Merge pull request DaGaMs#2 from neomorphic/master

Minor updates to the code. Mostly cleanup.

HMM.pm

@@ -5,9 +5,9 @@ HMM - representation of hidden markov moddels for computational biology
 =head1 SYNOPSIS
 
   use HMM;
-    
+
   my $hmm = HMM->new(-hmmerfile=>$file) || die("Couldn't open $file!\n"); #try to create a new hmm-object from the file
-    
+
   print $hmm->name(); #output the name of the model
   print $hmm->transitions(); #show the matrix of transition probabilities
 
@@ -26,6 +26,7 @@ it: L<PDL>.
 package HMM;
 
 use strict;
+use warnings;
 use PDL::LiteF;
 
 our $VERSION = '0.81';
@@ -100,7 +101,7 @@ sub name : lvalue {
     $self->{'modelName'};
 }
 
-    
+
 =head2 alphabet()
 
  Usage      : my @alphabet = $pHMM->alphabet()
@@ -113,7 +114,7 @@ sub alphabet : lvalue {
     $self->{'alphabet'};
 }
 
-    
+
 =head2 length()
 
  Usage      : my $length = $pHMM->length()

HMM/Alignment.pm

@@ -37,6 +37,7 @@ a graphical representation of the alignment. It is an extension of the HMM Logo
 package HMM::Alignment;
 
 use strict;
+use warnings;
 use vars '@ISA'; #inheritance
 use PDL::LiteF;
 use Imager ':handy';
@@ -588,9 +589,21 @@ sub draw_logo {
 #                     y2  => $middleMargin+5,
 #                     aa  => 0);
     }
-    
+
     # Finally, draw the logo
-    return $i->write(file=>$args{'-file'});
+    if ($args{'-file'}) {
+        $i->write(type=>'png', file=>$args{'-file'});
+    }
+    elsif ($args{'-fh'}) {
+        $i->write(type=>'png', fh=>$args{'-file'});
+    }
+    elsif ($args{'-data'}) {
+        $i->write(type=>'png', data=>$args{'-data'});
+    }
+    else {
+        warn __PACKAGE__." WARN No data output handle passed!\n";
+        return;
+    }
 }
 
 =head2 toPRC