/*
* 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;
import htsjdk.samtools.util.CloseableIterator;
import htsjdk.samtools.util.PeekableIterator;
import java.util.Comparator;
/**
* Iterator for SAM records that implements comparable to enable sorting of iterators.
* The comparison is performed by comparing the next record in the iterator to the next
* record in another iterator and returning the ordering between those SAM records.
*/
class ComparableSamRecordIterator extends PeekableIterator<SAMRecord> implements Comparable<ComparableSamRecordIterator> {
private final Comparator<SAMRecord> comparator;
private final SAMFileReader reader;
/**
* Constructs a wrapping iterator around the given iterator that will be able
* to compare itself to other ComparableSamRecordIterators using the given comparator.
*
* @param iterator the wrapped iterator.
* @param comparator the Comparator to use to provide ordering fo SAMRecords
*/
public ComparableSamRecordIterator(final SAMFileReader sam, final CloseableIterator<SAMRecord> iterator, final Comparator<SAMRecord> comparator) {
super(iterator);
this.reader = sam;
this.comparator = comparator;
}
/** Returns the reader from which this iterator was constructed. */
public SAMFileReader getReader() {
return reader;
}
/**
* Compares this iterator to another comparable iterator based on the next record
* available in each iterator. If the two comparable iterators have different
* comparator types internally an exception is thrown.
*
* @param that another iterator to compare to
* @return a negative, 0 or positive number as described in the Comparator interface
*/
public int compareTo(final ComparableSamRecordIterator that) {
if (this.comparator.getClass() != that.comparator.getClass()) {
throw new IllegalStateException("Attempt to compare two ComparableSAMRecordIterators that " +
"have different orderings internally");
}
final SAMRecord record = this.peek();
final SAMRecord record2 = that.peek();
return comparator.compare(record, record2);
}
@Override
public boolean equals(final Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
return compareTo((ComparableSamRecordIterator)o) == 0;
}
@Override
public int hashCode() {
throw new UnsupportedOperationException("ComparableSamRecordIterator should not be hashed because it can change value");
}
}