/*
* 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.filter;
import htsjdk.samtools.SAMRecord;
import java.util.Arrays;
import java.util.List;
/**
* Filter class for matching tag attributes in SAMRecords
*
* $Id$
*/
public class TagFilter implements SamRecordFilter {
private final String tag; // The key of the tag to match
private final List<Object> values; // The list of matching values
/**
* Constructor for a single value
*
* @param tag the key of the tag to match
* @param value the value to match
*/
public TagFilter(String tag, Object value) {
this.tag = tag;
this.values = Arrays.asList(value);
}
/**
* Constructor for multiple values
*
* @param tag the key of the tag to match
* @param values the matching values
*/
public TagFilter(String tag, List<Object> values) {
this.tag = tag;
this.values = values;
}
/**
* Determines whether a SAMRecord matches this filter
*
* @param record the SAMRecord to evaluate
* @return true if the SAMRecord matches the filter, otherwise false
*/
public boolean filterOut(SAMRecord record) {
return values.contains(record.getAttribute(tag));
}
/**
* Determines whether a paired of SAMRecord matches this filter
*
* @param first the first SAMRecord to evaluate
* @param second the second SAMRecord to evaluate
*
* @return true if the SAMRecords matches the filter, otherwise false
*/
public boolean filterOut(final SAMRecord first, final SAMRecord second) {
// both first and second must have the tag in order for it to be filtered out
return values.contains(first.getAttribute(tag)) && values.contains(second.getAttribute(tag));
}
}