X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=jpred%2Flib%2FFASTA%2FFile.pm;fp=jpred%2Flib%2FFASTA%2FFile.pm;h=ddf639d486e8c4e0305d666f23eb3068a516ec09;hb=eb3001dc41bf6cd46e20fd13fe3efbe9dedf6013;hp=a4356d0f27e487c3fff4fdee95dc84332a473380;hpb=2cf032f4b987ba747c04159965aed78e3820d942;p=jpred.git

diff --git a/jpred/lib/FASTA/File.pm b/jpred/lib/FASTA/File.pm
index a4356d0..ddf639d 100644
--- a/jpred/lib/FASTA/File.pm
+++ b/jpred/lib/FASTA/File.pm
@@ -8,63 +8,64 @@ use base qw(Sequence::File);
 use FASTA;
 
 sub old_read {
-	my ($self, $fh) = @_;
-
-	my ($id, $seq, @seqs);
-	while (<$fh>) {
-		chomp;
-		next if /^\s+$/;
-
-		if (s/^>//) {
-			push @seqs, [ $id, $seq ] if $id and $seq;
-			$seq = undef;
-			$id = $_;
-		}
-		else { $seq .= $_ }
-	}
-	push @seqs, [ $id, $seq ] if $id and $seq;
-
-	for (@seqs) {
-		my $new = FASTA->new(id => ${$_}[0]);
-		$new->seq(split //, ${$_}[1]);
-		$self->add_entries($new);
-	}
-
-	1;
+  my ( $self, $fh ) = @_;
+
+  my ( $id, $seq, @seqs );
+  while (<$fh>) {
+    chomp;
+    next if /^\s+$/;
+
+    if (s/^>//) {
+      push @seqs, [ $id, $seq ] if $id and $seq;
+      $seq = undef;
+      $id  = $_;
+    } else {
+      $seq .= $_;
+    }
+  }
+  push @seqs, [ $id, $seq ] if $id and $seq;
+
+  for (@seqs) {
+    my $new = FASTA->new( id => ${$_}[0] );
+    $new->seq( split //, ${$_}[1] );
+    $self->add_entries($new);
+  }
+
+  1;
 }
 
 sub read {
-	my ($self, $fh) = @_;
-	local $/ = "\n>";
-	while (<$fh>) {
-		s/^>//g;
-		s/>$//g;
+  my ( $self, $fh ) = @_;
+  local $/ = "\n>";
+  while (<$fh>) {
+    s/^>//g;
+    s/>$//g;
 
-		my ($id, @data) = split /\n/, $_;
-		my $entry = FASTA->new(id => $id);
-		$entry->seq( split //, join("", @data) );
+    my ( $id, @data ) = split /\n/, $_;
+    my $entry = FASTA->new( id => $id );
+    $entry->seq( split //, join( "", @data ) );
 
-		$self->add_entries($entry);
-	}
+    $self->add_entries($entry);
+  }
 
-	1;
+  1;
 }
 
 sub write {
-	my ($self, $fh) = @_;
+  my ( $self, $fh ) = @_;
 
-	local $| = 1;
-	
-	for ($self->get_entries) {
-		my $id = $_->id;
-		my @seq = $_->seq;
+  local $| = 1;
 
-		my $seq = join '', @seq;
-		$seq =~ s/\s*//g;
-		$seq =~ s/(.{72})/$1\n/g;
+  for ( $self->get_entries ) {
+    my $id  = $_->id;
+    my @seq = $_->seq;
 
-		print $fh ">$id\n$seq\n";
-	}
+    my $seq = join '', @seq;
+    $seq =~ s/\s*//g;
+    $seq =~ s/(.{72})/$1\n/g;
+
+    print $fh ">$id\n$seq\n";
+  }
 }
 
 1;