picard.analysis

Class MergeableMetricBase

java.lang.Object

htsjdk.samtools.metrics.MetricBase

picard.analysis.MergeableMetricBase

Direct Known Subclasses:

CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics, CollectVariantCallingMetrics.VariantCallingSummaryMetrics, DuplicationMetrics, ErrorMetric, ErrorSummaryMetrics, IndependentReplicateMetric, MendelianViolationMetrics, WgsMetrics

public abstract class MergeableMetricBase
extends htsjdk.samtools.metrics.MetricBase

An extension of MetricBase that knows how to merge-by-adding fields that are appropriately annotated (MergeByAdding). It also provides an interface for calculating derived fields calculateDerivedFields() (and an annotation that informs that said fields are derived NoMergingIsDerived). Finally, it also allows for an annotation that suggests that a field will be used as an ID and thus merging will simply ensure that these fields are equal MergeByAssertEquals. Other annotations are available, though they all currently imply that no implicit action will be taken MergingIsManual and NoMergingKeepsValue.

MergeByAdding is only enabled for the following types: int, Integer, float, Float, double, Double, short, Short, long, Long, byte, Byte. Overflow will be detected (for the short, and byte types) and an exception thrown.

Every (non-static) field in this class must be @Annotated by one of: MergeByAdding, MergeByAssertEquals, NoMergingIsDerived, MergingIsManual, NoMergingKeepsValue. Static fields may be annotated, but not with MergeByAdding, there will be no automatic modification of static fields

MergeByAdding

When merging another metric into this one, the value of the field in the other class will be added to the value in this. This will happen automatically!

MergeByAssertEquals

When merging another metric into this one, the code will assert that value of the field in the other class is equal to the value in this.

NoMergingIsDerived

When merging another metric into this one, no action will be taken since the value of this field should be derived from the other field. This derivation should happen in the "calculateDerivedFields" method.

MergingIsManual

When merging another metric into this one, the resulting value will be calculated "manually", i.e. by custom code in the merge method. The resulting value can depend on both this and other objects.

NoMergingKeepsValue

When merging another metric into this one, the value of the field in this remains unchanged by design.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static interface	MergeableMetricBase.MergeByAdding Metrics whose values can be merged by adding.
protected static interface	MergeableMetricBase.MergeByAssertEquals Metrics whose values should be equal when merging.
protected static interface	MergeableMetricBase.MergingIsManual Metrics that are merged manually in the merge(MergeableMetricBase) ()}.
protected static interface	MergeableMetricBase.NoMergingIsDerived Metrics that are not merged, but are subsequently derived from other metrics, for example by calculateDerivedFields().
protected static interface	MergeableMetricBase.NoMergingKeepsValue Metrics that are not merged.

Constructor Summary

Constructors

Constructor and Description
MergeableMetricBase()

Method Summary

Modifier and Type	Method and Description
void	calculateDerivedFields() Placeholder method that will calculate the derived fields from the other ones.
boolean	canMerge(MergeableMetricBase other) Checks if this instance can be merged with another Other must have all the fields that this instance has, and the fields that are annotated as MergeByAssertEquals must contain the same value
MergeableMetricBase	merge(java.util.Collection<? extends MergeableMetricBase> many) for a collection of MergeableMetricBase, merge them all into "this" one.
MergeableMetricBase	merge(MergeableMetricBase other) Merge another metric into this one
boolean	mergeIfCan(MergeableMetricBase other) Merges another MergableMetricBase if possible

Methods inherited from class htsjdk.samtools.metrics.MetricBase

equals, hashCode, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

MergeableMetricBase

public MergeableMetricBase()

Method Detail

canMerge

public boolean canMerge(MergeableMetricBase other)

Checks if this instance can be merged with another Other must have all the fields that this instance has, and the fields that are annotated as MergeByAssertEquals must contain the same value

Parameters:

other - metric that will be merged into this one.

Returns:

true if the other metric can be merged into this one.

mergeIfCan

public boolean mergeIfCan(MergeableMetricBase other)

Merges another MergableMetricBase if possible

Parameters:

other - another MergableMetricBase instance to merge, must of the same class as this.

Returns:

true if the other metric can be merged into this one.

merge

public MergeableMetricBase merge(java.util.Collection<? extends MergeableMetricBase> many)

for a collection of MergeableMetricBase, merge them all into "this" one.

Parameters:

many - a Collection of MergeableMetricBase

merge

public MergeableMetricBase merge(MergeableMetricBase other)

Merge another metric into this one

Parameters:

other - metric to merge into this one.

calculateDerivedFields

public void calculateDerivedFields()

Placeholder method that will calculate the derived fields from the other ones. Classes that are derived from non-trivial derived classes should consider calling super.calculateDerivedFields() as well. Fields whose value will change due to this method should be annotated with NoMergingKeepsValue.