Merge branch 'JABAWS_Release_2_5' into develop

[jabaws.git] / binaries / src / jpred / lib / Pairwise.pm

diff --git a/binaries/src/jpred/lib/Pairwise.pm b/binaries/src/jpred/lib/Pairwise.pm
new file mode 100644 (file)
index 0000000..e8abdb2
--- /dev/null
+++ b/binaries/src/jpred/lib/Pairwise.pm
@@ -0,0 +1,63 @@
+package Pairwise;
+
+use strict;
+use warnings;
+use Carp;
+use File::Temp;
+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 "Pairwise::run: path to pairwise not defined";
+    }
+  }
+}
+
+sub run {
+  my ( $self, $fasta ) = @_;
+
+  local $/ = undef;
+  local $? = 0;
+
+  my $f1 = File::Temp->new->filename;
+  my $f2 = File::Temp->new->filename;
+  $fasta->write_file($f1);
+  my $pairwise = $self->path;
+  system("$pairwise $f1 > $f2");
+  check( $pairwise, $? ) or croak "Pairwise::run: $pairwise was naughty\n";
+  open( my $fh, "<", $f2 );
+  my @output = join "\n", split "\n", <$fh>;
+  close $fh;
+  unlink $f1;
+  unlink $f2;
+
+  return @output;
+}
+
+sub old_run {
+  my ( $self, $fasta ) = @_;
+
+  local ( $/, $? ) = ( undef, 0 );
+
+  my $f = File::Temp->new->filename;
+  $fasta->write_file($f);
+
+  my $pid = open my $fh, $self->path . " $f |" or die $!;
+
+  my @output = join "\n", split "\n", <$fh>;
+
+  waitpid $pid, 0;
+  check( $self->path, $? ) or die "Pairwise was naughty\n";
+
+  return @output;
+}
+
+1;