/*
* Copyright (c) 2007-2012 The Broad Institute, Inc.
* SOFTWARE COPYRIGHT NOTICE
* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*/
package org.broad.igv.session;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.renderer.ColorScale;
import org.broad.igv.renderer.ColorScaleFactory;
import org.broad.igv.track.DataSourceTrack;
import org.broad.igv.track.DataTrack;
import org.broad.igv.ui.color.ColorUtilities;
import javax.xml.bind.annotation.adapters.XmlAdapter;
/**
* User: jacob
* Date: 2013-Jan-02
*/
public class SessionXmlAdapters{
public static class Color extends XmlAdapter<String, java.awt.Color>{
@Override
public String marshal(java.awt.Color value) throws Exception {
if (value != null) {
return ColorUtilities.colorToString(value);
}
return null;
}
@Override
public java.awt.Color unmarshal(String colorString) throws Exception {
if (colorString != null) {
return ColorUtilities.stringToColor(colorString);
}
return null;
}
}
public static class Renderer extends XmlAdapter<String, org.broad.igv.renderer.Renderer>{
@Override
public String marshal(org.broad.igv.renderer.Renderer renderer) throws Exception {
if (renderer != null) {
RendererFactory.RendererType type = RendererFactory.getRenderType(renderer);
if (type != null) {
return type.name();
}
}
return null;
}
@Override
public org.broad.igv.renderer.Renderer unmarshal(String rendererType) throws Exception {
if (rendererType != null) {
Class rendererClass = RendererFactory.getRendererClass(rendererType);
if (rendererClass != null) {
return (org.broad.igv.renderer.Renderer) rendererClass.newInstance();
}
}
return null;
}
}
public static class ContinuousColorScale extends XmlAdapter<String, org.broad.igv.renderer.ContinuousColorScale>{
@Override
public String marshal(org.broad.igv.renderer.ContinuousColorScale colorScale) throws Exception {
if (colorScale != null && !colorScale.isDefault()) {
return colorScale.asString();
}
return null;
}
@Override
public org.broad.igv.renderer.ContinuousColorScale unmarshal(String colorScaleString) throws Exception {
if (colorScaleString != null) {
ColorScale cs = ColorScaleFactory.getScaleFromString(colorScaleString);
if(cs instanceof org.broad.igv.renderer.ContinuousColorScale){
return (org.broad.igv.renderer.ContinuousColorScale) cs;
}
}
return null;
}
}
public static class Height extends XmlAdapter<String, Integer>{
@Override
public String marshal(Integer height) throws Exception {
if(height > 0){
return "" + height;
}
return null;
}
@Override
public Integer unmarshal(String heightString) throws Exception {
if(heightString != null){
return Integer.parseInt(heightString);
}
return null;
}
}
public static class Genome extends XmlAdapter<String, org.broad.igv.feature.genome.Genome>{
@Override
public String marshal(org.broad.igv.feature.genome.Genome v) throws Exception {
return v.getId();
}
@Override
public org.broad.igv.feature.genome.Genome unmarshal(String v) throws Exception {
org.broad.igv.feature.genome.Genome genome = GenomeManager.getInstance().getCurrentGenome();
if(genome != null && !genome.getId().equals(v)){
throw new IllegalStateException("Must load the proper genome before unmarshalling");
}
return genome;
}
}
public static class DataTrackIDAdapter extends XmlAdapter<String, org.broad.igv.track.DataTrack> {
@Override
public String marshal(DataTrack dataTrack) throws Exception {
return dataTrack.getId();
}
@Override
public DataTrack unmarshal(String trackId) throws Exception {
DataTrack dataTrack = (DataTrack) IGVSessionReader.getMatchingTrack(trackId, null);
if(dataTrack == null){
dataTrack = new DataSourceTrack(null, trackId, null, null);
}
return dataTrack;
}
}
}