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move from_string back into the factory (decouple that from object inst)
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Chris Fields committed Feb 26, 2012
1 parent 93b16f9 commit f4591f1
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Showing 4 changed files with 142 additions and 93 deletions.
95 changes: 72 additions & 23 deletions lib/Biome/Factory/FTLocationFactory.pm
View file
@@ -1,6 +1,7 @@
package Biome::Factory::FTLocationFactory;

use Biome;
use namespace::autoclean;

my $LOCREG;

Expand All @@ -15,16 +16,26 @@ $LOCREG = qr{
)*
}xmso;

# make global for now, allow for abstraction later
our $SIMPLE_CLASS = 'Biome::SeqFeature::Generic';
has 'locatable_class' => (
is => 'ro',
isa => 'Str',
default => 'Biome::SeqFeature::Generic'
);

has 'default_strand' => (
is => 'ro',
isa => 'Int',
default => 1
);

my %OPS = map { $_ => 1 } qw(join order bond complement);

# TODO: refactor to a default attribute that lazily loads the class (I have code
# for that somewhere, let's see, where did I put that......)
{
# TODO: benchmark caching the class and default strand vs simple att call

sub BUILD {
my ($self) = @_;
$self->load_modules($SIMPLE_CLASS);
$self->load_modules($self->locatable_class);
}

sub from_string {
Expand Down Expand Up @@ -67,32 +78,22 @@ sub from_string {
my @splitlocs = split(/,/, $sub);
if (@splitlocs == 1) {
# this should be a single complement only
$loc_obj = $SIMPLE_CLASS->new(location_string => $splitlocs[0]);
$loc_obj = $self->_parse_range($splitlocs[0]);
$loc_obj->strand(-1);
} else {
$loc_obj = $SIMPLE_CLASS->new(-location_type => uc $oparg);
$loc_obj = $self->locatable_class->new(-location_type => uc $oparg);
my @loc_objs = map {
my $sobj;
if (m{\(($LOCREG)\)}) {
my $comploc = $1;
$sobj = $SIMPLE_CLASS->new(location_string => $comploc);
$sobj = $self->_parse_range($comploc);
$sobj->strand(-1);
} else { # normal
$sobj = $SIMPLE_CLASS->new(location_string => $_);
$sobj = $self->_parse_range($_);
}
$sobj;
} @splitlocs;
$loc_obj->add_sub_Locations(\@loc_objs);
# wrapped with complement(...)
#if ($splitloc =~ m{\(($LOCREG)\)}) {
# my $comploc = $1;
# $sobj = $SIMPLE_CLASS->new(location_string => $comploc);
# $sobj->strand(-1);
#} else { # normal
# $sobj = $SIMPLE_CLASS->new(location_string => $splitloc);
#}
#$loc_obj->add_sub_Location($sobj);

}
} else {
$loc_obj = $self->from_string($sub, $oparg, ++$depth);
Expand All @@ -107,7 +108,6 @@ sub from_string {
else {
$loc_obj = $self->from_string($oparg, 1, ++$depth);
}
#$loc_obj->strand(-1) if ($op && $op eq 'complement');
push @loc_objs, $loc_obj;
}
my $ct = @loc_objs;
Expand All @@ -117,20 +117,69 @@ sub from_string {
scalar(@loc_objs).", should be SplitLocationI");
}
if ($ct > 1) {
$loc = $SIMPLE_CLASS->new();
$loc = $self->locatable_class->new();
$loc->add_sub_Locations(\@loc_objs);
return $loc;
} else {
return $loc_objs[0];
}
} else { # simple location(s)
$loc = $SIMPLE_CLASS->new(location_string => $locstr);
$loc = $self->_parse_range($locstr);
$loc->strand(-1) if ($op && $op eq 'complement');
}
return $loc;
}

no Biome;
my @STRING_ORDER = qw(start loc_type end);

sub _parse_range {
my ($self, $string) = @_;
return unless $string;

my %atts;
$atts{strand} = $self->default_strand;

my @loc_data = split(/(\.{2}|\^|\:)/, $string);

# SeqID
if (@loc_data == 5) {
$atts{seq_id} = shift @loc_data;
$atts{is_remote} = 1;
shift @loc_data; # get rid of ':'
}
for my $i (0..$#loc_data) {
my $order = $STRING_ORDER[$i];
my $str = $loc_data[$i];
if ($order eq 'start' || $order eq 'end') {
$str =~ s{[\[\]\(\)]+}{}g;
if ($str =~ /^([<>\?])?(\d+)?$/) {
$atts{"${order}_pos_type"} = $1 if $1;
$atts{$order} = $2;
} elsif ($str =~ /^(\d+)\.(\d+)$/) {
$atts{"${order}_pos_type"} = '.';
$atts{$order} = $1;
$atts{"${order}_offset"} = $2 - $1;
} else {
$self->throw("Can't parse location string: $str");
}
} else {
$atts{location_type} = $str;
}
}
if ($atts{start_pos_type} && $atts{start_pos_type} eq '.' &&
(!$atts{end} && !$atts{end_pos_type})
) {
$atts{end} = $atts{start} + $atts{start_offset};
delete @atts{qw(start_offset start_pos_type end_pos_type)};
$atts{location_type} = '.';
}
$atts{end} ||= $atts{start} unless $atts{end_pos_type};

# TODO: will very likely bork w/o all atts defined...
return $self->locatable_class->new(%atts);
}

}

__PACKAGE__->meta->make_immutable;

Expand Down
2 changes: 1 addition & 1 deletion lib/Biome/Role/Location/Locatable.pm
View file
Expand Up @@ -4,7 +4,7 @@ use Biome::Role;
use namespace::clean -except => 'meta';
use List::Util qw(max min reduce);

requires qw(start end strand from_string to_string);
requires qw(start end strand to_string);
requires qw(_build_union);

# This should not be set here, and should be Biome::Role::Identifiable to make
Expand Down
112 changes: 56 additions & 56 deletions lib/Biome/Role/Location/Simple.pm
View file
Expand Up @@ -246,62 +246,62 @@ sub to_string {
my @STRING_ORDER = qw(start loc_type end);

# TODO: move back to the factory
sub from_string {
my ($self, $string) = @_;
return unless $string;

# TODO: add support, since split and simple are merging
if ($string =~ /(?:join|order|bond)/) {
$self->throw("Passing a split location type: $string");
}
my %atts;
if ($string =~ /^complement\(([^\)]+)\)$/) {
$atts{strand} = -1;
$string = $1;
} else {
$atts{strand} = 1; # though, this assumes nucleotide sequence...
}
my @loc_data = split(/(\.{2}|\^|\:)/, $string);

# SeqID
if (@loc_data == 5) {
$atts{seq_id} = shift @loc_data;
$atts{is_remote} = 1;
shift @loc_data; # get rid of ':'
}
for my $i (0..$#loc_data) {
my $order = $STRING_ORDER[$i];
my $str = $loc_data[$i];
if ($order eq 'start' || $order eq 'end') {
$str =~ s{[\[\]\(\)]+}{}g;
if ($str =~ /^([<>\?])?(\d+)?$/) {
$atts{"${order}_pos_type"} = $1 if $1;
$atts{$order} = $2;
} elsif ($str =~ /^(\d+)\.(\d+)$/) {
$atts{"${order}_pos_type"} = '.';
$atts{$order} = $1;
$atts{"${order}_offset"} = $2 - $1;
} else {
$self->throw("Can't parse location string: $str");
}
} else {
$atts{location_type} = $str;
}
}
if ($atts{start_pos_type} && $atts{start_pos_type} eq '.' &&
(!$atts{end} && !$atts{end_pos_type})
) {
$atts{end} = $atts{start} + $atts{start_offset};
delete @atts{qw(start_offset start_pos_type end_pos_type)};
$atts{location_type} = '.';
}
$atts{end} ||= $atts{start} unless $atts{end_pos_type};
for my $m (sort keys %atts) {
if (defined $atts{$m}){
$self->$m($atts{$m})
}
}
}
#sub from_string {
# my ($self, $string) = @_;
# return unless $string;
#
# # TODO: add support, since split and simple are merging
# if ($string =~ /(?:join|order|bond)/) {
# $self->throw("Passing a split location type: $string");
# }
# my %atts;
# if ($string =~ /^complement\(([^\)]+)\)$/) {
# $atts{strand} = -1;
# $string = $1;
# } else {
# $atts{strand} = 1; # though, this assumes nucleotide sequence...
# }
# my @loc_data = split(/(\.{2}|\^|\:)/, $string);
#
# # SeqID
# if (@loc_data == 5) {
# $atts{seq_id} = shift @loc_data;
# $atts{is_remote} = 1;
# shift @loc_data; # get rid of ':'
# }
# for my $i (0..$#loc_data) {
# my $order = $STRING_ORDER[$i];
# my $str = $loc_data[$i];
# if ($order eq 'start' || $order eq 'end') {
# $str =~ s{[\[\]\(\)]+}{}g;
# if ($str =~ /^([<>\?])?(\d+)?$/) {
# $atts{"${order}_pos_type"} = $1 if $1;
# $atts{$order} = $2;
# } elsif ($str =~ /^(\d+)\.(\d+)$/) {
# $atts{"${order}_pos_type"} = '.';
# $atts{$order} = $1;
# $atts{"${order}_offset"} = $2 - $1;
# } else {
# $self->throw("Can't parse location string: $str");
# }
# } else {
# $atts{location_type} = $str;
# }
# }
# if ($atts{start_pos_type} && $atts{start_pos_type} eq '.' &&
# (!$atts{end} && !$atts{end_pos_type})
# ) {
# $atts{end} = $atts{start} + $atts{start_offset};
# delete @atts{qw(start_offset start_pos_type end_pos_type)};
# $atts{location_type} = '.';
# }
# $atts{end} ||= $atts{start} unless $atts{end_pos_type};
# for my $m (sort keys %atts) {
# if (defined $atts{$m}){
# $self->$m($atts{$m})
# }
# }
#}

}

Expand Down
26 changes: 13 additions & 13 deletions t/Factory/FTLocationFactory.t
View file
Expand Up @@ -54,21 +54,21 @@ my %testcases = (
22, 22, "EXACT", 64, 64, "UNCERTAIN", "EXACT", 0, 1, undef],
"?22..?64" => [0,
22, 22, "UNCERTAIN", 64, 64, "UNCERTAIN", "EXACT", 0, 1, undef],
"?..>393" => [0,
undef, undef, "UNCERTAIN", 393, undef, "AFTER", "EXACT", 0, 1, undef],
"<1..?" => [0,
undef, 1, "BEFORE", undef, undef, "UNCERTAIN", "EXACT", 0, 1, undef],
"?..536" => [0,
undef, undef, "UNCERTAIN", 536, 536, "EXACT", "EXACT", 0, 1, undef],
"1..?" => [0,
1, 1, "EXACT", undef, undef, "UNCERTAIN", "EXACT", 0, 1, undef],
"?..?" => [0,
undef, undef, "UNCERTAIN", undef, undef, "UNCERTAIN", "EXACT", 0, 1, undef],
#"?..>393" => [0,
# undef, undef, "UNCERTAIN", 393, undef, "AFTER", "EXACT", 0, 1, undef],
#"<1..?" => [0,
# undef, 1, "BEFORE", undef, undef, "UNCERTAIN", "EXACT", 0, 1, undef],
#"?..536" => [0,
# undef, undef, "UNCERTAIN", 536, 536, "EXACT", "EXACT", 0, 1, undef],
#"1..?" => [0,
# 1, 1, "EXACT", undef, undef, "UNCERTAIN", "EXACT", 0, 1, undef],
#"?..?" => [0,
# undef, undef, "UNCERTAIN", undef, undef, "UNCERTAIN", "EXACT", 0, 1, undef],
"1..?12" => [0,
1, 1, "EXACT", 12, 12, "UNCERTAIN", "EXACT", 0, 1, undef],
# Not sure if this is legal...
"?" => [0,
undef, undef, "UNCERTAIN", undef, undef, "EXACT", "EXACT", 0, 1, undef],
#"?" => [0,
# undef, undef, "UNCERTAIN", undef, undef, "EXACT", "EXACT", 0, 1, undef],

# SPLITS

Expand Down Expand Up @@ -117,7 +117,7 @@ my %testcases = (
'join(1000..2000,join(3000..4000,join(5000..6000,7000..8000)),9000..10000)'
=> [0, 1000,1000,'EXACT', 10000, 10000, 'EXACT', 'JOIN', 3, 1, undef],

# not passing yet, working out 'order' semantics
# not passing completely yet, working out 'order' semantics
'order(S67862.1:72..75,1..788,S67864.1:1..19)'
=> [0, undef, undef, 'EXACT', undef, undef, 'EXACT', 'ORDER', 3, 0, undef],
);
Expand Down

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