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The IO bundle for Geneweaver.
There is a newer version: 2.7.12
/*-
 * 
 * Copyright 2018, 2020  The Jackson Laboratory Inc.
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 * 
 * @author Matthew Gerring
 */
package org.geneweaver.domain;

import java.util.Arrays;
import java.util.Collection;
import java.util.Objects;

import javax.annotation.processing.Generated;

import com.fasterxml.jackson.annotation.JsonIgnore;

@Generated("POJO")
public class Anchor extends AbstractEntity implements AnchoredEntity {

	private String chr;
	
	private int start;
	
	private int end;

	private int intensity;

	public Anchor() {
		
	}
	
	public Anchor(String chr, int start, int end) {
		this.chr = chr;
		this.start = start;
		this.end   = end;
	}
	
	public Anchor(String chr, int start, int end, int intensity) {
		this.chr = chr;
		this.start = start;
		this.end   = end;
		this.intensity   = intensity;
	}

	/**
	 * @return the chrom
	 */
	public String getChr() {
		return chr;
	}

	/**
	 * @param chrom the chrom to set
	 */
	public void setChr(String chrom) {
		this.chr = chrom;
	}

	/**
	 * @return the start
	 */
	public int getStart() {
		return start;
	}

	/**
	 * @param start the start to set
	 */
	public void setStart(int start) {
		this.start = start;
	}

	/**
	 * @return the end
	 */
	public int getEnd() {
		return end;
	}

	/**
	 * @param end the end to set
	 */
	public void setEnd(int end) {
		this.end = end;
	}

	@Override
	public int hashCode() {
		final int prime = 31;
		int result = super.hashCode();
		result = prime * result + Objects.hash(chr, end, intensity, start);
		return result;
	}

	@Override
	public boolean equals(Object obj) {
		if (this == obj)
			return true;
		if (!super.equals(obj))
			return false;
		if (!(obj instanceof Anchor))
			return false;
		Anchor other = (Anchor) obj;
		return Objects.equals(chr, other.chr) && end == other.end && intensity == other.intensity
				&& start == other.start;
	}


	@Override
	public Collection anchors() {
		return Arrays.asList(this);
	}

	/**
	 * @return the intensity
	 */
	public int getIntensity() {
		return intensity;
	}

	/**
	 * @param intensity the intensity to set
	 */
	public void setIntensity(int intensity) {
		this.intensity = intensity;
	}

	/**
	 * Span between start and end of bases
	 * @return
	 */
	@JsonIgnore
	public int span() {
		return end-start;
	}


}