Field Detail

• scheme

  protected final Map<GenotypeConcordanceStates.TruthAndCallStates,GenotypeConcordanceStates.ContingencyState[]> scheme

  The underlying scheme

• NA

  public static final GenotypeConcordanceStates.ContingencyState[] NA

  These are convenience variables for defining a scheme. NA means that such a tuple should never be observed.

• EMPTY

  protected static final GenotypeConcordanceStates.ContingencyState[] EMPTY

• TP_ONLY

  protected static final GenotypeConcordanceStates.ContingencyState[] TP_ONLY

• FP_ONLY

  protected static final GenotypeConcordanceStates.ContingencyState[] FP_ONLY

• TN_ONLY

  protected static final GenotypeConcordanceStates.ContingencyState[] TN_ONLY

• FN_ONLY

  protected static final GenotypeConcordanceStates.ContingencyState[] FN_ONLY

• TP_FN

  protected static final GenotypeConcordanceStates.ContingencyState[] TP_FN

• TP_FP

  protected static final GenotypeConcordanceStates.ContingencyState[] TP_FP

• TP_TN

  protected static final GenotypeConcordanceStates.ContingencyState[] TP_TN

• FP_FN

  protected static final GenotypeConcordanceStates.ContingencyState[] FP_FN

• FP_TN

  protected static final GenotypeConcordanceStates.ContingencyState[] FP_TN

• FP_TN_FN

  protected static final GenotypeConcordanceStates.ContingencyState[] FP_TN_FN

• TP_FP_FN

  protected static final GenotypeConcordanceStates.ContingencyState[] TP_FP_FN

• TN_FN

  protected static final GenotypeConcordanceStates.ContingencyState[] TN_FN

Constructor Detail

• GenotypeConcordanceScheme

  public GenotypeConcordanceScheme()

Method Detail

• initiateScheme

  protected abstract void initiateScheme()

• addRow

  protected void addRow(GenotypeConcordanceStates.CallState callState,
                        GenotypeConcordanceStates.ContingencyState[]... concordanceStateArrays)

  Adds a row to the scheme

  Parameters:

  callState - the call state (row)

  concordanceStateArrays - the concordance state arrays for each truth value, in order

• getConcordanceStateArray

  public GenotypeConcordanceStates.ContingencyState[] getConcordanceStateArray(GenotypeConcordanceStates.TruthState truthState,
                                                                               GenotypeConcordanceStates.CallState callState)

  Get the concordance state array associate with the given truth state and call state tuple.

• getConcordanceStateArray

  public GenotypeConcordanceStates.ContingencyState[] getConcordanceStateArray(GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates)

  Get the concordance state array associate with the given truth state and call state tuple.

• getContingencyStateString

  public String getContingencyStateString(GenotypeConcordanceStates.TruthState truthState,
                                          GenotypeConcordanceStates.CallState callState)

  Get the contingency state array as a parse-able string

• getContingencyStateSet

  public Set<GenotypeConcordanceStates.ContingencyState> getContingencyStateSet(GenotypeConcordanceStates.ContingencyState[] contingencyStateArray)

  Get the contingency state array as a set

  Parameters:

  contingencyStateArray -

  Returns:

• validateScheme

  public void validateScheme()
                      throws PicardException

  Check that all cells in the scheme exist.

  Throws:

  PicardException - if a missing tuple was found.