JPRED-2 copy the portable branch into Git

[jpred.git] / jpred / lib / PSIBLAST / Run.pm

diff --git a/jpred/lib/PSIBLAST/Run.pm b/jpred/lib/PSIBLAST/Run.pm
index bf74c71..56cb471 100644 (file)
--- a/jpred/lib/PSIBLAST/Run.pm
+++ b/jpred/lib/PSIBLAST/Run.pm
@@ -16,11 +16,8 @@ sub new {
   # -b max number of alignments reported (default 250)
   # -v max number of sequences described (default 500)
   # -j max number of itterations (default 1)
-  $self->args("-e0.05 -h0.01 -m6 -b10000 -v10000 -j3");
-
-  #$self->args("-a2 -e0.05 -h0.01 -m6 -b20000 -v20000 -j15");
-  #    $self->BLASTMAT("/software/jpred_bin/blast");
-  #    $self->BLASTDB("/software/jpred_uniprot_all_filt");
+  # $self->args("-e0.05 -h0.01 -m6 -b10000 -v10000 -j3");
+  # $self->args("-a2 -e0.05 -h0.01 -m6 -b20000 -v20000 -j15");
 
   # Automatically run any arguments passed to the constructor
   for ( keys %args ) {
@@ -37,7 +34,7 @@ sub database { defined $_[1] ? $_[0]->{data}   = "-d $_[1]" : $_[0]->{data} }
 sub input    { defined $_[1] ? $_[0]->{input}  = "-i $_[1]" : $_[0]->{input} }
 sub output   { defined $_[1] ? $_[0]->{output} = "-o $_[1]" : $_[0]->{output} }
 sub matrix   { defined $_[1] ? $_[0]->{matrix} = "-Q $_[1]" : $_[0]->{matrix} }
-sub debug    { defined $_[1] ? $_[0]->{debug}  = $_[1]      : $_[0]->{debug} }    # CC corrected - now works as expected. Before, debug was always on.
+sub debug    { defined $_[1] ? $_[0]->{debug}  = $_[1]      : $_[0]->{debug} }
 sub BLASTMAT { $ENV{BLASTMAT} = $_[1] }
 sub BLASTDB  { $ENV{BLASTDB}  = $_[1] }
 
@@ -59,11 +56,7 @@ sub run {
   my $cmd = join " ", @cmd;
 
   # Execute PSIBLAST and check it ran okay
-  if ( $self->debug ) {
-
-    #for (keys %ENV) { warn "$_=$ENV{$_}\n" }
-    warn "$cmd\n";
-  }
+  warn "$cmd\n" if ( $self->debug );
 
   system($cmd) == 0 or check( "blastpgp", $? ) and die "blastpgp was naughty";