Bio::DB::GFF::Adaptor::dbi oracle
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::DB::GFF::Adaptor::dbi::oracle -- Database adaptor for a specific oracle schema
Package variables
No package variables defined.
Included modules
Bio::DB::GFF::Util::Binning
Bio::DB::GFF::Util::Rearrange
Inherit
Bio::DB::GFF::Adaptor::dbi
Synopsis
See Bio::DB::GFF
Description
This adaptor implements a specific oracle database schema that is
compatible with Bio::DB::GFF. It inherits from
Bio::DB::GFF::Adaptor::dbi, which itself inherits from Bio::DB::GFF.
The schema uses several tables:
    fdata
    This is the feature data table. Its columns are:
    fid	           feature ID (integer)
fref reference sequence name (string)
fstart start position relative to reference (integer)
fstop stop postion relative to reference (integer)
ftypeid feature type ID (integer)
fscore feature score (float); may be null
fstrand strand; one of "+" or "-"; may be null
fphase phase; one of 0, 1 or 2; may be null
gid group ID (integer)
ftarget_start for similarity features, the target start position (integer)
ftarget_stop for similarity features, the target stop position (integer)
    Note that it would be desirable to normalize the reference sequence
name, since there are usually many features that share the same
reference feature. However, in the current schema, query performance
suffers dramatically when this additional join is added.
    fgroup
    This is the group table. There is one row for each group. Columns:
    gid	      the group ID (integer)
gclass the class of the group (string)
gname the name of the group (string)
    The group table serves multiple purposes. As you might expect, it is
used to cluster features that logically belong together, such as the
multiple exons of the same transcript. It is also used to assign a
name and class to a singleton feature. Finally, the group table is
used to identify the target of a similarity hit. This is consistent
with the way in which the group field is used in the GFF version 2
format.
    The fgroup.gid field joins with the fdata.gid field.
    Examples:
  sql> select * from fgroup where gname='sjj_2L52.1';
+-------+-------------+------------+
| gid | gclass | gname |
+-------+-------------+------------+
| 69736 | PCR_product | sjj_2L52.1 |
+-------+-------------+------------+
1 row in set (0.70 sec)
sql> select fref,fstart,fstop from fdata,fgroup where gclass='PCR_product' and gname = 'sjj_2L52.1' and fdata.gid=fgroup.gid; +---------------+--------+-------+ | fref | fstart | fstop | +---------------+--------+-------+ | CHROMOSOME_II | 1586 | 2355 | +---------------+--------+-------+ 1 row in set (0.03 sec)
    ftype
    This table contains the feature types, one per row. Columns are:
    ftypeid      the feature type ID (integer)
fmethod the feature type method name (string)
fsource the feature type source name (string)
    The ftype.ftypeid field joins with the fdata.ftypeid field. Example:
  sql> select fref,fstart,fstop,fmethod,fsource from fdata,fgroup,ftype 
where gclass='PCR_product'
and gname = 'sjj_2L52.1'
and fdata.gid=fgroup.gid
and fdata.ftypeid=ftype.ftypeid;
+---------------+--------+-------+-------------+-----------+
| fref | fstart | fstop | fmethod | fsource |
+---------------+--------+-------+-------------+-----------+
| CHROMOSOME_II | 1586 | 2355 | PCR_product | GenePairs |
+---------------+--------+-------+-------------+-----------+
1 row in set (0.08 sec)
    fdna
    This table holds the raw DNA of the reference sequences. It has three
columns:
    fref          reference sequence name (string)
foffset offset of this sequence
fdna the DNA sequence (longblob)
    To overcome problems loading large blobs, DNA is automatically
fragmented into multiple segments when loading, and the position of
each segment is stored in foffset. The fragment size is controlled by
the -clump_size argument during initialization.
    fattribute_to_feature
    This table holds "attributes", which are tag/value pairs stuffed into
the GFF line. The first tag/value pair is treated as the group, and
anything else is treated as an attribute (weird, huh?).
 CHR_I assembly_tag Finished     2032 2036 . + . Note "Right: cTel33B"
CHR_I assembly_tag Polymorphism 668 668 . + . Note "A->C in cTel33B"
    The columns of this table are:
    fid                 feature ID (integer)
fattribute_id ID of the attribute (integer)
fattribute_value text of the attribute (text)
    The fdata.fid column joins with fattribute_to_feature.fid.
    fattribute
    This table holds the normalized names of the attributes. Fields are:
  fattribute_id      ID of the attribute (integer)
fattribute_name Name of the attribute (varchar)
In addition to implementing the abstract SQL-generating methods of
Bio::DB::GFF::Adaptor::dbi, this module also implements the data
loading functionality of Bio::DB::GFF.
 Title   : new
Usage : $db = Bio::DB::GFF->new(@args)
Function: create a new adaptor
Returns : a Bio::DB::GFF object
Args : see below
Status : Public
The new constructor is identical to the "dbi" adaptor's new() method,
except that the prefix "dbi:oracle" is added to the database DSN identifier
automatically if it is not there already.
  Argument       Description
-------- -----------
-dsn the DBI data source, e.g. 'dbi:mysql:ens0040' or "ens0040" -user username for authentication -pass the password for authentication
Methods
new
No description
Code
schemaDescriptionCode
setup_loadDescriptionCode
load_gff_lineDescriptionCode
get_table_idDescriptionCode
insertid
No description
Code
insert_sequence
No description
Code
search_notesDescriptionCode
make_meta_set_queryDescriptionCode
make_classes_query
No description
Code
chunk_size
No description
Code
getseqcoords_query
No description
Code
getaliascoords_query
No description
Code
getforcedseqcoords_query
No description
Code
getaliaslike_query
No description
Code
make_features_select_part
No description
Code
make_features_from_part_bkup
No description
Code
default_meta_values
No description
Code
min_bin
No description
Code
max_bin
No description
Code
straight_join_limit
No description
Code
Methods description
schemacode    nextTop
 Title   : schema
Usage : $schema = $db->schema
Function: return the CREATE script for the schema
Returns : a list of CREATE statemetns
Args : none
Status : protected
This method returns a list containing the various CREATE statements
needed to initialize the database tables.
setup_loadcodeprevnextTop
 Title   : setup_load
Usage : $db->setup_load
Function: called before load_gff_line()
Returns : void
Args : none
Status : protected
This method performs schema-specific initialization prior to loading a
set of GFF records. It prepares a set of DBI statement handlers to be
used in loading the data.
load_gff_linecodeprevnextTop
 Title   : load_gff_line
Usage : $db->load_gff_line($fields)
Function: called to load one parsed line of GFF
Returns : true if successfully inserted
Args : hashref containing GFF fields
Status : protected
This method is called once per line of the GFF and passed a series of
parsed data items that are stored into the hashref $fields. The keys are:
 ref          reference sequence
source annotation source
method annotation method
start annotation start
stop annotation stop
score annotation score (may be undef)
strand annotation strand (may be undef)
phase annotation phase (may be undef)
group_class class of annotation's group (may be undef)
group_name ID of annotation's group (may be undef)
target_start start of target of a similarity hit
target_stop stop of target of a similarity hit
attributes array reference of attributes, each of which is a [tag=>value] array ref
get_table_idcodeprevnextTop
 Title   : get_table_id
Usage : $integer = $db->get_table_id($table,@ids)
Function: get the ID of a group or type
Returns : an integer ID or undef
Args : none
Status : private
This internal method is called by load_gff_line to look up the integer
ID of an existing feature type or group. The arguments are the name
of the table, and two string identifiers. For feature types, the
identifiers are the method and source. For groups, the identifiers
are group name and class.
This method requires that a statement handler named lookup_$table,
have been created previously by setup_load(). It is here to overcome
deficiencies in mysql's INSERT syntax.
search_notescodeprevnextTop
 Title   : search_notes
Usage : @search_results = $db->search_notes("full text search string",$limit)
Function: Search the notes for a text string, using mysql full-text search
Returns : array of results
Args : full text search string, and an optional row limit
Status : public
This is a mysql-specific method. Given a search string, it performs a
full-text search of the notes table and returns an array of results.
Each row of the returned array is a arrayref containing the following fields:
  column 1     A Bio::DB::GFF::Featname object, suitable for passing to segment()
column 2 The text of the note
column 3 A relevance score.
column 4 A Bio::DB::GFF::Typename object
make_meta_set_querycodeprevnextTop
 Title   : make_meta_set_query
Usage : $sql = $db->make_meta_set_query
Function: return SQL fragment for setting a meta parameter
Returns : SQL fragment
Args : none
Status : public
By default this does nothing; meta parameters are not stored or
retrieved.
Methods code
newdescriptionprevnextTop
sub new {
  my $class = shift;
  my ($dsn,$other) = rearrange([
				[qw(FEATUREDB DB DSN)],
			       ],@_);
  $dsn = "dbi:Oracle:$dsn" if !ref($dsn) && $dsn !~ /^(dbi|DBI):/;
  my $self = $class->SUPER::new(-dsn=>$dsn,%$other);
  $self;
}
schemadescriptionprevnextTop
sub schema {
  my %schema = (
		fdata =>{
table=> q{
create table fdata (
fid INTEGER NOT NULL,
fref VARCHAR(100) DEFAULT '' NOT NULL,
fstart INTEGER DEFAULT '0' NOT NULL,
fstop INTEGER DEFAULT '0' NOT NULL,
fbin NUMBER DEFAULT '0.000000' NOT NULL,
ftypeid INTEGER DEFAULT '0' NOT NULL,
fscore NUMBER ,
fstrand VARCHAR2(3) CHECK (fstrand IN ('+','-')),
fphase VARCHAR2(3) CHECK (fphase IN ('0','1','2')),
gid INTEGER DEFAULT '0' NOT NULL,
ftarget_start INTEGER ,
ftarget_stop INTEGER ,
CONSTRAINT fdata_pk PRIMARY KEY (fid)
)
}
, # fdata table
index=>{ fdata_fref_idx => q{
CREATE UNIQUE INDEX fdata_fref_idx ON fdata (fref,fbin,fstart,fstop,ftypeid,gid)
}
, fdata_ftypeid_idx => q{
CREATE INDEX fdata_ftypeid_idx ON fdata (ftypeid)
}
, fdata_gid_idx => q{
CREATE INDEX fdata_gid_idx ON fdata (gid)
}
}, # fdata indexes
sequence=> { fdata_fid_sq => q{
CREATE SEQUENCE fdata_fid_sq START WITH 1
}
}, # fdata sequences
trigger=> { fdata_fid_ai => q{
CREATE OR REPLACE TRIGGER fdata_fid_ai
BEFORE INSERT ON fdata
FOR EACH ROW WHEN (new.fid IS NULL OR new.fid = 0)
BEGIN
SELECT fdata_fid_sq.nextval INTO :new.fid FROM dual;
END;
}
}# fdata triggers
}, # fdata
fgroup => { table => q{
CREATE TABLE fgroup (
gid INTEGER NOT NULL,
gclass VARCHAR(100) ,
gname VARCHAR(100) ,
CONSTRAINT fgroup_pk PRIMARY KEY (gid)
)
}
, # fgroup table
index => { fgroup_gclass_idx => q{
CREATE UNIQUE INDEX fgroup_gclass_idx ON fgroup (gclass,gname)
}
}, # fgroup indexes
sequence => { fgroup_gid_sq => q{
CREATE SEQUENCE fgroup_gid_sq START WITH 1
}
}, # fgroup sequences
trigger => { fgroup_gid_ai => q{
CREATE OR REPLACE TRIGGER fgroup_gid_ai
BEFORE INSERT ON fgroup
FOR EACH ROW WHEN (new.gid IS NULL OR new.gid = 0)
BEGIN
SELECT fgroup_gid_sq.nextval INTO :new.gid FROM dual;
END;
}
} # fgroup triggers
}, # fgroup
ftype => { table => q{
CREATE TABLE ftype (
ftypeid INTEGER NOT NULL,
fmethod VARCHAR(100) DEFAULT '' NOT NULL,
fsource VARCHAR(100),
CONSTRAINT ftype_pk PRIMARY KEY (ftypeid)
)
}
, # ftype table
index => { ftype_fmethod_idx => q{
CREATE INDEX ftype_fmethod_idx ON ftype (fmethod)
}
, ftype_fsource_idx => q{
CREATE INDEX ftype_fsource_idx ON ftype (fsource)
}
, ftype_ftype_idx => q{
CREATE UNIQUE INDEX ftype_ftype_idx ON ftype (fmethod,fsource)
}
}, # ftype indexes
sequence => { ftype_ftypeid_sq => q{
CREATE SEQUENCE ftype_ftypeid_sq START WITH 1
}
}, #ftype sequences
trigger => { ftype_ftypeid_ai => q{
CREATE OR REPLACE TRIGGER ftype_ftypeid_ai
BEFORE INSERT ON ftype
FOR EACH ROW WHEN (new.ftypeid IS NULL OR new.ftypeid = 0)
BEGIN
SELECT ftype_ftypeid_sq.nextval INTO :new.ftypeid FROM dual;
END;
}
} #ftype triggers
}, # ftype
fdna => { table => q{
CREATE TABLE fdna (
fref VARCHAR(100) DEFAULT '' NOT NULL,
foffset INTEGER DEFAULT '0' NOT NULL,
fdna LONG /* LONGBLOB */ ,
CONSTRAINT fdna_pk PRIMARY KEY (fref,foffset)
)
}
#fdna table
}, #fdna
fmeta => { table => q{
CREATE TABLE fmeta (
fname VARCHAR(255) DEFAULT '' NOT NULL,
fvalue VARCHAR(255) DEFAULT '' NOT NULL,
CONSTRAINT fmeta_pk PRIMARY KEY (fname)
)
}
# fmeta table
}, # fmeta
fattribute => { table => q{
CREATE TABLE fattribute (
fattribute_id INTEGER NOT NULL,
fattribute_name VARCHAR(255) DEFAULT '' NOT NULL,
CONSTRAINT fattribute_pk PRIMARY KEY (fattribute_id)
)
}
, # fattribute table
sequence=> { fattribute_fattribute_id_sq => q{
CREATE SEQUENCE fattribute_fattribute_id_sq START WITH 1
}
}, # fattribute sequences
trigger => { fattribute_fattribute_id_ai => q{
CREATE OR REPLACE TRIGGER fattribute_fattribute_id_ai
BEFORE INSERT ON fattribute
FOR EACH ROW WHEN (new.fattribute_id IS NULL OR new.fattribute_id = 0)
BEGIN
SELECT fattribute_fattribute_id_sq.nextval INTO :new.fattribute_id FROM dual;
END;
}
} # fattribute triggers
}, # fattribute
fattribute_to_feature => { table => q{
CREATE TABLE fattribute_to_feature (
fid INTEGER DEFAULT '0' NOT NULL,
fattribute_id INTEGER DEFAULT '0' NOT NULL,
fattribute_value VARCHAR2(255) /* TEXT */
)
}
, # fattribute_to_feature table
index => { fattribute_to_feature_fid => q{
CREATE INDEX fattribute_to_feature_fid ON fattribute_to_feature (fid,fattribute_id)
}
} # fattribute_to_feature indexes
}, # fattribute_to_feature
finterval_stats => { table=> q{
CREATE TABLE "finterval_stats" (
"ftypeid" integer DEFAULT '0' NOT NULL,
"fref" VARCHAR(100) DEFAULT '' NOT NULL,
"fbin" integer DEFAULT '0' NOT NULL,
"fcum_count" integer DEFAULT '0' NOT NULL,
CONSTRAINT finterval_stats_pk PRIMARY KEY (ftypeid,fref,fbin)
)
}
# finterval_stats table
},# finterval_stats
); return\% schema;
}
setup_loaddescriptionprevnextTop
sub setup_load {
  my $self      = shift;
  my $schema = $self->schema; 

  my $dbh = $self->features_db;

  if ($self->lock_on_load) {
    my @tables = map { "$_ WRITE"} $self->tables;
    my $tables = join ', ',@tables;
    $dbh->do("LOCK TABLES $tables");
  }

  my $lookup_type = $dbh->prepare_delayed('SELECT ftypeid FROM ftype WHERE fmethod=? AND fsource=?');
  my $insert_type = $dbh->prepare_delayed('INSERT INTO ftype (fmethod,fsource) VALUES (?,?)');
  my $sequence_type = (keys %{$schema->{ftype}{sequence}})[0];
  my $insertid_type = $dbh->prepare_delayed("SELECT $sequence_type.CURRVAL FROM dual");

  my $lookup_group = $dbh->prepare_delayed('SELECT gid FROM fgroup WHERE gname=? AND gclass=?');
  my $insert_group = $dbh->prepare_delayed('INSERT INTO fgroup (gname,gclass) VALUES (?,?)');
  my $sequence_group = (keys %{$schema->{fgroup}{sequence}})[0];
  my $insertid_group = $dbh->prepare_delayed("SELECT $sequence_group.CURRVAL FROM dual");

  my $lookup_attribute = $dbh->prepare_delayed('SELECT fattribute_id FROM fattribute WHERE fattribute_name=?');
  my $insert_attribute = $dbh->prepare_delayed('INSERT INTO fattribute (fattribute_name) VALUES (?)');
  my $sequence_attribute = (keys %{$schema->{fattribute}{sequence}})[0];
  my $insertid_attribute = $dbh->prepare_delayed("SELECT $sequence_attribute.CURRVAL FROM dual");

  my $insert_attribute_value = $dbh->prepare_delayed('INSERT INTO fattribute_to_feature (fid,fattribute_id,fattribute_value) VALUES (?,?,?)');

  my $insert_data  = $dbh->prepare_delayed(<<END);
INSERT INTO fdata (fref,fstart,fstop,fbin,ftypeid,fscore,
		   fstrand,fphase,gid,ftarget_start,ftarget_stop)
       VALUES(?,?,?,?,?,?,?,?,?,?,?)
END
;
  my $delete_existing_data = $dbh->prepare_delayed('DELETE FROM fdata WHERE fref=? AND fstart=? AND fstop=? AND fbin=? AND ftypeid=? AND GID=?');
  my $sequence_data =  (keys %{$schema->{fdata}{sequence}})[0];
  my $insertid_data = $dbh->prepare_delayed("SELECT $sequence_data.CURRVAL FROM dual");



  $self->{load_stuff}{sth}{lookup_ftype}     = $lookup_type;
  $self->{load_stuff}{sth}{insert_ftype}     = $insert_type;
  $self->{load_stuff}{sth}{insertid_ftype}   = $insertid_type;
  $self->{load_stuff}{sth}{lookup_fgroup}    = $lookup_group;
  $self->{load_stuff}{sth}{insert_fgroup}    = $insert_group;
  $self->{load_stuff}{sth}{insertid_fgroup}  = $insertid_group;
  $self->{load_stuff}{sth}{insert_fdata}     = $insert_data;
  $self->{load_stuff}{sth}{insertid_fdata}   = $insertid_data;
  $self->{load_stuff}{sth}{delete_existing_fdata} = $delete_existing_data;
  $self->{load_stuff}{sth}{lookup_fattribute} = $lookup_attribute;
  $self->{load_stuff}{sth}{insert_fattribute} = $insert_attribute;
  $self->{load_stuff}{sth}{insertid_fattribute} = $insertid_attribute;
  $self->{load_stuff}{sth}{insert_fattribute_value} = $insert_attribute_value;
  $self->{load_stuff}{types}  = {};
  $self->{load_stuff}{groups} = {};
  $self->{load_stuff}{counter} = 0;
}
load_gff_linedescriptionprevnextTop
sub load_gff_line {
  my $self = shift;
  my $gff = shift;
  
  if (defined $gff->{phase}){
     chomp($gff->{phase}); 
     undef($gff->{phase}) if $gff->{phase} eq '.';
   }

  if (defined $gff->{strand} && $gff->{strand} eq '.'){undef($gff->{strand})}; 
  if (defined $gff->{score}  && $gff->{score} eq '.'){undef($gff->{score})};

  my $s    = $self->{load_stuff};
  my $dbh  = $self->features_db;
  local $dbh->{PrintError} = 0;

  defined(my $typeid  = $self->get_table_id('ftype', $gff->{method} => $gff->{source})) or return;
  defined(my $groupid = $self->get_table_id('fgroup',$gff->{gname}  => $gff->{gclass})) or return;

  my $bin =  bin($gff->{start},$gff->{stop},$self->min_bin);
  my $result = $s->{sth}{insert_fdata}->execute($gff->{ref},
					       $gff->{start},$gff->{stop},$bin,
					       $typeid,
					       $gff->{score},$gff->{strand},$gff->{phase},
					       $groupid,
					       $gff->{tstart},$gff->{tstop});
  if (defined ($dbh->errstr)){
    print  $dbh->errstr,"\n" ,%$gff,"\n";
    if ($dbh->errstr =~ /ORA-02290: check constraint/){
      print "PHASE=$gff->{phase}"."===","\n";
    }

    if ($dbh->errstr =~ /ORA-00001: unique constraint/){
      $result = $s->{sth}{delete_existing_fdata}->execute($gff->{ref},
    							   $gff->{start},$gff->{stop},$bin,
    							   $typeid,
    							   $groupid);
    
      print "delete row result=$result\n";
      $result = $s->{sth}{insert_fdata}->execute($gff->{ref},
    					       $gff->{start},$gff->{stop},$bin,
    					       $typeid,
    					       $gff->{score},$gff->{strand},$gff->{phase},
    					       $groupid,
    					       $gff->{tstart},$gff->{tstop}); 
    
      print "insert row result=$result\n";
    }
  }
  warn $dbh->errstr,"\n" and print "ref=",$gff->{ref}," start=",$gff->{start}," stop=",$gff->{stop}," bin=",$bin," typeid=",$typeid," groupid=",$groupid,"\n" 
    and return unless $result;
  
  my $fid = $self->insertid($s->{sth},'fdata')
    || $self->get_feature_id($gff->{ref},$gff->{start},$gff->{stop},$typeid,$groupid);


  # insert attributes
# print STDERR map {"$fid attribute:". $_->[0]."=".$_->[1]."\n"} @{$gff->{attributes}};
foreach (@{$gff->{attributes}}) { defined(my $attribute_id = $self->get_table_id('fattribute',$_->[0])) or return; $s->{sth}{insert_fattribute_value}->execute($fid,$attribute_id,$_->[1]); } if ( (++$s->{counter} % 1000) == 0) { print STDERR "$s->{counter} records loaded..."; print STDERR -t STDOUT && !$ENV{EMACS} ? "\r" : "\n"; } $fid;
}
get_table_iddescriptionprevnextTop
sub get_table_id {
  my $self   = shift;
  my $table  = shift;
  my @ids    = @_;

  # irritating warning for null id
my $id_key; { local $^W=0; $id_key = join ':',@ids; } my $s = $self->{load_stuff}; my $sth = $s->{sth}; my $dbh = $self->features_db; unless (defined($s->{$table}{$id_key})) { $sth->{"lookup_$table"}->execute(@ids); my @result = $sth->{"lookup_$table"}->fetchrow_array; if (@result > 0) { $s->{$table}{$id_key} = $result[0]; } else { $sth->{"insert_$table"}->execute(@ids) && ($s->{$table}{$id_key} = $self->insertid($sth,$table)); #&& ($s->{$table}{$id_key} = $self->insertid($sth->{"insertid_$table"}));
#&& ($s->{$table}{$id_key} = $sth->{"insert_$table"}->insertid);
} } my $id = $s->{$table}{$id_key}; unless (defined $id) { warn "No $table id for $id_key ",$dbh->errstr," Record skipped.\n"; return; } $id;
}
insertiddescriptionprevnextTop
sub insertid {
  my $self = shift;
  my $sth = shift ;
  my $table = shift;

  my $insert_id;
  if ($sth->{"insertid_$table"}->execute()){
     $insert_id = ($sth->{"insertid_$table"}->fetchrow_array)[0];
  }
  else{
    warn "No CURRVAL for SEQUENCE of table $table ",$sth->errstr,"\n";
    return;
  }
  return $insert_id;
}


#sub insertid {
# my $self = shift;
# my $insertid_sth = shift ;
# my $insert_id;
# if ($insertid_sth->execute){
# $insert_id = ($insertid_sth->fetchrow_array)[0];
# }
# else{
# warn "No CURRVAL for SEQUENCE ",$insertid_sth->errstr,"\n";
# return;
# }
# return $insert_id;
#
}
insert_sequencedescriptionprevnextTop
sub insert_sequence {
  my $self = shift;
  my($id,$offset,$seq) = @_;
  my $sth = $self->{_insert_sequence}
    ||= $self->dbh->prepare_delayed('insert into fdna values (?,?,?)');
  $sth->execute($id,$offset,$seq) or $self->throw($sth->errstr);
}
search_notesdescriptionprevnextTop
sub search_notes {
  my $self = shift;
  my ($search_string,$limit) = @_;

  $search_string =~ tr/*?//d;

  my @words  = $search_string =~ /(\w+)/g;
  my $regex  = join '|',@words;
  my @searches = map {"fattribute_value LIKE '%${_}%'"} @words;
  my $search   = join(' OR ',@searches);

  my $query = <<END;
SELECT distinct gclass,gname,fattribute_value,fmethod,fsource
FROM fgroup,fattribute_to_feature,fdata,ftype
WHERE fgroup.gid=fdata.gid
AND fdata.fid=fattribute_to_feature.fid
AND fdata.ftypeid=ftype.ftypeid
AND ($search)
END
; my $sth = $self->dbh->do_query($query); my @results; while (my ($class,$name,$note,$method,$source) = $sth->fetchrow_array) { next unless $class && $name; # sorry, ignore NULL objects
my @matches = $note =~ /($regex)/g; my $relevance = 10*@matches; my $featname = Bio::DB::GFF::Featname->new($class=>$name); my $type = Bio::DB::GFF::Typename->new($method,$source); push @results,[$featname,$note,$relevance,$type]; last if $limit && @results >= $limit; } @results;
}
make_meta_set_querydescriptionprevnextTop
sub make_meta_set_query {
   return 'INSERT INTO fmeta VALUES (?,?)';
}
make_classes_querydescriptionprevnextTop
sub make_classes_query {
  my $self = shift;
  return 'SELECT DISTINCT gclass FROM fgroup WHERE NOT gclass IS NULL';
}
chunk_sizedescriptionprevnextTop
sub chunk_size {
  my $self = shift;
  $self->meta('chunk_size') || DEFAULT_CHUNK;
}
getseqcoords_querydescriptionprevnextTop
sub getseqcoords_query {
   my $self = shift;
   return GETSEQCOORDS ;
}
getaliascoords_querydescriptionprevnextTop
sub getaliascoords_query {
  my $self = shift;
  return GETALIASCOORDS ;
}
getforcedseqcoords_querydescriptionprevnextTop
sub getforcedseqcoords_query {
  my $self = shift;
  return GETFORCEDSEQCOORDS ;
}
getaliaslike_querydescriptionprevnextTop
sub getaliaslike_query {
  my $self = shift;
  return GETALIASLIKE ;
}
make_features_select_partdescriptionprevnextTop
sub make_features_select_part {
  my $self = shift;
  my $options = shift || {};
  my $s;
  if (my $b = $options->{bin_width}) {

    $s = <<END;
fref,
1+$b*floor(fstart/$b) as fstart,
$b*(1+floor(fstart/$b)) as fstop,
NVL2(fsource,fmethod||':'||fsource,fmethod),'bin',
count(*) as fscore,
'.','.','bin',
NVL2(fsource , fref||':'||fmethod||':'||fsource , fref||':'||fmethod),
NULL,NULL,NULL,NULL
END
; } else { $s = <<END;
fref,fstart,fstop,fsource,fmethod,fscore,fstrand,fphase,gclass,gname,ftarget_start,ftarget_stop,fdata.fid,fdata.gid
END
; } $s .= ",count(fdata.fid)" if $options->{attributes} && keys %{$options->{attributes}}>1; $s;
}
make_features_from_part_bkupdescriptionprevnextTop
sub make_features_from_part_bkup {
  my $self = shift;
  my $sparse = shift;
  my $options = shift || {};
  #my $index = $sparse ? ' USE INDEX(ftypeid)': '';
my $index = ''; return $options->{attributes} ? "fdata${index},ftype,fgroup,fattribute,fattribute_to_feature\n" : "fdata${index},ftype,fgroup\n"; } ####################################
# moved from mysqlopt.pm
###################################
# meta values
}
default_meta_valuesdescriptionprevnextTop
sub default_meta_values {
  my $self = shift;
  my @values = $self->SUPER::default_meta_values;
  return (
	  @values,
	  max_bin => MAX_BIN,
	  min_bin => MIN_BIN,
	  straight_join_limit => STRAIGHT_JOIN_LIMIT,
	 );
}
min_bindescriptionprevnextTop
sub min_bin {
  my $self = shift;
  return $self->meta('min_bin') || MIN_BIN;
}
max_bindescriptionprevnextTop
sub max_bin {
  my $self = shift;
  return $self->meta('max_bin') || MAX_BIN;
}
straight_join_limitdescriptionprevnextTop
sub straight_join_limit {
  my $self = shift;
  return $self->meta('straight_join_limit') || STRAIGHT_JOIN_LIMIT;
}

1;
}
General documentation
do_initializeTop
 Title   : do_initialize
Usage : $success = $db->do_initialize($drop_all)
Function: initialize the database
Returns : a boolean indicating the success of the operation
Args : a boolean indicating whether to delete existing data
Status : protected
This method will load the schema into the database. If $drop_all is
true, then any existing data in the tables known to the schema will be
deleted.
Internally, this method calls schema() to get the schema data.
drop_allTop
 Title   : drop_all
Usage : $db->drop_all
Function: empty the database
Returns : void
Args : none
Status : protected
This method drops the tables known to this module. Internally it
calls the abstract tables() method.