htsjdk.tribble.bed.BEDFeature Maven / Gradle / Ivy
/*
* The MIT License
*
* Copyright (c) 2013 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.tribble.bed;
import htsjdk.tribble.Feature;
import htsjdk.tribble.annotation.Strand;
import java.awt.*;
/**
* @author jrobinso
* @date Dec 24, 2009
*
* BED feature start and end positions must adhere to the Feature interval specifications.
* This is different than the 0-based representation in a BED file. This conversion is handled by {@link BEDCodec}.
* Anyone writing a bed file should be aware of this difference.
*/
public interface BEDFeature extends Feature {
Strand getStrand();
String getType();
Color getColor();
String getDescription();
java.util.List getExons();
String getName();
float getScore();
String getLink();
}