/*
* 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 java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
/**
* Collection of SAMSequenceRecords.
*/
public class SAMSequenceDictionary {
private List<SAMSequenceRecord> mSequences = new ArrayList<SAMSequenceRecord>();
private final Map<String, SAMSequenceRecord> mSequenceMap = new HashMap<String, SAMSequenceRecord>();
public SAMSequenceDictionary() {
}
public SAMSequenceDictionary(final List<SAMSequenceRecord> list) {
this();
setSequences(list);
}
public List<SAMSequenceRecord> getSequences() {
return Collections.unmodifiableList(mSequences);
}
public SAMSequenceRecord getSequence(final String name) {
return mSequenceMap.get(name);
}
/**
* Replaces the existing list of SAMSequenceRecords with the given list.
*
* @param list This value is used directly, rather than being copied.
*/
public void setSequences(final List<SAMSequenceRecord> list) {
mSequences = list;
mSequenceMap.clear();
int index = 0;
for (final SAMSequenceRecord record : list) {
record.setSequenceIndex(index++);
if (mSequenceMap.put(record.getSequenceName(), record) != null) {
throw new IllegalArgumentException("Cannot add sequence that already exists in SAMSequenceDictionary: " +
record.getSequenceName());
}
}
}
public void addSequence(final SAMSequenceRecord sequenceRecord) {
if (mSequenceMap.containsKey(sequenceRecord.getSequenceName())) {
throw new IllegalArgumentException("Cannot add sequence that already exists in SAMSequenceDictionary: " +
sequenceRecord.getSequenceName());
}
sequenceRecord.setSequenceIndex(mSequences.size());
mSequences.add(sequenceRecord);
mSequenceMap.put(sequenceRecord.getSequenceName(), sequenceRecord);
}
/**
* @return The SAMSequenceRecord with the given index, or null if index is out of range.
*/
public SAMSequenceRecord getSequence(final int sequenceIndex) {
if (sequenceIndex < 0 || sequenceIndex >= mSequences.size()) {
return null;
}
return mSequences.get(sequenceIndex);
}
/**
* @return The index for the given sequence name, or -1 if the name is not found.
*/
public int getSequenceIndex(final String sequenceName) {
final SAMSequenceRecord record = mSequenceMap.get(sequenceName);
if (record == null) {
return -1;
}
return record.getSequenceIndex();
}
public int size() {
return mSequences.size();
}
/**
* @return The sum of the lengths of the sequences in this dictionary
*/
public long getReferenceLength() {
long len = 0L;
for (final SAMSequenceRecord seq : getSequences()) {
len += seq.getSequenceLength();
}
return len;
}
public boolean isEmpty() {
return mSequences.isEmpty();
}
private static String DICT_MISMATCH_TEMPLATE = "SAM dictionaries are not the same: %s.";
/**
* Non-comprehensive {@link #equals(Object)}-assertion: instead of calling {@link SAMSequenceRecord#equals(Object)} on constituent
* {@link SAMSequenceRecord}s in this dictionary against its pair in the target dictionary, in order, call
* {@link SAMSequenceRecord#isSameSequence(SAMSequenceRecord)}.
*
* @throws AssertionError When the dictionaries are not the same, with some human-readable information as to why
*/
public void assertSameDictionary(final SAMSequenceDictionary that) {
if (this == that) return;
final Iterator<SAMSequenceRecord> thatSequences = that.mSequences.iterator();
for (final SAMSequenceRecord thisSequence : mSequences) {
if (!thatSequences.hasNext())
throw new AssertionError(String.format(DICT_MISMATCH_TEMPLATE, thisSequence + " is present in only one dictionary"));
else {
final SAMSequenceRecord thatSequence = thatSequences.next();
if(!thatSequence.isSameSequence(thisSequence))
throw new AssertionError(
String.format(DICT_MISMATCH_TEMPLATE, thatSequence + " was found when " + thisSequence + " was expected")
);
}
}
if (thatSequences.hasNext())
throw new AssertionError(String.format(DICT_MISMATCH_TEMPLATE, thatSequences.next() + " is present in only one dictionary"));
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
SAMSequenceDictionary that = (SAMSequenceDictionary) o;
if (!mSequences.equals(that.mSequences)) return false;
return true;
}
@Override
public int hashCode() {
return mSequences.hashCode();
}
}