%{
#include "dyna.h"

%}

matrix DnaMatchBlock
query type="DNA" name="query"
target type="DNA" name="target"
resource type="DnaMatrix*" name="comp65"
resource type="DnaMatrix*" name="comp75"
resource type="DnaMatrix*" name="comp85"
resource type="DnaMatrix*" name="comp95"
resource type="Score" name="g" 
resource type="Score" name="u"
resource type="Score" name="v"
resource type="Score" name="s"
resource type="Score" name="b"
state MATCH65
  source MATCH65 offi="1" offj="1"
    calc="comp65->score[DNA_BASE(query,i)][DNA_BASE(target,j)] + s"
    endsource
  source MATCH65 offi="0" offj="1"
    calc="g"
    target_label  MI65
    endsource
  source MATCH65 offi="1" offj="0"
    calc="g"
    query_label  MI65
    endsource
  source UNMATCHED_TARGET offi="1" offj="1"
    calc="comp65->score[DNA_BASE(query,i)][DNA_BASE(target,j)] + v"
    endsource
  query_label  MM65
  target_label MM65
endstate
state MATCH75
  source MATCH75 offi="1" offj="1"
    calc="comp75->score[DNA_BASE(query,i)][DNA_BASE(target,j)] + s"
    endsource
  source MATCH75 offi="0" offj="1"
    calc="g"
    target_label  MI75
    endsource
  source MATCH75 offi="1" offj="0"
    calc="g"
    query_label  MI75
    endsource
  source UNMATCHED_TARGET offi="1" offj="1"
    calc="comp75->score[DNA_BASE(query,i)][DNA_BASE(target,j)] + v"
    endsource
  query_label  MM75
  target_label MM75
endstate
state MATCH85
  source MATCH85 offi="1" offj="1"
    calc="comp85->score[DNA_BASE(query,i)][DNA_BASE(target,j)] + s"
    endsource
  source MATCH85 offi="0" offj="1"
    calc="g"
    target_label  MI85
    endsource
  source MATCH85 offi="1" offj="0"
    calc="g"
    query_label  MI85
    endsource
  source UNMATCHED_TARGET offi="1" offj="1"
    calc="comp85->score[DNA_BASE(query,i)][DNA_BASE(target,j)] + v"
    endsource
  query_label  MM85
  target_label MM85
endstate
state MATCH95
  source MATCH95 offi="1" offj="1"
    calc="comp95->score[DNA_BASE(query,i)][DNA_BASE(target,j)] + s"
    endsource
  source MATCH95 offi="0" offj="1"
    calc="g"
    target_label  MI95
    endsource
  source MATCH95 offi="1" offj="0"
    calc="g"
    query_label  MI95
    endsource
  source UNMATCHED_TARGET offi="1" offj="1"
    calc="comp95->score[DNA_BASE(query,i)][DNA_BASE(target,j)] + v"
    endsource
  query_label  MM95
  target_label MM95
endstate
state UNMATCHED_QUERY offi="1" offj="0"
  source MATCH65
    calc="b"
    endsource
  source MATCH75
    calc="b"
    endsource
  source MATCH85
    calc="b"
    endsource
  source MATCH95
    calc="b"
    endsource
  source UNMATCHED_QUERY 
    calc="u"
    endsource
  source START !top !left
    calc="0"
    endsource
  query_label  UM
  target_label UI
endstate
state UNMATCHED_TARGET offi="0" offj="1"
  source UNMATCHED_QUERY
    calc="v"
    endsource
  source UNMATCHED_TARGET
    calc="u"
    endsource
  target_label UM
  query_label  UI
endstate
state START !special !start
  query_label  START
  target_label START
endstate
state END !special !end
  source UNMATCHED_TARGET !right !bottom 
    calc="0"
    endsource
  query_label  END
  target_label END
endstate
endmatrix