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/*
* The MIT License
*
* Copyright (c) 2016 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*
*/
package picard.analysis;
import htsjdk.samtools.metrics.MetricBase;
import java.lang.annotation.Annotation;
import java.lang.annotation.ElementType;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
import java.lang.annotation.Target;
import java.lang.reflect.Field;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.List;
/**
* 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
*/
abstract public class MergeableMetricBase extends MetricBase {
/** Metrics whose values can be merged by adding. */
@Retention(RetentionPolicy.RUNTIME)
@Target(ElementType.FIELD)
protected @interface MergeByAdding {}
/** Metrics whose values should be equal when merging. */
@Retention(RetentionPolicy.RUNTIME)
@Target(ElementType.FIELD)
protected @interface MergeByAssertEquals {}
/** Metrics that are not merged, but are subsequently derived from other metrics, for example by
* {@link #calculateDerivedFields()}. */
@Retention(RetentionPolicy.RUNTIME)
@Target(ElementType.FIELD)
protected @interface NoMergingIsDerived {}
/** Metrics that are merged manually in the {@link #merge(MergeableMetricBase)} ()}. Typically these metrics need
* access to both metrics being merged. */
@Retention(RetentionPolicy.RUNTIME)
@Target(ElementType.FIELD)
protected @interface MergingIsManual {}
/** Metrics that are not merged. */
@Retention(RetentionPolicy.RUNTIME)
@Target(ElementType.FIELD)
protected @interface NoMergingKeepsValue {}
/** 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
*
* @param other metric that will be merged into this one.
* @return true if the other metric can be merged into this one.
*/
public boolean canMerge(final MergeableMetricBase other) {
try {
for (final Field field : this.getClass().getDeclaredFields()) {
if (field.isSynthetic()) continue;
//try to get field from other, will throw exception if other instance doesn't have the
field.get(other);
final Annotation[] equalAnnotations = field.getAnnotationsByType(MergeByAssertEquals.class);
if (equalAnnotations.length != 0) {
if (field.get(this) == null) return true;
if (field.get(other) == null) return true;
if (!field.get(this).equals(field.get(other))) return false;
}
}
} catch (final Exception e) {
return false;
}
return true;
}
/**
* Merges another MergableMetricBase if possible
*
* @param other another MergableMetricBase instance to merge, must of the same class as this.
* @return true if the other metric can be merged into this one.
*/
public boolean mergeIfCan(final MergeableMetricBase other) {
if (canMerge(other)) {
merge(other);
return true;
} else {
return false;
}
}
/**
* for a collection of MergeableMetricBase, merge them all into "this" one.
*
* @param many a Collection of MergeableMetricBase
*/
public MergeableMetricBase merge(final Collection many) {
many.stream().forEach(this::merge);
calculateDerivedFields();
return this;
}
/**
* Merge another metric into this one
*
* @param other metric to merge into this one.
*/
public MergeableMetricBase merge(final MergeableMetricBase other) {
for (final Field field : getAllFields(this.getClass())) {
if (field.isSynthetic()) continue;
if (field.getAnnotationsByType(MergeByAdding.class).length +
field.getAnnotationsByType(MergeByAssertEquals.class).length +
field.getAnnotationsByType(NoMergingIsDerived.class).length +
field.getAnnotationsByType(MergingIsManual.class).length +
field.getAnnotationsByType(NoMergingKeepsValue.class).length == 0) {
throw new IllegalStateException("All fields of this class must be annotated with @MergeByAdding, @NoMergingIsDerived, or @MergeByAssertEquals. " +
"Field " + field.getName() + " isn't annotated.");
}
final Annotation[] summableAnnotations = field.getAnnotationsByType(MergeByAdding.class);
field.setAccessible(true);
if (summableAnnotations.length != 0) {
try {
if (field.getType() == Integer.class) {
field.set(this, (Integer) field.get(this) + (Integer) field.get(other));
} else if (field.getType() == int.class) {
field.set(this, (int) field.get(this) + (int) field.get(other));
} else if (field.getType() == Float.class) {
field.set(this, (Float) field.get(this) + (Float) field.get(other));
} else if (field.getType() == float.class) {
field.set(this, (float) field.get(this) + (float) field.get(other));
} else if (field.getType() == Double.class) {
field.set(this, (Double) field.get(this) + (Double) field.get(other));
} else if (field.getType() == double.class) {
field.set(this, (double) field.get(this) + (double) field.get(other));
} else if (field.getType() == Long.class) {
field.set(this, (Long) field.get(this) + (Long) field.get(other));
} else if (field.getType() == long.class) {
field.set(this, (long) field.get(this) + (long) field.get(other));
} else if (field.getType() == Byte.class) {
final Integer result = (Byte) field.get(this) + (Byte) field.get(other);
if (result > Byte.MAX_VALUE)
throw new IllegalArgumentException("Overflow detected in adding " + field.get(this) + " to " + field.get(other));
field.set(this, (byte) (int) result);
} else if (field.getType() == byte.class) {
final int result = (byte) field.get(this) + (byte) field.get(other);
if (result > Byte.MAX_VALUE)
throw new IllegalArgumentException("Overflow detected in adding " + field.get(this) + " to " + field.get(other));
field.set(this, (byte) result);
} else if (field.getType() == Short.class) {
final Integer result = (Short) field.get(this) + (Short) field.get(other);
if (result > Short.MAX_VALUE)
throw new IllegalArgumentException("Overflow detected in adding " + field.get(this) + " to " + field.get(other));
field.set(this, (Short) (short) (int) result);
} else if (field.getType() == short.class) {
final Integer result = (short) field.get(this) + (short) field.get(other);
if (result > Short.MAX_VALUE)
throw new IllegalArgumentException("Overflow detected in adding " + field.get(this) + " to " + field.get(other));
field.set(this, (short) (int) result);
} else
throw new IllegalArgumentException("I don't know how to MergeByAdding type " + field.getDeclaringClass().getCanonicalName() +
" of field " + field.getName() + "please teach me!");
} catch (IllegalAccessException e) {
e.printStackTrace();
}
}
final Annotation[] equalAnnotations = field.getAnnotationsByType(MergeByAssertEquals.class);
if (equalAnnotations.length != 0) {
try {
if (field.get(this) == null) {
field.set(this, field.get(other));
} else if (field.get(other) != null && !field.get(this).equals(field.get(other))) {
throw new IllegalStateException("Field " + field.getName() +
" is annotated as @MergeByAssertEquals, but found two different values: " + field.get(this) + " & " + field.get(other));
}
} catch (IllegalAccessException e) {
e.printStackTrace();
}
}
}
return this;
}
private static List getAllFields(Class clazz){
final List fields = new ArrayList<>();
fields.addAll(Arrays.asList(clazz.getDeclaredFields()));
final Class superClass = clazz.getSuperclass();
if (superClass != null) fields.addAll(getAllFields(superClass));
return fields;
}
/**
* 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.
*/
public void calculateDerivedFields() {}
}
