public abstract class GenotypeConcordanceScheme
extends java.lang.Object
Constructor and Description |
---|
GenotypeConcordanceScheme() |
Modifier and Type | Method and Description |
---|---|
protected void |
addRow(GenotypeConcordanceStates.CallState callState,
GenotypeConcordanceStates.ContingencyState[]... concordanceStateArrays)
Adds a row to the scheme
|
GenotypeConcordanceStates.ContingencyState[] |
getConcordanceStateArray(GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates)
Get the concordance state array associate with the given truth state and call state tuple.
|
GenotypeConcordanceStates.ContingencyState[] |
getConcordanceStateArray(GenotypeConcordanceStates.TruthState truthState,
GenotypeConcordanceStates.CallState callState)
Get the concordance state array associate with the given truth state and call state tuple.
|
java.util.Set<GenotypeConcordanceStates.ContingencyState> |
getContingencyStateSet(GenotypeConcordanceStates.ContingencyState[] contingencyStateArray)
Get the contingency state array as a set
|
java.lang.String |
getContingencyStateString(GenotypeConcordanceStates.TruthState truthState,
GenotypeConcordanceStates.CallState callState)
Get the contingency state array as a parse-able string
|
protected abstract void |
initiateScheme() |
void |
validateScheme()
Check that all cells in the scheme exist.
|
protected final java.util.Map<GenotypeConcordanceStates.TruthAndCallStates,GenotypeConcordanceStates.ContingencyState[]> scheme
public static final GenotypeConcordanceStates.ContingencyState[] NA
protected static final GenotypeConcordanceStates.ContingencyState[] EMPTY
protected static final GenotypeConcordanceStates.ContingencyState[] TP_ONLY
protected static final GenotypeConcordanceStates.ContingencyState[] FP_ONLY
protected static final GenotypeConcordanceStates.ContingencyState[] TN_ONLY
protected static final GenotypeConcordanceStates.ContingencyState[] FN_ONLY
protected static final GenotypeConcordanceStates.ContingencyState[] TP_FN
protected static final GenotypeConcordanceStates.ContingencyState[] TP_FP
protected static final GenotypeConcordanceStates.ContingencyState[] TP_TN
protected static final GenotypeConcordanceStates.ContingencyState[] FP_FN
protected static final GenotypeConcordanceStates.ContingencyState[] FP_TN
protected static final GenotypeConcordanceStates.ContingencyState[] FP_TN_FN
protected static final GenotypeConcordanceStates.ContingencyState[] TP_FP_FN
protected static final GenotypeConcordanceStates.ContingencyState[] TN_FN
protected abstract void initiateScheme()
protected void addRow(GenotypeConcordanceStates.CallState callState, GenotypeConcordanceStates.ContingencyState[]... concordanceStateArrays)
callState
- the call state (row)concordanceStateArrays
- the concordance state arrays for each truth value, in orderpublic GenotypeConcordanceStates.ContingencyState[] getConcordanceStateArray(GenotypeConcordanceStates.TruthState truthState, GenotypeConcordanceStates.CallState callState)
public GenotypeConcordanceStates.ContingencyState[] getConcordanceStateArray(GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates)
public java.lang.String getContingencyStateString(GenotypeConcordanceStates.TruthState truthState, GenotypeConcordanceStates.CallState callState)
public java.util.Set<GenotypeConcordanceStates.ContingencyState> getContingencyStateSet(GenotypeConcordanceStates.ContingencyState[] contingencyStateArray)
contingencyStateArray
- public void validateScheme() throws PicardException
PicardException
- if a missing tuple was found.