/*
 * 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.
 */


//chr2:128,565,093-128,565,156

package org.broad.igv.variant;

import htsjdk.tribble.Feature;
import htsjdk.variant.variantcontext.GenotypeType;
import org.broad.igv.Globals;
import org.broad.igv.event.IGVEventBus;
import org.broad.igv.event.IGVEventObserver;
import org.broad.igv.event.TrackGroupEvent;
import org.broad.igv.feature.FeatureUtils;
import org.broad.igv.jbrowse.CircularViewUtilities;
import org.broad.igv.logging.LogManager;
import org.broad.igv.logging.Logger;
import org.broad.igv.prefs.IGVPreferences;
import org.broad.igv.prefs.PreferencesManager;
import org.broad.igv.renderer.GraphicUtils;
import org.broad.igv.track.*;
import org.broad.igv.ui.FontManager;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.panel.*;
import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.util.*;
import org.broad.igv.variant.vcf.MateVariant;
import org.w3c.dom.Document;
import org.w3c.dom.Element;

import java.awt.*;
import java.awt.event.MouseEvent;
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.text.DecimalFormat;
import java.util.List;
import java.util.*;
import java.util.stream.Collectors;

import static org.broad.igv.prefs.Constants.*;

/**
 * @author Jesse Whitworth, Jim Robinson, Fabien Campagne
 */

public class VariantTrack extends FeatureTrack implements IGVEventObserver {


    private static Logger log = LogManager.getLogger(VariantTrack.class);

    static final DecimalFormat numFormat = new DecimalFormat("#.###");

    private static final Color CIRC_VIEW_DEFAULT_COLOR = new Color(27, 192, 249);
    private static final int GROUP_BORDER_WIDTH = 3;
    private static final Color BAND1_COLOR = new Color(245, 245, 245);
    private static final Color BAND2_COLOR = Color.white;
    private static final Color SELECTED_BAND_COLOR = new Color(210, 210, 210);
    private static final Color borderGray = new Color(200, 200, 200);

    private final static int DEFAULT_EXPANDED_GENOTYPE_HEIGHT = 15;
    private final int DEFAULT_SQUISHED_HEIGHT = 4;
    private final static int DEFAULT_EXPANDED_VARIANT_HEIGHT = 25;
    private final static int DEFAULT_SQUISHED_VARIANT_HEIGHT = 6;
    private final static int MAX_FILTER_LINES = 15;
    private final static int WG_TRACK_HEIGHT = 40;


    // TODO -- this needs to be settable
    public static int METHYLATION_MIN_BASE_COUNT = 10;

    public static boolean isVCF(String format) {
        return (format.equals("vcf3") ||
                format.equals("vcf4") ||
                format.equals("vcf") ||
                format.equals("bcf"));
    }


    private VariantRenderer renderer;

    /**
     * When this flag is true, we have detected that the VCF file contains the FORMAT MR column representing
     * methylation data. This will enable the "Color By/Methylation Rate" menu item.
     */
    private boolean enableMethylationRateSupport;

    /**
     * Top (y) position of this track.  This is updated whenever the track is drawn.
     */
    private int top;

    private boolean showGenotypes;

    /**
     * The height of a single row in in squished mode
     */
    private int squishedHeight = DEFAULT_SQUISHED_HEIGHT;

    /**
     * List of all samples, in the order they appear in the file.
     */
    List<String> allSamples;

    /**
     * Boolean indicating if samples are grouped.
     */
    private boolean grouped;

    /**
     * The id of the group used to group samples.
     */
    private String groupByAttribute;

    /**
     * Map of group -> samples.  Each entry defines a group, the key is the group name and the value the list of
     * samples in the group.
     */
    LinkedHashMap<String, List<String>> samplesByGroups = new LinkedHashMap<String, List<String>>();


    /**
     * Current coloring option
     */
    private ColorMode genotypeColorMode = ColorMode.GENOTYPE;


    private ColorMode siteColorMode;

    /**
     * When true, variants that are marked filtering are not drawn.
     */
    private boolean hideFiltered = false;

    /**
     * The currently selected variant.  This is a transient variable, set only while the popup menu is up.
     */
    private Variant selectedVariant;

    /**
     * Transient list to keep track of the vertical bounds of each sample.  Set when rendering names, used to
     * select correct sample for popup text.  We use a list and linear lookup for now, some sort of tree structure
     * would be faster.
     */
    private List<SampleBounds> sampleBounds = new ArrayList<SampleBounds>();

    /**
     * List of selected samples.
     */
    private List<String> selectedSamples = new ArrayList<String>();

    /**
     * Experimental "mode" to couple VCF & BAM files
     */

    //private boolean vcfToBamMode = false;

    /**
     * Map of sample name -> associated bam file
     */
    Map<String, String> alignmentFiles;

    public void setRenderer(VariantRenderer renderer) {
        this.renderer = renderer;
    }


    public VariantTrack() {
    }

    public VariantTrack(String name, FeatureSource source) {
        this(null, source, Collections.<String>emptyList(), false);
        this.setName(name);
    }

    public VariantTrack(ResourceLocator locator, FeatureSource source, List<String> samples,
                        boolean enableMethylationRateSupport) {
        super(locator, source);

        IGVPreferences prefMgr = PreferencesManager.getPreferences();

        String path = locator == null ? null : locator.getPath();

        this.renderer = new VariantRenderer(this);

        this.enableMethylationRateSupport = enableMethylationRateSupport;
        if (enableMethylationRateSupport) {
            // also set the default color mode to Methylation rate:
            genotypeColorMode = ColorMode.METHYLATION_RATE;
        }

        this.siteColorMode = prefMgr.getAsBoolean(VARIANT_COLOR_BY_ALLELE_FREQ) ?
                ColorMode.ALLELE_FREQUENCY :
                ColorMode.ALLELE_FRACTION;

        this.allSamples = samples;

        // this handles the new attribute grouping mechanism:
        setupGroupsFromAttributes();

        setDisplayMode(DisplayMode.EXPANDED);

        int sampleCount = allSamples.size();
        final int groupCount = samplesByGroups.size();
        final int margins = (groupCount - 1) * 3;
        squishedHeight = sampleCount == 0 || showGenotypes == false ? DEFAULT_SQUISHED_HEIGHT :
                Math.min(DEFAULT_SQUISHED_HEIGHT, Math.max(1, (height - getVariantBandHeight() - margins) / sampleCount));
        showGenotypes = defaultShowGenotypes();


        // If sample->bam list file is supplied enable vcfToBamMode.
        String vcfToBamMapping = locator == null ? null : locator.getMappingPath();

        boolean bypassFileAutoDiscovery = prefMgr.getAsBoolean(BYPASS_FILE_AUTO_DISCOVERY);
        if (vcfToBamMapping == null && path != null && !bypassFileAutoDiscovery) {
	    String mappingFile = "";
            int queryStart = path.indexOf("?");
            if (queryStart > -1)
            {
                String query =  path.substring(queryStart);
                path = path.substring(0,queryStart);
                mappingFile = path + ".mapping" + query;
            }

            if (ParsingUtils.fileExists(mappingFile)) {
                vcfToBamMapping = mappingFile;
            }
        }

        if (vcfToBamMapping != null && !vcfToBamMapping.equals(".")) {
            loadAlignmentMappings(vcfToBamMapping);
        }

        // Set visibility window.  These values are appropriate for human dbsnp/1kg files, probably conservative otherwise
        // Ugly test on source is to avoid having to add "isIndexed" to a zillion feature source classes.  The intent
        // is to skip this if using a non-indexed source.
        if (!(source instanceof TribbleFeatureSource && ((TribbleFeatureSource) source).isIndexed() == false)) {
            int defVisibilityWindow = prefMgr.getAsInt(DEFAULT_VISIBILITY_WINDOW);
            if (defVisibilityWindow > 0) {
                setVisibilityWindow(defVisibilityWindow * 1000);
            } else {
                int vw = Math.max(10000, (100000 - 100 * (allSamples.size() - 1)));
                setVisibilityWindow(vw);
            }
        }

        IGVEventBus.getInstance().subscribe(TrackGroupEvent.class, this);

    }

    private boolean defaultShowGenotypes() {
        return allSamples.size() > 0;
    }

    private void loadAlignmentMappings(String bamListPath) {
        alignmentFiles = new HashMap<String, String>();
        BufferedReader br = null;

        try {
            br = ParsingUtils.openBufferedReader(bamListPath);
            String nextLine;
            while ((nextLine = br.readLine()) != null) {
                String[] tokens = ParsingUtils.TAB_PATTERN.split(nextLine);
                if (tokens.length < 2) {
                    log.warn("Skipping bam mapping file line: " + nextLine);
                } else {

                    String alignmentPath = tokens[1];
                    boolean isAbsolute;
                    if (alignmentPath.startsWith("http://") || alignmentPath.startsWith("ftp:")) {
                        isAbsolute = true;
                    } else {
                        String absolutePath = (new File(alignmentPath)).getAbsolutePath();
                        String prefix = absolutePath.substring(0, 3);
                        isAbsolute = alignmentPath.startsWith(prefix);
                    }
                    if (!isAbsolute) {
                        alignmentPath = FileUtils.getAbsolutePath(alignmentPath, bamListPath);
                    }


                    alignmentFiles.put(tokens[0], alignmentPath);
                }
            }
        } catch (IOException e) {
            MessageUtils.showMessage("<html>Error loading bam mapping file: " + bamListPath + "<br>" + e.getMessage());
        } finally {
            if (br != null) {
                try {
                    br.close();
                } catch (IOException e) {

                }
            }
        }
    }

    String getBamFileForSample(String sample) {
        return alignmentFiles == null ? null : alignmentFiles.get(sample);
    }


    /**
     * Set groups from global sample information attributes.
     */
    private void setupGroupsFromAttributes() {
        // setup groups according to the attribute used for sorting (loaded from a sample information file):

        AttributeManager manager = AttributeManager.getInstance();
        String newGroupByAttribute = !IGV.hasInstance() ? null : IGV.getInstance().getGroupByAttribute();

        // The first equality handles the case where both are null
        if ((newGroupByAttribute == groupByAttribute) ||
                (newGroupByAttribute != null && newGroupByAttribute.equals(groupByAttribute))) {
            // Nothing to do
            return;
        }


        samplesByGroups.clear();

        groupByAttribute = newGroupByAttribute;

        if (groupByAttribute == null) {
            grouped = false;
            return;
        }

        for (String sample : allSamples) {

            String sampleGroup = manager.getAttribute(sample, newGroupByAttribute);

            List<String> sampleList = samplesByGroups.get(sampleGroup);
            if (sampleList == null) {
                sampleList = new ArrayList<String>();
                samplesByGroups.put(sampleGroup, sampleList);
            }
            sampleList.add(sample);
        }

        grouped = samplesByGroups.size() > 1;
        groupByAttribute = newGroupByAttribute;
    }

    /**
     * Sort samples.  Sort both the master list and groups, if any.
     *
     * @param comparator the comparator to sort by
     */
    public void sortSamples(Comparator<String> comparator) {
        Collections.sort(allSamples, comparator);
        for (List<String> samples : samplesByGroups.values()) {
            Collections.sort(samples, comparator);
        }
    }


    public boolean isEnableMethylationRateSupport() {
        return enableMethylationRateSupport;
    }


    /**
     * Returns the height of a single sample (genotype) band
     *
     * @return
     */
    public int getGenotypeBandHeight() {
        switch (getDisplayMode()) {
            case SQUISHED:
                return getSquishedHeight();
            case COLLAPSED:
                return 0;
            default:
                return DEFAULT_EXPANDED_GENOTYPE_HEIGHT;

        }
    }

    /**
     * Returns the total height of the track (including all sample/genotypes)
     *
     * @return
     */
    public int getHeight() {
        int sampleCount = allSamples.size();
        int h;
        if (getDisplayMode() == DisplayMode.COLLAPSED || sampleCount == 0 || showGenotypes == false) {
            h = getVariantsHeight();
        } else {
            final int groupCount = samplesByGroups.size();
            int margins = groupCount * 3;
            h = getVariantsHeight() + margins + (sampleCount * getGenotypeBandHeight());
        }
        return Math.max(WG_TRACK_HEIGHT, h);
    }

    public Object getHeader() {
        if (source instanceof TribbleFeatureSource) {
            return ((TribbleFeatureSource) source).getHeader();
        }
        return null;
    }

    /**
     * Return the height of the variant section only (no samples/genotypes)
     *
     * @return
     */
    private int getVariantsHeight() {
        return getVariantBandHeight() * getNumberOfFeatureLevels();
    }

    /**
     * Set the height of the track.
     *
     * @param height
     */
    public void setHeight(int height) {

        final DisplayMode displayMode = getDisplayMode();

        // If collapsed there's nothing we can do to affect height
        if (displayMode == DisplayMode.COLLAPSED) {
            return;
        }

        // If height is < expanded height try "squishing" track, otherwise expand it
        final int groupCount = samplesByGroups.size();
        final int margins = (groupCount - 1) * 3;
        int sampleCount = showGenotypes == false ? 0 : allSamples.size();
        final int expandedHeight = getVariantBandHeight() + margins + (sampleCount * getGenotypeBandHeight());
        if (height < expandedHeight) {
            setDisplayMode(DisplayMode.SQUISHED);
        } else {
            if (displayMode != DisplayMode.EXPANDED) {
                setDisplayMode(DisplayMode.EXPANDED);
            }
        }

        squishedHeight = showGenotypes == false ? DEFAULT_SQUISHED_HEIGHT :
                Math.min(DEFAULT_SQUISHED_HEIGHT, Math.max(1, (height - getVariantBandHeight() - margins) / sampleCount));
    }


    /**
     * Render the features in the supplied rectangle.
     *
     * @param context
     * @param trackRectangle
     * @param packedFeatures
     */
    @Override
    protected void renderFeatureImpl(RenderContext context, Rectangle trackRectangle, PackedFeatures packedFeatures) {

        Graphics2D g2D = context.getGraphics();

        top = trackRectangle.y;
        Rectangle visibleRectangle = context.getVisibleRect();

        // A disposable rect -- note this gets modified all over the place, bad practice
        Rectangle tmpRect = new Rectangle(trackRectangle);
        tmpRect.height = getGenotypeBandHeight();
        tmpRect.y = trackRectangle.y;

        Rectangle bandRect = new Rectangle(tmpRect);
        bandRect.y += getVariantsHeight();
        drawBackground(g2D, bandRect, visibleRectangle, BackgroundType.DATA);

        List<PackedFeatures.FeatureRow> rows = packedFeatures.getRows();

        int overallFeatureRectHeight = getVariantsHeight();
        int overallSampleRectHeight = trackRectangle.height - overallFeatureRectHeight;
        Rectangle overallSampleRect = new Rectangle(trackRectangle.x, top + overallFeatureRectHeight, trackRectangle.width, overallSampleRectHeight);

        int curRowTop = top;

        if (rows.size() > 0) {
            final double locScale = context.getScale();
            final double origin = context.getOrigin();

            final double pXMin = tmpRect.getMinX();
            final double pXMax = tmpRect.getMaxX();
            tmpRect.height = getVariantBandHeight();

            int lastEndX = -1;
            int minSpacing = 3;
            for (PackedFeatures.FeatureRow row : rows) {
                List<Feature> features = row.getFeatures();
                for (Feature feature : features) {
                    Variant variant = (Variant) feature;

                    if (hideFiltered && variant.isFiltered()) {
                        continue;
                    }

                    int start = variant.getStart();
                    int end = variant.getEnd();
                    int pX = (int) ((start - origin) / locScale);
                    int dX = (int) Math.max(2, (end - start) / locScale);

                    if (pX + dX < pXMin) {
                        continue;
                    }
                    if (pX > pXMax) {
                        break;
                    }
                    int w = dX;
                    int x = pX;

                    if (w < 3) {
                        w = 3;
                        x--;
                    }

                    //Make sure we have some whitespace between this
                    //feature and the previous one, but only if they don't
                    //actually overlap and the current size is reasonably large
                    int spacing = x - lastEndX;
                    if (spacing > 0 && spacing < minSpacing && w > 2 * minSpacing) {
                        x += minSpacing - spacing;
                    }

                    tmpRect.y = curRowTop;
                    if (tmpRect.intersects(visibleRectangle)) {
                        renderer.renderSiteBand(variant, tmpRect, x, w, context);
                        lastEndX = x + w - 1;
                    }

                    if (showGenotypes) {
                        renderSamples(g2D, visibleRectangle, variant, context, overallSampleRect, x, w);
                        boolean isSelected = selectedVariant != null && selectedVariant == variant;
                        if (isSelected) {
                            Graphics2D selectionGraphics = context.getGraphic2DForColor(Color.black);
                            selectionGraphics.drawRect(x, curRowTop, w, getHeight());
                        }
                    }

                }

                curRowTop += getVariantBandHeight();
                lastEndX = -1;

            }
        } else {
            tmpRect.height = getVariantBandHeight();
            tmpRect.y = trackRectangle.y;
            g2D.setColor(Color.gray);
            GraphicUtils.drawCenteredText("No Variants Found", trackRectangle, g2D);
        }

        renderBoundaryLines(g2D, trackRectangle, visibleRectangle);

    }

    private void drawLineIfVisible(Graphics2D g2D, Rectangle visibleRectangle, Color color, int yLoc, int left, int right) {
        if (yLoc >= visibleRectangle.y && yLoc <= visibleRectangle.getMaxY()) {
            if (color != null) g2D.setColor(color);
            g2D.drawLine(left, yLoc, right, yLoc);
        }
    }

    private void drawVariantBandBorder(Graphics2D g2D, Rectangle visibleRectangle, int variantBandY, int left, int right) {
        if (allSamples.size() > 0 && showGenotypes) {
            drawLineIfVisible(g2D, visibleRectangle, Color.lightGray, variantBandY, left, right);
        }
    }

    private void renderSamples(Graphics2D g2D, Rectangle visibleRectangle, Variant variant, RenderContext context, Rectangle overallSampleRect, int x, int w) {

        Rectangle tmpRect = new Rectangle(overallSampleRect);
        tmpRect.height = getGenotypeBandHeight();
        if (grouped) {
            for (Map.Entry<String, List<String>> entry : samplesByGroups.entrySet()) {
                for (String sample : entry.getValue()) {
                    if (overallSampleRect.intersects(visibleRectangle)) {
                        renderer.renderGenotypeBandSNP(variant, context, tmpRect, x, w, sample, genotypeColorMode, hideFiltered);
                    }
                    tmpRect.y += tmpRect.height;
                }
                tmpRect.y += GROUP_BORDER_WIDTH;
            }
        } else {

            for (String sample : allSamples) {

                if (tmpRect.intersects(visibleRectangle)) {
                    renderer.renderGenotypeBandSNP(variant, context, tmpRect, x, w, sample, genotypeColorMode, hideFiltered);
                }
                tmpRect.y += tmpRect.height;
            }
        }
    }

    /**
     * Renders the top line, bottom track line, and border between variants / genotypes
     *
     * @param g2D
     * @param trackRectangle
     * @param visibleRectangle
     */
    private void renderBoundaryLines(Graphics2D g2D, Rectangle trackRectangle, Rectangle visibleRectangle) {
        top = trackRectangle.y;
        final int left = trackRectangle.x;
        final int right = (int) trackRectangle.getMaxX();

        //Top line
        // drawLineIfVisible(g2D, visibleRectangle, Color.black, top + 1, left, right);

        // Bottom border
        int bottomY = trackRectangle.y + trackRectangle.height;
        drawLineIfVisible(g2D, visibleRectangle, borderGray, bottomY, left, right);

        // Variant / Genotype border
        if (allSamples.size() > 0 && showGenotypes) {
            int variantGenotypeBorderY = trackRectangle.y + getVariantsHeight();
            drawVariantBandBorder(g2D, visibleRectangle, variantGenotypeBorderY, left, right);

            if (grouped) {
                g2D.setColor(Color.black);
                int y = trackRectangle.y + getVariantsHeight();
                for (Map.Entry<String, List<String>> entry : samplesByGroups.entrySet()) {
                    y += entry.getValue().size() * getGenotypeBandHeight() + GROUP_BORDER_WIDTH;
                    g2D.drawLine(trackRectangle.x, y, trackRectangle.x + trackRectangle.width, y);
                }
            }
        }
    }

    /**
     * Render the name panel.
     * <p/>
     * NOTE:  The sample names are actually drawn in the drawBackground method.
     *
     * @param g2D
     * @param trackRectangle
     * @param visibleRectangle
     */
    @Override
    public void renderName(Graphics2D g2D, Rectangle trackRectangle, Rectangle visibleRectangle) {

        top = trackRectangle.y;

        Rectangle rect = new Rectangle(trackRectangle);
        g2D.setFont(FontManager.getFont(fontSize));
        g2D.setColor(BAND2_COLOR);


        g2D.setColor(Color.black);
        rect.height = getVariantsHeight();
        if (rect.intersects(visibleRectangle)) {
            Rectangle intersectedRect = rect.intersection(visibleRectangle);
            GraphicUtils.drawWrappedText(getName(), intersectedRect, g2D, false);
        }

        rect.y += rect.height;
        rect.height = getGenotypeBandHeight();

        // The sample bounds list will get reset when  the names are drawn.
        sampleBounds.clear();
        drawBackground(g2D, rect, visibleRectangle, BackgroundType.NAME);


        renderBoundaryLines(g2D, trackRectangle, visibleRectangle);

    }

    /**
     * Render sample attributes, if any.
     *
     * @param g2D
     * @param trackRectangle
     * @param visibleRectangle
     * @param attributeNames
     * @param mouseRegions
     */

    public void renderAttributes(Graphics2D g2D, Rectangle trackRectangle, Rectangle visibleRectangle,
                                 List<String> attributeNames, List<MouseableRegion> mouseRegions) {

        if (showGenotypes == false) return;

        top = trackRectangle.y;
        Rectangle rect = new Rectangle(trackRectangle);

        rect.height = getVariantsHeight();
        if (rect.intersects(visibleRectangle)) {
            super.renderAttributes(g2D, rect, visibleRectangle, attributeNames, mouseRegions);
        }

        if (getDisplayMode() == DisplayMode.COLLAPSED) {
            return;
        }

        rect.y += rect.height;
        rect.height = getGenotypeBandHeight();
        Rectangle bandRectangle = new Rectangle(rect);  // Make copy for later use


        drawBackground(g2D, rect, visibleRectangle, BackgroundType.ATTRIBUTE);

        if (grouped) {
            for (List<String> sampleList : samplesByGroups.values()) {
                renderAttributeBand(g2D, bandRectangle, visibleRectangle, attributeNames, sampleList, mouseRegions);
                bandRectangle.y += GROUP_BORDER_WIDTH;

            }
        } else {
            renderAttributeBand(g2D, bandRectangle, visibleRectangle, attributeNames, allSamples, mouseRegions);

        }

        renderBoundaryLines(g2D, trackRectangle, visibleRectangle);

    }

    /**
     * Render attributes for a sample.   This is mostly a copy of AbstractTrack.renderAttributes().
     * TODO -- refactor to eliminate duplicate code from AbstractTrack
     *
     * @param g2D
     * @param bandRectangle
     * @param visibleRectangle
     * @param attributeNames
     * @param sampleList
     * @param mouseRegions
     * @return
     */
    private void renderAttributeBand(Graphics2D g2D, Rectangle bandRectangle, Rectangle visibleRectangle,
                                     List<String> attributeNames, List<String> sampleList, List<MouseableRegion> mouseRegions) {


        for (String sample : sampleList) {

            if (bandRectangle.intersects(visibleRectangle)) {

                int x = bandRectangle.x;

                for (String name : attributeNames) {

                    String key = name.toUpperCase();
                    String attributeValue = AttributeManager.getInstance().getAttribute(sample, key);
                    if (attributeValue != null) {
                        Rectangle rect = new Rectangle(x, bandRectangle.y, AttributeHeaderPanel.ATTRIBUTE_COLUMN_WIDTH,
                                bandRectangle.height);
                        g2D.setColor(AttributeManager.getInstance().getColor(key, attributeValue));
                        g2D.fill(rect);
                        mouseRegions.add(new MouseableRegion(rect, key, attributeValue));
                    }
                    x += AttributeHeaderPanel.ATTRIBUTE_COLUMN_WIDTH + AttributeHeaderPanel.COLUMN_BORDER_WIDTH;
                }

            }
            bandRectangle.y += bandRectangle.height;

        }
    }

    /**
     * Draws the "greenbar" type background.  Also, rather bizarrely, draws the sample names.
     *
     * @param g2D
     * @param bandRectangle
     * @param visibleRectangle
     * @param type
     */
    private void drawBackground(Graphics2D g2D, Rectangle bandRectangle, Rectangle visibleRectangle,
                                BackgroundType type) {


        if (getDisplayMode() == DisplayMode.COLLAPSED || showGenotypes == false) {
            return;
        }

        boolean coloredLast = true;
        Rectangle textRectangle = new Rectangle(bandRectangle);
        textRectangle.height--;

        int bandFontSize = Math.min(fontSize, (int) bandRectangle.getHeight() - 1);
        Font font = FontManager.getFont(bandFontSize);
        Font oldFont = g2D.getFont();
        g2D.setFont(font);

        if (grouped) {
            for (Map.Entry<String, List<String>> sampleGroup : samplesByGroups.entrySet()) {
                int y0 = bandRectangle.y;

                List<String> sampleList = sampleGroup.getValue();
                coloredLast = colorBand(g2D, bandRectangle, visibleRectangle, coloredLast, textRectangle, sampleList, type);
                bandRectangle.y += GROUP_BORDER_WIDTH;

                if (type == BackgroundType.NAME && bandRectangle.height < 3) {
                    String group = sampleGroup.getKey();
                    if (group != null) {
                        g2D.setColor(Color.black);
                        g2D.setFont(oldFont);
                        int y2 = bandRectangle.y;
                        Rectangle textRect = new Rectangle(bandRectangle.x, y0, bandRectangle.width, y2 - y0);
                        GraphicUtils.drawWrappedText(group, textRect, g2D, true);
                    }
                }

            }

        } else {
            coloredLast = colorBand(g2D, bandRectangle, visibleRectangle, coloredLast, textRectangle, allSamples, type);
        }
        g2D.setFont(oldFont);
    }


    private boolean colorBand(Graphics2D g2D, Rectangle bandRectangle, Rectangle visibleRectangle,
                              boolean coloredLast, Rectangle textRectangle, List<String> sampleList,
                              BackgroundType type) {

        boolean supressFill = (getDisplayMode() == DisplayMode.SQUISHED && squishedHeight < 4);

        for (String sample : sampleList) {

            if (coloredLast) {
                g2D.setColor(BAND1_COLOR);
                coloredLast = false;
            } else {
                g2D.setColor(BAND2_COLOR);
                coloredLast = true;
            }

            if (bandRectangle.intersects(visibleRectangle)) {
                if (!supressFill) {
                    if (selectedSamples.contains(sample) && hasAlignmentFiles()) {
                        g2D.setColor(SELECTED_BAND_COLOR);
                    }
                    g2D.fillRect(bandRectangle.x, bandRectangle.y, bandRectangle.width, bandRectangle.height);
                }

                if (type == BackgroundType.NAME) {
                    sampleBounds.add(new SampleBounds(bandRectangle.y, bandRectangle.y + bandRectangle.height, sample));
                    if (bandRectangle.height >= 3) {
                        String printName = sample;
                        textRectangle.y = bandRectangle.y + 1;
                        g2D.setColor(Color.black);
                        GraphicUtils.drawWrappedText(printName, bandRectangle, g2D, false);
                    }


                } else if (type == BackgroundType.ATTRIBUTE) {

                }
            }
            bandRectangle.y += bandRectangle.height;

        }
        return coloredLast;
    }

    public boolean getHideFiltered() {
        return hideFiltered;
    }

    public void setHideFiltered(boolean value) {
        this.hideFiltered = value;
    }

    public ColorMode getGenotypeColorMode() {
        return genotypeColorMode;
    }

    public void setGenotypeColorMode(ColorMode mode) {
        this.genotypeColorMode = mode;
    }

    public ColorMode getSiteColorMode() {
        return siteColorMode;
    }

    public void setSiteColorMode(ColorMode siteColorMode) {
        this.siteColorMode = siteColorMode;
    }

    @Override
    public void setColor(Color color) {
        // Setting color implicitly turns of "color by" modes
        this.genotypeColorMode = ColorMode.NONE;
        this.siteColorMode = ColorMode.NONE;
        super.setColor(color);
    }

    public String getNameValueString(int y) {
        if (y < top + getVariantsHeight()) {
            return super.getNameValueString(y);
        } else {
            String sample = getSampleAtPosition(y);
            return sample;
        }
    }

    /**
     * Return popup text for the given position
     *
     * @param chr
     * @param position - position in UCSC "0 based"  genomic coordinates
     * @param mouseX
     * @param frame    @return
     */
    public String getValueStringAt(String chr, double position, int mouseX, int mouseY, ReferenceFrame frame) {

        try {
            double maxDistance = 10 * frame.getScale();
            if (mouseY < top + getVariantsHeight()) {
                int modY = mouseY;
                Variant variant = getFeatureClosest(position, modY, frame.getName(), maxDistance);
                if (variant == null) return null;

                return getVariantToolTip(variant);
            } else {
                if (sampleBounds == null || sampleBounds.isEmpty()) return null;
                String sample = getSampleAtPosition(mouseY);
                if (sample == null) return null;

                Variant variant = getFeatureClosest(position, -1, frame.getName(), maxDistance);
                return getSampleToolTip(sample, variant);
            }
        } catch (Exception e) {
            log.error("Error getting value string", e);
            return null;
        }
    }

    /**
     * Return the sample at the give pixel position
     *
     * @param y - screen position in pixels
     * @return
     */
    private String getSampleAtPosition(int y) {

        if (sampleBounds.isEmpty()) {
            return null;
        }
        String sample = null;

        // Estimate the index of the sample, then do a linear search
        final int sampleCount = sampleBounds.size();

        int firstSampleY = sampleBounds.get(0).top;
        int idx = Math.max(0, Math.min((y - firstSampleY) / getGenotypeBandHeight(), sampleCount - 1));

        SampleBounds bounds = sampleBounds.get(idx);
        if (bounds.contains(y)) {
            sample = bounds.sample;
        } else if (bounds.top > y) {
            while (idx > 0) {
                idx--;
                bounds = sampleBounds.get(idx);
                if (bounds.contains(y)) {
                    sample = bounds.sample;
                }
            }
        } else {
            while (idx < sampleCount - 1) {
                idx++;
                bounds = sampleBounds.get(idx);
                if (bounds.contains(y)) {
                    sample = bounds.sample;
                }
            }
        }
        return sample;
    }

    /**
     * Return the variant closest to the genomic position in the given reference frame, within the prescribed tolerance
     *
     * @param position
     * @param y           pixel position in panel coordinates (i.e. not track coordinates)
     * @param frameName
     * @param maxDistance
     * @return
     */
    protected Variant getFeatureClosest(double position, int y, String frameName, double maxDistance) {

        PackedFeatures<Feature> packedFeatures = packedFeaturesMap.get(frameName);

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

        Feature feature = null;
        List<Feature> features;

        //We search only the specified row if y is a meaningful value.
        //Otherwise we search everything
        int row = ((y - top) / getVariantBandHeight());
        if (y < 0 || row >= getNumberOfFeatureLevels()) {
            features = packedFeatures.getFeatures();
        } else {
            features = packedFeatures.getRows().get(row).getFeatures();
        }

        if (features != null) {
            feature = FeatureUtils.getFeatureClosest(position, features);
        }
        if (feature == null ||
                ((position < feature.getStart() - maxDistance) || (position > feature.getEnd() + maxDistance))) {
            return null;
        } else {
            return (Variant) feature;
        }


    }

    private String getVariantToolTip(Variant variant) {
        String id = variant.getID();

        StringBuffer toolTip = new StringBuffer();
        toolTip.append("Chr: " + variant.getChr());
        toolTip.append("<br>Position: " + variant.getPositionString());
        toolTip.append("<br>ID: " + id);
        toolTip.append("<br>Reference: " + variant.getReference());
        List<Allele> alternates = variant.getAlternateAlleles();
        String alternateString = null;
        if (alternates.size() > 0) {
            alternateString = StringUtils.join(alternates, ",");
            toolTip.append("<br>Alternate: " + alternateString);
        }

        double qual = variant.getPhredScaledQual();
        String qualString = variant.hasLog10PError() ? numFormat.format(qual) : ".";
        toolTip.append("<br>Qual: " + qualString);
        toolTip.append("<br>Type: " + variant.getType());
        if (variant.isFiltered()) {
            toolTip.append("<br>Is Filtered Out: Yes</b>");
            toolTip = toolTip.append(getFilterTooltip(variant));
        } else {
            toolTip.append("<br>Is Filtered Out: No</b><br>");
        }

        if (alternateString != null) {
            toolTip.append("<br><b>Alleles:</b>");

            toolTip.append("<br>Alternate Alleles: " + alternateString);

            int[] ac = variant.getAlleleCounts();
            if (ac != null) {
                String acString = ac.length > 1 ? "<br>Allele Counts: " : "<br>Allele Count: ";
                for (int i = 0; i < ac.length; i++) {
                    acString += Integer.toString(ac[i]);
                    if (i < ac.length - 1) acString += ", ";
                }
                toolTip.append(acString);
            }

            int totalAlleleCount = variant.getTotalAlleleCount();
            if (totalAlleleCount > 0) {
                toolTip.append("<br>Total # Alleles: " + String.valueOf(totalAlleleCount));
            }

            double[] af = variant.getAlleleFreqs();
            String afString = af.length > 1 ? "<br>Allele Fequencies: " : "<br>Allele Frequency: ";
            for (int i = 0; i < af.length; i++) {
                afString += Double.toString(af[i]);
                if (i < af.length - 1) afString += ", ";
            }
            toolTip.append(afString);
        }
        if (variant.getAttributes().size() > 0) {
            toolTip.append(getVariantInfo(variant));
        }


        return toolTip.toString();
    }

    protected String getVariantInfo(Variant variant) {
        Set<String> keys = variant.getAttributes().keySet();
        if (keys.size() > 0) {
            String toolTip = "<br><br><b>Variant Attributes</b>";
            int count = 0;

            // Put AF and GMAF and put at the top, if present
            String k = "AF";
            String afValue = variant.getAttributeAsString(k);
            if (afValue != null && afValue.length() > 0 && !afValue.equals("null")) {
                toolTip = toolTip.concat("<br>" + getFullName(k) + ": " + variant.getAttributeAsString(k));
            }

            k = "GMAF";
            afValue = variant.getAttributeAsString(k);
            if (afValue != null && afValue.length() > 0 && !afValue.equals("null")) {
                toolTip = toolTip.concat("<br>" + getFullName(k) + ": " + variant.getAttributeAsString(k));
            }
            int maxFilterLines = getMaxFilterLines();
            for (String key : keys) {
                count++;

                if (key.equals("AF") || key.equals("GMAF")) continue;

                if (count > maxFilterLines) {
                    toolTip = toolTip.concat("<br>....");
                    break;
                }
                toolTip = toolTip.concat("<br>" + getFullName(key) + ": " + variant.getAttributeAsString(key));

            }
            return toolTip;
        }
        return " ";
    }

    /**
     * The maximum number of filter lines to show for variants.
     * We show more info if the user is displaying a separate window than
     * if using tooltip
     *
     * @return
     */
    private int getMaxFilterLines() {
        return IGV.getInstance().isShowDetailsOnHover() ? MAX_FILTER_LINES : 1000;
    }

    private String getGenotypeInfo(Genotype genotype) {
        final Map<String, Object> attributes = genotype.getAttributes();
        Set<String> keys = attributes.keySet();
        if (keys.size() > 0) {
            String tooltip = "<br><b>Genotype Attributes</b>";
            for (String key : keys) {
                tooltip = tooltip.concat("<br>" + getFullName(key) + ": " + attributes.get(key));
            }
            return tooltip;
        }
        return null;
    }

    public void clearSelectedVariant() {
        selectedVariant = null;
    }

    public List<String> getAllSamples() {
        return allSamples;
    }

    public int getSquishedHeight() {
        return squishedHeight;
    }

    public void setSquishedHeight(int squishedHeight) {
        this.squishedHeight = squishedHeight;
    }

    @Override
    public void receiveEvent(Object event) {
        if (event instanceof TrackGroupEvent) {
            setupGroupsFromAttributes();
        }
    }

    public boolean hasAlignmentFiles() {
        return alignmentFiles != null && !alignmentFiles.isEmpty();
    }

    public Collection<String> getSelectedSamples() {
        return selectedSamples;
    }

    public boolean isShowGenotypes() {
        return showGenotypes;
    }

    public void setShowGenotypes(boolean showGenotypes) {
        this.showGenotypes = showGenotypes;
    }

    /**
     * The height of the top band representing the variant call
     */
    public int getVariantBandHeight() {
        return getDisplayMode() == DisplayMode.SQUISHED ? DEFAULT_SQUISHED_VARIANT_HEIGHT : DEFAULT_EXPANDED_VARIANT_HEIGHT;
    }

    public enum ColorMode {
        GENOTYPE, METHYLATION_RATE, ALLELE_FREQUENCY, NONE, ALLELE_FRACTION
    }

    public static enum BackgroundType {
        NAME, ATTRIBUTE, DATA;
    }


    static Map<String, String> fullNames = new HashMap();

    static {
        fullNames.put("AA", "Ancestral Allele");
        fullNames.put("AC", "Allele Count");
        fullNames.put("AN", "Total Alleles");
        fullNames.put("AF", "Allele Frequency");
        fullNames.put("DP", "Depth");
        fullNames.put("MQ", "Mapping Quality");
        fullNames.put("NS", "Number of Samples with Data");
        fullNames.put("BQ", "RMS Base Quality");
        fullNames.put("SB", "Strand Bias");
        fullNames.put("DB", "dbSNP Membership");
        fullNames.put("GQ", "Genotype Quality");
        fullNames.put("GL", "Genotype Likelihoods");  //Hom-ref, het, hom-var break this down into a group
    }

    static String getFullName(String key) {
        return fullNames.containsKey(key) ? fullNames.get(key) : key;
    }


    private String getSampleToolTip(String sample, Variant variant) {

        if (variant == null) return null;
        double goodBaseCount = variant.getGenotype(sample).getAttributeAsDouble("GB");
        if (Double.isNaN(goodBaseCount)) goodBaseCount = 0;
        if (isEnableMethylationRateSupport() && goodBaseCount < 10) {
            return sample;
        }
        String id = variant.getID();
        StringBuffer toolTip = new StringBuffer();
        toolTip = toolTip.append("Chr: " + variant.getChr());
        toolTip = toolTip.append("<br>Position: " + variant.getPositionString());
        toolTip = toolTip.append("<br>ID: " + id + "<br>");
        toolTip = toolTip.append("<br><b>Genotype Information</b>");
        toolTip = toolTip.append("<br>Sample: " + sample);

        Genotype genotype = variant.getGenotype(sample);
        if (genotype != null) {
            toolTip = toolTip.append("<br>Genotype: " + genotype.getGenotypeString());
            toolTip = toolTip.append("<br>Quality: " + numFormat.format(genotype.getPhredScaledQual()));
            toolTip = toolTip.append("<br>Type: " + genotype.getTypeString());
        }
        if (variant.isFiltered()) {
            toolTip = toolTip.append("<br>Is Filtered Out: Yes</b>");
            toolTip = toolTip.append(getFilterTooltip(variant));
        } else {
            toolTip = toolTip.append("<br>Is Filtered Out: No</b><br>");
        }

        if (genotype != null) {
            String sInfoStr = getGenotypeInfo(genotype);
            if (sInfoStr != null) {
                toolTip = toolTip.append(sInfoStr + "<br>");
            }
        }
        return toolTip.toString();
    }


    private String getFilterTooltip(Variant variant) {
        Collection filters = variant.getFilters();
        String toolTip = "<br>";
        for (Object filter : filters) {
            toolTip = toolTip.concat("- " + (String) filter + "<br>");
        }

        return toolTip;
    }


    /**
     * Return the {@code Variant} object closest to the specified event
     *
     * @param te
     * @return
     * @api
     */
    public Variant getSelectedVariant(final TrackClickEvent te) {
        final ReferenceFrame referenceFrame = te.getFrame();
        Variant selVariant = null;
        if (referenceFrame != null && referenceFrame.getName() != null) {
            final double position = te.getChromosomePosition();
            double maxDistance = 10 * referenceFrame.getScale();
            selVariant = getFeatureClosest(position, te.getMouseEvent().getY(), referenceFrame.getName(), maxDistance);
        }
        return selVariant;
    }


    public IGVPopupMenu getPopupMenu(final TrackClickEvent te) {
        selectedVariant = getSelectedVariant(te);
        if (selectedVariant != null) {
            repaint();
        }
        return new VariantMenu(this, selectedVariant, te);
    }


    /**
     * Handle a mouse click from the name panel.
     *
     * @param e
     */
    @Override
    public void handleNameClick(MouseEvent e) {
        String sampleAtPosition = getSampleAtPosition(e.getY());

        if (e.isPopupTrigger()) {
            return;
        }

        if (e.isMetaDown() || e.isControlDown()) {
            if (sampleAtPosition != null) {
                if (selectedSamples.contains(sampleAtPosition)) {
                    //    selectedSamples.remove(sampleAtPosition);
                } else {
                    selectedSamples.add(sampleAtPosition);
                }
            }
        } else if (e.isShiftDown() && !selectedSamples.isEmpty()) {
            int idx = getSampleIndex(sampleAtPosition);
            int lastIDX = getSampleIndex(selectedSamples.get(selectedSamples.size() - 1));
            if (idx >= 0 && lastIDX >= 0) {
                selectedSamples.clear();
                for (int i = Math.min(idx, lastIDX); i <= (Math.max(idx, lastIDX)); i++) {
                    String s = sampleBounds.get(i).sample;
                    selectedSamples.add(s);
                }
            }

        } else {
            if (sampleAtPosition != null) {
                if (selectedSamples.size() == 1 && selectedSamples.contains(sampleAtPosition)) {
                    selectedSamples.clear();
                    repaint();
                    return;     // <-  TODO fix, bad practice
                } else {
                    selectedSamples.clear();
                }
                selectedSamples.add(sampleAtPosition);
            }
        }
        repaint();

    }


    /**
     * Return the index for the sample.  This is a very inefficient implementation, but we don't care because
     * these lists are tiny.
     *
     * @param sample
     * @return
     */
    private int getSampleIndex(String sample) {
        for (int i = 0; i < sampleBounds.size(); i++) {
            if (sample.equals(sampleBounds.get(i).sample)) {
                return i;
            }
        }
        return -1;
    }

    /**
     * Handle a mouse click from the data panel.
     *
     * @param te - wraps the MouseClickEvent and reference frame.
     * @return true if the click is handled, false otherwise
     */
    @Override
    public boolean handleDataClick(TrackClickEvent te) {

        if (hasAlignmentFiles()) {
            final ReferenceFrame referenceFrame = te.getFrame();
            final double position = te.getChromosomePosition();
            double maxDistance = 10 * referenceFrame.getScale();

            Variant f = getFeatureClosest(position, te.getMouseEvent().getY(), te.getFrame().getName(), maxDistance);
            selectedSamples.clear();
            if (f != null) {
                String selectedSample = getSampleAtPosition(te.getMouseEvent().getY());
                if (selectedSample != null) {
                    // Select clicked sample and all other adjacent with the same genotype
                    Genotype genotype = f.getGenotype(selectedSample);
                    GenotypeType type = genotype.getType();

                    int idx = getSampleIndex(selectedSample);
                    for (int i = idx; i < sampleBounds.size(); i++) {
                        String s = sampleBounds.get(i).sample;
                        Genotype gt = f.getGenotype(s);
                        if (gt != null && type == gt.getType()) {
                            selectedSamples.add(s);
                        } else {
                            break;
                        }
                    }
                    for (int i = idx - 1; i >= 0; i--) {
                        String s = sampleBounds.get(i).sample;
                        Genotype gt = f.getGenotype(s);
                        if (gt != null && type == gt.getType()) {
                            selectedSamples.add(s);
                        } else {
                            break;
                        }
                    }
                }
            }
            repaint();
        }

        if (IGV.getInstance().isShowDetailsOnClick()) {
            openTooltipWindow(te);
        }

        return true;
    }

    public void loadSelectedBams() {
        Runnable runnable = new Runnable() {
            public void run() {
                // Use a set to enforce uniqueness
                final int nSamples = selectedSamples.size();
                if (nSamples == 0) {
                    return;
                }

                Set<String> bams = new HashSet<String>(nSamples);
                String name = "";
                int n = 0;
                for (String sample : selectedSamples) {
                    bams.add(getBamFileForSample(sample));
                    n++;
                    if (n < 7) {
                        if (n == 6) {
                            name += "...";
                        } else {
                            name += sample;
                            if (n < nSamples) name += ", ";
                        }
                    }
                }

                if (bams.size() > 20) {
                    boolean proceed = MessageUtils.confirm("Are you sure you want to load " + nSamples + " bams?");
                    if (!proceed) return;
                }

                String bamList = "";
                for (String bam : bams) {
                    bamList += bam + ",";

                }
                ResourceLocator loc = new ResourceLocator(bamList);
                loc.setFormat("alist");
                loc.setName(name);
                List<Track> tracks = null;
                try {
                    tracks = IGV.getInstance().load(loc);
                } catch (Exception e) {
                    log.error("Error loading bam: " + loc.getPath(), e);
                }

                TrackPanel panel = IGV.getInstance().getVcfBamPanel();
                panel.clearTracks();
                panel.addTracks(tracks);
            }
        };

        LongRunningTask.submit(runnable);
    }

    /**
     * Return the nextLine or previous feature relative to the center location.
     * <p/>
     * Loop through "next feature from super implementation until first non-filtered variant is found.
     *
     * @param chr
     * @param center
     * @param forward
     * @return
     * @throws IOException
     */
    @Override
    public Feature nextFeature(String chr, double center, boolean forward, ReferenceFrame frame) throws IOException {

        if (getHideFiltered()) {
            Feature f;
            while ((f = super.nextFeature(chr, center, forward, frame)) != null) {
                if (!(f instanceof Variant) || !((Variant) f).isFiltered()) {
                    return f;
                } else {
                    chr = f.getChr();
                    center = (f.getStart() + f.getEnd()) / 2 + 1;
                }
            }
            return null;
        } else {
            return super.nextFeature(chr, center, forward, frame);
        }
    }

    static class SampleBounds {
        int top;
        int bottom;
        String sample;

        SampleBounds(int top, int bottom, String sample) {
            this.top = top;
            this.bottom = bottom;
            this.sample = sample;
        }

        boolean contains(int y) {
            return y >= top && y <= bottom;
        }
    }

    void sendToCircularView(TrackClickEvent e) {

        List<Feature> visibleFeatures;
        if (e.getFrame() == null) {
            visibleFeatures = new ArrayList<>();
            for (ReferenceFrame frame : FrameManager.getFrames()) {
                visibleFeatures.addAll(getVisibleFeatures(frame));
            }
        } else {
            visibleFeatures = getVisibleFeatures(e.getFrame());
        }

        List<Feature> svFeatures = visibleFeatures.stream().filter(f -> {
            Variant v = f instanceof MateVariant ? ((MateVariant) f).mate : (Variant) f;
            Map<String, Object> attrs = v.getAttributes();
            return attrs.containsKey("CHR2") && attrs.containsKey("END");
        }).collect(Collectors.toList());

        if (svFeatures.isEmpty()) {
            MessageUtils.showMessage("No structural variants found.");
        } else {
            CircularViewUtilities.sendVariantsToJBrowse(svFeatures, getName(), CIRC_VIEW_DEFAULT_COLOR);
        }
    }

    @Override
    public List<Feature> getVisibleFeatures(ReferenceFrame frame) {
        if (frame.getChrName().equals(Globals.CHR_ALL) &&
                this.source instanceof TribbleFeatureSource.NonIndexedFeatureSource) {
            try {
                return ((TribbleFeatureSource.NonIndexedFeatureSource) this.source).getAllFeatures();
            } catch (IOException e) {
                return Collections.emptyList();
            }
        } else {
            return super.getVisibleFeatures(frame);
        }
    }


    @Override
    public void marshalXML(Document document, Element element) {

        super.marshalXML(document, element);

        if (showGenotypes != defaultShowGenotypes()) {
            element.setAttribute("showGenotypes", String.valueOf(showGenotypes));
        }

        if (this.squishedHeight != DEFAULT_SQUISHED_HEIGHT) {
            element.setAttribute("squishedHeight", String.valueOf(squishedHeight));
        }

        if (genotypeColorMode != ColorMode.GENOTYPE) {
            element.setAttribute("genotypeColorMode", genotypeColorMode.toString());
        }

        if (siteColorMode != null) {
            element.setAttribute("siteColorMode", siteColorMode.toString());
        }

    }

    @Override
    public void unmarshalXML(Element element, Integer version) {

        super.unmarshalXML(element, version);

        if (element.hasAttribute("showGenotypes")) {
            this.showGenotypes = Boolean.parseBoolean(element.getAttribute("showGenotypes"));
        }

        if (element.hasAttribute("squishedHeight")) {
            this.squishedHeight = Integer.parseInt(element.getAttribute("squishedHeight"));
        }

        if (element.hasAttribute("genotypeColorMode")) {
            this.genotypeColorMode = ColorMode.valueOf(element.getAttribute("genotypeColorMode"));
        } else if (element.hasAttribute("coloring")) {
            // backward compatibility
            this.genotypeColorMode = ColorMode.valueOf(element.getAttribute("coloring"));
        }

        if (element.hasAttribute("siteColorMode")) {
            this.siteColorMode = ColorMode.valueOf(element.getAttribute("siteColorMode"));

        }
    }

}
