/*
 * 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.track;

import com.google.common.eventbus.Subscribe;
import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.cli_plugin.PluginFeatureSource;
import org.broad.igv.cli_plugin.PluginSource;
import org.broad.igv.feature.*;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.renderer.*;
import org.broad.igv.session.IGVSessionReader;
import org.broad.igv.session.SubtlyImportant;
import org.broad.igv.tools.FeatureSearcher;
import org.broad.igv.tools.motiffinder.MotifFinderSource;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.UIConstants;
import org.broad.igv.ui.event.DataLoadedEvent;
import org.broad.igv.ui.panel.ReferenceFrame;
import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.util.*;
import org.broad.igv.variant.VariantTrack;
import htsjdk.tribble.Feature;
import htsjdk.tribble.TribbleException;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;

import javax.swing.*;
import javax.xml.bind.JAXBElement;
import javax.xml.bind.JAXBException;
import javax.xml.bind.MarshalException;
import javax.xml.bind.Marshaller;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlSeeAlso;
import javax.xml.bind.annotation.XmlType;
import javax.xml.namespace.QName;
import java.awt.*;
import java.awt.event.MouseEvent;
import java.io.IOException;
import java.util.*;
import java.util.List;

/**
 * Track which displays features, typically showing regions of the genome
 * in a qualitative way. Features are rendered using the specified FeatureRenderer.
 * The gene track is an example of a feature track.
 *
 * @author jrobinso
 */
@XmlType(factoryMethod = "getNextTrack")
@XmlSeeAlso({VariantTrack.class, PluginFeatureSource.class, MotifFinderSource.class})
public class FeatureTrack extends AbstractTrack {

    private static Logger log = Logger.getLogger(FeatureTrack.class);

    //All tracks have label "Track", we need to specify the type sometimes
    //but still preserve backwards compatibility
    @XmlAttribute
    protected Class clazz = FeatureTrack.class;

    public static final int MINIMUM_FEATURE_SPACING = 5;
    public static final int DEFAULT_MARGIN = 5;
    public static final int NO_FEATURE_ROW_SELECTED = -1;
    protected static final Color SELECTED_FEATURE_ROW_COLOR = new Color(100, 100, 100, 30);
    private static final int DEFAULT_EXPANDED_HEIGHT = 35;
    private static final int DEFAULT_SQUISHED_HEIGHT = 12;

    private int expandedRowHeight = DEFAULT_EXPANDED_HEIGHT;
    private int squishedRowHeight = DEFAULT_SQUISHED_HEIGHT;

    boolean fatalLoadError = false;

    Track.DisplayMode lastFeatureMode = null;  // Keeps track of the feature display mode before an auto-switch to COLLAPSE


    protected List<Rectangle> levelRects = new ArrayList();

    // TODO -- this is a memory leak, this cache needs cleared when the reference frame collection (gene list) changes
    /**
     * Map of reference frame name -> packed features
     */
    protected Map<String, PackedFeatures<IGVFeature>> packedFeaturesMap = Collections.synchronizedMap(new HashMap<String, PackedFeatures<IGVFeature>>());

    private FeatureRenderer renderer;

    private DataRenderer coverageRenderer;

    // true == features,  false =  coverage
    private boolean showFeatures = true;

    protected FeatureSource source;

    protected boolean featuresLoading = false;

    //track which row of the expanded track is selected by the user.
    //Selection goes away if tracks are collpased
    protected int selectedFeatureRowIndex = NO_FEATURE_ROW_SELECTED;

    //Feature selected by the user.  This is repopulated on each handleDataClick() call.
    protected IGVFeature selectedFeature = null;

    int margin = DEFAULT_MARGIN;

    private static boolean drawBorder = true;

    private boolean alternateExonColor = false;

    private static final String PLUGIN_SOURCE = "PluginSource";
    private static final String SEQUENCE_MATCH_SOURCE = "SequenceMatchSource";

    private static Object loadLock = new Object();

    //Force this track to load data synchronously.
    //With this set to false, it chooses depending on the source
    private boolean forceLoadSync = false;

    // TODO -- there are WAY too many constructors for this class

    /**
     * Construct with no feature source.  Currently this is only used for the SpliceJunctionFinderTrack subclass.
     *
     * @param id
     * @param name
     */
    public FeatureTrack(String id, String name) {
        super(id, name);
        setSortable(false);
    }

    public FeatureTrack(ResourceLocator locator, String id, String name) {
        super(locator, id, name);
        setSortable(false);
    }

    /**
     * Constructor with no ResourceLocator.  Note:  tracks using this constructor will not be recorded in the
     * "Resources" section of session files.
     *
     * @param id
     * @param name
     * @param source
     * @api
     */
    public FeatureTrack(String id, String name, FeatureSource source) {
        super(id, name);
        init(source, null);
        setSortable(false);
    }


    /**
     * Constructor specifically for BigWig data source
     *
     * @param locator
     * @param id
     * @param name
     * @param source
     */
    public FeatureTrack(ResourceLocator locator, String id, String name, FeatureSource source) {
        super(locator, id, name);
        init(source, locator.getPath());
        setSortable(false);
    }


    public FeatureTrack(ResourceLocator locator, FeatureSource source) {
        super(locator);
        init(source, locator != null ? locator.getPath() : null);
        setSortable(false);
    }


    public FeatureTrack(ResourceLocator locator, String id, FeatureSource source) {
        super(locator, id);
        init(source, locator.getPath());
    }

    /**
     * Create a new track which is a shallow copy of this one
     *
     * @param featureTrack
     */
    public FeatureTrack(FeatureTrack featureTrack) {
        this(featureTrack.getId(), featureTrack.getName(), featureTrack.source);
    }

    protected void init(FeatureSource source, String path) {

        this.source = source;
        setMinimumHeight(10);
        setColor(Color.blue.darker());

        coverageRenderer = new BarChartRenderer();
        if (source.getFeatureWindowSize() > 0) {
            visibilityWindow = source.getFeatureWindowSize();
        }

        this.renderer = path != null && path.endsWith("junctions.bed") ?
                new SpliceJunctionRenderer() : new IGVFeatureRenderer();

    }

    @Override
    public boolean isFilterable() {
        return false; // Don't filter "feature" tracks
    }

    @Override
    public int getHeight() {
        if (!isVisible()) {
            return 0;
        }
        int rowHeight = getDisplayMode() == DisplayMode.SQUISHED ? squishedRowHeight : expandedRowHeight;
        int minHeight = rowHeight * Math.max(1, getNumberOfFeatureLevels());
        return Math.max(minHeight, super.getHeight());
    }

    public int getExpandedRowHeight() {
        return expandedRowHeight;
    }

    public void setExpandedRowHeight(int expandedRowHeight) {
        this.expandedRowHeight = expandedRowHeight;
    }

    public int getSquishedRowHeight() {
        return squishedRowHeight;
    }

    public void setSquishedRowHeight(int squishedRowHeight) {
        this.squishedRowHeight = squishedRowHeight;
    }

    public int getFeatureWindowSize() {
        return source.getFeatureWindowSize();
    }

    public void setRendererClass(Class rc) {
        try {
            renderer = (FeatureRenderer) rc.newInstance();
        } catch (Exception ex) {
            log.error("Error instatiating renderer ", ex);
        }
    }

    public void setMargin(int margin) {
        this.margin = margin;
    }

    @Override
    public void setProperties(TrackProperties trackProperties) {
        super.setProperties(trackProperties);
        if (trackProperties.getFeatureVisibilityWindow() >= 0) {
            setVisibilityWindow(trackProperties.getFeatureVisibilityWindow());
        }
        alternateExonColor = trackProperties.isAlternateExonColor();

    }


    public void setWindowFunction(WindowFunction type) {
        // Ignored for feature tracks
    }


    /**
     * Return the maximum number of features for any panel in this track.  In whole genome view there is a single panel,
     * but there are multiple in gene list view (one for each gene list).
     *
     * @return
     */
    public int getNumberOfFeatureLevels() {
        if (areFeaturesStacked() && packedFeaturesMap.size() > 0) {
            int n = 0;
            synchronized (packedFeaturesMap) {
                for (PackedFeatures pf : packedFeaturesMap.values()) {
                    //dhmay adding null check.  To my mind this shouldn't be necessary, but we're encountering
                    //it intermittently.  Food for future thought
                    if (pf != null) {
                        n = Math.max(n, pf.getRowCount());
                    }
                }
            }
            return n;
        }
        return 1;
    }


    /**
     * @return Whether features are displayed stacked on top of one another, rather than overlapping
     */
    protected boolean areFeaturesStacked() {
        return getDisplayMode() != DisplayMode.COLLAPSED;
    }

    /**
     * Return a score over the interval.  This is required by the track interface to support sorting.
     */
    public float getRegionScore(String chr, int start, int end, int zoom, RegionScoreType scoreType, String frameName) {

        try {
            Iterator<Feature> features = source.getFeatures(chr, start, end);
            if (features != null) {
                if (scoreType == RegionScoreType.MUTATION_COUNT && this.getTrackType() == TrackType.MUTATION) {
                    int count = 0;
                    while (features.hasNext()) {
                        Feature f = features.next();
                        if (f.getStart() > end) {
                            break;
                        }
                        if (f.getEnd() >= start) {
                            count++;
                        }
                    }

                    return count;
                } else if (scoreType == RegionScoreType.SCORE) {
                    // Average score of features in region.  Note: Should the score be weighted by genomic size?
                    float regionScore = 0;
                    int nValues = 0;
                    while (features.hasNext()) {
                        Feature f = features.next();
                        if (f instanceof IGVFeature) {
                            if ((f.getEnd() >= start) && (f.getStart() <= end)) {
                                float value = ((IGVFeature) f).getScore();
                                regionScore += value;
                                nValues++;
                            }
                        }
                    }
                    if (nValues == 0) {
                        // No scores in interval
                        return -Float.MAX_VALUE;
                    } else {
                        return regionScore / nValues;
                    }
                }
            }
        } catch (IOException e) {
            log.error("Error counting features.", e);
        }
        return -Float.MAX_VALUE;
    }


    public FeatureRenderer getRenderer() {
        if (renderer == null) {
            setRendererClass(IGVFeatureRenderer.class);
        }
        return renderer;
    }

    /**
     * Return a string for popup text.
     *
     * @param chr
     * @param position in genomic coordinates
     * @param y        - pixel position in panel coordinates (i.e. not track coordinates)
     * @return
     */
    public String getValueStringAt(String chr, double position, int y, ReferenceFrame frame) {


        if (showFeatures) {

            List<Feature> allFeatures = getAllFeatureAt(position, y, frame);
            if (allFeatures == null) {
                return null;
            }

            StringBuffer buf = new StringBuffer();
            boolean firstFeature = true;
            int maxNumber = 10;
            int n = 1;
            for (Feature feature : allFeatures) {
                if (feature != null && feature instanceof IGVFeature) {
                    if (!firstFeature) {
                        buf.append("<br/>--------------<br/>");
                    }

                    IGVFeature igvFeature = (IGVFeature) feature;
                    String vs = igvFeature.getValueString(position, null);
                    buf.append(vs);

                    if (IGV.getInstance().isShowDetailsOnClick()) {
                        // URL
                        String url = getFeatureURL(igvFeature);

                        if (url != null) {
                            buf.append("<br/><a href=\"" + url + "\">" + url + "</a>");
                        }
                    }

                    firstFeature = false;

                    if (n > maxNumber) {
                        buf.append("...");
                        break;
                    }
                }
                n++;
            }

            return buf.toString();
        } else {
            int zoom = Math.max(0, frame.getZoom());
            if (source == null) {
                return null;
            }
            List<LocusScore> scores = source.getCoverageScores(chr, (int) position - 10, (int) position + 10, zoom);

            if (scores == null) {
                return "";
            } else {
                // give a +/- 2 pixel buffer, otherwise very narrow features will be missed.
                double bpPerPixel = frame.getScale();
                int minWidth = (int) (2 * bpPerPixel);    /* * */
                LocusScore score = (LocusScore) FeatureUtils.getFeatureAt(position, minWidth, scores);
                return score == null ? null : "Mean count: " + score.getScore();
            }

        }
    }


    private String getFeatureURL(IGVFeature igvFeature) {
        String url = igvFeature.getURL();
        if (url == null) {
            String trackURL = getUrl();
            if (trackURL != null && igvFeature.getIdentifier() != null) {
                String encodedID = StringUtils.encodeURL(igvFeature.getIdentifier());
                url = trackURL.replaceAll("\\$\\$", encodedID);
            }
        }
        return url;
    }


    /**
     * Get all features which overlap the specified locus
     *
     * @return
     */
    public List<Feature> getFeatures(String chr, int start, int end) {
        List<Feature> features = new ArrayList<Feature>();
        try {
            Iterator<Feature> iter = source.getFeatures(chr, start, end);
            while (iter.hasNext()) {
                features.add(iter.next());
            }
        } catch (IOException e) {
            throw new RuntimeException(e);
        }
        return features;
    }

    /**
     * @param position in genomic coordinates
     * @param y        pixel location in panel coordinates.  // TODO offset by track origin before getting here?
     * @param frame
     * @return
     */
    private List<Feature> getAllFeatureAt(double position, int y, ReferenceFrame frame) {
        // Determine the level number (for expanded tracks)
        int featureRow = getFeatureRow(y);
        return getFeaturesAtPositionInFeatureRow(position, featureRow, frame);
    }

    /**
     * Determine which row the user clicked in and return the appropriate feature
     *
     * @param y
     * @return
     */
    private int getFeatureRow(int y) {
        // Determine the level number (for expanded tracks).
        int featureRow = 0;
        if (levelRects != null) {
            for (int i = 0; i < levelRects.size(); i++) {
                Rectangle r = levelRects.get(i);
                if ((y >= r.y) && (y <= r.getMaxY())) {
                    featureRow = i;
                    break;
                }
            }
        }
        return featureRow;
    }

    /**
     * Knowing the feature row, figure out which feature is at {@code position}. If not expanded,
     * featureRow is ignored
     *
     * @param position
     * @param featureRow
     * @param frame
     * @return
     */
    public List<Feature> getFeaturesAtPositionInFeatureRow(double position, int featureRow, ReferenceFrame frame) {

        PackedFeatures<IGVFeature> packedFeatures = packedFeaturesMap.get(frame.getName());

        if (packedFeatures == null) {
            return null;
        }

        //If features are stacked we look at only the row.
        //If they are collapsed on top of each other, we get all features in all rows
        int nLevels = areFeaturesStacked() ? packedFeatures.getRowCount() : 1;
        List<IGVFeature> possFeatures = null;
        if ((nLevels > 1) && (featureRow < nLevels)) {
            possFeatures = packedFeatures.getRows().get(featureRow).getFeatures();
        } else {
            possFeatures = packedFeatures.getFeatures();
        }

        List<Feature> featureList = null;
        if (possFeatures != null) {
            // give a 2 pixel window, otherwise very narrow features will be missed.
            double bpPerPixel = frame.getScale();
            double minWidth = MINIMUM_FEATURE_SPACING * bpPerPixel;
            int maxFeatureLength = packedFeatures.getMaxFeatureLength();
            featureList = FeatureUtils.getAllFeaturesAt(position, maxFeatureLength, minWidth, possFeatures);
        }
        return featureList;
    }


    public WindowFunction getWindowFunction() {
        return WindowFunction.count;
    }

    @Override
    public boolean handleDataClick(TrackClickEvent te) {

        MouseEvent e = te.getMouseEvent();

        //Selection of an expanded feature row
        if (areFeaturesStacked()) {
            if (levelRects != null) {
                for (int i = 0; i < levelRects.size(); i++) {
                    Rectangle rect = levelRects.get(i);
                    if (rect.contains(e.getPoint())) {
                        if (i == selectedFeatureRowIndex)
                            setSelectedFeatureRowIndex(FeatureTrack.NO_FEATURE_ROW_SELECTED);
                        else {
                            //make this track selected
                            setSelected(true);
                            //select the appropriate row
                            setSelectedFeatureRowIndex(i);
                        }
                        IGV.getInstance().doRefresh();
                        break;
                    }
                }
            }
        }

        //For feature selection
        selectedFeature = null;

        Feature f = getFeatureAtMousePosition(te);
        if (f != null && f instanceof IGVFeature) {
            IGVFeature igvFeature = (IGVFeature) f;
            if (selectedFeature != null && igvFeature.contains(selectedFeature) && (selectedFeature.contains(igvFeature))) {
                //If something already selected, then if it's the same as this feature, deselect, otherwise, select
                //this feature.
                //todo: contains() might not do everything I want it to.
                selectedFeature = null;
            } else {
                //if nothing already selected, or something else selected,
                // select this feature
                selectedFeature = igvFeature;
            }

            if (IGV.getInstance().isShowDetailsOnClick()) {
                openTooltipWindow(te);
            } else {
                String url = getFeatureURL(igvFeature);
                if (url != null) {
                    try {
                        BrowserLauncher.openURL(url);
                    } catch (IOException e1) {
                        log.error("Error launching url: " + url);
                    }
                    e.consume();
                    return true;
                }
            }
        }

        return false;
    }

    public Feature getFeatureAtMousePosition(TrackClickEvent te) {
        MouseEvent e = te.getMouseEvent();
        final ReferenceFrame referenceFrame = te.getFrame();
        if (referenceFrame != null) {
            double location = referenceFrame.getChromosomePosition(e.getX());
            List<Feature> features = getAllFeatureAt(location, e.getY(), referenceFrame);
            return (features != null && features.size() > 0) ? features.get(0) : null;
        } else {
            return null;
        }
    }

    /**
     * Required by the interface, really not applicable to feature tracks
     */
    public boolean isLogNormalized() {
        return true;
    }


    public void overlay(RenderContext context, Rectangle rect) {
        renderFeatures(context, rect);
    }

    @Override
    public void setDisplayMode(DisplayMode mode) {
        // Explicity setting the display mode overrides the automatic switch
        lastFeatureMode = null;
        super.setDisplayMode(mode);
    }

    @Override
    public void load(RenderContext context) {
        ReferenceFrame frame = context.getReferenceFrame();
        PackedFeatures packedFeatures = packedFeaturesMap.get(frame.getName());
        String chr = context.getChr();
        int start = (int) context.getOrigin();
        int end = (int) context.getEndLocation();
        if (packedFeatures == null || !packedFeatures.containsInterval(chr, start, end)) {
            try {
                context.getReferenceFrame().getEventBus().unregister(FeatureTrack.this);
            } catch (IllegalArgumentException e) {
                //Don't care
            }
            loadFeatures(frame.getChrName(), (int) frame.getOrigin(), (int) frame.getEnd(), context);
        }
    }

    @Override
    public void render(RenderContext context, Rectangle rect) {
        Rectangle renderRect = new Rectangle(rect);
        renderRect.y = renderRect.y + margin;
        renderRect.height -= margin;


        showFeatures = isShowFeatures(context);
        if (showFeatures) {
            if (lastFeatureMode != null) {
                super.setDisplayMode(lastFeatureMode);
                lastFeatureMode = null;
            }
            renderFeatures(context, renderRect);
        } else {
            if (getDisplayMode() != DisplayMode.COLLAPSED) {
                // An ugly hack, but we want to prevent this for vcf tracks
                if (!(this instanceof VariantTrack)) {
                    lastFeatureMode = getDisplayMode();
                    super.setDisplayMode(DisplayMode.COLLAPSED);
                }
            }
            renderCoverage(context, renderRect);
        }

        if (FeatureTrack.drawBorder) {
            Graphics2D borderGraphics = context.getGraphic2DForColor(UIConstants.TRACK_BORDER_GRAY);
            borderGraphics.drawLine(rect.x, rect.y, rect.x + rect.width, rect.y);
            //TODO Fix height for variant track
            borderGraphics.drawLine(rect.x, rect.y + rect.height, rect.x + rect.width, rect.y + rect.height);
        }

    }

    protected boolean isShowFeatures(RenderContext context) {

        if (context.getChr().equals(Globals.CHR_ALL)) {
            return false;
        } else {
            double windowSize = context.getEndLocation() - context.getOrigin();
            int vw = getVisibilityWindow();
            return (vw <= 0 || windowSize <= vw);
        }
    }

    protected void renderCoverage(RenderContext context, Rectangle inputRect) {
        if (source == null) {
            return;
        }

        final String chr = context.getChr();

        List<LocusScore> scores = chr.equals(Globals.CHR_ALL) ?
                source.getCoverageScores(chr, (int) context.getOrigin(),
                        (int) context.getEndLocation(), context.getZoom()) :
                null;

        if (scores == null) {
            Graphics2D g = context.getGraphic2DForColor(Color.gray);
            Rectangle textRect = new Rectangle(inputRect);

            // Keep text near the top of the track rectangle
            textRect.height = Math.min(inputRect.height, 20);
            String message = chr.equals(Globals.CHR_ALL) ? "Zoom in to see features." :
                    "Zoom in to see features, or right-click to increase Feature Visibility Window.";
            GraphicUtils.drawCenteredText(message, textRect, g);

        } else {
            float max = getMaxEstimate(scores);
            ContinuousColorScale cs = getColorScale();
            if (cs != null) {
                cs.setPosEnd(max);
            }
            setDataRange(new DataRange(0, 0, max));
            coverageRenderer.render(scores, context, inputRect, this);
        }
    }

    private float getMaxEstimate(List<LocusScore> scores) {
        float max = 0;
        int n = Math.min(200, scores.size());
        for (int i = 0; i < n; i++) {
            max = Math.max(max, scores.get(i).getScore());
        }
        return max;
    }

    /**
     * Render features in the given input rectangle.
     *
     * @param context
     * @param inputRect
     */
    protected void renderFeatures(RenderContext context, Rectangle inputRect) {

        if (featuresLoading || fatalLoadError) {
            return;
        }

        if (log.isTraceEnabled()) {
            String msg = String.format("renderFeatures: %s frame: %s", getName(), context.getReferenceFrame().getName());
            log.trace(msg);
        }

        //Attempt to load the relevant data. Note that there is no guarantee
        //the data will be loaded once preload exits, as loading may be asynchronous
        load(context);
        PackedFeatures packedFeatures = packedFeaturesMap.get(context.getReferenceFrame().getName());

        if (packedFeatures == null || !packedFeatures.overlapsInterval(context.getChr(), (int) context.getOrigin(), (int) context.getEndLocation() + 1)) {
            return;
        }

        try {
            renderFeatureImpl(context, inputRect, packedFeatures);
        } catch (TribbleException e) {
            log.error("Tribble error", e);
            //Error loading features.  We'll let the user decide if this is "fatal" or not.  
            if (!fatalLoadError) {
                fatalLoadError = true;
                boolean unload = MessageUtils.confirm("<html> Error loading features: " + e.getMessage() +
                        "<br>Unload track " + getName() + "?");
                if (unload) {
                    Collection<Track> tmp = Arrays.asList((Track) this);
                    IGV.getInstance().removeTracks(tmp);
                    IGV.getInstance().doRefresh();
                } else {
                    fatalLoadError = false;
                }
            }
        }


    }

    protected void renderFeatureImpl(RenderContext context, Rectangle inputRect, PackedFeatures packedFeatures) {


        FeatureRenderer renderer = getRenderer();
        if (areFeaturesStacked()) {
            List<PackedFeatures.FeatureRow> rows = packedFeatures.getRows();
            if (rows != null && rows.size() > 0) {

                int nLevels = rows.size();
                synchronized (levelRects) {

                    levelRects.clear();

                    // Divide rectangle into equal height levels
                    double h = inputRect.getHeight() / nLevels;
                    Rectangle rect = new Rectangle(inputRect.x, inputRect.y, inputRect.width, (int) h);
                    int i = 0;

                    renderer.reset();
                    for (PackedFeatures.FeatureRow row : rows) {
                        levelRects.add(new Rectangle(rect));
                        renderer.render(row.features, context, levelRects.get(i), this);
                        if (selectedFeatureRowIndex == i) {
                            Graphics2D fontGraphics = context.getGraphic2DForColor(SELECTED_FEATURE_ROW_COLOR);
                            fontGraphics.fillRect(rect.x, rect.y, rect.width, rect.height);
                        }
                        rect.y += h;
                        i++;
                    }
                }
            }
        } else {
            List<IGVFeature> features = packedFeatures.getFeatures();
            if (features != null) {
                renderer.render(features, context, inputRect, this);
            }
        }
    }


    /**
     * Loads and segregates features into rows such that they do not overlap.  Loading is done in a background
     * thread.
     *
     * @param chr
     * @param start
     * @param end
     */
    protected void loadFeatures(final String chr, final int start, final int end, final RenderContext context) {

        boolean aSync = !forceLoadSync && !(source instanceof FeatureCollectionSource);


        NamedRunnable runnable = new NamedRunnable() {
            public void run() {
                try {
                    featuresLoading = true;

                    synchronized (loadLock) {
                        if (log.isTraceEnabled()) {
                            log.trace(String.format("Loading features: %s:%d-%d", chr, start, end));
                        }


                        int delta = (end - start) / 2;
                        int expandedStart = start - delta;
                        int expandedEnd = end + delta;

                        //Make sure we are only querying within the chromosome
                        //we allow for somewhat pathological cases of start
                        //being negative and end being outside, but
                        //only if directly queried. Our expansion should not
                        //set start < 0 or end > chromosomeLength
                        if (start >= 0) {
                            expandedStart = Math.max(0, expandedStart);
                        }


                        Genome genome = GenomeManager.getInstance().getCurrentGenome();
                        if (genome != null) {
                            Chromosome c = genome.getChromosome(chr);
                            if (c != null && end < c.getLength()) expandedEnd = Math.min(c.getLength(), expandedEnd);
                        }

                        Iterator<Feature> iter = source.getFeatures(chr, expandedStart, expandedEnd);
                        if (iter == null) {
                            PackedFeatures pf = new PackedFeatures(chr, expandedStart, expandedEnd);
                            packedFeaturesMap.put(context.getReferenceFrame().getName(), pf);
                        } else {
                            //dhmay putting a switch in for different packing behavior in splice junction tracks.
                            //This should probably be switched somewhere else, but that would require a big refactor.
                            PackedFeatures pf = new PackedFeatures(chr, expandedStart, expandedEnd, iter, getName());
                            packedFeaturesMap.put(context.getReferenceFrame().getName(), pf);
                        }
                    }

                    //Now that features are loaded, we may need to repaint
                    //to accommodate.
                    context.getReferenceFrame().getEventBus().post(new DataLoadedEvent(context));
                } catch (Exception e) {
                    // Mark the interval with an empty feature list to prevent an endless loop of load
                    // attempts.
                    PackedFeatures pf = new PackedFeatures(chr, start, end);
                    packedFeaturesMap.put(context.getReferenceFrame().getName(), pf);
                    String msg = "Error loading features for interval: " + chr + ":" + start + "-" + end + " <br>" + e.toString();
                    MessageUtils.showMessage(msg);
                    log.error(msg, e);
                } finally {
                    featuresLoading = false;
                }
            }

            public String getName() {
                return "Load features: " + FeatureTrack.this.getName();
            }
        };

        if (aSync) {
            context.getReferenceFrame().getEventBus().register(FeatureTrack.this);
            LongRunningTask.submit(runnable);
        } else {
            runnable.run();
        }

    }

    public void setForceLoadSync(boolean forceLoadSync){
        this.forceLoadSync = forceLoadSync;
    }

    /**
     * Called after features are finished loading, which can be asynchronous
     *
     * @param event
     */
    @Subscribe
    private void receiveDataLoaded(DataLoadedEvent event) {
        if (IGV.hasInstance()) {
            // TODO -- WHY IS THIS HERE????
            //TODO Assuming this is necessary, there can be many data loaded events in succession,
            //don't want to layout for each one
            IGV.getInstance().layoutMainPanel();
        }
        JComponent panel = event.context.getPanel();
        if (panel != null) panel.repaint();
    }

    /**
     * Return the nextLine or previous feature relative to the center location.
     * TODO -- investigate delegating this method to FeatureSource, where it might be possible to simplify the implementation
     *
     * @param chr
     * @param center
     * @param forward
     * @return
     * @throws IOException
     */
    public Feature nextFeature(String chr, double center, boolean forward, ReferenceFrame frame) throws IOException {

        Feature f = null;
        boolean canScroll = (forward && !frame.windowAtEnd()) || (!forward && frame.getOrigin() > 0);
        PackedFeatures packedFeatures = packedFeaturesMap.get(frame.getName());

        if (packedFeatures != null && packedFeatures.containsInterval(chr, (int) center - 1, (int) center + 1)) {
            if (packedFeatures.getFeatures().size() > 0 && canScroll) {
                f = (forward ? FeatureUtils.getFeatureAfter(center + 1, packedFeatures.getFeatures()) :
                        FeatureUtils.getFeatureBefore(center - 1, packedFeatures.getFeatures()));
            }

            if (f == null) {
                FeatureSource rawSource = source;
                if (source instanceof CachingFeatureSource) {
                    rawSource = ((CachingFeatureSource) source).getSource();
                }
                if (rawSource instanceof MotifFinderSource || rawSource instanceof PluginFeatureSource) {
                    FeatureTrackUtils.nextFeatureSearch(source, chr, packedFeatures.getStart(), packedFeatures.getEnd(),
                            forward, new FeatureSearcher.GotoFeatureHandler());
                } else {
                    f = FeatureTrackUtils.nextFeature(source, chr, packedFeatures.getStart(), packedFeatures.getEnd(), forward);
                }

            }
        }

        return f;
    }

    public void setVisibilityWindow(int windowSize) {
        super.setVisibilityWindow(windowSize);
        packedFeaturesMap.clear();
        source.setFeatureWindowSize(visibilityWindow);
    }

    public int getSelectedFeatureRowIndex() {
        return selectedFeatureRowIndex;
    }

    public void setSelectedFeatureRowIndex(int selectedFeatureRowIndex) {
        this.selectedFeatureRowIndex = selectedFeatureRowIndex;
    }

    public IGVFeature getSelectedFeature() {
        return selectedFeature;
    }

    public static boolean isDrawBorder() {
        return drawBorder;
    }

    public static void setDrawBorder(boolean drawBorder) {
        FeatureTrack.drawBorder = drawBorder;
    }

    public boolean isAlternateExonColor() {
        return alternateExonColor;
    }

    @SubtlyImportant
    private static FeatureTrack getNextTrack() {
        FeatureTrack out = (FeatureTrack) IGVSessionReader.getNextTrack();
        if (out == null) out = new FeatureTrack((String) null, null);
        return out;
    }

    @Override
    public void restorePersistentState(Node node, int version) throws JAXBException {
        super.restorePersistentState(node, version);
        if (node.hasChildNodes()) {
            NodeList childNodes = node.getChildNodes();
            for (int ii = 0; ii < childNodes.getLength(); ii++) {
                Node child = childNodes.item(ii);
                String nodeName = child.getNodeName();
                if (nodeName.contains("#text")) continue;

                if (nodeName.equalsIgnoreCase(PLUGIN_SOURCE)) {
                    source = IGVSessionReader.getJAXBContext().createUnmarshaller().unmarshal(child, PluginFeatureSource.class).getValue();
                } else if (nodeName.equalsIgnoreCase(SEQUENCE_MATCH_SOURCE)) {
                    FeatureSource rawSource = IGVSessionReader.getJAXBContext().createUnmarshaller().unmarshal(child, MotifFinderSource.class).getValue();
                    source = new CachingFeatureSource(rawSource);
                } else {
                    try {
                        FeatureSource newSource = (FeatureSource) IGVSessionReader.getJAXBContext().createUnmarshaller().unmarshal(child, Class.forName(nodeName)).getValue();
                        source = newSource;
                    } catch (Exception e) {
                        //Lots can go wrong, it just means this isn't a FeatureSource
                        //Probably not an error
                    }
                }
            }
        }
    }

    /**
     * @param m
     * @param trackElement
     * @throws JAXBException
     */
    public void marshalSource(Marshaller m, Element trackElement) throws JAXBException {
        if (source == null) return;
        FeatureSource rawSource = source;
        if (rawSource instanceof CachingFeatureSource) {
            rawSource = ((CachingFeatureSource) rawSource).getSource();
        }


        //We apply special treatment for a few classes
        if (rawSource instanceof PluginSource) {
            JAXBElement element = new JAXBElement<PluginSource>(new QName("", PLUGIN_SOURCE), PluginSource.class,
                    (PluginSource) rawSource);
            m.marshal(element, trackElement);
        } else if (rawSource instanceof MotifFinderSource) {
            JAXBElement element = new JAXBElement<MotifFinderSource>(new QName("", SEQUENCE_MATCH_SOURCE), MotifFinderSource.class,
                    (MotifFinderSource) rawSource);
            m.marshal(element, trackElement);
        } else {
            //Users can write their own FeatureSources, we tag with the fully qualified class name
            Class<? extends FeatureSource> srcClazz = rawSource.getClass();
            JAXBElement element = new JAXBElement(new QName("", srcClazz.getName()), srcClazz, rawSource);
            try {
                m.marshal(element, trackElement);
            } catch (MarshalException e) {
                //This happens if the source is not marshallable
                //Many of our classes can't, and that's not an error
            }
        }
    }

    /**
     * This method exists for Plugin tracks. When restoring a session there is no guarantee of track
     * order, so arguments referring to other tracks may fail to resolve. We update those references
     * here after all tracks have been processed
     *
     * @param allTracks
     */
    public void updateTrackReferences(List<Track> allTracks) {
        if (source instanceof PluginSource) {
            ((PluginSource) source).updateTrackReferences(allTracks);
        }
    }

    /**
     * Features are packed upon loading, effectively a cache.
     * This clears that cache. Used to force a refresh
     *
     * @api
     */
    public void clearPackedFeatures() {
        this.packedFeaturesMap.clear();
    }

}

