X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=jpred%2Flib%2FSequence.pm;fp=jpred%2Flib%2FSequence.pm;h=ea342d36ae9b0e2c5d5fc4e5813773c7a655e92c;hb=eb3001dc41bf6cd46e20fd13fe3efbe9dedf6013;hp=6a53af14b14f6e8a6deea01ed59d1509903e1254;hpb=2cf032f4b987ba747c04159965aed78e3820d942;p=jpred.git

diff --git a/jpred/lib/Sequence.pm b/jpred/lib/Sequence.pm
index 6a53af1..ea342d3 100644
--- a/jpred/lib/Sequence.pm
+++ b/jpred/lib/Sequence.pm
@@ -6,33 +6,34 @@ use Carp;
 use base qw(Root);
 
 sub id {
-	my ($self, $id) = @_;
-	defined $id ?
-		$self->{__PACKAGE__."id"} = $id :
-		return $self->{__PACKAGE__."id"};
+  my ( $self, $id ) = @_;
+  defined $id
+    ? $self->{ __PACKAGE__ . "id" } = $id
+    : return $self->{ __PACKAGE__ . "id" };
 }
 
 sub seq {
-	my ($self, @entries) = @_;
-	if (@entries) { $self->{__PACKAGE__."seq"} = [ @entries ] }
-	else {
-		if (wantarray) {
-			return defined $self->{__PACKAGE__."seq"} ?
-				@{ $self->{__PACKAGE__."seq"} } :
-				();
-		}
-		else { return $self->{__PACKAGE__."seq"} }
-	}
+  my ( $self, @entries ) = @_;
+  if (@entries) { $self->{ __PACKAGE__ . "seq" } = [@entries] }
+  else {
+    if (wantarray) {
+      return defined $self->{ __PACKAGE__ . "seq" }
+        ? @{ $self->{ __PACKAGE__ . "seq" } }
+        : ();
+    } else {
+      return $self->{ __PACKAGE__ . "seq" };
+    }
+  }
 }
 
 sub length {
-	my ($self) = @_;
-	return scalar @{ [ $self->seq ] };
+  my ($self) = @_;
+  return scalar @{ [ $self->seq ] };
 }
 
 #sub numeric {
 #	my ($self, $set) = @_;
-#	return $set ? 
+#	return $set ?
 #		$self->{__PACKAGE__."numeric"} = $set :
 #		$self->{__PACKAGE__."numeric"};
 #}
@@ -58,38 +59,39 @@ sub length {
 #}
 
 sub sub_seq {
-	my ($self, @segments) = @_;
-
-	my $package = ref $self;
-
-	return $self->seq unless @segments;
-	confess "Passed an uneven number of segments" unless @segments % 2 == 0;
-
-	{
-		my %segments = @segments;
-		# Find out if there are overlapping segments
-		for my $pri (sort keys %segments) {
-			for my $test (sort keys %segments) {
-				next if $pri == $test;
-				croak "Overlapping segments" if $test < $segments{$pri};
-			}
-		}
-	}
-	
-	my @sections;
-	my ($i, @seq) = (0, $self->seq);
-	do {
-		my ($start, $end) = @segments[$i, $i + 1];
-
-		# Create a new sequence object in the correct package, and put the
-		# segment into it
-		my $new_seq = $package->new(id => $self->id);
-		$new_seq->seq( @seq[ $start .. $end ] );
-		push @sections, $new_seq;
-		$i += 2;
-	} while ($i < @segments);
-
-	return @sections;
+  my ( $self, @segments ) = @_;
+
+  my $package = ref $self;
+
+  return $self->seq unless @segments;
+  confess "Passed an uneven number of segments" unless @segments % 2 == 0;
+
+  {
+    my %segments = @segments;
+
+    # Find out if there are overlapping segments
+    for my $pri ( sort keys %segments ) {
+      for my $test ( sort keys %segments ) {
+        next if $pri == $test;
+        croak "Overlapping segments" if $test < $segments{$pri};
+      }
+    }
+  }
+
+  my @sections;
+  my ( $i, @seq ) = ( 0, $self->seq );
+  do {
+    my ( $start, $end ) = @segments[ $i, $i + 1 ];
+
+    # Create a new sequence object in the correct package, and put the
+    # segment into it
+    my $new_seq = $package->new( id => $self->id );
+    $new_seq->seq( @seq[ $start .. $end ] );
+    push @sections, $new_seq;
+    $i += 2;
+  } while ( $i < @segments );
+
+  return @sections;
 }
 
 1;