Class SimpleDataType

Method Details

• getState

  public final int getState(char c)

  Handles gap char and then passes on to getStateImpl

  Specified by:

  getState in interface DataType

  Parameters:

  c - character

  Returns:

  state

• getChar

  public final char getChar(int state)

  Handles gap state and then passes on to getStateImpl

  Specified by:

  getChar in interface DataType

  Parameters:

  state - state return corresponding character

• getStateImpl

  protected abstract int getStateImpl(char c)

  For sub classes to implement main functionality of getState. Gaps do not need to be considered

• getCharImpl

  protected abstract char getCharImpl(int state)

• getPreferredChar

  public final char getPreferredChar(char c)

  Automatically handles Gaps for sub classes

  Specified by:

  getPreferredChar in interface DataType

• getPreferredCharImpl

  protected char getPreferredCharImpl(char c)

  Can be overidden by subclasses. Default implementation get's character's state and that get's the character for that state

• isUnknownChar

  public final boolean isUnknownChar(char c)

  Specified by:

  isUnknownChar in interface DataType

  Returns:

  true if this state is unknown (or a gap)

• isUnknownState

  public final boolean isUnknownState(int state)

  Checks if state is a gap state (then returns true), otherwise passes on to isUnknownStateImpl

  Specified by:

  isUnknownState in interface DataType

  Returns:

  true if this state is an unknown state (the same as check if a state is >= the number of states... but neater)

• isUnknownStateImpl

  protected abstract boolean isUnknownStateImpl(int state)

  For subclasses to handle, without regard for gaps

• toString

  public String toString()

  Overrides:

  toString in class Object

• getRecommendedUnknownState

  public int getRecommendedUnknownState()

  Specified by:

  getRecommendedUnknownState in interface DataType

  Returns:

  -1 (not getNumStates())

• isAmbiguous

  public boolean isAmbiguous()

  Specified by:

  isAmbiguous in interface DataType

  Returns:

  false

• getAmbiguousVersion

  public AmbiguousDataType getAmbiguousVersion()

  Specified by:

  getAmbiguousVersion in interface DataType

  Returns:

  null

• hasGap

  public final boolean hasGap()

  Specified by:

  hasGap in interface DataType

  Returns:

  true

• isGapChar

  public final boolean isGapChar(char c)

  Specified by:

  isGapChar in interface DataType

  Returns:

  true if this character is a '.' or a '_'

• isGapState

  public final boolean isGapState(int state)

  Specified by:

  isGapState in interface DataType

  Returns:

  true if state is gap state (-2), false other wise

• getRecommendedGapState

  public final int getRecommendedGapState()

  Specified by:

  getRecommendedGapState in interface DataType

  Returns:

  GAP_STATE (-2)