JPRED-2 copy the portable branch into Git

[jpred.git] / jpred / lib / Index / EMBOSS.pm

diff --git a/jpred/lib/Index/EMBOSS.pm b/jpred/lib/Index/EMBOSS.pm
index 4d2d06c..484c4f1 100644 (file)
--- a/jpred/lib/Index/EMBOSS.pm
+++ b/jpred/lib/Index/EMBOSS.pm
@@ -14,38 +14,40 @@ use FASTA::File;
 sub read_index { 1 }
 
 sub get_sequence {
-       my ($self, $key) = @_;
-       croak "No value for get_sequence" unless $key;
-
-       my @cmd = split / /, "seqret -filter $key";
-
-       my $pid = open3(undef, \*RD, \*ERR, @cmd);
-
-       my $seqs = FASTA::File->new(read => \*RD);
-       my @err = <ERR>;
-
-       pop @err;
-       pop @err;
-
-       close RD; close ERR;
-       waitpid $pid, 0;
-       
-       # Everything was okay...
-       if (WIFEXITED($?) and not WEXITSTATUS($?)) { return $seqs }
-       # Non-zero exit
-       elsif (WIFEXITED($?) and WEXITSTATUS($?)) {
-               carp "seqret had a problem: $?; $!";
-               carp @err;
-       }
-       # Was it stopped by an external program
-       elsif (WIFSIGNALED($?)) {
-               carp "seqret halted by external signal ".WTERMSIG($?)
-       }
-       else {
-               carp "seqret suffered from a random pantwetting event"
-       }
-
-       return undef;
+  my ( $self, $key ) = @_;
+  croak "No value for get_sequence" unless $key;
+
+  my @cmd = split / /, "seqret -filter $key";
+
+  my $pid = open3( undef, \*RD, \*ERR, @cmd );
+
+  my $seqs = FASTA::File->new( read => \*RD );
+  my @err = <ERR>;
+
+  pop @err;
+  pop @err;
+
+  close RD;
+  close ERR;
+  waitpid $pid, 0;
+
+  # Everything was okay...
+  if ( WIFEXITED($?) and not WEXITSTATUS($?) ) { return $seqs }
+
+  # Non-zero exit
+  elsif ( WIFEXITED($?) and WEXITSTATUS($?) ) {
+    carp "seqret had a problem: $?; $!";
+    carp @err;
+  }
+
+  # Was it stopped by an external program
+  elsif ( WIFSIGNALED($?) ) {
+    carp "seqret halted by external signal " . WTERMSIG($?);
+  } else {
+    carp "seqret suffered from a random pantwetting event";
+  }
+
+  return undef;
 }
 
 1;