From 64c246ca3a549d00f67d2fdbf6e1f8610e1709f1 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 21 Oct 2009 06:04:03 +0000
Subject: [PATCH] fixed dna/DNA bug in Align.pm

git-svn-id: http://biopieces.googlecode.com/svn/trunk@699 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/bowtie_seq         |  1 +
 code_perl/Maasha/Align.pm |  4 ++--
 code_perl/Maasha/XHTML.pm | 17 ++++++++++++++++-
 3 files changed, 19 insertions(+), 3 deletions(-)

diff --git a/bp_bin/bowtie_seq b/bp_bin/bowtie_seq
index dc8b09e..6c1659b 100755
--- a/bp_bin/bowtie_seq
+++ b/bp_bin/bowtie_seq
@@ -160,6 +160,7 @@ sub bowtie2biopiece
     $record->{ 'SCORES' }     = $entry->[ 5 ];
     $record->{ 'SCORE' }      = $entry->[ 6 ] + 1;
     $record->{ 'DESCRIPTOR' } = $entry->[ 7 ];
+    $record->{ 'S_LEN' }      = length $entry->[ 4 ];
     $record->{ 'SEQ_LEN' }    = length $entry->[ 4 ];
     $record->{ 'S_END' }      = $record->{ 'S_BEG' } + $record->{ 'SEQ_LEN' } - 1;
     $record->{ 'SCORES' }     =~ s/(.)/ord( $1 ) - 33 . ";"/ge; # http://maq.sourceforge.net/fastq.shtml
diff --git a/code_perl/Maasha/Align.pm b/code_perl/Maasha/Align.pm
index 55b4c2f..622846d 100644
--- a/code_perl/Maasha/Align.pm
+++ b/code_perl/Maasha/Align.pm
@@ -480,9 +480,9 @@ sub align_tile
 
         $type = Maasha::Seq::seq_guess_type( $seq1 );
 
-        if ( $type eq "rna" ) {
+        if ( $type =~ /rna/i ) {
             $seq2 = Maasha::Seq::rna_revcomp( $seq1 );
-        } elsif ( $type eq "dna" ) {
+        } elsif ( $type =~ /dna/i ) {
             $seq2 = Maasha::Seq::dna_revcomp( $seq1 );
         } else {
             Maasha::Common::error( qq(Bad sequence type->$type) );
diff --git a/code_perl/Maasha/XHTML.pm b/code_perl/Maasha/XHTML.pm
index 4aeba31..44a72ba 100755
--- a/code_perl/Maasha/XHTML.pm
+++ b/code_perl/Maasha/XHTML.pm
@@ -622,7 +622,7 @@ sub mailto
 }
 
 
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> IMG <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> IMG & OBJECT <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 sub img
@@ -640,6 +640,21 @@ sub img
 }
 
 
+sub object
+{
+    # Martin A. Hansen, October 2009.
+
+    # HTML <object> element
+
+    my ( %args,
+       ) = @_;
+
+    # Returns string
+
+    return &tag_single( "object", \%args );
+}
+
+
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DIV & SPAN <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-- 
2.39.5