/*
 * 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.
 */

/*
 * To change this template, choose Tools | Templates
 * and open the template in the editor.
 */
package org.broad.igv.sam;

import com.google.common.eventbus.Subscribe;
import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.PreferenceManager;
import org.broad.igv.data.CoverageDataSource;
import org.broad.igv.feature.FeatureUtils;
import org.broad.igv.feature.LocusScore;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.goby.GobyCountArchiveDataSource;
import org.broad.igv.renderer.BarChartRenderer;
import org.broad.igv.renderer.DataRange;
import org.broad.igv.renderer.DataRenderer;
import org.broad.igv.session.IGVSessionReader;
import org.broad.igv.session.SubtlyImportant;
import org.broad.igv.tdf.TDFDataSource;
import org.broad.igv.tdf.TDFReader;
import org.broad.igv.track.*;
import org.broad.igv.ui.DataRangeDialog;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.color.ColorUtilities;
import org.broad.igv.ui.event.DataLoadedEvent;
import org.broad.igv.ui.event.ViewChange;
import org.broad.igv.ui.panel.FrameManager;
import org.broad.igv.ui.panel.IGVPopupMenu;
import org.broad.igv.ui.panel.ReferenceFrame;
import org.broad.igv.ui.util.FileDialogUtils;
import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.StringUtils;

import javax.swing.*;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.File;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;

/**
 * @author jrobinso
 */
@XmlType(factoryMethod = "getNextTrack")
public class CoverageTrack extends AbstractTrack {

    private static Logger log = Logger.getLogger(CoverageTrack.class);
    public static final int TEN_MB = 10000000;

    char[] nucleotides = {'a', 'c', 'g', 't', 'n'};
    public static Color lightBlue = new Color(0, 0, 150);
    private static Color coverageGrey = new Color(175, 175, 175);
    public static final Color negStrandColor = new Color(140, 140, 160);
    public static final Color posStrandColor = new Color(160, 140, 140);

    public static final boolean DEFAULT_AUTOSCALE = true;
    public static final boolean DEFAULT_SHOW_REFERENCE = false;

    // User settable state -- these attributes should be stored in the session file
    @XmlAttribute private float snpThreshold;
    //TODO This appears to not be used anywhere, remove?
    @XmlAttribute boolean showReference;

    AlignmentDataManager dataManager;
    CoverageDataSource dataSource;
    DataRenderer dataSourceRenderer;
    IntervalRenderer intervalRenderer;
    PreferenceManager prefs;
    JMenuItem dataRangeItem;
    JMenuItem autoscaleItem;
    Genome genome;

    /**
     * Whether to autoscale across all ReferenceFrames
     * Default is true because we usually do, SashimiPlot does not
     */
    private boolean globalAutoScale = true;

    public void setRenderOptions(AlignmentTrack.RenderOptions renderOptions) {
        this.renderOptions = renderOptions;
    }

    AlignmentTrack.RenderOptions getRenderOptions(){
        return this.renderOptions;
    }

    private AlignmentTrack.RenderOptions renderOptions = null;

    public CoverageTrack(CoverageTrack track){
        this(track.getResourceLocator(), track.getName(), track.genome);
        if(track.dataManager != null) this.setDataManager(track.dataManager);
        if(track.dataSource != null) this.setDataSource(track.dataSource);
    }

    public CoverageTrack(ResourceLocator locator, String name, Genome genome) {
        super(locator, locator.getPath() + "_coverage", name);
        super.setDataRange(new DataRange(0, 0, 60));
        this.genome = genome;
        intervalRenderer = new IntervalRenderer();
        setMaximumHeight(40);

        setColor(coverageGrey);

        prefs = PreferenceManager.getInstance();
        snpThreshold = prefs.getAsFloat(PreferenceManager.SAM_ALLELE_THRESHOLD);
        autoScale = DEFAULT_AUTOSCALE;
        showReference = DEFAULT_SHOW_REFERENCE;
        //TODO  logScale = prefs.


    }

    public void setDataManager(AlignmentDataManager dataManager) {
        this.dataManager = dataManager;
        this.dataManager.getEventBus().register(this);
    }

    public void setDataSource(CoverageDataSource dataSource) {
        this.dataSource = dataSource;
        dataSourceRenderer = new BarChartRenderer();
        setDataRange(new DataRange(0, 0, 1.5f * (float) dataSource.getDataMax()));

    }

    public void setSnpThreshold(float snpThreshold){
        this.snpThreshold = snpThreshold;
    }

    public float getSnpThreshold() {
        return snpThreshold;
    }

    public boolean isShowReference() {
        return showReference;
    }

    /**
     * Rescale as necessary, and tell components to repaint
     * @param e
     */
    @Subscribe
    public void receiveDataLoaded(DataLoadedEvent e){
        ReferenceFrame frame = e.context.getReferenceFrame();
        rescale(frame);
        frame.getEventBus().post(new ViewChange.Result());
    }

    public void rescale(ReferenceFrame iframe) {
        List<ReferenceFrame> frameList = new ArrayList<ReferenceFrame>();
        if(iframe != null) frameList.add(iframe);
        if(globalAutoScale){
            frameList.addAll(FrameManager.getFrames());
        }

        if (autoScale && dataManager != null) {

            int max = 10;
            for (ReferenceFrame frame : frameList) {
                AlignmentInterval interval = dataManager.getLoadedInterval(frame.getCurrentRange());
                if (interval == null) continue;

                int origin = (int) frame.getOrigin();
                int end = (int) frame.getEnd() + 1;

                int intervalMax = interval.getMaxCount(origin, end);
                max = intervalMax > max ? intervalMax : max;
            }

            DataRange newRange = new DataRange(0, max);
            newRange.setType(getDataRange().getType());
            super.setDataRange(newRange);

        }
    }

    public void render(RenderContext context, Rectangle rect){

        overlay(context, rect);

        drawBorder(context, rect);
        List<LocusScore> scores = getSummaryScores(context);
        if (scores != null) {
            dataSourceRenderer.renderBorder(this, context, rect);
        }

        if(!isRepeatY(rect)){
            lastRenderY = rect.y;
            if(dataSourceRenderer != null){
                dataSourceRenderer.renderAxis(this, context, rect);
            }
            if(FrameManager.isExomeMode()){
                int x = context.getGraphics().getClipBounds().x;
                Rectangle scaleRect = new Rectangle(x, rect.y, rect.width, rect.height);
                drawScale(context, scaleRect);
            }

        }

    }

    private List<LocusScore> getSummaryScores(RenderContext context){
        List<LocusScore> scores = null;
        if(dataSource != null){
            String chr = context.getChr();
            int start = (int) context.getOrigin();
            int end = (int) context.getEndLocation();
            int zoom = context.getZoom();
            scores = dataSource.getSummaryScoresForRange(chr, start, end, zoom);
        }
        return scores;
    }

    public void overlay(RenderContext context, Rectangle rect) {

        float maxRange = PreferenceManager.getInstance().getAsFloat(PreferenceManager.SAM_MAX_VISIBLE_RANGE);
        float minVisibleScale = (maxRange * 1000) / 700;

        if (context.getScale() < minVisibleScale && !context.getChr().equals(Globals.CHR_ALL)) {
            //Show coverage calculated from intervals if zoomed in enough
            AlignmentInterval interval = null;
            if (dataManager != null) {
                dataManager.load(context, renderOptions, true);
                interval = dataManager.getLoadedInterval(context.getReferenceFrame().getCurrentRange());
            }
            if (interval != null) {
                if (interval.contains(context.getChr(), (int) context.getOrigin(), (int) context.getEndLocation())) {
                    if(autoScale) rescale(context.getReferenceFrame());
                    intervalRenderer.paint(context, rect, interval.getCounts());
                    return;
                }
            }
        }

        //Use precomputed scores, if available
        List<LocusScore> scores = getSummaryScores(context);
        if (scores != null) {
            dataSourceRenderer.renderScores(this, scores, context, rect);
        }

    }

    /**
     * Draw border and scale
     * @param context
     * @param rect
     */
    private void drawBorder(RenderContext context, Rectangle rect) {
        context.getGraphic2DForColor(Color.gray).drawLine(
                rect.x, rect.y + rect.height,
                rect.x + rect.width, rect.y + rect.height);

        if(!FrameManager.isExomeMode()){
            drawScale(context, rect);
        }
    }

    public void drawScale(RenderContext context, Rectangle rect) {
        DataRenderer.drawScale(getDataRange(), context, rect);
    }

    public boolean isLogNormalized() {
        return false;
    }

    public String getValueStringAt(String chr, double position, int y, ReferenceFrame frame) {

        float maxRange = PreferenceManager.getInstance().getAsFloat(PreferenceManager.SAM_MAX_VISIBLE_RANGE);
        float minVisibleScale = (maxRange * 1000) / 700;
        if (frame.getScale() < minVisibleScale) {
            AlignmentInterval interval = dataManager.getLoadedInterval(frame.getCurrentRange());
            if (interval == null) return null;

            if (interval.contains(chr, (int) position, (int) position)) {
                AlignmentCounts counts = interval.getCounts();
                if (counts != null) {
                    return counts.getValueStringAt((int) position);
                }
            }
        } else {
            return getPrecomputedValueString(chr, position, frame);
        }
        return null;
    }

    private String getPrecomputedValueString(String chr, double position, ReferenceFrame frame) {

        if (dataSource == null) {
            return "";
        }
        int zoom = Math.max(0, frame.getZoom());
        List<LocusScore> scores = dataSource.getSummaryScoresForRange(chr, (int) position - 10, (int) position + 10, zoom);

        // give a 2 pixel window, otherwise very narrow features will be missed.
        double bpPerPixel = frame.getScale();
        double minWidth = 2 * bpPerPixel;    /* * */

        if (scores == null) {
            return "";
        } else {
            LocusScore score = (LocusScore) FeatureUtils.getFeatureAt(position, 0, scores);
            return score == null ? "" : "Mean count: " + score.getScore();
        }
    }

    public float getRegionScore(String chr, int start, int end, int zoom, RegionScoreType type, String frameName) {
        return 0;
    }

    /**
     * Class to render coverage track, including mismatches.
     * <p/>
     * NOTE:  This class has been extensively optimized with the aid of a profiler,  attempts to "clean up" this code
     * should be done with frequent profiling, or it will likely have detrimental performance impacts.
     */
    class IntervalRenderer {

        private void paint(RenderContext context, Rectangle rect, AlignmentCounts alignmentCounts) {

            Color color = getColor();
            Graphics2D graphics = context.getGraphic2DForColor(color);

            DataRange range = getDataRange();
            double maxRange = range.isLog() ? Math.log10(range.getMaximum()) : range.getMaximum();

            final double rectX = rect.getX();
            final double rectMaxX = rect.getMaxX();
            final double rectY = rect.getY();
            final double rectMaxY = rect.getMaxY();
            final double rectHeight = rect.getHeight();
            final double origin = context.getOrigin();
            final double colorScaleMax = getColorScale().getMaximum();
            final double scale = context.getScale();

            boolean bisulfiteMode = dataManager.getExperimentType() == AlignmentTrack.ExperimentType.BISULFITE;


            // First pass, coverage
            int lastpX = -1;
            //for (AlignmentCounts alignmentCounts : countList) {
            int start = alignmentCounts.getStart();
            int nPoints = alignmentCounts.getNumberOfPoints();
            boolean isSparse = alignmentCounts instanceof SparseAlignmentCounts;

            for (int idx = 0; idx < nPoints; idx++) {

                int pos = isSparse ? ((SparseAlignmentCounts) alignmentCounts).getPosition(idx) : start + idx;
                int pX = (int) (rectX + (pos - origin) / scale);

                if (pX > rectMaxX) {
                    break; // We're done,  data is position sorted so we're beyond the right-side of the view
                }

                int dX = (int) (rectX + (pos + 1 - origin) / scale) - pX;
                dX = dX < 1 ? 1 : dX;
                if (pX + dX > lastpX) {
                    int pY = (int) rectMaxY - 1;
                    int totalCount = alignmentCounts.getTotalCount(pos);
                    double tmp = range.isLog() ? Math.log10(totalCount) / maxRange : totalCount / maxRange;
                    int height = (int) (tmp * rectHeight);

                    height = Math.min(height, rect.height - 1);
                    int topY = (pY - height);
                    if (dX > 3) {
                        dX--; // Create a little space between bars when there is room.
                    }
                    if (height > 0) {
                        graphics.fillRect(pX, topY, dX, height);

                    }
                    lastpX = pX + dX;
                }
            }
            //}


            // Second pass - mark mismatches
            lastpX = -1;
            //for (AlignmentCounts alignmentCounts : countList) {

            BisulfiteCounts bisulfiteCounts = alignmentCounts.getBisulfiteCounts();
            final int intervalEnd = alignmentCounts.getEnd();
            final int intervalStart = alignmentCounts.getStart();
            byte[] refBases = null;

            // Dont try to compute mismatches for intervals > 10 MB
            if ((intervalEnd - intervalStart) < TEN_MB) {
                refBases = genome.getSequence(context.getChr(), intervalStart, intervalEnd);
            }


            start = alignmentCounts.getStart();
            nPoints = alignmentCounts.getNumberOfPoints();
            isSparse = alignmentCounts instanceof SparseAlignmentCounts;

            for (int idx = 0; idx < nPoints; idx++) {
                int pos = isSparse ? ((SparseAlignmentCounts) alignmentCounts).getPosition(idx) : start + idx;

                BisulfiteCounts.Count bc = null;
                if (bisulfiteMode && bisulfiteCounts != null) {
                    bc = bisulfiteCounts.getCount(pos);
                }

                int pX = (int) (rectX + (pos - origin) / scale);

                if (pX > rectMaxX) {
                    break; // We're done,  data is position sorted so we're beyond the right-side of the view
                }

                int dX = (int) (rectX + (pos + 1 - origin) / scale) - pX;
                dX = dX < 1 ? 1 : dX;
                if (pX + dX > lastpX) {


                    // Test to see if any single nucleotide mismatch  (nucleotide other than the reference)
                    // has a quality weight > 20% of the total
                    // Skip this test if the position is in the list of known snps or if the reference is unknown
                    boolean mismatch = false;

                    if (refBases != null) {
                        int refIdx = pos - intervalStart;
                        if (refIdx >= 0 && refIdx < refBases.length) {
                            if (bisulfiteMode) {
                                mismatch = (bc != null && (bc.methylatedCount + bc.unmethylatedCount) > 0);
                            } else {
                                byte ref = refBases[refIdx];
                                mismatch = alignmentCounts.isMismatch(pos, ref, context.getChr(), snpThreshold);
                            }
                        }
                    }

                    if (!mismatch) {
                        continue;
                    }

                    int pY = (int) rectMaxY - 1;

                    int totalCount = alignmentCounts.getTotalCount(pos);
                    double tmp = range.isLog() ? Math.log10(totalCount) / maxRange : totalCount / maxRange;
                    int height = (int) (tmp * rectHeight);

                    height = Math.min(height, rect.height - 1);

                    if (dX > 3) {
                        dX--; // Create a little space between bars when there is room.
                    }

                    if (height > 0) {
                        if (bisulfiteMode) {
                            if (bc != null) {
                                drawBarBisulfite(context, pos, rect, totalCount, maxRange,
                                        pY, pX, dX, bc, range.isLog());
                            }
                        } else {
                            drawBar(context, pos, rect, totalCount, maxRange,
                                    pY, pX, dX, alignmentCounts, range.isLog());
                        }
                    }
                    lastpX = pX + dX;

                }
            }
            //}

        }
    }

    /**
     * Draw a colored bar to represent a mismatch to the reference.   The height is proportional to the % of
     * reads with respect to the total.  If "showAllSnps == true"  the bar is shaded by avg read quality.
     *
     * @param context
     * @param pos
     * @param rect
     * @param max
     * @param pY
     * @param pX
     * @param dX
     * @param interval
     * @return
     */

    int drawBar(RenderContext context,
                int pos,
                Rectangle rect,
                double totalCount,
                double max,
                int pY,
                int pX,
                int dX,
                AlignmentCounts interval,
                boolean isLog) {

        for (char nucleotide : nucleotides) {

            int count = interval.getCount(pos, (byte) nucleotide);

            Color c = Globals.nucleotideColors.get(nucleotide);

            Graphics2D tGraphics = context.getGraphic2DForColor(c);

            double tmp = isLog ?
                    (count / totalCount) * Math.log10(totalCount) / max :
                    count / max;
            int height = (int) (tmp * rect.getHeight());

            height = Math.min(pY - rect.y, height);
            int baseY = pY - height;

            if (height > 0) {
                tGraphics.fillRect(pX, baseY, dX, height);
            }

            pY = baseY;
        }
        return pX + dX;
    }

    int drawBarBisulfite(RenderContext context,
                         int pos,
                         Rectangle rect,
                         double totalCount,
                         double maxRange,
                         int pY,
                         int pX0,
                         int dX,
                         BisulfiteCounts.Count count,
                         boolean isLog) {

        // If bisulfite mode, we expand the rectangle to make it more visible.  This code is copied from
        // AlignmentRenderer
        int pX = pX0;
        if (dX < 3) {
            int expansion = dX;
            pX -= expansion;
            dX += (2 * expansion);
        }


        double nMethylated = count.methylatedCount;
        double unMethylated = count.unmethylatedCount;
        Color c = Color.red;
        Graphics2D tGraphics = context.getGraphic2DForColor(c);

        //Not all reads at a position are informative,  color by % of informative reads
        // double totalInformative = count.methylatedCount + count.unmethylatedCount;
        // double mult = totalCount / totalInformative;
        // nMethylated *= mult;
        // unMethylated *= mult;

        double tmp = isLog ?
                (nMethylated / totalCount) * Math.log10(totalCount) / maxRange :
                nMethylated / maxRange;
        int height = (int) (tmp * rect.getHeight());

        height = Math.min(pY - rect.y, height);
        int baseY = pY - height;
        if (height > 0) {
            tGraphics.fillRect(pX, baseY, dX, height);
        }
        pY = baseY;

        c = Color.blue;
        tGraphics = context.getGraphic2DForColor(c);

        tmp = isLog ?
                (unMethylated / totalCount) * Math.log10(totalCount) / maxRange :
                unMethylated / maxRange;
        height = (int) (tmp * rect.getHeight());

        height = Math.min(pY - rect.y, height);
        baseY = pY - height;
        if (height > 0) {
            tGraphics.fillRect(pX, baseY, dX, height);

        }
        return pX + dX;
    }


    /**
     * Strand-specific
     *
     * @param context
     * @param pos
     * @param rect
     * @param maxCount
     * @param pY
     * @param pX
     * @param dX
     * @param isPositive
     * @param interval
     * @return
     */
    void drawStrandBar(RenderContext context,
                       int pos,
                       Rectangle rect,
                       double maxCount,
                       int pY,
                       int pX,
                       int dX,
                       boolean isPositive,
                       AlignmentCounts interval) {


        for (char nucleotide : nucleotides) {

            Color c = Globals.nucleotideColors.get(nucleotide);
            Graphics2D tGraphics = context.getGraphic2DForColor(c);

            int count = isPositive ? interval.getPosCount(pos, (byte) nucleotide) :
                    interval.getNegCount(pos, (byte) nucleotide);

            int height = (int) Math.round(count * rect.getHeight() / maxCount);
            height = isPositive ? Math.min(pY - rect.y, height) :
                    Math.min(rect.y + rect.height - pY, height);
            int baseY = (int) (isPositive ? (pY - height) : pY);

            if (height > 0) {
                tGraphics.fillRect(pX, baseY, dX, height);
            }
            pY = isPositive ? baseY : baseY + height;
        }
    }


    static float[] colorComps = new float[3];

    private Color getShadedColor(int qual, Color backgroundColor, Color color) {
        float alpha = 0;
        int minQ = prefs.getAsInt(PreferenceManager.SAM_BASE_QUALITY_MIN);
        ColorUtilities.getRGBColorComponents(color);
        if (qual < minQ) {
            alpha = 0.1f;
        } else {
            int maxQ = prefs.getAsInt(PreferenceManager.SAM_BASE_QUALITY_MAX);
            alpha = Math.max(0.1f, Math.min(1.0f, 0.1f + 0.9f * (qual - minQ) / (maxQ - minQ)));
        }
        // Round alpha to nearest 0.1, for effeciency;
        alpha = ((int) (alpha * 10 + 0.5f)) / 10.0f;

        if (alpha >= 1) {
            return color;
        } else {
            return ColorUtilities.getCompositeColor(backgroundColor, color, alpha);
        }
    }

    /**
     * Override to return a specialized popup menu
     *
     * @return
     */
    @Override
    public IGVPopupMenu getPopupMenu(TrackClickEvent te) {

        IGVPopupMenu popupMenu = new IGVPopupMenu();

        JLabel popupTitle = new JLabel("  " + getName(), JLabel.CENTER);

        Font newFont = popupMenu.getFont().deriveFont(Font.BOLD, 12);
        popupTitle.setFont(newFont);
        if (popupTitle != null) {
            popupMenu.add(popupTitle);
        }

        popupMenu.addSeparator();

        ArrayList<Track> tmp = new ArrayList();
        tmp.add(this);

        popupMenu.add(TrackMenuUtils.getChangeTrackHeightItem(tmp));
        popupMenu.add(TrackMenuUtils.getTrackRenameItem(tmp));
        addCopyDetailsItem(popupMenu, te);

        addAutoscaleItem(popupMenu, te.getFrame());
        addLogScaleItem(popupMenu);
        dataRangeItem = addDataRangeItem(IGV.getMainFrame(), popupMenu, tmp);

        this.addSnpTresholdItem(popupMenu);

        popupMenu.addSeparator();
        addLoadCoverageDataItem(popupMenu);
        popupMenu.addSeparator();

        popupMenu.add(TrackMenuUtils.getRemoveMenuItem(tmp));

        return popupMenu;
    }

    private void addCopyDetailsItem(IGVPopupMenu popupMenu, TrackClickEvent te) {
        JMenuItem copyDetails = new JMenuItem("Copy Details to Clipboard");
        copyDetails.setEnabled(false);
        if (te.getFrame() != null) {
            final String details = getValueStringAt(te.getFrame().getChrName(), te.getChromosomePosition(), te.getMouseEvent().getY(), te.getFrame());
            copyDetails.addActionListener(new ActionListener() {
                @Override
                public void actionPerformed(ActionEvent e) {
                    if (details != null) {
                        String deets = details.replace("<br>", System.getProperty("line.separator"));
                        StringUtils.copyTextToClipboard(deets);
                    }
                }
            });
            copyDetails.setEnabled(details != null);
        }
        popupMenu.add(copyDetails);
    }


    public static JMenuItem addDataRangeItem(final Frame parentFrame, JPopupMenu menu, final Collection<? extends Track> selectedTracks) {
        JMenuItem maxValItem = new JMenuItem("Set Data Range");

        maxValItem.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {
                if (selectedTracks.size() > 0) {

                    DataRange prevAxisDefinition = selectedTracks.iterator().next().getDataRange();
                    DataRangeDialog dlg = new DataRangeDialog(parentFrame, prevAxisDefinition);
                    dlg.setHideMid(true);
                    dlg.setVisible(true);
                    if (!dlg.isCanceled()) {
                        float min = Math.min(dlg.getMin(), dlg.getMax());
                        float max = Math.max(dlg.getMin(), dlg.getMax());
                        float mid = dlg.getBase();
                        if (mid < min) mid = min;
                        else if (mid > max) mid = max;
                        DataRange dataRange = new DataRange(min, mid, max);
                        dataRange.setType(dlg.getDataRangeType());

                        for (Track track : selectedTracks) {
                            track.setDataRange(dataRange);
                            track.setAutoScale(false);
                        }
                        parentFrame.repaint();
                    }
                }

            }
        });
        if (menu != null) menu.add(maxValItem);

        return maxValItem;
    }

    public JMenuItem addSnpTresholdItem(JPopupMenu menu) {
        JMenuItem maxValItem = new JMenuItem("Set allele frequency threshold...");

        maxValItem.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {

                String value = JOptionPane.showInputDialog("Allele frequency threshold: ", Float.valueOf(snpThreshold));
                if (value == null) {
                    return;
                }
                try {
                    float tmp = Float.parseFloat(value);
                    snpThreshold = tmp;
                    IGV.getInstance().repaintDataPanels();
                } catch (Exception exc) {
                    //log
                }

            }
        });
        menu.add(maxValItem);

        return maxValItem;
    }

    public void addLoadCoverageDataItem(JPopupMenu menu) {
        // Change track height by attribute
        final JMenuItem item = new JCheckBoxMenuItem("Load coverage data...");
        item.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {

                final PreferenceManager prefs = PreferenceManager.getInstance();
                File initDirectory = prefs.getLastTrackDirectory();
                File file = FileDialogUtils.chooseFile("Select coverage file", initDirectory, FileDialog.LOAD);
                if (file != null) {
                    prefs.setLastTrackDirectory(file.getParentFile());
                    String path = file.getAbsolutePath();
                    if (path.endsWith(".tdf") || path.endsWith(".tdf")) {
                        TDFReader reader = TDFReader.getReader(file.getAbsolutePath());
                        TDFDataSource ds = new TDFDataSource(reader, 0, getName() + " coverage", genome);
                        setDataSource(ds);
                        IGV.getInstance().repaintDataPanels();
                    } else if (path.endsWith(".counts")) {
                        CoverageDataSource ds = new GobyCountArchiveDataSource(file);
                        setDataSource(ds);
                        IGV.getInstance().repaintDataPanels();
                    } else {
                        MessageUtils.showMessage("Coverage data must be in .tdf format");
                    }
                }
            }
        });

        menu.add(item);

    }

    public void addAutoscaleItem(JPopupMenu menu,final ReferenceFrame frame) {
        // Change track height by attribute
        autoscaleItem = new JCheckBoxMenuItem("Autoscale");
        autoscaleItem.setSelected(autoScale);
        autoscaleItem.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {

                autoScale = autoscaleItem.isSelected();
                dataRangeItem.setEnabled(!autoScale);
                if (autoScale) {
                    rescale(frame);
                }
                IGV.getInstance().repaintDataPanels();

            }
        });

        menu.add(autoscaleItem);
    }

    public void addLogScaleItem(JPopupMenu menu) {
        // Change track height by attribute
        final DataRange dataRange = getDataRange();
        final JCheckBoxMenuItem logScaleItem = new JCheckBoxMenuItem("Log scale");
        final boolean logScale = dataRange.getType() == DataRange.Type.LOG;
        logScaleItem.setSelected(logScale);
        logScaleItem.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {

                DataRange.Type scaleType = logScaleItem.isSelected() ?
                        DataRange.Type.LOG :
                        DataRange.Type.LINEAR;
                dataRange.setType(scaleType);
                IGV.getInstance().repaintDataPanels();
            }
        });

        menu.add(logScaleItem);
    }

    @SubtlyImportant
    private static CoverageTrack getNextTrack() {
        return (CoverageTrack) IGVSessionReader.getNextTrack();
    }

    public void setGlobalAutoScale(boolean globalAutoScale) {
        this.globalAutoScale = globalAutoScale;
    }

}
