Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
tree: 2f35affbf3
Fetching contributors…

Cannot retrieve contributors at this time

executable file 2162 lines (1803 sloc) 55.18 kb
# $Id: HIVQueryHelper.pm 231 2008-12-11 14:32:00Z maj $
#
# BioPerl module for Bio::DB::HIV::HIVQueryHelper
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Mark A. Jensen <maj@fortinbras.us>
#
# Copyright Mark A. Jensen
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::DB::HIV::HIVQueryHelper - Routines and packages used by Bio::DB::HIV and
Bio::DB::Query::HIVQuery
=head1 SYNOPSIS
Used in Bio::DB::Query::HIVQuery. No need to use directly.
=head1 DESCRIPTION
C<Bio::DB::HIV::HIVQueryHelper> contains a number of packages for use
by L<Bio::DB::Query::HIVQuery>. Package C<HIVSchema> parses the
C<lanl-schema.xml> file, and allows access to it in the context of the
relational database it represents (see APPENDIX for excruciating
detail). Packages C<QRY>, C<R>, and C<Q> together create the query
string parser that enables NCBI-like queries to be understood by
C<Bio::DB::Query::HIVQuery>. They provide objects and operators to
perform and simplify logical expressions involving C<AND>, C<OR>, and
C<()> and return hash structures that can be handled by
C<Bio::DB::Query::HIVQuery> routines.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Mark A. Jensen
Email maj@fortinbras.us
=head1 CONTRIBUTORS
Mark A. Jensen
=head1 APPENDIX
The rest of the documentation details each of the contained packages.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::DB::HIV::HIVQueryHelper;
use strict;
use Bio::Root::Root;
# globals
BEGIN {
#exceptions
@Bio::QueryStringSyntax::Exception::ISA = qw( Bio::Root::Exception);
}
1;
=head2 HIVSchema - objects/methods to manipulate a version of the LANL HIV DB schema
=head3 HIVSchema SYNOPSIS
$schema = new HIVSchema( 'lanl-schema.xml' );
@tables = $schema->tables;
@validFields = $schema->fields;
@validAliases = $schema->aliases;
@query_aliases_for_coreceptor = $schema->aliases( 'SEQ_SAMple.SSAM_second_receptor' );
$pk_for_SequenceEntry = $schema->primarykey('SequenceEntry'); # returns 'SequenceEntry.SE_id'
$fk_for_SEQ_SAMple_to_SequenceEntry =
$schema->foreignkey('SEQ_SAMple', 'SequenceEntry'); # returns 'SEQ_SAMple.SSAM_SE_id'
$table = $schema->tablepart('SEQ_SAMple.SSAM_badseq'); # returns 'SEQ_SAMple'
$column = $schema->columnpart('SEQ_SAMple.SSAM_badseq'); # returns 'SSAM_badseq'
=head3 HIVSchema DESCRIPTION
HIVSchema methods are used in L<Bio::DB::Query::HIVQuery> for table,
column, primary/foreign key manipulations based on the observed Los
Alamos HIV Sequence Database (LANL DB) naming conventions for their
CGI parameters. The schema is contained in an XML file
(C<lanl-schema.xml>) which is read into an HIVSchema object, in turn a
property of the HIVQuery object. HIVSchema methods are used to build
correct cgi queries in a way that attempts to preserve the context of
the relational database the query parameters represent.
=cut
package # hide from PAUSE
HIVSchema;
# objects/methods to manipulate a version of the LANL HIV DB schema
# stored in XML
use XML::Simple;
use Bio::Root::Root;
use strict;
### constructor
=head3 HIVSchema CONSTRUCTOR
=head4 HIVSchema::new
Title : new
Usage : $schema = new HIVSchema( "lanl-schema.xml ");
Function:
Example :
Returns : an HIVSchema object
Args : XML filename
=cut
sub new {
my $class = shift;
my @args = @_;
my $self = {};
if ($args[0]) {
$self->{schema_ref} = loadHIVSchema($args[0]);
}
bless($self, $class);
return $self;
}
### object methods
=head3 HIVSchema INSTANCE METHODS
=head4 HIVSchema tables
Title : tables
Usage : $schema->tables()
Function: get all table names in schema
Example :
Returns : array of table names
Args : none
=cut
sub tables {
# return array of all tables in schema
local $_;
my $self = shift;
my $sref = $self->{schema_ref};
Bio::Root::Root->throw("schema not initialized") unless $sref;
my @k = grep(/\./, keys %$sref);
my %ret;
foreach (@k) {
s/\..*$//;
$ret{$_}++;
}
@k = sort keys %ret;
return @k;
}
=head4 HIVSchema columns
Title : columns
Usage : $schema->columns( [$tablename] );
Function: return array of columns for specified table, or all columns in
schema, if called w/o args
Example :
Returns :
Args : tablename or fieldname string
=cut
sub columns {
# return array of columns for specified table
# all columns in schema, if called w/o args
local $_;
my $self = shift;
my ($tbl) = @_;
my $sref = $self->{schema_ref};
Bio::Root::Root->throw("schema not initialized") unless $sref;
# trim column name
$tbl =~ s/\..*$//;
# check if table exists
return () unless grep(/^$tbl$/i, $self->tables);
my @k = sort keys %$sref;
@k = grep (/^$tbl\./i, @k);
foreach (@k) {
s/^$tbl\.//;
}
return @k;
}
=head4 HIVSchema fields
Title : fields
Usage : $schema->fields();
Function: return array of all fields in schema, in format "table.column"
Example :
Returns : array of all fields
Args : none
=cut
sub fields {
# return array of all fields (Table.Column format) in schema
my $self = shift;
my $sref = $self->{schema_ref};
Bio::Root::Root->throw("schema not initialized") unless $sref;
my @k = sort keys %{$sref};
return @k;
}
=head4 HIVSchema options
Title : options
Usage : $schema->options(@fieldnames)
Function: get array of options (i.e., valid match data strings) available
to specified field
Example :
Returns : array of match data strings
Args : [array of] fieldname string[s] in "table.column" format
=cut
sub options {
# return array of options available to specified field
my $self = shift;
my ($sfield) = @_;
my $sref = $self->{schema_ref};
Bio::Root::Root->throw("schema not initialized") unless $sref;
return $$sref{$sfield}{option} ? @{$$sref{$sfield}{option}} : ();
}
=head4 HIVSchema aliases
Title : aliases
Usage : $schema->aliases(@fieldnames)
Function: get array of aliases to specified field[s]
Example :
Returns : array of valid query aliases for fields as spec'd in XML file
Args : [an array of] fieldname[s] in "table.column" format
=cut
sub aliases {
# return array of aliases to specified field
my $self = shift;
my ($sfield) = @_;
my $sref = $self->{schema_ref};
my @ret;
Bio::Root::Root->throw("schema not initialized") unless $sref;
if ($sfield) {
return $$sref{$sfield}{alias} ? @{$$sref{$sfield}{alias}} : ();
}
else { # all valid aliases
map {push @ret, @{$$sref{$_}{alias}} if $$sref{$_}{alias}} $self->fields;
return @ret;
}
}
=head4 HIVSchema ankh
Title : ankh (annotation key hash)
Usage : $schema->ankh(@fieldnames)
Function: return a hash translating fields to annotation keys for the
spec'd fields.
(Annotation keys are used for parsing the tab-delimited response
to Bio::DB::Query::HIVQuery::_do_lanl_request.)
Example :
Returns : hash ref
Args : [an array of] fieldname[s] in "table.column" format
=cut
sub ankh {
# return hash translating sfields to annotation keys for specified sfield(s)
my $self = shift;
my %ret = ();
my @sfields = @_;
my $sref = $self->{schema_ref};
Bio::Root::Root->throw("schema not initialized") unless $sref;
foreach (@sfields) {
next unless $$sref{$_}{ankey};
$ret{$_} = {'ankey'=>$$sref{$_}{ankey},'antype'=>$$sref{$_}{antype}};
}
return %ret;
}
=head4 HIVSchema tablepart
Title : tablepart (alias: tbl)
Usage : $schema->tbl(@fieldnames)
Function: return the portion of the fieldname[s] that refer to the
db table
Example : $schema->tbl('SequenceEntry.SE_id'); # returns 'SequenceEntry'
Returns : table name as string
Args : [an array of] fieldname[s] in "table.column" format
=cut
sub tablepart {
# return the 'Table' part of the specified field(s)
my $self = shift;
my @sfields = @_;
Bio::Root::Root->throw("schema not initialized") unless $self->{schema_ref};
my ($squish,@ret, %ret);
if ($sfields[0] eq '-s') {
# squish : remove duplicates from the returned array
$squish=1;
shift @sfields;
}
foreach (@sfields) {
push @ret, /^(.*)\./;
}
if ($squish) {
# arg order is clobbered
@ret{@ret} = undef;
@ret = keys %ret;
}
return (wantarray ? @ret : $ret[0]);
}
sub tbl {
# tablepart alias
shift->tablepart(@_);
}
=head4 HIVSchema columnpart
Title : columnpart (alias: col)
Usage : $schema->col(@fieldnames)
Function: return the portion of the fieldname[s] that refer to the
db column
Example : $schema->col('SequenceEntry.SE_id'); # returns 'SE_id'
Returns : column name as string
Args : [an array of] fieldname[s] in "table.column" format
=cut
sub columnpart {
# return the 'Column' part of the specified field(s)
my $self = shift;
my @sfields = @_;
Bio::Root::Root->throw("schema not initialized") unless $self->{schema_ref};
my @ret;
foreach (@sfields) {
push @ret, /\.(.*)$/;
}
return (wantarray ? @ret : $ret[0]);
}
sub col {
# columnpart alias
shift->columnpart(@_);
}
=head4 HIVSchema primarykey
Title : primarykey [alias: pk]
Usage : $schema->pk(@tablenames);
Function: return the primary key of the specified table[s], as judged by
the syntax of the table's[s'] fieldnames
Example : $schema->pk('SequenceEntry') # returns 'SequenceEntry.SE_id'
Returns : primary key fieldname[s] in "table.column" format, or null if
no pk exists
Args : [an array of] table name[s] (fieldnames are ok, table part used)
=cut
sub primarykey {
# return the primary key (in Table.Column format) of specified table(s)
my $self = shift;
my @tbl = @_;
my @ret;
Bio::Root::Root->throw("schema not initialized") unless $self->{schema_ref};
foreach my $tbl (@tbl) {
# trim column name
$tbl =~ s/\..*$//;
grep(/^$tbl$/i, $self->tables) ?
push(@ret, grep(/\.[0-9a-zA-Z]+_id/, grep(/$tbl/i,$self->fields))) :
push(@ret, "");
}
return (wantarray ? @ret : $ret[0]);
}
sub pk {
# primarykey alias
shift->primarykey(@_);
}
=head4 HIVSchema foreignkey
Title : foreignkey [alias: fk]
Usage : $schema->fk($intable [, $totable])
Function: return foreign key fieldname in table $intable referring to
table $totable, or all foreign keys in $intable if $totable
unspec'd
Example : $schema->fk('AUthor', 'SequenceEntry'); # returns 'AUthor_AU_SE_id'
Returns : foreign key fieldname[s] in "table.column" format
Args : tablename [, optional foreign table name] (fieldnames are ok,
table part used)
=cut
sub foreignkey {
# return foreign key in in-table ($intbl) to to-table ($totbl)
# or all foreign keys in in-table if to-table not specified
# keys returned in Table.Column format
my $self = shift;
my ($intbl, $totbl) = @_;
Bio::Root::Root->throw("schema not initialized") unless $self->{schema_ref};
# trim col names
$intbl =~ s/\..*$//;
$totbl =~ s/\..*$// if $totbl;
# check if in-table exists
return () unless grep( /^$intbl/i, $self->tables);
my @ret = grep( /$intbl\.(?:[0-9a-zA-Z]+_){2,}id/i, $self->fields);
if ($totbl) {
my $tpk = $self->primarykey($totbl);
return (wantarray ? () : "") unless grep( /^$totbl/i, $self->tables) && $tpk;
($tpk) = ($tpk =~ /\.(.*)$/);
@ret = grep( /$tpk$/, @ret);
return (wantarray ? @ret : $ret[0]);
}
else {
# return all foreign keys in in-table
return @ret;
}
}
sub fk {
# foreignkey alias
shift->foreignkey(@_);
}
=head4 HIVSchema foreigntable
Title : foreigntable [alias ftbl]
Usage : $schema->ftbl( @foreign_key_fieldnames );
Function: return tablename of table that foreign keys points to
Example : $schema->ftbl( 'AUthor.AU_SE_id' ); # returns 'SequenceEntry'
Returns : tablename
Args : [an array of] fieldname[s] in "table.column" format
=cut
sub foreigntable {
# return table name that foreign key(s) point(s) to
my $self = shift;
my @fk = @_;
my @ret;
Bio::Root::Root->throw("schema not initialized") unless $self->{schema_ref};
foreach (@fk) {
my ($mnem, $fmnem) = /\.([0-9a-zA-Z]+)_([0-9a-zA-Z]+)_.*$/;
next unless $mnem && $fmnem;
# lookup based on Table.Column format of fields
my $sf = [grep( /^[0-9a-zA-Z]+\.$fmnem\_/, $self->fields )]->[0];
next unless $sf;
($sf) = ($sf =~ /^([0-9a-zA-Z]+)\./);
push @ret, $sf;
}
return (wantarray ? @ret : $ret[0]);
}
sub ftbl {
# foreigntable alias
shift->foreigntable(@_);
}
=head4 HIVSchema find_join
Title : find_join
Usage : $sch->find_join('Table1', 'Table2')
Function: Retrieves a set of foreign and primary keys (in table.column
format) that represents a join path from Table1 to Table2
Example :
Returns : an array of keys (as table.column strings) -or- an empty
array if Table1 == Table2 -or- undef if no path exists
Args : two table names as strings
=cut
sub find_join {
my $self = shift;
my ($tgt, $tbl) = @_;
my ($stack, $revstack, $found, $revcut) = ([],[], 0, 4);
$self->_find_join_guts($tgt, $tbl, $stack, \$found);
if ($found) {
if (@$stack > $revcut) {
# reverse order of tables, see if a shorter path emerges
$found = 0;
$self->_find_join_guts($tgt, $tbl, $revstack, \$found, 1);
return (@$stack <= @$revstack ? @$stack : @$revstack);
}
return @$stack;
}
else {
return undef;
}
}
=head4 HIVSchema _find_join_guts
Title : _find_join_guts
Usage : $sch->_find_join_guts($table1, $table2, $stackref, \$found, $reverse)
(call with $stackref = [], $found=0)
Function: recursive guts of find_join
Example :
Returns : if a path is found, $found==1 and @$stackref contains the keys
in table.column format representing the path; if a path is not
found, $found == 0 and @$stackref contains garbage
Args : $table1, $table2 : table names as strings
$stackref : an arrayref to an empty array
\$found : a scalar ref to the value 0
$rev : if $rev==1, the arrays of table names will be reversed;
this can give a shorter path if cycles exist in the
schema graph
=cut
sub _find_join_guts {
my $self = shift;
my ($tbl, $tgt, $stack, $found, $rev) = @_;
return () if $tbl eq $tgt;
my $k = $self->pk($tbl);
if ($k) {
# all fks pointing to pk
my @fk2pk = map {
$self->fk($_, $k) || ()
} ($rev ? reverse $self->tables : $self->tables);
# skip keys already on stack
if (@$stack) {
(@$stack == 1) && do {
@fk2pk = grep (!/$$stack[0]/, @fk2pk);
};
(@$stack > 1 ) && do {
@fk2pk = map { my $f=$_; grep(/$f/, @$stack) ? () : $f } @fk2pk;
};
}
foreach my $f2p (@fk2pk) { # tables with fks pointing to pk
push @$stack, $f2p;
if ($self->tbl($f2p) eq $tgt) { # this fk's table is the target
# found it
$$found = 1;
return;
}
else {
#keep looking
$self->_find_join_guts($self->tbl($f2p), $tgt, $stack, $found, $rev);
return if $$found;
}
}
}
# all fks in $tbl
my @fks = ($rev ? reverse $self->fk($tbl) : $self->fk($tbl));
#skip keys already on stack
if (@$stack) {
(@$stack == 1) && do {
@fks = grep(!/$$stack[0]/, @fks);
};
(@$stack > 1) && do {
@fks = map { my $f=$_; grep(/$f/, @$stack) ? () : $f } @fks;
};
}
# all fks in table
if (@fks) {
for my $f (@fks) {
push @$stack, $f;
if ($self->ftbl($f) eq $tgt) { #found it
$$found = 1;
return;
}
else {
$self->_find_join_guts($self->ftbl($f), $tgt, $stack, $found, $rev);
$$found ? return : pop @$stack;
}
}
}
else {
pop @$stack;
return;
}
}
=head4 HIVSchema loadSchema
Title : loadHIVSchema [alias: loadSchema]
Usage : $schema->loadSchema( $XMLfilename )
Function: read (LANL DB) schema spec from XML
Example : $schema->loadSchema('lanl-schema.xml');
Returns : hashref to schema data
Keys are fieldnames in "table.column" format.
Each value is a hashref with the following properties:
{name} : HIVWEB 'table.column' format fieldname,
can be used directly in the cgi query
{aliases} : ref to array containing valid aliases/shortcuts for
{name}; can be used in routines creating the HTML query
{options} : ref to array containing valid matchdata for this field
can be used directly in the HTML query
{ankey} : contains the annotation key for this field used with
Bioperl annotation objects
{..attr..}: ..value_of_attr.. for this field (app-specific metadata)
Args :
=cut
sub loadHIVSchema {
my $fn = shift;
Bio::Root::Root->throw("loadHIVSchema: schema file not found") unless -e $fn;
my $q = XML::Simple->new(ContentKey=>'name',NormalizeSpace=>2,ForceArray=>1);
my %ret;
my $ref = $q->XMLin($fn);
my @sf = keys %{$$ref{sfield}};
foreach (@sf) {
my $h = $$ref{sfield}{$_};
$ret{$_} = $h;
foreach my $ptr ($$h{option}, $$h{alias}) {
if ($ptr) {
# kludge for XMLin: appears to convert to arrays, if there
# exists a tag without content, but to convert to hashes
# with content as key, if all tags possess content
if (ref($ptr) eq 'HASH') {
my @k = keys %{$ptr};
if (grep /desc/, keys %{$ptr->{$k[0]}}) {
# slurp the desc's
$$h{desc} = [ map { $$ptr{$_}->{desc} } @k ];
}
# now overwrite with keys (descs in same order...)
$ptr = [@k];
}
elsif (ref($ptr) eq 'ARRAY') {
$ptr = [map { ref eq 'HASH' ? $_->{name} : $_ } @{$ptr}]
}
else {
1; # stub : doh!
}
}
}
for my $ptr ($$h{ankey}) {
# flatten
my $ank = [keys %{$ptr}]->[0];
if (!defined $ank) {
delete $$h{ankey};
}
else {
$h->{antype} = $ptr->{$ank}{antype};
$ptr = $ank;
}
}
}
return \%ret;
}
sub loadSchema {
my $self = shift;
$self->{schema_ref} = loadHIVSchema(shift);
}
# below, dangerous
=head4 HIVSchema _sfieldh
Title : _sfieldh
Usage : $schema->_sfieldh($fieldname)
Function: get hashref to the specified field hash
Example :
Returns : hashref
Args : fieldname in "table.column" format
=cut
sub _sfieldh {
# return reference to the specified field hash
my $self = shift;
my ($sfield) = @_;
return ${$self->{schema_ref}}{$sfield};
}
1;
=head2 Class QRY - a query algebra for HIVQuery
=head3 QRY SYNOPSIS
$Q = new QRY(
new R(
new Q('coreceptor', 'CXCR4'),
new Q('country', 'ZA')
)
);
QRY::Eq(QRY::And($Q, $Q), $Q); # returns 1
QRY::Eq(QRY::Or($Q, $Q), $Q); # returns 1
$Q2 = $Q1->clone;
$Q2 = new QRY(
new R(
new Q( 'coreceptor', 'CCR5' ),
new Q( 'country', 'ZA')
)
);
(QRY::And($Q, $Q2))->isnull; # returns 1
$Q3 = QRY::Or($Q, $Q2);
print $Q3->A; # prints '(CCR5 CXCR4)[coreceptor] (ZA)[country]'
=head3 QRY DESCRIPTION
The QRY package provides a query parser for
L<Bio::DB::Query::HIVQuery>. Currently, the parser supports AND, OR,
and () operations. The structure of the LANL cgi makes it tricky to
perform NOTs, though this could be implemented if the desire were
great.
Two class methods do the work. C<QRY::_parse_q> does a first-pass
parse of the query string. C<QRY::_make_q> interprets the parse tree
as returned by C<QRY::_parse_q> and produces an array of hash
structures that can be used directly by C<Bio::DB::Query::HIVQuery>
query execution methods. Validation of query fields and options is
performed at the C<Bio::DB::Query::HIVQuery> level, not here.
C<QRY> objects are collections of C<R> (or request) objects, which are
in turn collections of C<Q> (or atomic query) objects. C<Q> objects
represent a query on a single field, with match data options C<OR>ed
together, e.g. C<(A B)[subtype]>. C<R> objects collect C<Q> objects
that could be processed in a single HTTP request; i.e., a set of
atomic queries each having different fields C<AND>ed together, such as
(A B)[subtype] AND ('CCR5')[coreceptor] AND (US CA)[country]
The C<QRY> object collects C<R>s that cannot be reduced (through
logical operations) to a single HTTP request, e.g.
((C)[subtype] AND (SI)[phenotype]) OR ( (D)[subtype] AND (NSI)[phenotype] ),
which cannot be got in one go through the current LANL cgi
implementation (as far as I can tell). The parser will simplify
something like
((C)[subtype] AND (SI)[phenotype]) OR ((C)[subtype] AND (NSI)[phenotype])
to the single request
(C)[subtype] AND (NSI SI)[phenotype]
however.
The operators C<&> and C<|> are overloaded to C<QRY::And> and
C<QRY::Or>, to get Perl precedence and grouping for free. C<bool> is
overloaded to get symbolic tests such as C<if ($QRY) {stuff}>. C<==>
is overloaded with C<QRY::Eq> for convenience. No overloading is done
for C<R> or C<Q>.
=cut
# a query algebra for HIVQuery
#
# Each Q object is an 'atomic' query, written as (data)[field]
# (a b ...)[X] equals (a)[X] | (b)[X] | ...
# Each R object represents a single HTTP request to the db
# contains an array of Q (atomic) objects (q1, q2, ...)
# the R object is interpreted as q1 & q2 & ...
# Each QRY object represents a series of HTTP requests to the db
# contains an array of R (request) objects (R1, R2, ...)
# the QRY object is interpreted as R1 | R2 | ...
#
# & and | operations are specified for each type
package # hide from PAUSE
QRY;
use strict;
$QRY::NULL = new QRY();
use overload
"|" => \&Or,
"&" => \&And,
"bool" => \&Bool,
"==" => \&Eq;
# query language emulator
# supports only AND and OR, any groupings
#
# syntax rules:
# query atom: bareword [field] OR (bareword ...) [field]
# only single bareword allowed between []
# annotation fields in {} (only bareword lists allowed between {})
# () can group query atoms joined by operators (AND or OR)
# () containing only barewords MUST be followed by a field descriptor [field]
# empty [] not allowed
# query atoms joined with AND by default
# barewords are associated (ORed within) the next field descriptor in the line
# follow the parse tree, creating new QRY objects as needed in @q, and
# construct a logical expression using & and | symbols.
# These are overloaded for doing ands and ors on QRY objects;
# to get the final QRY object, eval the resulting expression $q_expr.
# QRY object will be translated into (possibly multiple) hashes
# conforming to HIVQuery parameter requirements.
=head4 QRY _make_q
Title : _make_q
Usage : QRY::_make_q($parsetree)
Function: creates hash structures suitable for HIVQuery from parse tree
returned by QRY::_parse_q
Example :
Returns : array of hashrefs of query specs
Args : a hashref
=cut
sub _make_q {
my $ptree = shift;
my ($q_expr, @q, @an, $query, @dbq);
_make_q_guts($ptree, \$q_expr, \@q, \@an);
$query = eval $q_expr;
throw Bio::Root::Root(-class=>'Bio::Root::Exception',
-text=>$@,
-value=>$q_expr) if $@;
return {} if $query->isnull;
foreach my $rq ($query->requests) {
my $h = {'query'=>{}};
foreach ($rq->atoms) {
my @d = split(/\s+/, $_->dta);
foreach my $d (@d) {
$d =~ s/[+]/ /g; ###! _ to [+]
$d =~ s/'//g;
}
$h->{'query'}{$_->fld} = (@d == 1) ? $d[0] : [@d];
}
$h->{'annot'} = [@an] if @an;
push @dbq, $h;
}
return @dbq;
}
=head4 QRY _make_q_guts
Title : _make_q_guts (Internal class method)
Usage : _make_q_guts($ptree, $q_expr, $qarry, $anarry)
Function: traverses the parse tree returned from QRY::_parse_q, checking
syntax and creating HIVQuery-compliant query structures
Example :
Returns :
Args : $parse_tree (hashref), $query_expression (scalar string ref),
$query_array (array ref : stack for returning query structures),
$annotation_array (array ref : stack for returning annotation
fields)
=cut
sub _make_q_guts {
my ($ptree, $q_expr, $qarry, $anarry) = @_;
my (@words, $o);
eval { # catch
foreach (@{$ptree->{cont}}) {
m{^AND$} && do {
$$q_expr .= "&";
next;
};
m{^OR$} && do {
$$q_expr .= "|";
next;
};
m{^HASH} && do {
for my $dl ($_->{delim}) {
($dl =~ m{\(}) && do {
if (grep /^HASH/, @{$_->{cont}}) {
$$q_expr .= "&" unless !$$q_expr || !length($$q_expr) || (substr($$q_expr, -1, 1) =~ /[&|(]/);
$$q_expr .= "(";
_make_q_guts($_,$q_expr,$qarry,$anarry);
$$q_expr .= ")";
}
else {
my @c;
my $c = join(' ',@{$_->{cont}});
$c =~ s/,/ /g;
Bio::Root::Root->throw("query syntax error: unmatched ['\"]") if (@c = ($c =~ /(['"])/g)) % 2;
@c = split(/\s*(['"])\s*/, $c);
do {
$c = shift @c;
if ($c =~ m{['"]}) {
$c = join('', ($c, shift @c, shift @c));
$c =~ s/\s+/+/g; ###! _ to +
push @words, $c;
}
else {
push @words, split(/\s+/,$c);
}
} while @c;
}
last;
};
($dl =~ m{\[}) && do {
Bio::Root::Root->throw("syntax error: empty field descriptor") unless @{$_->{cont}};
Bio::Root::Root->throw("syntax error: more than one field descriptor in square brackets") unless @{$_->{cont}} == 1;
push @{$qarry}, new QRY( new R( new Q( $_->{cont}->[0], @words)));
# add default operation if nec
$$q_expr .= "&" unless !$$q_expr || !length($$q_expr) || (substr($$q_expr, -1, 1) =~ /[&|(]/);
$$q_expr .= "\$q[".$#$qarry."]";
@words = ();
last;
};
($dl =~ m{\{}) && do {
foreach my $an (@{$_->{cont}}) {
($an =~ /^HASH/) && do {
if ($an->{delim} eq '[') {
push @$anarry, @{$an->{cont}};
}
else {
Bio::Root::Root->throw("query syntax error: only field descriptors (with or without square brackets) allowed in annotation spec");
}
next;
};
do { #else
push @$anarry, $an;
next;
};
}
last;
};
do {
1; #else stub
};
}
next;
};
do { # else, bareword
if ($o) {
$words[-1] .= "+$_"; ####! _ to +
}
else {
push @words, $_;
}
m/['"]/ && ($o = !$o);
};
} # @{ptree->{cont}}
Bio::Root::Root->throw("query syntax error: no search fields specified")
unless $$q_expr =~ /q\[[0-9]+\]/;
};
$@ ?
throw Bio::Root::Root(-class=>'Bio::QueryStringSyntax::Exception',
-text=>$@,
-value=>$$q_expr)
: return 1;
}
=head4 QRY _parse_q
Title : _parse_q
Usage : QRY::_parse_q($query_string)
Function: perform first pass parse of a query string with some syntax
checking, return a parse tree suitable for QRY::_make_q
Example : QRY::_parse_q(" to[be] OR (not to)[be] ");
Returns : hashref
Args : query string
=cut
# parse qry string into a branching tree structure
# each branch tagged by the opening delimiter ( key 'delim' )
# content (tokens and subbranch hashes) placed in l2r order in
# @{p->{cont}}
sub _parse_q {
local $_;
my $qstr = shift;
my $illegal = qr/[^a-zA-Z0-9-_<>=,\.\(\[\{\}\]\)\s'"]/;
my $pdlm = qr/[\{\[\(\)\]\}]/;
my %md = ('('=>')', '['=>']','{'=>'}');
my @tok = grep !/^\s*$/, split /($pdlm)/, $qstr;
return {} unless @tok;
my @pstack = ();
my @dstack = ();
my ($ptree, $p);
eval { #catch
Bio::Root::Root->throw("query syntax error: illegal character") if $qstr =~ /$illegal/;
$ptree = $p = {'delim'=>'*'};
foreach (@tok) {
#trim whsp
s/^\s+//;
s/\s+$//;
m{[\(\[\{]} && do {
my $new = {'delim'=>$_};
$p->{cont} = [] unless $p->{cont};
push @{$p->{cont}}, $new;
push @pstack, $p;
push @dstack, $_;
$p = $new;
next;
};
m{[\)\]\}]} && do {
my $d = pop @dstack;
if ($md{$d} eq $_) {
$p = pop @pstack;
Bio::Root::Root->throw("query syntax error: unmatched \"$_\"") unless $p;
}
else {
Bio::Root::Root->throw("query syntax error: saw \"$_\" before matching \"$md{$d}\"");
}
next;
};
do { # else
$p->{cont} = [] unless $p->{cont};
push @{$p->{cont}}, split(/\s+/);
};
}
};
$@ ?
throw Bio::Root::Root(-class=>'Bio::QueryStringSyntax::Exception',
-text=>$@,
-value=>"")
: return $ptree;
}
## QRY constructor
=head3 QRY CONSTRUCTOR
=head4 QRY Constructor
Title : QRY constructor
Usage : $QRY = new QRY()
Function:
Example :
Returns :
Args : array of R objects, optional
=cut
sub new {
my $class = shift;
my @args = @_;
my $self = {};
$self->{requests} = [];
bless($self, $class);
$self->put_requests(@args) if @args;
return $self;
}
## QRY instance methods
=head3 QRY INSTANCE METHODS
=head4 QRY requests
Title : requests
Usage : $QRY->requests
Function: get/set array of requests comprising this QRY object
Example :
Returns :
Args : array of class R objects
=cut
sub requests {
my $self = shift;
$self->put_requests(@_) if @_;
return @{$self->{'requests'}};
}
=head4 QRY put_requests
Title : put_requests
Usage : $QRY->put_request(@R)
Function: add object of class R to $QRY
Example :
Returns :
Args : [an array of] of class R object[s]
=cut
sub put_requests {
my $self = shift;
my @args = @_;
foreach (@args) {
Bio::Root::Root->throw('requires type R (request)') unless ref && $_->isa('R');
push @{$self->{requests}}, $_;
}
return @args;
}
=head4 QRY isnull
Title : isnull
Usage : $QRY->isnull
Function: test if QRY object is null
Example :
Returns : 1 if null, 0 otherwise
Args :
=cut
sub isnull {
my $self = shift;
return ($self->requests) ? 0 : 1;
}
=head4 QRY A
Title : A
Usage : print $QRY->A
Function: get a string representation of QRY object
Example :
Returns : string scalar
Args :
=cut
sub A {
my $self = shift;
return join( "\n", map {$_->A} $self->requests );
}
=head4 QRY len
Title : len
Usage : $QRY->len
Function: get number of class R objects contained by QRY object
Example :
Returns : scalar
Args :
=cut
sub len {
my $self = shift;
return scalar @{$self->{'requests'}};
}
=head4 QRY clone
Title : clone
Usage : $QRY2 = $QRY1->clone;
Function: create and return a clone of the object
Example :
Returns : object of class QRY
Args :
=cut
sub clone {
local $_;
my $self = shift;
my $ret = QRY->new();
foreach ($self->requests) {
$ret->put_requests($_->clone);
}
return $ret;
}
## QRY class methods
=head3 QRY CLASS METHODS
=head4 QRY Or
Title : Or
Usage : $QRY3 = QRY::Or($QRY1, $QRY2)
Function: logical OR for QRY objects
Example :
Returns : a QRY object
Args : two class QRY objects
=cut
sub Or {
local $_;
my ($q, $r, $rev_f) = @_;
Bio::Root::Root->throw('requires type QRY') unless ref($q) && $q->isa('QRY');
Bio::Root::Root->throw('requires type QRY') unless ref($r) && $r->isa('QRY');
if ($q->isnull) {
return $r->clone;
}
elsif ($r->isnull) {
return $q->clone;
}
do {my $qq = $q; $q=$r; $r=$qq} if ($q->len > $r->len);
my @rq_r = $r->requests;
my @rq_q = $q->requests;
my (@cand_rq, @ret_rq);
# search for simplifications
my @now = @rq_q;
my @nxt =();
foreach (@rq_r) {
my $found = 0;
while (my $rq = pop @now) {
my @result = R::Or($rq, $_);
if (@result==1) {
push @cand_rq, $result[0]->clone;
$found = 1;
last;
}
else {
push @nxt, $rq;
}
}
push @cand_rq, $_->clone unless ($found);
# @now becomes unexamined @rq_q's plus failed @rq_q's
@now = (@now, @nxt);
}
push @cand_rq, map {$_->clone} @now; # add all failed @rq_q's
# squeeze out redundant requests
while (my $rq = pop @cand_rq) {
push @ret_rq, $rq unless @cand_rq && grep {R::Eq($rq, $_)} @cand_rq;
}
return new QRY( @ret_rq );
}
=head4 QRY And
Title : And
Usage : $QRY3 = QRY::And($QRY1, $QRY2)
Function: logical AND for QRY objects
Example :
Returns : a QRY object
Args : two class QRY objects
=cut
sub And {
my ($q, $r, $rev_f) = @_;
Bio::Root::Root->throw('requires type QRY') unless ref($q) && $q->isa('QRY');
Bio::Root::Root->throw('requires type QRY') unless ref($r) && $r->isa('QRY');
return ($QRY::NULL) if ($q->isnull || $r->isnull);
my (@cand_rq, @ret_rq);
foreach my $rq_r ($r->requests) {
foreach my $rq_q ($q->requests) {
my ($rq) = R::And($rq_r, $rq_q);
push @cand_rq, $rq unless $rq->isnull;
}
}
return $QRY::NULL unless @cand_rq;
# squeeze out redundant requests
while (my $rq = pop @cand_rq) {
push @ret_rq, $rq unless @cand_rq && grep {R::Eq($rq, $_)} @cand_rq;
}
return new QRY( @ret_rq );
}
=head4 QRY Bool
Title : Bool
Usage : QRY::Bool($QRY1)
Function: allows symbolic testing of QRY object when bool overloaded
Example : do {stuff} if $QRY1 *same as* do {stuff} if !$QRY1->isnull
Returns :
Args : a class QRY object
=cut
sub Bool {
my $q = shift;
Bio::Root::Root->throw('requires type QRY') unless ref($q) && $q->isa('QRY');
return $q->isnull ? 0 : 1;
}
=head4 QRY Eq
Title : Eq
Usage : QRY::Eq($QRY1, $QRY2)
Function: test if R objects in two QRY objects are the same
(irrespective of order)
Example :
Returns : 1 if equal, 0 otherwise
Args : two class QRY objects
=cut
sub Eq {
my ($q, $r, $rev_f) = @_;
Bio::Root::Root->throw('requires type QRY') unless ref($q) && $q->isa('QRY');
Bio::Root::Root->throw('requires type QRY') unless ref($r) && $r->isa('QRY');
return 0 unless $q->len == $r->len;
foreach my $rq_q ($q->requests) {
my $found = 0;
foreach my $rq_r ($r->requests) {
if (R::Eq($rq_q,$rq_r)) {
$found = 1;
last;
}
}
return 0 unless $found;
}
return 1;
}
1;
=head2 Class R - request objects for QRY algebra
=head3 R SYNOPSIS
$R = new R( $q1, $q2 );
$R->put_atoms($q3);
$R->del_atoms('coreceptor', 'phenotype');
return $R->clone;
$R1 = new R( new Q('subtype', 'B') );
$R2 = new R( new Q('subtype', 'B C'),
new Q('country', 'US') );
R::Eq( (R::And($R1, $R2))[0],
new R( new Q('subtype', 'B' ),
new Q('country', 'US') )); # returns 1
QRY::Eq( new QRY(R::Or($R1, $R2)), new QRY($R1, $R2) ); # returns 1
R::In( (R::And($R1, $R2))[0], $R1 ); # returns 1
=head3 R DESCRIPTION
Class R objects contain a list of atomic queries (class Q
objects). Each class R object represents a single HTTP request to the
LANL DB. When converted to a DB query, the class Q objects contained
by an R object are effectively C<AND>ed.
=cut
package # hide from PAUSE
R;
use strict;
$R::NULL = R->new();
## R constructor
=head3 R CONSTRUCTOR
=head4 R constructor
Title : R constructor
Usage : $R = new R()
Function: create a new R (request) object
Example :
Returns : class R (request) object
Args : optional, array of class Q objects
=cut
sub new {
my $class = shift;
my @args = @_;
my $self = {};
$self->{atoms} = {};
bless($self, $class);
$self->put_atoms(@args) if @args;
return $self;
}
## R instance methods
=head3 R INSTANCE METHODS
=head4 R len
Title : len
Usage : $R->len
Function: get number of class Q objects contained in R object
Example :
Returns : scalar
Args :
=cut
sub len {
my $self = shift;
return scalar @{[keys %{$self->{'atoms'}}]};
}
=head4 R atoms
Title : atoms
Usage : $R->atoms( [optional $field])
Function: get array of class Q (atomic query) objects in class R object
Example : $R->atoms(); $R->atoms('coreceptor')
Returns : array of class Q objects (all Qs or those corresponding to $field
if present)
Args : optional, scalar string
=cut
sub atoms {
local $_;
# returns an array of atoms
# no arg: all atoms;
# args: atoms with specified fields
my $self = shift;
my @flds = (@_ ? @_ : keys %{$self->{'atoms'}});
return wantarray ? map { $self->{'atoms'}->{$_} } @flds : $self->{'atoms'}->{$flds[0]};
}
=head4 R fields
Title : fields
Usage : $R->fields
Function: get array of fields of all Q objects contained in $R
Example :
Returns : array of scalars
Args :
=cut
sub fields {
my $self = shift;
return keys %{$self->{'atoms'}};
}
=head4 R put_atoms
Title : put_atoms
Usage : $R->put_atoms( @q )
Function: AND an atomic query (class Q object) to the class R object's list
Example :
Returns : void
Args : an [array of] class Q object[s]
=cut
sub put_atoms {
# AND this atom to the request
local $_;
my $self = shift;
my @args = @_;
foreach (@args) {
Bio::Root::Root->throw('requires type Q (atom)') unless ref && $_->isa('Q');
if ($self->atoms($_->fld)) {
my $a = Q::qand( $self->atoms($_->fld), $_ );
if ($a->isnull) {
delete $self->{'atoms'}->{$_->fld};
}
else {
$self->{atoms}->{$_->fld} = $a->clone;
}
}
else {
$self->{atoms}->{$_->fld} = $_->clone;
}
}
return;
}
=head4 R del_atoms
Title : del_atoms
Usage : $R->del_atoms( @qfields )
Function: removes class Q objects from R object's list according to the
field names given in arguments
Example :
Returns : the class Q objects deleted
Args : scalar array of field names
=cut
sub del_atoms {
# remove atoms by field from request
local $_;
my $self = shift;
my @args = @_;
return () unless @args;
my @ret;
foreach (@args) {
push @ret, delete $self->{'atoms'}->{$_};
}
return @ret;
}
=head4 R isnull
Title : isnull
Usage : $R->isnull
Function: test if class R object is null
Example :
Returns : 1 if null, 0 otherwise
Args :
=cut
sub isnull {
my $self = shift;
return ($self->len) ? 0 : 1;
}
=head4 R A
Title : A
Usage : print $R->A
Function: get a string representation of class R object
Example :
Returns : string scalar
Args :
=cut
sub A {
my $self = shift;
my @a = sort {$a->fld cmp $b->fld} $self->atoms;
return join(" ", map {$_->A} @a);
}
=head4 R clone
Title : clone
Usage : $R2 = $R1->clone;
Function: create and return a clone of the object
Example :
Returns : object of class R
Args :
=cut
sub clone {
local $_;
my $self = shift;
my $ret = R->new();
foreach ($self->atoms) {
$ret->put_atoms($_->clone);
}
return $ret;
}
## R class methods
=head3 R CLASS METHODS
=head4 R In
Title : In
Usage : R::In($R1, $R2)
Function: tests whether the query represented by $R1 would return a subset
of items returned by the query represented by $R2
Example : print "R2 gets those and more" if R::In($R1, $R2);
Returns : 1 if R1 is subset of R2, 0 otherwise
Args : two class R objects
=cut
sub In {
local $_;
my ($s, $t) = @_;
Bio::Root::Root->throw('requires type R (request)') unless ref($s) && $s->isa('R');
Bio::Root::Root->throw('requires type R (request)') unless ref($t) && $t->isa('R');
return 1 if ($s->isnull);
# common fields
my @cf = grep {defined} map {my $f=$_; grep /^$f$/,$s->fields} $t->fields;
return 0 unless @cf==$t->len;
foreach (@cf) {
my @sd = split(/\s+/, $s->atoms($_)->dta);
my @td = split(/\s+/, $t->atoms($_)->dta);
my @cd = grep {defined} map {my $d=$_; grep /^$d$/, @td} @sd;
return 0 unless @cd==@sd;
}
return 1;
}
=head4 R And
Title : And
Usage : @Rresult = R::And($R1, $R2)
Function: logical AND for R objects
Example :
Returns : an array containing class R objects
Args : two class R objects
=cut
sub And {
local $_;
my ($s, $t) = @_;
Bio::Root::Root->throw('requires type R (request)') unless ref($s) && $s->isa('R');
Bio::Root::Root->throw('requires type R (request)') unless ref($t) && $t->isa('R');
return ($R::NULL) if ($s->isnull || $t->isnull);
do { my $ss = $s; $s = $t; $t = $ss } if ( $s->len > $t->len );
# $t has at least as many fields defined than $s ($t is more restrictive)
# common fields
my @cf = grep {defined} map {my $sf = $_; grep /$sf/, $t->fields } $s->fields;
my $ret = R->new();
my $v = $t->clone;
$v->del_atoms(@cf);
my $u = $s->clone;
$u->del_atoms(@cf);
# And the atoms with identical fields
foreach (@cf) {
my ($a) = Q::qand($s->atoms($_), $t->atoms($_));
if ($a->isnull) {
return $R::NULL;
}
else {
$ret->put_atoms($a);
}
}
# put the private atoms
$ret->put_atoms($u->atoms, $v->atoms);
return ($ret);
}
=head4 R Or
Title : Or
Usage : @Rresult = R::Or($R1, $R2)
Function: logical OR for R objects
Example :
Returns : an array containing class R objects
Args : two class R objects
=cut
sub Or {
local $_;
my ($s, $t) = @_;
Bio::Root::Root->throw('requires type R (request)') unless ref($s) && $s->isa('R');
Bio::Root::Root->throw('requires type R (request)') unless ref($t) && $t->isa('R');
if ($s->isnull) {
return $t->clone;
}
elsif ($t->isnull) {
return $s->clone;
}
return $s->clone if (R::In($t, $s));
return $t->clone if (R::In($s, $t));
# try simplifying
do { my $ss = $s; $s = $t; $t = $ss } if ( $s->len > $t->len );
# common fields
my @cf = grep {defined} map {my $sf = $_; grep /$sf/, $t->fields } $s->fields;
#
if ($t->len == @cf) {
# all atoms equal within fields but one? If yes, simplify...
my @df = grep {!Q::qeq($s->atoms($_), $t->atoms($_))} @cf;
if (@df == 1) {
my ($a) = Q::qor($s->atoms($df[0]), $t->atoms($df[0]));
my $ret = $s->clone;
$ret->del_atoms($df[0]);
$ret->put_atoms($a);
return ($ret);
}
}
# neither request contains the other, and the requests cannot be
# simplified; reflect back (clones of) the input...
return ($s->clone, $t->clone);
}
=head4 R Eq
Title : Eq
Usage : R::Eq($R1, $R2)
Function: test if class Q objects in two R objects are the same
(irrespective of order)
Example :
Returns : 1 if equal, 0 otherwise
Args : two class R objects
=cut
sub Eq {
local $_;
my ($s, $t) = @_;
Bio::Root::Root->throw('requires type R (request)') unless ref($s) && $s->isa('R');
Bio::Root::Root->throw('requires type R (request)') unless ref($t) && $t->isa('R');
my @sf = $s->fields;
my @tf = $t->fields;
return 0 unless @sf==@tf;
my @cf = grep {defined} map {my $f=$_; grep /^$f$/,@sf} @tf;
return 0 unless @cf==@tf;
foreach (@cf) {
return 0 unless Q::qeq($s->atoms($_), $t->atoms($_));
}
return 1;
}
1;
=head2 Class Q - atomic query objects for QRY algebra
=head3 Q SYNOPSIS
$q = new Q('coreceptor', 'CXCR4 CCR5');
$u = new Q('coreceptor', 'CXCR4');
$q->fld; # returns 'coreceptor'
$q->dta; # returns 'CXCR4 CCR5'
print $q->A; # prints '(CXCR4 CCR5)[coreceptor]
Q::qeq($q, $u); # returns 0
Q::qeq( Q::qor($q, $q), $q ); # returns 1
Q::qin($u, $q) # returns 1
Q::qeq(Q::qand($u, $q), $u ); # returns 1
=head3 Q DESCRIPTION
Class Q objects represent atomic queries, that can be described by a
single LANL cgi parameter=value pair. Class R objects (requests) are
built from class Qs. The logical operations at the higher levels
(C<QRY, R>) ultimately depend on the lower level operations on Qs:
C<qeq, qin, qand, qor>.
=cut
package # hide from PAUSE
Q;
use strict;
$Q::NULL = Q->new();
## Q constructor
=head3 Q CONSTRUCTOR
=head4 Q constructor
Title : Q constructor
Usage : $q = new Q($field, $data)
Function: create a new Q (atomic query) object
Example :
Returns : class Q object
Args : optional $field, $data strings
=cut
sub new {
local $_;
my ($class,@args) = @_;
my $self={};
foreach (@args) { s/^\s+//; s/\s+$//; }
my ($fld, @dta) = @args;
$self->{fld}=$fld;
$self->{dta}=join(" ", @dta);
bless($self, $class);
return $self;
}
## Q instance methods
=head3 Q INSTANCE METHODS
=head4 Q isnull
Title : isnull
Usage : $q->isnull
Function: test if class Q object is null
Example :
Returns : 1 if null, 0 otherwise
Args :
=cut
sub isnull {
my $self = shift;
Bio::Root::Root->throw("requires type Q (atom)") unless ref($self) && $self->isa('Q');
return 1 unless (($self->fld && length($self->fld)) || ($self->dta && length($self->dta)));
return 0;
}
=head4 Q fld
Title : fld
Usage : $q->fld($field)
Function: get/set fld (field name) property
Example :
Returns : scalar
Args : scalar
=cut
sub fld {
my $self = shift;
Bio::Root::Root->throw("requires type Q (atom)") unless ref($self) && $self->isa('Q');
my $f = shift;
if ($f) {
$f =~ s/^\s+//;
$f =~ s/\s+$//;
return $self->{fld}=$f;
}
return $self->{fld};
}
=head4 Q dta
Title : dta
Usage : $q->dta($data)
Function: get/set dta (whsp-separated data string) property
Example :
Returns : scalar
Args : scalar
=cut
sub dta {
my $self = shift;
Bio::Root::Root->throw("requires type Q (atom)") unless ref($self) && $self->isa('Q');
my $d = join(" ", @_);
if ($d) {
$d =~ s/^\s+//;
$d =~ s/\s+$//;
return $self->{dta} = $d;
}
return $self->{dta};
}
=head4 Q A
Title : A
Usage : print $q->A
Function: get a string representation of class Q object
Example :
Returns : string scalar
Args :
=cut
sub A {
my $self = shift;
Bio::Root::Root->throw("requires type Q (atom)") unless ref($self) && $self->isa('Q');
my @a = split(/\s+/, $self->dta);
return "(".join(' ', sort {$a cmp $b} @a).")[".$self->fld."]";
}
=head4 Q clone
Title : clone
Usage : $q2 = $q1->clone;
Function: create and return a clone of the object
Example :
Returns : object of class Q
Args :
=cut
sub clone {
my $self = shift;
Bio::Root::Root->throw("requires type Q (atom)") unless ref($self) && $self->isa('Q');
my $ret = Q->new($self->fld, $self->dta);
return $ret;
}
### Q class methods
=head3 Q CLASS METHODS
=head4 Q qin
Title : qin
Usage : Q::qin($q1, $q2)
Function: tests whether the query represented by $q1 would return a subset
of items returned by the query represented by $q2
Example : print "q2 gets those and more" if Q::qin($q1, $q2);
Returns : 1 if q1 is subset of q2, 0 otherwise
Args : two class Q objects
=cut
sub qin {
my ($a, $b) = @_;
Bio::Root::Root->throw('requires type Q (atom)') unless (ref $a) && $a->isa('Q') && (ref $b) && $b->isa('Q');
return 0 unless $a->fld eq $b->fld;
return Q::qeq( $b, Q::qor($a, $b) );
}
=head4 Q qeq
Title : qeq
Usage : Q::qeq($q1, $q2)
Function: test if fld and dta properties in two class Q objects are the same
(irrespective of order)
Example :
Returns : 1 if equal, 0 otherwise
Args : two class Q objects
=cut
sub qeq {
local $_;
my ($a, $b) = @_;
Bio::Root::Root->throw('requires type Q (atom)') unless (ref $a) && $a->isa('Q') && (ref $b) && $b->isa('Q');
return 0 unless $a->fld eq $b->fld;
my @ad = unique(split(/\s+/,$a->dta));
my @bd = unique(split(/\s+/,$b->dta));
return 0 unless @ad==@bd;
my @cd = grep {defined} map {my $f = $_; grep /^$f$/, @ad} @bd;
return @cd == @bd;
}
=head4 Q qor
Title : qor
Usage : @qresult = Q::qor($q1, $q2)
Function: logical OR for Q objects
Example :
Returns : an array of class Q objects
Args : two class Q objects
=cut
sub qor {
local $_;
my @a = @_;
foreach (@a) {
Bio::Root::Root->throw("requires type Q (atom)") unless ref && $_->isa('Q');
}
my @ret;
my (%f, @f);
@a = grep {!$_->isnull} @a;
return ($Q::NULL) unless @a > 0;
# list of unique flds
@f = unique(map {$_->fld} @a);
foreach my $f (@f) {
my @fobjs = grep {$_->fld eq $f} @a;
my @d = unique(map {split(/\s/, $_->dta)} @fobjs );
my $r = Q->new($f, @d);
push @ret, $r;
}
return @ret;
}
=head4 Q qand
Title : qand
Usage : @qresult = Q::And($q1, $q2)
Function: logical AND for R objects
Example :
Returns : an array of class Q objects
Args : two class Q objects
=cut
sub qand {
local $_;
my ($a, $b) = @_;
Bio::Root::Root->throw('requires type Q (atom)') unless (ref $a) && $a->isa('Q') && (ref $b) && $b->isa('Q');
my @ret;
if (ref $a eq 'ARRAY') {
foreach my $ea (@$a) {
push @ret, qand( $ea, $b );
}
return qor(@ret); # simplify
}
elsif (ref $b eq 'ARRAY') {
foreach my $eb (@$b) {
push @ret, qand( $a, $eb);
1;
}
return qor(@ret); # simplify
}
else {
return ($Q::NULL) if ($a->isnull || $b->isnull);
if ($a->fld eq $b->fld) {
# find intersection of data
my (%ad, @ad, @bd);
@ad = split(/\s+/, $a->dta);
@ad{@ad} = (1) x @ad;
@bd = split(/\s+/, $b->dta);
foreach (@bd) {
$ad{$_}++;
}
my $r = Q->new($a->fld,
grep {$_}
map {$ad{$_} == 2 ? $_ : undef} keys %ad);
return (length($r->dta) > 0) ? ($r) : ($Q::NULL);
}
else {
return ($a, $b);
}
}
}
=head3 Q INTERNALS
=head4 Q unique
Title : unique
Usage : @ua = unique(@a)
Function: return contents of @a with duplicates removed
Example :
Returns :
Args : an array
=cut
sub unique {
my @a = @_;
my %a;
@a{@a} = undef;
return keys %a;
}
1;
=head2 Additional tools for Bio::AnnotationCollectionI
=head3 Bio::AnnotationCollectionI SYNOPSIS (additional methods)
$seq->annotation->put_value('patient_id', 1401)
$seq->annotation->get_value('patient_ids') # returns 1401
$seq->annotation->put_value('patient_group', 'MassGenH')
$seq->annotation->put_value(['clinical', 'cd4count'], 503);
$seq->annotation->put_value(['clinical', 'virus_load'], 150805);
foreach ( qw( cd4count virus_load ) ) {
$blood_readings{$_} = $seq->annonation->get_value(['clinical', $_]);
}
=head3 Bio::AnnotationCollectionI DESCRIPTION (additional methods)
C<get_value()> and C<put_value> allow easy creation of and access to an
annotation collection tree with nodes of L<Bio::Annotation::SimpleValue>. These
methods obiviate direct accession of the SimpleValue objects.
=cut
package Bio::AnnotationCollectionI;
use strict;
use Bio::Annotation::SimpleValue;
=head2 get_value
Title : get_value
Usage : $ac->get_value($tagname) -or-
$ac->get_value( $tag_level1, $tag_level2,... )
Function: access the annotation value assocated with the given tags
Example :
Returns : a scalar
Args : an array of tagnames that descend into the annotation tree
=cut
sub get_value {
local $_;
my $self = shift;
my @args = @_;
my @h;
return "" unless @_;
while ($_ = shift @args) {
@h = $self->get_Annotations($_);
if (ref($h[0]->{value})) {
$self = $h[0]->{value}; # must be another Bio::AnnotationCollectionI
}
else {
last;
}
}
return $h[0] && $h[0]->{value} ; # now the last value.
}
=head2 put_value
Title : put_value
Usage : $ac->put_value($tagname, $value) -or-
$ac->put_value([$tag_level1, $tag_level2, ...], $value) -or-
$ac->put_value( [$tag_level1, $tag_level2, ...] )
Function: create a node in an annotation tree, and assign a scalar value to it
if a value is specified
Example :
Returns : scalar or a Bio::AnnotationCollection object
Args : $tagname, $value scalars (can be specified as -KEYS=>$tagname,
-VALUE=>$value) -or-
\@tagnames, $value (or as -KEYS=>\@tagnames, -VALUE=>$value )
Note : If intervening nodes do not exist, put_value creates them, replacing
existing nodes. So if $ac->put_value('x', 10) was done, then later,
$ac->put_value(['x', 'y'], 20), the original value of 'x' is trashed,
and $ac->get_value('x') will now return the annotation collection
with tagname 'y'.
=cut
sub put_value {
local $_;
my $self = shift;
my @args = @_;
my ($keys, $value) = $self->_rearrange([qw( KEYS VALUE )], @args);
my (@keys, $lastkey);
# $value ||= new Bio::Annotation::Collection;
@keys = (ref($keys) eq 'ARRAY') ? @$keys : ($keys);
$lastkey = pop @keys;
foreach (@keys) {
my $a = $self->get_value($_);
if (ref($a) && $a->isa('Bio::Annotation::Collection')) {
$self = $a;
}
else {
# replace an old value
$self->remove_Annotations($_) if $a;
my $ac = Bio::Annotation::Collection->new();
$self->add_Annotation(Bio::Annotation::SimpleValue->new(
-tagname => $_,
-value => $ac
)
);
$self = $ac;
}
}
if ($self->get_value($lastkey)) {
# replace existing value
($self->get_Annotations($lastkey))[0]->{value} = $value;
}
else {
$self->add_Annotation(Bio::Annotation::SimpleValue->new(
-tagname=>$lastkey,
-value=>$value
));
}
return $value;
}
=head2 get_keys
Title : get_keys
Usage : $ac->get_keys($tagname_level_1, $tagname_level_2,...)
Function: Get an array of tagnames underneath the named tag nodes
Example : # prints the values of the members of Category 1...
print map { $ac->get_value($_) } $ac->get_keys('Category 1') ;
Returns : array of tagnames or empty list if the arguments represent a leaf
Args : [array of] tagname[s]
=cut
sub get_keys {
my $self = shift;
my @keys = @_;
foreach (@keys) {
my $a = $self->get_value($_);
if (ref($a) && $a->isa('Bio::Annotation::Collection')) {
$self = $a;
}
else {
return ();
}
}
return $self->get_all_annotation_keys();
}
1;
Jump to Line
Something went wrong with that request. Please try again.