%{
#include "dyna.h"

%}

matrix ProteinBlockAligner
query name="q" type="PROTEIN"
target name="t" type="PROTEIN"
resource name="m" type="COMPMAT"
resource name="bentry" type="Score"
resource name="bexit"  type="Score"
resource name="bfor_trans" type="Score"
resource name="b_self_trans" type="Score"
resource name="b3exit" type="Score"
state BLOCK_1
  calc="AAMATCH(m,AMINOACID(q,i),AMINOACID(t,j))"
  source BLOCK_1 offi="1" offj="1"
    calc="b_self_trans"
    endsource
  source START offi="1" offj="1"
    calc="0"
    endsource
  source UNALIGNED offi="1" offj="1"
    calc="bentry"
    endsource
  query_label SEQUENCE_BLOCK_1
  target_label SEQUENCE_BLOCK_1
endstate
state BLOCK_2
  calc="AAMATCH(m,AMINOACID(q,i),AMINOACID(t,j))"
  source BLOCK_2 offi="1" offj="1"
    calc="b_self_trans"
    endsource
  source BLOCK_1 offi="1" offj="1"
    calc="bfor_trans"
    endsource
  query_label SEQUENCE_BLOCK_2
  target_label SEQUENCE_BLOCK_2
endstate
state BLOCK_3
  calc="AAMATCH(m,AMINOACID(q,i),AMINOACID(t,j))"
  source BLOCK_3 offi="1" offj="1"
    calc="b_self_trans"
    endsource
  source BLOCK_2 offi="1" offj="1"
    calc="bfor_trans"
    endsource
  query_label SEQUENCE_BLOCK_2
  target_label SEQUENCE_BLOCK_2
endstate
state UNALIGNED
  source BLOCK_1 offi="0" offj="1"
    calc="bexit"
    endsource
  source BLOCK_1 offi="1" offj="0"
    calc="bexit"
    endsource
  source BLOCK_2 offi="0" offj="1"
    calc="b3exit"
    endsource
  source BLOCK_2 offi="1" offj="0"
    calc="b3exit"
    endsource
  source UNALIGNED offi="0" offj="1"
    calc="0"
    endsource
  source UNALIGNED offi="1" offj="0"
    calc="0"
    endsource
  query_label UNALIGNED
  target_label UNALIGNED
endstate
state START !start !special
endstate
state END !end !special
  source UNALIGNED 
    calc="0"
    endsource
  source BLOCK_1 
    calc="0"
    endsource
  query_label END
  target_label END
endstate
endmatrix

%{
#include "pba.h"


%}