fixed minor bug in write_align of pairwise protein alignments

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1077 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_perl/Maasha/Align.pm b/code_perl/Maasha/Align.pm
index a01ec4b8cadc86660a9bd69965ca14564a04035f..262ee48255634929b0e7383224952b3800fc88aa 100644 (file)
--- 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 eq "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 .= " ";