X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=code_perl%2FMaasha%2FAlign.pm;h=262ee48255634929b0e7383224952b3800fc88aa;hb=c401b3387e7713ee622638150609f11ee9305928;hp=55b4c2f9f0f6b9a698aa1278317a1599626479e4;hpb=e85ab3ff25098befde19f6f0839292f68739b785;p=biopieces.git

diff --git a/code_perl/Maasha/Align.pm b/code_perl/Maasha/Align.pm
index 55b4c2f..262ee48 100644
--- a/code_perl/Maasha/Align.pm
+++ b/code_perl/Maasha/Align.pm
@@ -272,18 +272,18 @@ sub align_pins
 
     $type ||= Maasha::Seq::seq_guess_type( $entry1->[ SEQ ] );
 
-    $blosum = blosum_read() if $type =~ /protein/;
+    $blosum = blosum_read() if $type =~ "PROTEIN";
 
     for ( $i = 0; $i < length $entry1->[ SEQ ]; $i++ )
     {
-        $char1 = substr $entry1->[ SEQ ], $i, 1;
-        $char2 = substr $entry2->[ SEQ ], $i, 1;
+        $char1 = uc substr $entry1->[ SEQ ], $i, 1;
+        $char2 = uc substr $entry2->[ SEQ ], $i, 1;
 
         if ( $blosum and $char1 eq $char2 ) {
             $pins .= $char1;
-        } elsif ( uc $char1 eq uc $char2 ) {
+        } elsif ( $char1 eq $char2 ) {
             $pins .= "|";
-        } elsif ( $blosum and $blosum->{ $char1 }->{ $char2 } > 0 ) {
+        } elsif ( $blosum and defined $blosum->{ $char1 }->{ $char2 } and $blosum->{ $char1 }->{ $char2 } > 0 ) {
             $pins .= "+";
         } else {
             $pins .= " ";
@@ -480,9 +480,9 @@ sub align_tile
 
         $type = Maasha::Seq::seq_guess_type( $seq1 );
 
-        if ( $type eq "rna" ) {
+        if ( $type eq "RNA" ) {
             $seq2 = Maasha::Seq::rna_revcomp( $seq1 );
-        } elsif ( $type eq "dna" ) {
+        } elsif ( $type eq "DNA" ) {
             $seq2 = Maasha::Seq::dna_revcomp( $seq1 );
         } else {
             Maasha::Common::error( qq(Bad sequence type->$type) );