JPRED-2 Current state of the SVN trank

[jpred.git] / jpred / lib / FASTA / File.pm

diff --git a/jpred/lib/FASTA/File.pm b/jpred/lib/FASTA/File.pm
index a4356d0..ddf639d 100644 (file)
--- 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;