_index_filehandle
 Usage   : $obj->primary_index_filehandle($newval)
 Function: 
 Example : 
 Returns : value of primary_index_filehandle
 Args    : newvalue (optional)

 Title   : format
 Usage   : $obj->format($newval)
 Function: 
 Example : 
 Returns : value of format
 Args    : newvalue (optional)

 Title   : write_flag
 Usage   : $obj->write_flag($newval)
 Function: 
 Example : 
 Returns : value of write_flag
 Args    : newvalue (optional)

 Title   : dbname
 Usage   : $obj->dbname($newval)
 Function: get/set database name
 Example : 
 Returns : value of dbname
 Args    : newvalue (optional)

 Title   : index_directory
 Usage   : $obj->index_directory($newval)
 Function: 
 Example : 
 Returns : value of index_directory
 Args    : newvalue (optional)

 Title   : record_size
 Usage   : $obj->record_size($newval)
 Function: 
 Example : 
 Returns : value of record_size
 Args    : newvalue (optional)

 Title   : primary_namespace
 Usage   : $obj->primary_namespace($newval)
 Function: 
 Example : 
 Returns : value of primary_namespace
 Args    : newvalue (optional)

 Title   : index_type
 Usage   : $obj->index_type($newval)
 Function: 
 Example : 
 Returns : value of index_type
 Args    : newvalue (optional)

 Title   : index_version
 Usage   : $obj->index_version($newval)
 Function: 
 Example : 
 Returns : value of index_version
 Args    : newvalue (optional)

 Title   : primary_pattern
 Usage   : $obj->primary_pattern($newval)
 Function: 
 Example : 
 Returns : value of primary_pattern
 Args    : newvalue (optional)

 Title   : start_pattern
 Usage   : $obj->start_pattern($newval)
 Function: 
 Example : 
 Returns : value of start_pattern
 Args    : newvalue (optional)

 Title   : secondary_patterns
 Usage   : $obj->secondary_patterns($newval)
 Function: 
 Example : 
 Returns : value of secondary_patterns
 Args    : newvalue (optional)

 Title   : secondary_namespaces
 Usage   : $obj->secondary_namespaces($newval)
 Function: 
 Example : 
 Returns : value of secondary_namespaces
 Args    : newvalue (optional)

Methods code

sub systell {

sysseek($_[0], 0, SEEK_CUR)

}

sub syseof {

sysseek($_[0], 0, SEEK_END)

}

sub new {

    my($class, @args) = @_;

    my $self = $class->SUPER::new(@args);

    bless $self, $class;

    my ($index_dir,$dbname,$format,$write_flag,$primary_pattern,
	$primary_namespace,$start_pattern,$secondary_patterns) =
	    $self->_rearrange([qw(DIRECTORY
				  DBNAME
				  FORMAT
				  WRITE_FLAG
				  PRIMARY_PATTERN
				  PRIMARY_NAMESPACE
				  START_PATTERN
				  SECONDARY_PATTERNS)], @args);

    $self->index_directory($index_dir);
    $self->dbname($dbname);

    if ($self->index_directory && $self->read_config_file) {
	
	my $fh = $self->primary_index_filehandle;
        my $record_width = $self->read_header($fh);
        $self->record_size($record_width);
    }
    $format ||= DEFAULT_FORMAT;
    $self->format            ($format);
    $self->write_flag        ($write_flag);

    if ($self->write_flag && ! $primary_namespace) {
      ($primary_namespace,$primary_pattern,
       $start_pattern,$secondary_patterns) =
	$self->_guess_patterns($self->format);
    }

    $self->primary_pattern   ($primary_pattern);
    $self->primary_namespace ($primary_namespace);
    $self->start_pattern     ($start_pattern);
    $self->secondary_patterns($secondary_patterns);

    return $self;

}

sub new_from_registry {

    my ($self,%config) =  @_;
   
    my $dbname   = $config{'dbname'};
    my $location = $config{'location'};
    
    my $index =  new Bio::DB::Flat::BinarySearch(-dbname    => $dbname,
						 -index_dir => $location,
						 );

}

sub get_Seq_by_id {

    my ($self,$id) = @_;

    my ($fh,$length) = $self->get_stream_by_id($id);

    unless (defined($self->format)) {
	$self->throw("Can't create sequence - format is not defined");
    }

    return unless $fh;

    unless ( defined($self->{_seqio}) ) {

	$self->{_seqio} = new Bio::SeqIO(-fh => $fh,
					 -format => $self->format);
    } else {
	$self->{_seqio}->fh($fh);
    }

    return $self->{_seqio}->next_seq;

}

sub get_entry_by_id {

    my ($self,$id) = @_;

    my ($fh,$length) = $self->get_stream_by_id($id);

    my $entry;

    sysread($fh,$entry,$length);

    return $entry;

}

sub get_stream_by_id {

    my ($self,$id) = @_;

    unless( $self->record_size ) {
	if ($self->index_directory && $self->read_config_file) {
	    
	    my $fh = $self->primary_index_filehandle;
	    my $record_width = $self->read_header($fh);
	    $self->record_size($record_width);
	}
    }
    my $indexfh = $self->primary_index_filehandle;
    syseof ($indexfh);

    my $filesize = systell($indexfh);
    
    $self->throw("file was not parsed properly, record size is empty") 
	unless $self->record_size;
    
    my $end = ($filesize - $self->{'_start_pos'}) / $self->record_size;
    my ($newid,$rest,$fhpos) = $self->find_entry($indexfh,0,$end,$id,$self->record_size);

    
    my ($fileid,$pos,$length) = split(/\t/,$rest);

    #print STDERR "BinarySearch Found id entry $newid $fileid $pos $length:$rest\n";

    if (!$newid) {
      return;
    }

    my $fh = $self->get_filehandle_by_fileid($fileid);
    my $file = $self->{_file}{$fileid};

    open (IN,"<$file");
    $fh =\* IN;

    my $entry;
    
    sysseek($fh,$pos,0);

    return ($fh,$length);

}

sub get_Seq_by_acc {

    my ($self,$acc) = @_;

    if ($self->primary_namespace eq "ACC") {
       return $self->get_Seq_by_id($acc);
    } else {
      return $self->get_Seq_by_secondary("ACC",$acc);
    }

}

sub get_Seq_by_secondary {

    my ($self,$name,$id) = @_;

    my @names = $self->secondary_namespaces;

    my $found = 0;
    foreach my $tmpname (@names) {
	if ($name eq $tmpname) {
	    $found = 1;
	}
    }

    if ($found == 0) {
	$self->throw("Secondary index for $name doesn't exist\n");
    }

    my $fh = $self->open_secondary_index($name);

    syseof ($fh);

    my $filesize = systell($fh);

    my $recsize = $self->{'_secondary_record_size'}{$name};
#    print "Name " . $recsize . "\n";

    my $end = ($filesize - $self->{'_start_pos'})/$recsize;

#    print "End $end $filesize\n";
    my ($newid,$primary_id,$pos) = $self->find_entry($fh,0,$end,$id,$recsize);

    sysseek($fh,$pos,0);

#    print "Found new id $newid $primary_id\n";    
    # We now need to shuffle up the index file to find the top secondary entry

    my $record = $newid;

    while ($record =~ /^$newid/ && $pos >= 0) {

	$record = $self->read_record($fh,$pos,$recsize);
	$pos = $pos - $recsize;
#	print "Up record = $record:$newid\n";
    }
    
    $pos += $recsize;

#    print "Top position is $pos\n";

    # Now we have to shuffle back down again to read all the secondary entries

    my $current_id = $newid;
    my %primary_id;

    $primary_id{$primary_id} = 1;

    while ($current_id eq $newid) {
	$record = $self->read_record($fh,$pos,$recsize);
	# print "Record is :$record:\n";
	my ($secid,$primary_id) = split(/\t/,$record,2);
	$current_id = $secid;

	if ($current_id eq $newid) {
	    $primary_id =~ s/ //g;
	#    print "Primary $primary_id\n";
	    $primary_id{$primary_id} = 1;
	    
	    $pos = $pos + $recsize;
	 #   print "Down record = $record\n";
	}
    }
	
    if (!defined($newid)) {
      return;
    }

    my @entry;

    foreach my $id (keys %primary_id) {
      push @entry,$self->get_Seq_by_id($id);
    }
    return wantarray ? @entry : $entry[0];

}

sub read_header {

    my ($self,$fh) = @_;

    my $record_width;

    sysread($fh,$record_width,HEADER_SIZE);

    $self->{'_start_pos'} = HEADER_SIZE;
    $record_width =~ s/ //g;
    $record_width = $record_width * 1;

    return $record_width;

}

sub read_record {

  my ($self,$fh,$pos,$len) = @_;

  sysseek($fh,$pos,0);

  my $record;
    
  sysread($fh,$record,$len);

  return $record;

}

sub get_all_primary_ids {

  my $self = shift;

  my $fh = $self->primary_index_filehandle;
  syseof($fh);
  my $filesize = systell($fh);
  my $recsize  = $self->record_size;
  my $end = $filesize;

  my @ids;
  for (my $pos=$self->{'_start_pos'}; $pos < $end; $pos += $recsize) {
    my $record = $self->read_record($fh,$pos,$recsize);
    my ($entryid)  = split(/\t/,$record);
    push @ids,$entryid;
  }
  @ids;

}

sub find_entry {

    my ($self,$fh,$start,$end,$id,$recsize) = @_;
    
    my $mid = int( ($end+1+$start) / 2);
    my $pos = ($mid-1)*$recsize + $self->{'_start_pos'};
    
    my ($record) = $self->read_record($fh,$pos,$recsize);
    my ($entryid,$rest)  = split(/\t/,$record,2);
    $rest =~ s/\s+$//;

#    print "Mid $recsize $mid $pos:$entryid:$rest:$record\n";
#    print "Entry :$id:$entryid:$rest\n";

    my ($first,$second) = $id le $entryid ? ($id,$entryid) : ($entryid,$id);

    if ($id eq $entryid) {

      return ($id,$rest,$pos-$recsize);

    } elsif ($first eq $id) {
	
      if ($end-$start <= 1) {
	return;
      }
      my $end = $mid;
#      print "Moving up $entryid $id\n";
      $self->find_entry($fh,$start,$end,$id,$recsize);

    } elsif ($second eq $id ) {
#	print "Moving down $entryid $id\n";
      if ($end-$start <= 1) {
	return;
      }

      $start = $mid;
      
      $self->find_entry($fh,$start,$end,$id,$recsize);
    }

}

sub build_index {

    my ($self,@files) = @_;
    $self->write_flag or 
	$self->throw('Cannot build index unless -write_flag is true');

    my $rootdir = $self->index_directory;

    if (!defined($rootdir)) {
	$self->throw("No index directory set - can't build indices");
    }

    if (! -d $rootdir) {
	$self->throw("Index directory [$rootdir] is not a directory. Cant' build indices");
    }

    my $dbpath = Bio::Root::IO->catfile($rootdir,$self->dbname);
    if (! -d $dbpath) {
      warn "Creating directory $dbpath\n";
      mkdir $dbpath,0777 or $self->throw("Couldn't create $dbpath: $!");
    }

    unless (@files ) {
	$self->throw("Must enter an array of filenames to index");
    }

    foreach my $file (@files) {
	$file = File::Spec->rel2abs($file)
	    unless File::Spec->file_name_is_absolute($file);
	unless ( -e $file) {
	    $self->throw("Can't index file [$file] as it doesn't exist");
	}
    }
    
    if (my $filehash = $self->{_dbfile}) {
      push @files,keys %$filehash;
    }

    my %seen;
    @files = grep {!$seen{$_}++} @files;

    # Lets index
    $self->make_config_file(\@files);
    my $entries = 0;
    foreach my $file (@files) {
      $entries += $self->_index_file($file);
    }

    # update alphabet if necessary
    $self->make_config_file(\@files);

    # And finally write out the indices
    $self->write_primary_index;
    $self->write_secondary_indices;

    $entries;

}

sub _index_file {

    my ($self,$file) = @_;
    my $v = $self->verbose;
    open(FILE,"<$file") || $self->throw("Can't open file [$file]");

    my $recstart = 0;
    my $fileid = $self->get_fileid_by_filename($file);
    my $found = 0;
    my $id;
    my $count = 0;

    my $primary       = $self->primary_pattern;
    my $start_pattern = $self->start_pattern;

    my $pos = 0;

    my $new_primary_entry;

    my $length;
    #my $pos = 0;
    my $fh =\* FILE;

    my $done = -1;

    my @secondary_names = $self->secondary_namespaces;
    my %secondary_id;
    my $last_one;

    while (<$fh>) {
      $last_one = $_;
      $self->{alphabet} ||= $self->guess_alphabet($_);		
      if ($_ =~ /$start_pattern/) {
	if ($done == 0) {
	  $id = $new_primary_entry;
	  $self->{alphabet} ||= $self->guess_alphabet($_);
	  
	  my $tmplen = (tell $fh) - length($_);

	  $length = $tmplen  - $pos;
		
	  unless( defined($id)) {
	    $self->throw("No id defined for sequence");
	  }
	  unless( defined($fileid)) {
	    $self->throw("No fileid defined for file $file");
	  }
	  unless( defined($pos)) {
	    $self->throw("No position defined for " . $id . "\n");
	  }
	  unless( defined($length)) {
	    $self->throw("No length defined for " . $id . "\n");
	  }
	  $self->_add_id_position($id,$pos,$fileid,$length,\%secondary_id);

	  $pos   = $tmplen;
		
	  if ($count > 0 && $count%1000 == 0) {
	    $self->debug( "Indexed $count ids\n") if $v > 0;
	  }
	    
	  $count++;
	} else {
	  $done = 0;
	}
      }

      if ($_ =~ /$primary/) {
	$new_primary_entry = $1;    
      }

      my $secondary_patterns = $self->secondary_patterns;

      foreach my $sec (@secondary_names) {
	my $pattern = $secondary_patterns->{$sec};

	if ($_ =~ /$pattern/) {
	  $secondary_id{$sec} = $1;
	}
      }
	
    }

    # Remember to add in the last one

    $id = $new_primary_entry;
    my $tmplen = (tell $fh) - length($last_one);

    $length = $tmplen  - $pos;
    
    if (!defined($id)) {
	$self->throw("No id defined for sequence");
    }
    if (!defined($fileid)) {
	$self->throw("No fileid defined for file $file");
    }
    if (!defined($pos)) {
	$self->throw("No position defined for " . $id . "\n");
    }
    if (!defined($length)) {
	$self->throw("No length defined for " . $id . "\n");
    }
    
    $self->_add_id_position($id,$pos,$fileid,$length,\%secondary_id);
    $count++;
    
    close(FILE);
    $count;

}

sub write_primary_index {

    my ($self) = @_;

    my @ids = keys %{$self->{_id}};

    @ids = sort {$a cmp $b} @ids;

    open (INDEX,">" . $self->primary_index_file) || 
	$self->throw("Can't open primary index file [" . 
		     $self->primary_index_file . "]");

    my $recordlength = $self->{_maxidlength} +
	               $self->{_maxfileidlength} + 
	               $self->{_maxposlength} +
   		       $self->{_maxlengthlength} + 3;
	
    
    print INDEX sprintf("%4d",$recordlength);

    foreach my $id (@ids) {

	if (!defined($self->{_id}{$id}{_fileid})) {
	    $self->throw("No fileid for $id\n");
	}
	if (!defined($self->{_id}{$id}{_pos})) {
	    $self->throw("No position for $id\n");
	}
	if (!defined($self->{_id}{$id}{_length})) {
	    $self->throw("No length for $id");
	}

	my $record =  $id              . "\t" . 
	    $self->{_id}{$id}{_fileid} . "\t" .
	    $self->{_id}{$id}{_pos}    . "\t" .
	    $self->{_id}{$id}{_length};

	print INDEX sprintf("%-${recordlength}s",$record);

    }
    close(INDEX);

}

sub write_secondary_indices {

    my ($self) = @_;

    # These are the different 
    my @names = keys (%{$self->{_secondary_id}});

    
    foreach my $name (@names) {

	my @seconds = keys %{$self->{_secondary_id}{$name}};

	# First we need to loop over to get the longest record.
	my $length = 0;

	foreach my $second (@seconds) {
	    my $tmplen = length($second) + 1;
	    my @prims = keys %{$self->{_secondary_id}{$name}{$second}};

	    foreach my $prim (@prims) {
		my $recordlen = $tmplen + length($prim);
	    
		if ($recordlen > $length) {
		    $length = $recordlen;
		}
	    }
	}

	# Now we can print the index
	
	my $fh = $self->new_secondary_filehandle($name);	

	print $fh sprintf("%4d",$length);
	@seconds = sort @seconds;
	
	foreach my $second (@seconds) {

	    my @prims = keys %{$self->{_secondary_id}{$name}{$second}};
	    my $tmp = $second;

	    foreach my $prim (@prims) {
		my $record = $tmp . "\t" . $prim;
		if (length($record) > $length) {
		    $self->throw("Something has gone horribly wrong - length of record is more than we thought [$length]\n");
		} else {
		    print $fh sprintf("%-${length}s",$record);
		    print $fh sprintf("%-${length}s",$record);
		}
	    }
	}
		
	close($fh);
    }

}

sub new_secondary_filehandle {

    my ($self,$name) = @_;

    my $indexdir = $self->_config_path;

    my $secindex = Bio::Root::IO->catfile($indexdir,"id_$name.index");

    my $fh;
    open($fh,">$secindex") || $self->throw($!);
    return $fh;

}

sub open_secondary_index {

    my ($self,$name) = @_;

    if (!defined($self->{_secondary_filehandle}{$name})) {

	my $indexdir = $self->_config_path;
	my $secindex = $indexdir . "/id_$name.index";
	
	if (! -e $secindex) {
	    $self->throw("Index is not present for namespace [$name]\n");
	}

        my $newfh;
	open($newfh,"<$secindex") || $self->throw($!);
	my $reclen = $self->read_header($newfh);

	$self->{_secondary_filehandle} {$name} = $newfh;
	$self->{_secondary_record_size}{$name} = $reclen;
    }

    return $self->{_secondary_filehandle}{$name};

}

sub _add_id_position {

  my ($self,$id,$pos,$fileid,$length,$secondary_id) = @_;

  if (!defined($id)) {
    $self->throw("No id defined. Can't add id position");
  }
  if (!defined($pos)) {
    $self->throw("No position defined. Can't add id position");
  }
  if ( ! defined($fileid)) {
    $self->throw("No fileid defined. Can't add id position");
  }
  if (! defined($length) || $length <= 0) {
    $self->throw("No length defined or <= 0 [$length]. Can't add id position");
  }

  $self->{_id}{$id}{_pos}    = $pos;
  $self->{_id}{$id}{_length} = $length;
  $self->{_id}{$id}{_fileid} = $fileid;

  # Now the secondary ids

  foreach my $sec (keys (%$secondary_id)) {
    my $value = $secondary_id->{$sec};

    $self->{_secondary_id}{$sec}{$value}{$id} = 1;
  }

  $self->{_maxidlength} = length($id)
    if !exists $self->{_maxidlength} or length($id) >= $self->{_maxidlength};

  $self->{_maxfileidlength} = length($fileid)
    if !exists $self->{_maxfileidlength} or length($fileid) >= $self->{_maxidlength};

  $self->{_maxposlength} = length($pos)
    if !exists $self->{_maxposlength} or length($pos) >= $self->{_maxposlength};

  $self->{_maxlengthlength} = length($length)
      if !exists $self->{_maxlengthlength} or length($length) >= $self->{_maxlengthlength};

}

sub make_config_file {

    my ($self,$files) = @_;
    
    my @files = @$files;

    my $configfile = $self->_config_file;

    open(CON,">$configfile") || $self->throw("Can't create config file [$configfile]");

    # First line must be the type of index - in this case flat
    print CON "index\tflat/1\n";

    # Now the fileids

    my $count = 0;

    foreach my $file (@files) {

	my $size = -s $file;

	print CON "fileid_$count\t$file\t$size\n";

	my $fh;
	open($fh,"<$file") || $self->throw($!);
	$self->{_fileid}{$count}   = $fh;
	$self->{_file}  {$count}   = $file;
	$self->{_dbfile}{$file}    = $count;
	$self->{_size}{$count}     = $size; 
	
	$count++;
    }

    # Now the namespaces

    print CON "primary_namespace\t" .$self->primary_namespace. "\n";
    
    # Needs fixing for the secondary stuff

    my $second_patterns = $self->secondary_patterns;

    my @second = keys %$second_patterns;

    if ((@second))  {
	print CON "secondary_namespaces";

	foreach my $second (@second) {
	    print CON "\t$second";
	}
        print CON "\n";
    }

    # Now the config format

    unless (defined ($self->format) ) {
	$self->throw("Format does not exist in module - can't write config file");
    } else {
	my $format = $self->format;
	my $alphabet = $self->alphabet;
	my $alpha    = $alphabet ? "/$alphabet" : '';
	print CON "format\t" . "URN:LSID:open-bio.org:$format$alpha\n";
    }
    close(CON);

}

sub read_config_file {

    my ($self) = @_;

    my $configfile = $self->_config_file;
    return unless -e $configfile;

    open(CON,"<$configfile") || $self->throw("Can't open configfile [$configfile]");

    # First line must be type

    my $line = <CON>; chomp($line);
    my $version;

    # This is hard coded as we only index flatfiles here
    if ($line =~ /index\tflat\/(\d+)/) {
	$version = $1;
    } else {
	$self->throw("First line not compatible with flat file index.  Should be something like\n\nindex\tflat/1");
    }

    $self->index_type("flat");
    $self->index_version($version);

    while (<CON>) {
	chomp;

	# Look for fileid lines
	if ($_ =~ /^fileid_(\d+)\t(\S+)\t(\d+)/) {
	    my $fileid   = $1;
	    my $filename = $2;
	    my $filesize = $3;
	    
	    if (! -e $filename) {
		$self->throw("File [$filename] does not exist!");
	    }
	    if (-s $filename != $filesize) {
		$self->throw("Flatfile size for $filename differs from what the index thinks it is. Real size [" . (-s $filename) . "] Index thinks it is [" . $filesize  . "]");
	    }
		
	    my $fh;
	    open($fh,"<$filename") || $self->throw($!);

	    $self->{_fileid}{$fileid}   = $fh;
	    $self->{_file}  {$fileid}   = $filename;
	    $self->{_dbfile}{$filename} = $fileid;
            $self->{_size}  {$fileid}   = $filesize; 

	}

	# Look for namespace lines
	if (/(.*)_namespaces?\t(.+)/) {
	    if ($1 eq "primary") {
		$self->primary_namespace($2);
	    } elsif ($1 eq "secondary") {
		$self->secondary_namespaces(split "\t",$2);
	    } else {
		$self->throw("Unknown namespace name in config file [$1");
	    }
	}
	
	# Look for format lines

	if ($_ =~ /format\t(\S+)/) {

	  # Check the format here?
	  my $format = $1;

	  # handle LSID format
	  if ($format =~ /^URN:LSID:open-bio\.org:(\w+)(?:\/(\w+))?/) {
	      $self->format($1);
	      $self->alphabet($2);
	  } else {  # compatibility with older versions
	    $self->format($1);
	  }
	}
    }
    close(CON);

    # Now check we have all that we need

    my @fileid_keys = keys (%{$self->{_fileid}});

    if (!(@fileid_keys)) {
	$self->throw("No flatfile fileid files in config - check the index has been made correctly");
    }

    if (!defined($self->primary_namespace)) {
	$self->throw("No primary namespace exists");
    }

    if (! -e $self->primary_index_file) {
	$self->throw("Primary index file [" . $self->primary_index_file . "] doesn't exist");
    }

    1;

}

sub get_fileid_by_filename {

    my ($self,$file) = @_;
    
    if (!defined($self->{_dbfile})) {
	$self->throw("No file to fileid mapping present.  Has the fileid file been read?");
    }

    
    return $self->{_dbfile}{$file};

}

sub get_filehandle_by_fileid {

    my ($self,$fileid) = @_;

    if (!defined($self->{_fileid}{$fileid})) {
	$self->throw("ERROR: undefined fileid in index [$fileid]");
    }
   
    return $self->{_fileid}{$fileid};

}

sub primary_index_file {

    my ($self) = @_;

    return Bio::Root::IO->catfile($self->_config_path,"key_" . $self->primary_namespace . ".key");

}

sub primary_index_filehandle {

    my ($self) = @_;

    unless (defined ($self->{'_primary_index_handle'})) {
	open($self->{'_primary_index_handle'}, "<" . $self->primary_index_file) || self->throw($@);
    }
    return $self->{'_primary_index_handle'};

}

sub format {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'format'} = $value;
    }
    return $obj->{'format'};

}

sub alphabet {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{alphabet} = $value;
    }
    return $obj->{alphabet};

}

sub write_flag {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'write_flag'} = $value;
    }
    return $obj->{'write_flag'};

}

sub dbname {

  my $self = shift;
  my $d = $self->{flat_dbname};
  $self->{flat_dbname} = shift if @_;
  $d;

}

sub index_directory {

    my ($self,$arg) = @_;

    if (defined($arg)) {
	if ($arg !~ /\/$/) {
	    $arg .= "/";
	}
	$self->{_index_directory} = $arg;
    }
    return $self->{_index_directory};

}

sub _config_path {

  my $self = shift;
  my $root = $self->index_directory;
  my $dbname = $self->dbname;
  Bio::Root::IO->catfile($root,$dbname);

}

sub _config_file {

  my $self = shift;
  my $path = $self->_config_path;
  Bio::Root::IO->catfile($path,CONFIG_FILE_NAME);

}

sub record_size {

    my $self = shift;
    $self->{_record_size} = shift if @_;
    return $self->{_record_size};

}

sub primary_namespace {

    my $self = shift;
    $self->{_primary_namespace} =  shift if @_;
    return $self->{_primary_namespace};

}

sub index_type {

    my $self = shift;
    $self->{_index_type} = shift if @_;
    return $self->{_index_type};

}

sub index_version {

    my $self = shift;
    $self->{_index_version} = shift if @_;
    return $self->{_index_version};

}

sub primary_pattern {

    my $obj = shift;
    $obj->{'primary_pattern'} = shift if @_;
    return $obj->{'primary_pattern'};

}

sub start_pattern {

    my $obj = shift;
    $obj->{'start_pattern'} = shift if @_;
    return $obj->{'start_pattern'};

}

sub secondary_patterns {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'secondary_patterns'} = $value;

      my @names = keys %$value;

      foreach my $name (@names) {
	  $obj->secondary_namespaces($name);
      }
    }
    return $obj->{'secondary_patterns'};

}

sub secondary_namespaces {

    my ($obj,@values) = @_;

    if (@values) {
	push(@{$obj->{'secondary_namespaces'}},@values);
    }
    return @{$obj->{'secondary_namespaces'} || []};

}

sub new_SWISSPROT_index {

    my ($self,$index_dir,@files) = @_;
    
    my %secondary_patterns;
    
    my $start_pattern = "^ID   (\\S+)";
    my $primary_pattern = "^AC   (\\S+)\\;";
    
    $secondary_patterns{"ID"} = $start_pattern;

    my $index =  new Bio::DB::Flat::BinarySearch
	(-index_dir          => $index_dir,
	 -format             => 'swissprot',
	 -primary_pattern    => $primary_pattern,
	 -primary_namespace  => "ACC",
	 -start_pattern      => $start_pattern,
	 -secondary_patterns =>\% secondary_patterns);
    
    $index->build_index(@files);

}

sub new_EMBL_index {

   my ($self,$index_dir,@files) = @_;
   
   my %secondary_patterns;

   my $start_pattern = "^ID   (\\S+)";
   my $primary_pattern = "^AC   (\\S+)\\;";
   my $primary_namespace = "ACC";

   $secondary_patterns{"ID"} = $start_pattern;

   my $index = new Bio::DB::Flat::BinarySearch
       (-index_dir          => $index_dir,
	-format             => 'embl',
	-primary_pattern    => $primary_pattern,
	-primary_namespace  => "ACC",
	-start_pattern      => $start_pattern,
	-secondary_patterns =>\% secondary_patterns);
   
    $index->build_index(@files);

   return $index;

}

sub new_FASTA_index {

   my ($self,$index_dir,@files) =  @_;

   my %secondary_patterns;

   my $start_pattern = "^>";
   my $primary_pattern = "^>(\\S+)";
   my $primary_namespace = "ACC"; 

   $secondary_patterns{"ID"} = "^>\\S+ +(\\S+)";

   my $index =  new Bio::DB::Flat::BinarySearch
       (-index_dir          => $index_dir,
	-format             => 'fasta',
	-primary_pattern    => $primary_pattern,
	-primary_namespace  => "ACC",
	-start_pattern      => $start_pattern,
	-secondary_patterns =>\% secondary_patterns);
   
   $index->build_index(@files);

   return $index;

}

sub guess_alphabet {

  my $self = shift;
  my $line = shift;

  my $format = $self->format;
  return 'protein' if $format eq 'swissprot';

  if ($format eq 'genbank') {
    return unless $line =~ /^LOCUS/;
    return 'dna' if $line =~ /\s+\d+\s+bp/i;
    return 'protein';
  }

  if ($format eq 'embl') {
    return unless $line =~ /^ID/;
    return 'dna' if $line =~ / DNA;/i;
    return 'rna' if $line =~ / RNA;/i;
    return 'protein';
  }

  return;

}

sub _guess_patterns {

  my $self = shift;
  my $format = shift;
  if ($format =~ /swiss(prot)?/i) {
    return ('ID',
	    "^ID   (\\S+)",
	    "^ID   (\\S+)",
	    {
	     ACC  => "^AC   (\\S+);"
	    });
  }

  if ($format =~ /embl/i) {
    return ('ID',
	    "^ID   (\\S+)",
	    "^ID   (\\S+)",
	    {
	     ACC     => q//^AC   (\S+);/,
	     VERSION => q//^SV\s+(\S+)/
	    });
  }

  if ($format =~ /genbank/i) {
    return ('ID',
	    q//^LOCUS\s+(\S+)/,
	    q//^LOCUS/,
	    {
	     ACC     => q//^ACCESSION\s+(\S+)/,
	     VERSION => q//^VERSION\s+(\S+)/
	    });
  }

  if ($format =~ /fasta/i) {
    return ('ACC',
	    "^>(\\S+)",
	    "^>",
	    {
	     ID => "^>\\S+ +(\\S+)"
	    }
	   );
  }

  $self->throw("I can't handle format $format");

}

General documentation

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

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 - michele@sanger.ac.uk

Jason Stajich, jason@bioperl.org

The rest of the documentation details each of the object methods. Internal
methods are usually preceded with an "_" (underscore).