VCFFeature.java

/*
 * The MIT License (MIT)
 *
 * Copyright (c) 2007-2015 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 org.broad.igv.feature.tribble;

import org.broad.igv.feature.Exon;
import org.broad.igv.feature.IGVFeature;
import org.broad.igv.feature.LocusScore;
import org.broad.igv.feature.Strand;
import org.broad.igv.track.WindowFunction;
import org.broad.igv.util.collections.MultiMap;

import java.awt.*;

/**
 * @author jrobinso
 */
public class VCFFeature implements IGVFeature, htsjdk.tribble.Feature {

    private String chr;
    private int start;
    private String id = "";
    private String name;
    private String ref;
    private String alt;
    private float quality;
    private String filter;
    private String info;

    public VCFFeature(String chr, int start, String id, String ref, String alt, float quality, String filter, String info) {
        this.chr =  chr;
        this.start = start;
        this.id = id;
        this.ref = ref;
        this.alt = alt;
        this.name = "";
        this.quality = quality;
        this.filter = filter;
        this.info = info.replace(";", "<br>");
    }

    public float getScore() {
        return getQuality();
    }

    public String getValueString(double position, int mouseX, WindowFunction windowFunction) {
        StringBuffer buf = new StringBuffer();
        if (id != null && id.length() > 0) {
            buf.append(id + "<br>");
        }
        buf.append(ref + "->" + alt +  "<br>");
        buf.append("QUAL = " + quality + "<br>");
        buf.append("FILTER = " + filter + "<br>");
        buf.append("--------------<br>");
        buf.append(info);
        return buf.toString();

    }

    public int getStart() {
        return start;
    }

    public void setStart(int start) {
        this.start = start;
    }

    public int getEnd() {
        return start + 1;
    }

    public String getIdentifier() {
        return id;  //To change body of implemented methods use File | Settings | File Templates.
    }

    public String getName() {
        return name;  //To change body of implemented methods use File | Settings | File Templates.
    }

    public String getDescription() {
        return name;  //To change body of implemented methods use File | Settings | File Templates.
    }

    public boolean hasScore() {
        return false;  //To change body of implemented methods use File | Settings | File Templates.
    }

    public LocusScore copy() {
        throw new java.lang.UnsupportedOperationException("Copy not supported");
    }

    public Strand getStrand() {
        return Strand.NONE;  //To change body of implemented methods use File | Settings | File Templates.
    }

    public boolean hasStrand() {
        return false;  //To change body of implemented methods use File | Settings | File Templates.
    }

    public void setName(String name) {
        throw new java.lang.UnsupportedOperationException("Copy not supported");
    }

    public Color getColor() {
        return null;  //To change body of implemented methods use File | Settings | File Templates.
    }

    public boolean contains(IGVFeature feature) {
        return false;  //To change body of implemented methods use File | Settings | File Templates.
    }

    public java.util.List<Exon> getExons() {
        return null;  //To change body of implemented methods use File | Settings | File Templates.
    }

    public int getLength() {
        return 1;  //To change body of implemented methods use File | Settings | File Templates.
    }

    public MultiMap<String, String> getAttributes() {
        return null;  //To change body of implemented methods use File | Settings | File Templates.
    }

    public boolean contains(double location) {
        return location >= start && location < start + 1;  //To change body of implemented methods use File | Settings | File Templates.
    }

    public String getURL() {
        return null;  //To change body of implemented methods use File | Settings | File Templates.
    }

    public Exon getExonAt(double location) {
        return null;  //To change body of implemented methods use File | Settings | File Templates.
    }

    public void setEnd(int end) {
        throw new java.lang.UnsupportedOperationException("setEnd not supported");

    }

    public String getType() {
        return "VCF";  //To change body of implemented methods use File | Settings | File Templates.
    }

    public String getChr() {
        return chr;
    }

    @Override
    public String getContig() {
        return chr;
    }

    public void setChr(String chr) {
        throw new java.lang.UnsupportedOperationException("setEnd not supported");
    }

    public float getQuality() {
        return quality;
    }


    public String getFilter() {
        return filter;
    }

    public String getInfo() {
        return info;
    }


    // TODO -- move this up
    public String getLocusString() {
        return getChr() + ":" + getStart() + ":" + getEnd();
    }

}