/*
* The MIT License (MIT)
*
* Copyright (c) 2016 University of California San Diego
* Author: Jim Robinson
*
* 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.bionano;
import org.broad.igv.feature.AbstractFeature;
import org.broad.igv.feature.Strand;
import org.broad.igv.track.WindowFunction;
import java.awt.*;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
public class SMAPFeature extends AbstractFeature {
private int linkId;
private String[] headers;
private String[] tokens;
double confidence;
List<SMAPFeature> partialFeatures;
public SMAPFeature(String chr, int start, int end, double confidence, String type, String[] headers, String[] tokens) {
super(chr, start, end, Strand.NONE);
// TODO -- check tokens length
this.tokens = tokens;
this.confidence = confidence;
this.type = type;
this.headers = headers;
}
public SMAPFeature(String chr, int start, int end, double conf, String t, String[] headers, String[] tokens, int linkId) {
this(chr, start, end, conf, t, headers, tokens);
this.linkId = linkId;
}
@Override
public Color getColor() {
if (colors.containsKey(type)) {
return colors.get(type);
} else {
return super.getColor();
}
}
public void addPartialFeature(SMAPFeature smapFeature) {
if (partialFeatures == null) {
partialFeatures = new ArrayList<SMAPFeature>();
}
partialFeatures.add(smapFeature);
}
@Override
public String getURL() {
return null;
}
@Override
public String getValueString(double position, int mouseX, WindowFunction windowFunction) {
StringBuffer buf = new StringBuffer();
buf.append("<b>Type: " + type + "</b>");
for (int i = 0; i < headers.length; i++) {
buf.append("<br>" + headers[i] + ": " + tokens[i]);
}
if(partialFeatures != null) {
for(SMAPFeature pf : partialFeatures) {
buf.append("<hr>");
buf.append(pf.getValueString(position, mouseX, windowFunction));
}
}
return buf.toString();
}
public int getLinkId() {
return linkId;
}
static Map<String, Color> colors = new HashMap<String, Color>();
static {
colors.put("insertion", new Color(0, 128, 0));
colors.put("deletion", new Color(255, 0, 0));
}
}