remove some cruft

cjfields · Jul 20, 2012 · 11f6b0f · 11f6b0f
1 parent e69cd0b
commit 11f6b0f
Show file tree

Hide file tree

Showing 2 changed files with 25 additions and 37 deletions.
diff --git a/lib/Biome/Role/Location.pm b/lib/Biome/Role/Location.pm
@@ -1,7 +1,6 @@
 package Biome::Role::Location;
 
 use Biome::Role;
-use Biome::Types qw/SequenceStrand CoordinatePolicy/;
 
 ##at this point making it independent of range
 #with 'Biome::Root::Range';
@@ -50,7 +49,7 @@ See L<Biome::Role::Location::CoordinatePolicy> for more information
 
 =cut
 
-requires 'start' ; 
+requires 'start' ;
 
 
 =head2 end
@@ -93,11 +92,11 @@ requires 'end';
 
 =cut
 
-has 'each_Location' => ( 
-	is => 'ro', 
-	builder => '_build_each_Location', 
-	lazy => 1, 
-); 
+has 'each_Location' => (
+	is => 'ro',
+	builder => '_build_each_Location',
+	lazy => 1,
+);
 
 =head2 to_FTstring
 
@@ -109,10 +108,10 @@ has 'each_Location' => (
 
 =cut
 
-has  'to_FTstring' => ( 
-	is => 'ro', 
-	builder => '_build_FTstring', 
-	lazy => 1, 
+has  'to_FTstring' => (
+	is => 'ro',
+	builder => '_build_FTstring',
+	lazy => 1,
 );
 
 
@@ -127,10 +126,10 @@ has  'to_FTstring' => (
 
 =cut
 
-has 'valid_Location' => ( 
-	is => 'ro', 
-	builder => '_build_valid_Location', 
-	lazy => 1, 
+has 'valid_Location' => (
+	is => 'ro',
+	builder => '_build_valid_Location',
+	lazy => 1,
 );
 
 sub _build_valid_Location {
@@ -193,16 +192,16 @@ requires 'coordinate_policy' ;
            kind of AB18375:450-900 which can be found in GenBank/EMBL
            feature tables.
 
- Example : 
+ Example :
  Returns : TRUE if the location is a remote location, and FALSE otherwise
- Args    : 
+ Args    :
 
 
 =cut
 
-has 'is_remote' => ( 
-	is => 'rw', 
-	isa => 'Int', 
+has 'is_remote' => (
+	is => 'rw',
+	isa => 'Int',
 );
 
 =head2 strand
@@ -272,7 +271,7 @@ requires 'max_start';
   Usage   : my $start_pos_type = $location->start_pos_type();
   Function: Get start position type encoded as text
 
-            Known valid values are 'BEFORE' (<5..100), 'AFTER' (>5..100), 
+            Known valid values are 'BEFORE' (<5..100), 'AFTER' (>5..100),
             'EXACT' (5..100), 'WITHIN' ((5.10)..100), 'BETWEEN', (5^6), with
             their meaning best explained by their GenBank/EMBL location string
             encoding in brackets.
@@ -289,7 +288,7 @@ requires 'start_pos_type';
 
   Title   : min_end
   Usage   : my $minend = $location->min_end();
-  Function: Get minimum ending point of feature. 
+  Function: Get minimum ending point of feature.
 
             Note that an implementation must not call end() in this method
             unless end() is overridden such as not to delegate to the
@@ -327,7 +326,7 @@ requires 'max_end';
   Usage   : my $end_pos_type = $location->end_pos_type();
   Function: Get end position encoded as text.
 
-            Known valid values are 'BEFORE' (5..<100), 'AFTER' (5..>100), 
+            Known valid values are 'BEFORE' (5..<100), 'AFTER' (5..>100),
             'EXACT' (5..100), 'WITHIN' (5..(90.100)), 'BETWEEN', (5^6), with
             their meaning best explained by their GenBank/EMBL location string
             encoding in brackets.
@@ -350,9 +349,9 @@ requires 'end_pos_type';
 
 =cut
 
-has 'seq_id' => ( 
-	is => 'rw', 
-	isa => 'Str', 
+has 'seq_id' => (
+	is => 'rw',
+	isa => 'Str',
 );
 
 

diff --git a/lib/Biome/Role/Location/Range.pm b/lib/Biome/Role/Location/Range.pm
@@ -17,17 +17,6 @@ has end     => (
     default => 0
 );
 
-sub ucsc_start {
-    my ($self, $newstart) = shift;
-    if (defined $newstart) {
-        $self->start($newstart + 1);
-    }
-    my $st = $self->start;
-    $st ? $st - 1 : 0;
-}
-
-sub ucsc_end {shift->end}
-
 sub length {$_[0]->end - $_[0]->start + 1;}
 
 sub to_string {