picard.analysis.replicates

Class MergeableMetricBase

java.lang.Object

htsjdk.samtools.metrics.MetricBase

picard.analysis.replicates.MergeableMetricBase

Direct Known Subclasses:

IndependentReplicateMetric

public class MergeableMetricBase
extends htsjdk.samtools.metrics.MetricBase

An extension of MetricBase that knows how to merge-by-adding fields that are appropriately annotated. It also provides an interface for calculating derived fields (and an annotation that informs that said fields are derived). Finally, it also allows for an annotation that suggests that a field will be used as an ID and thus merging will simply require that these fields are equal. merge-by-adding 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.

Author:

Yossi Farjoun

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static interface	MergeableMetricBase.MergeByAdding
protected static interface	MergeableMetricBase.MergeByAssertEquals
protected static interface	MergeableMetricBase.NoMergingIsDerived

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
void	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 void 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 base classes should consider calling super.calculateDerivedFields() as well.