Restored strict and warnings pragmas to modules

There were a number of modules where the strict and warnings pragmas
had been removed. I restored these and fixed the warning message in
HMM/Profile (caused by PDL returning the string 'BAD' instead
of a number) by checking the string to make sure it is numeric, before
testing it.

HMM.pm

@@ -26,6 +26,7 @@ it: L<PDL>.
 package HMM;
 
 use strict;
+use warnings;
 use PDL::LiteF;
 
 our $VERSION = '0.81';

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';

HMM/Profile.pm

@@ -480,12 +480,11 @@ sub draw_logo {
         #get all the values for one column from the matrix
         my @infValues = list $ICM->slice($k);
 
-
         my $l=0;
 
         #fill infContent-Hash with Values
         foreach my $key (@alphabet){
-            unless(($infValues[$l]*$yStep)<1){ # if the character would print lower than 1 pixel, discard it
+            if( $infValues[$l] !~ /^BAD$/ && ($infValues[$l] * $yStep) > 1){ # if the character would print lower than 1 pixel, discard it
                 $infContent{$key} = sprintf('%.16f', $infValues[$l]);
             }
             ++$l; # this is the index of the information-content of the next character in the infValues vector

HMM/Utilities3.pm

@@ -1,8 +1,9 @@
 package HMM::Utilities3;
-use vars qw(@ISA @EXPORTER @EXPORT_OK);
+use strict;
+use warnings;
 use Exporter;
-@ISA = qw(Exporter);
-@EXPORT = ();
+our @ISA = qw(Exporter);
+our @EXPORT = ();
 
 use PDL::LiteF;
 

make_profile.pl

@@ -17,7 +17,7 @@
 my $xsize       = $logo->length() * 34;
 my $greyscale   = 0;
 
-if (0==1) {
+=for comment
 $logo->print_logo_dimensions(
     -xsize          => $xsize,
     -ysize          => $ysize,
@@ -27,7 +27,7 @@
     -greyscale      => $greyscale,
     -height_logodds => $height_logodds
   )  or die "Error writing $outfile!\n";
-}
+=cut
 
 #Now go and make the logos
 print STDOUT "Drawing Logo...\n";