X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=binaries%2Fsrc%2Fmafft%2Fcore%2Fmafft-homologs.tmpl;h=c06743c53ee4ba8813bf7cbc11bf77b182913596;hb=HEAD;hp=63a7116e1cb2237ca4a03fac48b822baa4d9ec22;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git

diff --git a/binaries/src/mafft/core/mafft-homologs.tmpl b/binaries/src/mafft/core/mafft-homologs.tmpl
index 63a7116..c06743c 100644
--- a/binaries/src/mafft/core/mafft-homologs.tmpl
+++ b/binaries/src/mafft/core/mafft-homologs.tmpl
@@ -300,7 +300,7 @@ for i in 0..(nin-1)
 			break if $_ =~ /<Hsp_hseq>(.*)<\/Hsp_hseq>/
 		end
 #		break if $1 == nil
-		target = $1.sub( /-/, "" )
+		target = $1.sub( /-/, "" ).sub( /U/, "X" )
 #		p target
 #		STDERR.puts "adding 1 seq"
 		ids.push( id )
@@ -340,11 +340,11 @@ outnam2 = []
 len = outseq.length
 for i in 0..(len-1)
 #	p outnam[i]
-	if fullout == 0 && outnam[i] =~ /^_addedbymaffte_/ then
+	if fullout == 0 && outnam[i] =~ /_addedbymaffte_/ then
 		next
 	end
 	outseq2.push( outseq[i] )
-	outnam2.push( outnam[i].sub( /^_addedbymaffte_/, "_ho_" ) )
+	outnam2.push( outnam[i].sub( /_addedbymaffte_/, "_ho_" ) )
 end
 
 nout = outseq2.length