get basic union function working by splitting up the build between roles

cjfields · Feb 20, 2012 · 2caef8f · 2caef8f
1 parent b3de5dc
commit 2caef8f
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Showing 4 changed files with 40 additions and 25 deletions.
diff --git a/lib/Biome/Role/Location/Locatable.pm b/lib/Biome/Role/Location/Locatable.pm
@@ -5,6 +5,7 @@ use namespace::clean -except => 'meta';
 use List::Util qw(max min reduce);
 
 requires qw(start end strand from_string to_string);
+requires qw(_build_union);
 
 # This should not be set here, and should be Biome::Role::Identifiable to make
 # the primary ID less Seq-specific
@@ -133,9 +134,6 @@ sub union {
 
 	unshift @given, $self if blessed($self) && $self->start && $self->end;
 
-	# cannot give union if a contained location is remote
-	return if grep { $_->is_remote } (@given);
-
     my $union_strand = $given[0]->strand;
 
     for my $r (@given[1..$#given]) {
@@ -154,12 +152,7 @@ sub union {
 
 	return unless $five_prime && $three_prime;
 
-	# TODO: do we assign offsets?
-	return (blessed $self)->new(-start 			=> $five_prime->start,
-								-start_pos_type	=> $five_prime->start_pos_type,
-								-end 			=> $three_prime->end,
-								-end_pos_type	=> $three_prime->end_pos_type,
-								-strand 		=> $union_strand);
+	return $self->_build_union($five_prime, $three_prime, $union_strand);
 }
 
 ### Other methods

diff --git a/lib/Biome/Role/Location/Range.pm b/lib/Biome/Role/Location/Range.pm
@@ -44,6 +44,13 @@ sub from_string {
 
 sub flip_strand {$_[0]->strand($_[0]->strand * -1);}
 
+sub _build_union {
+    my ($self, $five_prime, $three_prime, $strand) = @_;
+    return (blessed $self)->new(-start 			=> $five_prime->start,
+                            -end 			=> $three_prime->end,
+                            -strand 		=> $strand);
+}
+
 1;
 
 __END__
@@ -280,12 +287,12 @@ BioPerl mailing lists. Your participation is much appreciated.
 
 Patches are always welcome.
 
-=head2 Support 
- 
+=head2 Support
+
 Please direct usage questions or support issues to the mailing list:
-  
+
 L<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

diff --git a/lib/Biome/Role/Location/Simple.pm b/lib/Biome/Role/Location/Simple.pm
@@ -326,6 +326,15 @@ sub flip_strand {
     $self->strand($self->strand * -1);
 }
 
+sub _build_union {
+    my ($self, $five_prime, $three_prime, $strand) = @_;
+    return (blessed $self)->new(-start 			=> $five_prime->start,
+                            -start_pos_type	=> $five_prime->start_pos_type,
+                            -end 			=> $three_prime->end,
+                            -end_pos_type	=> $three_prime->end_pos_type,
+                            -strand 		=> $strand);
+}
+
 1;
 
 __END__

diff --git a/lib/Biome/Role/Location/Split.pm b/lib/Biome/Role/Location/Split.pm
@@ -34,12 +34,19 @@ has     'auto_expand'   => (
     default     => 1
 );
 
+sub add_sub_Location {
+    $_[0]->add_sub_Locations([$_[1]])
+}
+
 sub add_sub_Locations {
     my ($self, $newlocs) = @_;
+    return unless ref $newlocs eq 'ARRAY';
 
     my $locs = $self->locations;
 
-    if ($self->auto_expand) {
+    my $remote = grep {$_->is_remote} @$newlocs;
+
+    if ($self->auto_expand && !$remote) {
         my $union_loc =  $self->union($newlocs);
         if (defined($union_loc)) {
             for my $att (qw(start end strand start_pos_type end_pos_type)) {
@@ -81,27 +88,26 @@ Biome::Role::Location::Split - Role describing split locations.
          other necessary roles...
     }
 
-    my $split = Foo->new(-start => 7, -end => 100, -strand => 1);
+    my $split = Foo->new();
 
     my $loc1 = Bar->new(-start => 1, -end => 50, -strand => -1);
     my $loc2 = Bar->new(-start => 75, -end => 150); # no strandedness defined
 
-    $split->add_subLocation($loc1);
-    $split->add_subLocation($loc2);
+    $split->add_sub_LocationS([$loc1, $loc2]);
 
-     Split locations autoexpand to whatever subLocations they contain by
-     default and the strand is defined by the subLocations. This is b/c this
-     implementation is just a simple top-level location that contains other
-     simple Locations, so the borders should match accordingly and the strand
-     be dictated by them. However, as this is a simple location, the strand
-     won't be affected.
+    # Split locations autoexpand to whatever subLocations they contain by
+    # default, the strand being defined by the subLocations. This is b/c this
+    # implementation is just a simple top-level location that contains other
+    # simple Locations, so the borders should match accordingly and the strand
+    # be dictated by them. However, as this is a simple location, the strand
+    # won't be affected.
 
     say $split->start; # 1
     say $split->end;   # 150
     say $split->strand; # 0, strand for sublocations is different
 
-     If you want to explicitly change the top-level coordinate in some way,
-     then do so after one has finished adding subLocations.
+    # If you want to explicitly change the top-level coordinate in some way,
+    # then do so after one has finished adding subLocations.
 
     $split->start(100);
     $split->strand(1);