%{
#include "dyna.h"

%}

matrix ProteinSW
query  type="PROTEIN"  name="query"  
target type="PROTEIN"  name="target"
resource type="COMPMAT" name="comp"
resource type="int"    name="gap"
resource type="int"    name="ext"
state MATCH offi="1" offj="1" 
	calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(target,j))"
	source MATCH
		calc="0"
		endsource
	source INSERT
		calc="0"
		endsource
	source DELETE
		calc="0"
		endsource
	source START
		calc="0"
		endsource
	query_label  SEQUENCE
	target_label SEQUENCE
endstate
state INSERT offi="0" offj="1"
	source MATCH
		calc="gap"
		endsource
	source INSERT
		calc="ext"
		endsource
	query_label  INSERT
	target_label SEQUENCE
endstate
state DELETE offi="1" offj="0"
	source MATCH
		calc="gap"
		endsource
	source DELETE
		calc="ext"
		endsource
	query_label  SEQUENCE
	target_label INSERT
endstate
state START !special !start
	query_label  START
	target_label START
endstate
state END !special !end
	source MATCH 
		calc="0"
		endsource
	query_label  END
	target_label END
endstate
endmatrix