/*
* 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 picard.illumina;
import htsjdk.samtools.util.SequenceUtil;
import htsjdk.samtools.util.StringUtil;
import picard.util.AdapterPair;
class CustomAdapterPair implements AdapterPair {
private final String fivePrime, threePrime, fivePrimeReadOrder;
private final byte[] fivePrimeBytes, threePrimeBytes, fivePrimeReadOrderBytes;
CustomAdapterPair(final String fivePrime, final String threePrime) {
this.threePrime = threePrime;
this.threePrimeBytes = StringUtil.stringToBytes(threePrime);
this.fivePrime = fivePrime;
this.fivePrimeReadOrder = SequenceUtil.reverseComplement(fivePrime);
this.fivePrimeBytes = StringUtil.stringToBytes(fivePrime);
this.fivePrimeReadOrderBytes = StringUtil.stringToBytes(fivePrimeReadOrder);
}
public String get3PrimeAdapter() { return threePrime; }
public String get5PrimeAdapter() { return fivePrime; }
public String get3PrimeAdapterInReadOrder() { return threePrime; }
public String get5PrimeAdapterInReadOrder() { return fivePrimeReadOrder; }
public byte[] get3PrimeAdapterBytes() { return threePrimeBytes; }
public byte[] get5PrimeAdapterBytes() { return fivePrimeBytes; }
public byte[] get3PrimeAdapterBytesInReadOrder() { return threePrimeBytes; }
public byte[] get5PrimeAdapterBytesInReadOrder() { return fivePrimeReadOrderBytes; }
public String getName() { return "Custom adapter pair"; }
}