JPRED-2 Current state of the SVN trank

[jpred.git] / jpred / lib / Pairwise.pm

diff --git a/jpred/lib/Pairwise.pm b/jpred/lib/Pairwise.pm
index d6d32bd..370d226 100644 (file)
--- a/jpred/lib/Pairwise.pm
+++ b/jpred/lib/Pairwise.pm
@@ -11,32 +11,32 @@ use base qw(Root Common);
 use Run qw(check);
 
 sub path {
-       my ($self, $path) = @_;
-       if (defined $path) { $self->{path}= $path }
-       else {
-               if (defined $self->{path}) { return $self->{path} }
-               else { croak "Path not defined" }
-       }
+  my ( $self, $path ) = @_;
+  if ( defined $path ) { $self->{path} = $path }
+  else {
+    if   ( defined $self->{path} ) { return $self->{path} }
+    else                           { croak "Path not defined" }
+  }
 }
 
 sub run {
-       my ($self, $fasta) = @_;
+  my ( $self, $fasta ) = @_;
 
-       croak "Non FASTA::File object passed to Pairwise::run" unless isa $fasta, 'FASTA::File';
+  croak "Non FASTA::File object passed to Pairwise::run" unless isa $fasta, 'FASTA::File';
 
-       local ($/, $?) = (undef, 0);
+  local ( $/, $? ) = ( undef, 0 );
 
-       my $f = File::Temp->new->filename;
-       $fasta->write_file($f);
+  my $f = File::Temp->new->filename;
+  $fasta->write_file($f);
 
-       my $pid = open my $fh, $self->path." $f |" or die $!;
+  my $pid = open my $fh, $self->path . " $f |" or die $!;
 
-       my @output = join "\n", split "\n", <$fh>;
+  my @output = join "\n", split "\n", <$fh>;
 
-       waitpid $pid, 0;
-       check($self->path, $?) or die "Pairwise was naughty\n";
+  waitpid $pid, 0;
+  check( $self->path, $? ) or die "Pairwise was naughty\n";
 
-       return @output;
+  return @output;
 }
 
 1;