Uses of Class
picard.vcf.GenotypeConcordanceStates.ContingencyState

Packages that use GenotypeConcordanceStates.ContingencyState

Package	Description
picard.vcf

Uses of GenotypeConcordanceStates.ContingencyState in picard.vcf

Fields in picard.vcf declared as GenotypeConcordanceStates.ContingencyState

Modifier and Type	Field and Description
protected static GenotypeConcordanceStates.ContingencyState[]	GenotypeConcordanceScheme.EMPTY
protected static GenotypeConcordanceStates.ContingencyState[]	GenotypeConcordanceScheme.FN_ONLY
protected static GenotypeConcordanceStates.ContingencyState[]	GenotypeConcordanceScheme.FP_FN
protected static GenotypeConcordanceStates.ContingencyState[]	GenotypeConcordanceScheme.FP_ONLY
protected static GenotypeConcordanceStates.ContingencyState[]	GenotypeConcordanceScheme.FP_TN
protected static GenotypeConcordanceStates.ContingencyState[]	GenotypeConcordanceScheme.FP_TN_FN
static GenotypeConcordanceStates.ContingencyState[]	GenotypeConcordanceScheme.NA These are convenience variables for defining a scheme.
protected static GenotypeConcordanceStates.ContingencyState[]	GenotypeConcordanceScheme.TN_FN
protected static GenotypeConcordanceStates.ContingencyState[]	GenotypeConcordanceScheme.TN_ONLY
protected static GenotypeConcordanceStates.ContingencyState[]	GenotypeConcordanceScheme.TP_FN
protected static GenotypeConcordanceStates.ContingencyState[]	GenotypeConcordanceScheme.TP_FP
protected static GenotypeConcordanceStates.ContingencyState[]	GenotypeConcordanceScheme.TP_FP_FN
protected static GenotypeConcordanceStates.ContingencyState[]	GenotypeConcordanceScheme.TP_ONLY
protected static GenotypeConcordanceStates.ContingencyState[]	GenotypeConcordanceScheme.TP_TN

Methods in picard.vcf that return GenotypeConcordanceStates.ContingencyState

Modifier and Type	Method and Description
GenotypeConcordanceStates.ContingencyState[]	GenotypeConcordanceScheme.getConcordanceStateArray(GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates) Get the concordance state array associate with the given truth state and call state tuple.
GenotypeConcordanceStates.ContingencyState[]	GenotypeConcordanceScheme.getConcordanceStateArray(GenotypeConcordanceStates.TruthState truthState, GenotypeConcordanceStates.CallState callState) Get the concordance state array associate with the given truth state and call state tuple.
static GenotypeConcordanceStates.ContingencyState	GenotypeConcordanceStates.ContingencyState.valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static GenotypeConcordanceStates.ContingencyState[]	GenotypeConcordanceStates.ContingencyState.values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods in picard.vcf that return types with arguments of type GenotypeConcordanceStates.ContingencyState

Modifier and Type	Method and Description
java.util.Map<GenotypeConcordanceStates.ContingencyState,java.lang.Long>	GenotypeConcordanceCounts.getContingencyStateCounts(GenotypeConcordanceScheme scheme) Returns the total number of times each contingency state is encountered, summed across all truth/call state pairs.
java.util.Set<GenotypeConcordanceStates.ContingencyState>	GenotypeConcordanceScheme.getContingencyStateSet(GenotypeConcordanceStates.ContingencyState[] contingencyStateArray) Get the contingency state array as a set

Methods in picard.vcf with parameters of type GenotypeConcordanceStates.ContingencyState

Modifier and Type	Method and Description
protected void	GenotypeConcordanceScheme.addRow(GenotypeConcordanceStates.CallState callState, GenotypeConcordanceStates.ContingencyState[]... concordanceStateArrays) Adds a row to the scheme
java.util.Set<GenotypeConcordanceStates.ContingencyState>	GenotypeConcordanceScheme.getContingencyStateSet(GenotypeConcordanceStates.ContingencyState[] contingencyStateArray) Get the contingency state array as a set