htsjdk.samtools.metrics.MetricBase Maven / Gradle / Ivy
/*
* The MIT License
*
* Copyright (c) 2009 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 htsjdk.samtools.metrics;
import htsjdk.samtools.SAMException;
import htsjdk.samtools.util.FormatUtil;
import java.lang.reflect.Field;
/**
* A base class from which all Metric classes should inherit.
*
* @author Tim Fennell
*/
public class MetricBase {
/**
* An equals method that checks equality by asserting that the classes are of the exact
* same type and that all public fields are equivalent. Equivalence is checked by formatting
* the field as it would be written to disk and then checking String equality.
*
* @param o an instance to compare to
* @return true if they are equal, false otherwise
*/
public boolean equals(final Object o) {
if (o == null) return false;
if (o.getClass() != getClass()) return false;
final FormatUtil formatter = new FormatUtil();
// Loop through all the fields and check that they are either
// null in both objects or equal in both objects
for (final Field f : getClass().getFields()) {
try {
final Object lhs = f.get(this);
final Object rhs = f.get(o);
if (lhs == null) {
if (rhs == null) {
// keep going
}
else {
return false;
}
}
else {
if (formatter.format(lhs).equals(formatter.format(rhs))) //compare based on the serialized representation
{
// keep going
}
else {
return false;
}
}
}
catch (IllegalAccessException iae) {
throw new SAMException("Could not read field " + f.getName() + " from a " + getClass().getSimpleName());
}
}
// If we got this far all the fields are equal
return true;
}
/**
* Computes a hashcode by formatting each field into its on disk representation
* and summing the hashcodes of all the fields.
*/
public int hashCode() {
int result = 0;
FormatUtil formatter = new FormatUtil();
for (final Field f : getClass().getFields()) {
try {
Object value = f.get(this);
value = formatter.format(value); //format the value the way it will be written to disk
final int fieldHash = value != null ? value.hashCode() : 0;
result = 31 * result + fieldHash;
} catch (IllegalAccessException e) {
throw new SAMException("Could not read field " + f.getName() + " from a " + getClass().getSimpleName());
}
}
return result;
}
/** Converts the metric class to a human readable string. */
public String toString() {
final StringBuilder buffer = new StringBuilder();
final FormatUtil formatter = new FormatUtil();
for (final Field f : getClass().getFields()) {
try {
buffer.append(f.getName());
buffer.append('\t');
buffer.append(formatter.format(f.get(this)));
buffer.append('\n');
}
catch (IllegalAccessException iae) {
throw new SAMException("Could not read field " + f.getName() + " from a " + getClass().getSimpleName());
}
}
return buffer.toString();
}
}