contralign.topology

####################################################
# Topology configuration file for PROBCONS aligner #
####################################################

## Track definitions ###############################

NewTrack {
  name = SEQUENCE
  suffix = ""
}

## Context definitions #############################

NewContext {
  name = MATCH_COMPRESSED_EMISSION
  param = param_MATCH_COMPRESSED_EMISSION
  state_type = StateType_MATCH
  type = ContextType_EMISSION
  track = SEQUENCE
  level = 1
  width = 1
  groups = { AGPST C DENQ FWY HKR ILMV }
}

NewContext {
  name = MATCH_EMISSION
  param = param_MATCH_EMISSION
  state_type = StateType_MATCH
  type = ContextType_EMISSION
  track = SEQUENCE
  level = 2
  width = 1
  groups = { A R N D C Q E G H I L K M F P S T W Y V }
}

NewContext {
  name = INSERT_COMPRESSED_EMISSION_X
  param = param_INSERT_COMPRESSED_EMISSION
  state_type = StateType_INSERT_X
  type = ContextType_EMISSION
  track = SEQUENCE
  level = 1
  width = 1
  groups = { AGPST C DENQ FWY HKR ILMV }
}

NewContext {
  name = INSERT_EMISSION_X
  param = param_INSERT_EMISSION
  state_type = StateType_INSERT_X
  type = ContextType_EMISSION
  track = SEQUENCE
  level = 2
  width = 1
  groups = { A R N D C Q E G H I L K M F P S T W Y V }
}

NewContext {
  name = INSERT_COMPRESSED_EMISSION_Y
  param = param_INSERT_COMPRESSED_EMISSION
  state_type = StateType_INSERT_Y
  type = ContextType_EMISSION
  track = SEQUENCE
  level = 1
  width = 1
  groups = { AGPST C DENQ FWY HKR ILMV }
}

NewContext {
  name = INSERT_EMISSION_Y
  param = param_INSERT_EMISSION
  state_type = StateType_INSERT_Y
  type = ContextType_EMISSION
  track = SEQUENCE
  level = 2
  width = 1
  groups = { A R N D C Q E G H I L K M F P S T W Y V }
}

NewContext {
  name = HYDROPHILIC_COUNT_X
  param = param_HYDROPHILIC_COUNT
  state_type = StateType_INSERT_X
  type = ContextType_COUNT
  track = SEQUENCE
  level = 1
  width = 6
  groups = { DEGKNQPRS }
}

NewContext {
  name = HYDROPHILIC_COUNT_Y
  param = param_HYDROPHILIC_COUNT
  state_type = StateType_INSERT_Y
  type = ContextType_COUNT
  track = SEQUENCE
  level = 1
  width = 6
  groups = { DEGKNQPRS }
}

NewContext {
  name = HYDROPHILIC_COUNT_X_CONTINUE
  param = param_HYDROPHILIC_COUNT_CONTINUE
  state_type = StateType_INSERT_X
  type = ContextType_COUNT
  track = SEQUENCE
  level = 1
  width = 6
  groups = { DEGKNQPRS }
}

NewContext {
  name = HYDROPHILIC_COUNT_Y_CONTINUE
  param = param_HYDROPHILIC_COUNT_CONTINUE
  state_type = StateType_INSERT_Y
  type = ContextType_COUNT
  track = SEQUENCE
  level = 1
  width = 6
  groups = { DEGKNQPRS }
}

## State definitions ###############################

NewState {
  name = MATCH
  param = param_MATCH_USAGE
  type = StateType_MATCH
  contexts = {
    MATCH_COMPRESSED_EMISSION
    MATCH_EMISSION
  }
}

NewState {
  name = INSERT_1_X
  param = param_INSERT_1_USAGE
  type = StateType_INSERT_X
  contexts = { 
    INSERT_COMPRESSED_EMISSION_X
    INSERT_EMISSION_X
  }
}

NewState {
  name = INSERT_1_Y
  param = param_INSERT_1_USAGE
  type = StateType_INSERT_Y
  contexts = {
    INSERT_COMPRESSED_EMISSION_Y
    INSERT_EMISSION_Y
  }
}

NewState {
  name = INSERT_2_X
  param = param_INSERT_2_USAGE
  type = StateType_INSERT_X
  contexts = { 
    INSERT_COMPRESSED_EMISSION_X
    INSERT_EMISSION_X
  }
}

NewState {
  name = INSERT_2_Y
  param = param_INSERT_2_USAGE
  type = StateType_INSERT_Y
  contexts = {
    INSERT_COMPRESSED_EMISSION_Y
    INSERT_EMISSION_Y
  }
}

## Transition definitions ##########################

NewTransition { from = MATCH      to = MATCH      param = param_MATCH_continue    contexts = { } }
NewTransition { from = MATCH      to = INSERT_1_X param = param_MATCH_to_INSERT_1 contexts = { HYDROPHILIC_COUNT_Y } }
NewTransition { from = MATCH      to = INSERT_1_Y param = param_MATCH_to_INSERT_1 contexts = { HYDROPHILIC_COUNT_X } }
NewTransition { from = INSERT_1_X to = MATCH      param = param_INSERT_1_to_MATCH contexts = { HYDROPHILIC_COUNT_Y } }
NewTransition { from = INSERT_1_Y to = MATCH      param = param_INSERT_1_to_MATCH contexts = { HYDROPHILIC_COUNT_X } }
NewTransition { from = INSERT_1_X to = INSERT_1_X param = param_INSERT_1_continue contexts = { HYDROPHILIC_COUNT_Y_CONTINUE } }
NewTransition { from = INSERT_1_X to = INSERT_1_Y param = param_INSERT_1_change   contexts = { } }
NewTransition { from = INSERT_1_Y to = INSERT_1_X param = param_INSERT_1_change   contexts = { } }
NewTransition { from = INSERT_1_Y to = INSERT_1_Y param = param_INSERT_1_continue contexts = { HYDROPHILIC_COUNT_X_CONTINUE } }

NewTransition { from = MATCH      to = INSERT_2_X param = param_MATCH_to_INSERT_2 contexts = { HYDROPHILIC_COUNT_Y } }
NewTransition { from = MATCH      to = INSERT_2_Y param = param_MATCH_to_INSERT_2 contexts = { HYDROPHILIC_COUNT_X } }
NewTransition { from = INSERT_2_X to = MATCH      param = param_INSERT_2_to_MATCH contexts = { HYDROPHILIC_COUNT_Y } }
NewTransition { from = INSERT_2_Y to = MATCH      param = param_INSERT_2_to_MATCH contexts = { HYDROPHILIC_COUNT_X } }
NewTransition { from = INSERT_2_X to = INSERT_2_X param = param_INSERT_2_continue contexts = { HYDROPHILIC_COUNT_Y_CONTINUE } }
NewTransition { from = INSERT_2_X to = INSERT_2_Y param = param_INSERT_2_change   contexts = { } }
NewTransition { from = INSERT_2_Y to = INSERT_2_X param = param_INSERT_2_change   contexts = { } }
NewTransition { from = INSERT_2_Y to = INSERT_2_Y param = param_INSERT_2_continue contexts = { HYDROPHILIC_COUNT_X_CONTINUE } }