/*
 * 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.renderer;

//~--- non-JDK imports --------------------------------------------------------

import org.apache.log4j.Logger;
import org.broad.igv.PreferenceManager;
import org.broad.igv.feature.*;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.track.FeatureTrack;
import org.broad.igv.track.RenderContext;
import org.broad.igv.track.Track;
import org.broad.igv.track.TrackType;
import org.broad.igv.ui.FontManager;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.color.ColorUtilities;

import java.awt.*;
import java.awt.font.LineMetrics;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

// Added by Solomon

/**
 * Renderer for the full "IGV" feature interface (classes implementing
 *
 * @author Enter your name here...
 * @version Enter version here..., 08/10/24
 */
public class IGVFeatureRenderer extends FeatureRenderer {

    static final Color AA_COLOR_1 = new Color(92, 92, 164);
    static final Color AA_COLOR_2 = new Color(12, 12, 120);
    static final Color DULL_BLUE = new Color(0, 0, 200);
    static final Color DULL_RED = new Color(200, 0, 0);
    /**
     * Field description
     */
    public static final int NON_CODING_HEIGHT = 8;
    private static Logger log = Logger.getLogger(IGVFeatureRenderer.class);
    protected boolean drawBoundary = false;


    float viewLimitMin = Float.NaN;
    float viewLimitMax = Float.NaN;


    // Use the max of these values to determine where
    // text should be drawn
    protected double lastFeatureLineMaxY = 0;
    protected double lastFeatureBoundsMaxY = 0;
    protected double lastRegionMaxY = 0;

    // Constants
    static protected final int NORMAL_STRAND_Y_OFFSET = 14;
    static protected final int ARROW_SPACING = 30;
    static protected final int NO_STRAND_THICKNESS = 2;
    static protected final int REGION_STRAND_THICKNESS = 4;
    static final int BLOCK_HEIGHT = 14;
    static final int THIN_BLOCK_HEIGHT = 6;

    int blockHeight = BLOCK_HEIGHT;
    int thinBlockHeight = THIN_BLOCK_HEIGHT;

    //Map from Exon to y offset
    //Could use more coordinates, but they are all contained in the Exon
    private Map<IExon, Integer> exonMap = new HashMap<IExon, Integer>(100);

    /**
     * Note:  assumption is that featureList is sorted by pStart position.
     *
     * @param featureList
     * @param context
     * @param trackRectangle
     * @param track
     */
    public void render(List<IGVFeature> featureList,
                       RenderContext context,
                       Rectangle trackRectangle,
                       Track track) {

        double origin = context.getOrigin();
        double locScale = context.getScale();

        final Track.DisplayMode displayMode = track.getDisplayMode();
        blockHeight = displayMode == Track.DisplayMode.SQUISHED ? BLOCK_HEIGHT / 2 : BLOCK_HEIGHT;
        thinBlockHeight = displayMode == Track.DisplayMode.SQUISHED ? THIN_BLOCK_HEIGHT / 2 : THIN_BLOCK_HEIGHT;

        // Clear values
        lastFeatureLineMaxY = 0;
        lastFeatureBoundsMaxY = 0;
        lastRegionMaxY = 0;


        // TODO -- use enum instead of string "Color"
        if ((featureList != null) && (featureList.size() > 0)) {

            // Create a graphics object to draw font names.  Graphics are not cached
            // by font, only by color, so its neccessary to create a new one to prevent
            // affecting other tracks.
            Font font = FontManager.getFont(track.getFontSize());
            Graphics2D fontGraphics = (Graphics2D) context.getGraphic2DForColor(Color.BLACK).create();
            fontGraphics.setFont(font);

            // Track coordinates
            double trackRectangleX = trackRectangle.getX();
            double trackRectangleMaxX = trackRectangle.getMaxX();
            double trackRectangleY = trackRectangle.getY();
            double trackRectangleMaxY = trackRectangle.getMaxY();

            // Draw the lines that represent the bounds of
            // a feature's region
            // TODO -- bugs in "Line Placement" style -- hardocde to fishbone


            int lastFeatureEndedAtPixelX = -9999;
            int lastPixelEnd = -1;
            int occludedCount = 0;
            int maxOcclusions = 2;


            boolean alternateExonColor = (track instanceof FeatureTrack && ((FeatureTrack) track).isAlternateExonColor());
            boolean colorToggle = true;

            IGVFeature featureArray[] = featureList.toArray(new IGVFeature[featureList.size()]);
            for (int i = 0; i < featureArray.length; i++) {

                IGVFeature feature = featureArray[i];

                // Get the pStart and pEnd of the entire feature  at extreme zoom levels the
                // virtual pixel value can be too large for an int, so the computation is
                // done in double precision and cast to an int only when its confirmed its
                // within the field of view.


                double virtualPixelStart = Math.round((feature.getStart() - origin) / locScale);
                double virtualPixelEnd = Math.round((feature.getEnd() - origin) / locScale);

                boolean hasExons = ((feature.getExons() != null) && (feature.getExons().size() > 0));

                // If the any part of the feature fits in the
                // Track rectangle draw it
                if ((virtualPixelEnd >= trackRectangleX) && (virtualPixelStart <= trackRectangleMaxX)) {

                    //
                    int pixelEnd = (int) Math.min(trackRectangleMaxX, virtualPixelEnd);
                    int pixelStart = (int) Math.max(trackRectangleX, virtualPixelStart);


                    if (pixelEnd <= lastPixelEnd) {
                        if (occludedCount >= maxOcclusions) {
                            continue;
                        } else {
                            occludedCount++;
                        }
                    } else {
                        occludedCount = 0;
                        lastPixelEnd = pixelEnd;
                    }

                    Color color = getFeatureColor(feature, track);

                    Graphics2D g2D = context.getGraphic2DForColor(color);

                    // Get the feature's direction
                    Strand strand = feature.getStrand();

                    // Draw block
                    int pixelThickStart = pixelStart;
                    int pixelThickEnd = pixelEnd;
                    if (feature instanceof BasicFeature) {
                        BasicFeature bf = (BasicFeature) feature;
                        pixelThickStart = (int) Math.max(trackRectangleX, (bf.getThickStart() - origin) / locScale);
                        pixelThickEnd = (int) Math.min(trackRectangleMaxX, (bf.getThickEnd() - origin) / locScale);
                    }

                    drawFeatureBlock(pixelStart, pixelEnd, pixelThickStart, pixelThickEnd, trackRectangle, strand, hasExons, g2D);

                    int pixelYCenter = trackRectangle.y + NORMAL_STRAND_Y_OFFSET / 2;
                    if ((pixelEnd - pixelStart < 3) && hasExons) {
                        drawFeatureBounds(pixelStart, pixelEnd, pixelYCenter, g2D);
                    } else {

                        Graphics2D arrowGraphics = hasExons
                                ? g2D
                                : context.getGraphic2DForColor(Color.WHITE);

                        // Draw the directional arrows
                        drawStrandArrows(feature, pixelStart, pixelEnd, pixelYCenter, displayMode, arrowGraphics);

                        if (hasExons) {
                            drawExons(feature, pixelYCenter, context, g2D, trackRectangle, displayMode,
                                    alternateExonColor, track.getColor(), track.getAltColor());
                        }

                    }

                    // Draw name
                    if (displayMode != Track.DisplayMode.SQUISHED) {
                        String name = feature.getName();
                        if (name != null) {
                            LineMetrics lineMetrics = font.getLineMetrics(name, g2D.getFontRenderContext());
                            int fontHeight = (int) Math.ceil(lineMetrics.getHeight());


                            // Draw feature name.  Center it over the feature extent,
                            // or if the feature extends beyond the track bounds over
                            // the track rectangle.
                            int nameStart = Math.max(0, pixelStart);
                            int nameEnd = Math.min(pixelEnd, (int) trackRectangle.getWidth());
                            int textBaselineY = getLastLargestMaxY() + fontHeight;

                            // Calculate the minimum amount of vertical track
                            // space required be we  draw the
                            // track name without drawing over the features
                            int verticalSpaceRequiredForText = textBaselineY - (int) trackRectangleY;

                            if (verticalSpaceRequiredForText <= trackRectangle.height) {

                                lastFeatureEndedAtPixelX = drawFeatureName(feature, nameStart, nameEnd,
                                        lastFeatureEndedAtPixelX, fontGraphics, textBaselineY);
                            }
                        }
                    }

                    // If this is the highlight feature highlight it
                    if (getHighlightFeature() == feature) {
                        int yStart = pixelYCenter - blockHeight / 2 - 1;
                        Graphics2D highlightGraphics = context.getGraphic2DForColor(Color.cyan);
                        highlightGraphics.drawRect(pixelStart - 1, yStart, (pixelEnd - pixelStart + 2), blockHeight + 2);


                    }

                }

            }

            if (drawBoundary) {
                Graphics2D g2D = context.getGraphic2DForColor(Color.LIGHT_GRAY);
                g2D.drawLine((int) trackRectangleX, (int) trackRectangleMaxY - 1,
                        (int) trackRectangleMaxX, (int) trackRectangleMaxY - 1);
            }
        }
    }

    /**
     * @param pixelStart
     * @param pixelEnd
     * @param trackRectangle
     * @param strand
     * @param hasRegions
     * @param g
     * @return The stroke used to draw the line.
     */
    final private void drawFeatureBlock(int pixelStart, int pixelEnd, int pixelThickStart, int pixelThickEnd,
                                        Rectangle trackRectangle, Strand strand, boolean hasRegions, Graphics2D g) {

        Graphics2D g2D = (Graphics2D) g.create();

        if (!hasRegions) {
            int yOffset = trackRectangle.y + NORMAL_STRAND_Y_OFFSET / 2;

            if (pixelThickStart > pixelStart) {
                g2D.fillRect(pixelStart, yOffset - (thinBlockHeight) / 2,
                        Math.max(1, pixelThickStart - pixelStart), (thinBlockHeight));
            }
            if (pixelThickEnd > 0 && pixelThickEnd < pixelEnd) {
                g2D.fillRect(pixelThickEnd, yOffset - (thinBlockHeight) / 2,
                        Math.max(1, pixelEnd - pixelThickEnd), (thinBlockHeight));
            }

            g2D.fillRect(pixelThickStart, yOffset - (blockHeight - 4) / 2,
                    Math.max(1, pixelThickEnd - pixelThickStart), (blockHeight - 4));
            lastFeatureLineMaxY = yOffset + blockHeight - 4;
        } else {

            // Draw the line that represents the entire feature
            int yOffset = trackRectangle.y + NORMAL_STRAND_Y_OFFSET / 2;
            float lineThickness = ((BasicStroke) g.getStroke()).getLineWidth();
            if (strand == null) {

                // Double the line thickness
                lineThickness *= NO_STRAND_THICKNESS;
                Stroke stroke = new BasicStroke(lineThickness);
                g2D.setStroke(stroke);
            }
            g2D.drawLine(pixelStart, yOffset, pixelEnd, yOffset);
            lastFeatureLineMaxY = yOffset + lineThickness;
        }
        g2D.dispose();
    }


    // If the width is < 3 there isn't room to draw the
    // feature, or orientation.  If the feature has any exons
    // at all indicate by filling a small rect

    private void drawFeatureBounds(int pixelStart, int pixelEnd, int yOffset, Graphics2D g2D) {

        if (pixelEnd == pixelStart) {
            int yStart = yOffset - blockHeight / 2;
            g2D.drawLine(pixelStart, yStart, pixelStart, yStart + blockHeight);
        } else {
            g2D.fillRect(pixelStart, yOffset - blockHeight / 2, pixelEnd - pixelStart, blockHeight);
        }

        lastFeatureBoundsMaxY = yOffset + blockHeight / 2;
    }

    protected void drawExons(IGVFeature gene, int yOffset, RenderContext context,
                             Graphics2D g2D, Rectangle trackRectangle, Track.DisplayMode mode,
                             boolean alternateExonColor, Color color1, Color color2) {

        Graphics exonNumberGraphics = g2D.create();
        exonNumberGraphics.setColor(Color.BLACK);
        exonNumberGraphics.setFont(FontManager.getFont(Font.BOLD, 8));

        // Now get the individual regions of the
        // feature are drawn here

        double theOrigin = context.getOrigin();
        double locationScale = context.getScale();

        Graphics2D fontGraphics = context.getGraphic2DForColor(Color.WHITE);

        boolean colorToggle = true;


        for (Exon exon : gene.getExons()) {

            // Parse expression from tags, if available
            //Credit Michael Poidinger and Solomonraj Wilson, Singapore Immunology Network.
            Float exprValue = null;

            Map<String, String> attributes = exon.getAttributes();
            if (attributes != null && attributes.containsKey("expr")) {
                try {
                    exprValue = Float.parseFloat(attributes.get("expr"));
                } catch (NumberFormatException e) {
                    log.error("Error parsing expression tag " + attributes.get("expr"), e);
                }
            }

            if (exprValue != null) {
                ContinuousColorScale colorScale = PreferenceManager.getInstance().getColorScale(TrackType.GENE_EXPRESSION);
                Color chartColor = colorScale.getColor(exprValue);
                g2D = context.getGraphic2DForColor(chartColor);
            }

            // Added by Solomon - End

            Graphics2D blockGraphics = g2D;
            if (alternateExonColor) {
                Color color = colorToggle ? color1 : color2;
                blockGraphics = context.getGraphic2DForColor(color);
                colorToggle = !colorToggle;
            }

            int curYOffset = yOffset;
//            IExon pExon = Exon.getExonProxy(exon);
//            if(exonMap.containsKey(pExon)){
//                curYOffset= exonMap.get(pExon);
//            }else{
//                exonMap.put(pExon, yOffset);
//            }

            int pStart = getPixelFromChromosomeLocation(exon.getChr(), exon.getStart(), theOrigin, locationScale);
            int pEnd = getPixelFromChromosomeLocation(exon.getChr(), exon.getEnd(), theOrigin, locationScale);


            if ((pEnd >= trackRectangle.getX()) && (pStart <= trackRectangle.getMaxX())) {
                int pCdStart =
                        Math.min(pEnd, Math.max(pStart,
                                getPixelFromChromosomeLocation(exon.getChr(),
                                        exon.getCdStart(), theOrigin, locationScale)));
                int pCdEnd = Math.max(pStart, Math.min(pEnd,
                        getPixelFromChromosomeLocation(exon.getChr(),
                                exon.getCdEnd(), theOrigin, locationScale)));

                // Entire exon is UTR
                if (exon.isUTR()) {
                    int pClippedStart = (int) Math.max(pStart, trackRectangle.getX());
                    int pClippedEnd = (int) Math.min(pEnd, trackRectangle.getMaxX());
                    int pClippedWidth = pClippedEnd - pClippedStart;
                    blockGraphics.fillRect(pClippedStart, curYOffset - NON_CODING_HEIGHT / 2, pClippedWidth, NON_CODING_HEIGHT);

                } else {// Exon contains 5' UTR -- draw non-coding part
                    if (pCdStart > pStart) {
                        int pClippedStart = (int) Math.max(pStart, trackRectangle.getX());
                        int pClippedEnd = (int) Math.min(pCdStart, trackRectangle.getMaxX());
                        int pClippedWidth = pClippedEnd - pClippedStart;
                        blockGraphics.fillRect(pClippedStart, curYOffset - NON_CODING_HEIGHT / 2, pClippedWidth, NON_CODING_HEIGHT);
                        pStart = pCdStart;
                    }
                    //  Exon contains 3' UTR  -- draw non-coding part
                    if (pCdEnd < pEnd) {
                        int pClippedStart = (int) Math.max(pCdEnd, trackRectangle.getX());
                        int pClippedEnd = (int) Math.min(pEnd, trackRectangle.getMaxX());
                        int pClippedWidth = pClippedEnd - pClippedStart;
                        blockGraphics.fillRect(pClippedStart, curYOffset - NON_CODING_HEIGHT / 2, pClippedWidth, NON_CODING_HEIGHT);
                        pEnd = pCdEnd;
                    }

                    // At least part of this exon is coding.  Draw the coding part.
                    if ((exon.getCdStart() < exon.getEnd()) && (exon.getCdEnd() > exon.getStart())) {
                        int pClippedStart = (int) Math.max(pStart, trackRectangle.getX());
                        int pClippedEnd = (int) Math.min(pEnd, trackRectangle.getMaxX());
                        int pClippedWidth = Math.max(2, pClippedEnd - pClippedStart);
                        blockGraphics.fillRect(pClippedStart, curYOffset - blockHeight / 2, pClippedWidth, blockHeight);

                    }
                }

                Graphics2D arrowGraphics = context.getGraphic2DForColor(Color.white);
                drawStrandArrows(gene, pStart + ARROW_SPACING / 2, pEnd, curYOffset, mode, arrowGraphics);


                if (locationScale < 0.25) {
                    labelAminoAcids(pStart, fontGraphics, theOrigin, context, gene, locationScale,
                            curYOffset, exon, trackRectangle);
                }

            }

            // TODO -- eliminate reference to lastRegionMaxY, a base class member.
            //
            lastRegionMaxY = yOffset - blockHeight / 2 + blockHeight;

        }

    }

    protected void drawStrandArrows(IGVFeature feature, int pixelStart, int pixelEnd, int yOffset, Track.DisplayMode mode,
                                    Graphics2D g2D) {

        // Don't draw strand arrows for very small regions
        if ((pixelEnd - pixelStart < 6)) {
            return;
        }

        // Limit drawing to visible region, we don't really know the viewport pEnd,
        int vStart = 0;
        int vEnd = 10000;

        // Draw the directional arrows on the feature
        final int sz = mode == Track.DisplayMode.EXPANDED ? 3 : 2;
        if (feature.getStrand().equals(Strand.POSITIVE)) {

            for (int i = pixelEnd; i > pixelStart; i -= ARROW_SPACING) {

                if (i < vStart) {
                    break;
                }
                if (i < vEnd) {
                    g2D.drawLine(i, yOffset, i - sz, yOffset + sz);
                    g2D.drawLine(i, yOffset, i - sz, yOffset - sz);
                }

            }
        } else if (feature.getStrand().equals(Strand.NEGATIVE)) {

            // Draw starting line.  Should we be doing this?
            g2D.drawLine(pixelEnd, yOffset + 2, pixelEnd, yOffset - 2);

            for (int i = pixelStart; i < pixelEnd; i += ARROW_SPACING) {
                if (i > vEnd) {
                    break;
                }
                if ((i > vStart) && (i < vEnd)) {
                    g2D.drawLine(i, yOffset, i + sz, yOffset + sz);
                    g2D.drawLine(i, yOffset, i + sz, yOffset - sz);
                }
            }
        }
    }

    final private int drawFeatureName(IGVFeature feature, int pixelStart, int pixelEnd,
                                      int lastFeatureEndedAtPixelX, Graphics2D g2D,
                                      int textBaselineY) {

        String name = feature.getName();
        if (name == null) {
            return lastFeatureEndedAtPixelX;
        }

        FontMetrics fm = g2D.getFontMetrics();
        int fontSize = fm.getFont().getSize();
        int nameWidth = fm.stringWidth(name);
        int nameStart = (pixelStart + pixelEnd - nameWidth) / 2;

        if (nameStart > (lastFeatureEndedAtPixelX + fontSize)) {

            // g2D.clearRect(xString2, textBaselineY, (int) stringBounds.getWidth(), (int) stringBounds.getHeight());
            g2D.drawString(name, nameStart, textBaselineY);
            lastFeatureEndedAtPixelX = nameStart + nameWidth;

        }

        return lastFeatureEndedAtPixelX;
    }

    /**
     * Method description
     *
     * @param pStart
     * @param fontGraphics
     * @param theOrigin
     * @param context
     * @param gene
     * @param locationScale
     * @param yOffset
     * @param exon
     * @param trackRectangle
     */
    public void labelAminoAcids(int pStart, Graphics2D fontGraphics, double theOrigin,
                                RenderContext context, IGVFeature gene, double locationScale,
                                int yOffset, Exon exon, Rectangle trackRectangle) {

        Genome genome = IGV.getInstance().getGenomeManager().getCurrentGenome();
        AminoAcidSequence aaSequence = exon.getAminoAcidSequence(genome);
        if ((aaSequence != null) && aaSequence.hasNonNullSequence()) {
            Rectangle aaRect = new Rectangle(pStart, yOffset - blockHeight / 2, 1, blockHeight);

            int aaSeqStartPosition = aaSequence.getStartPosition();
            int firstFullAcidIndex = (int) Math.floor((aaSeqStartPosition - exon.getReadingShift()) / 3);
            //calculated oddness or evenness of first amino acid. This is also done independently in SequenceRenderer
            boolean odd = (firstFullAcidIndex % 2) == 1;

            if (aaSeqStartPosition > exon.getStart()) {

                // The codon for the first amino acid is split between this and the previous exon
                // TODO -- get base from previous exon and compute aaSequence.  For now skipping drawing
                // the AA label
                int cdStart = Math.max(exon.getCdStart(), exon.getStart());
                aaRect.x = getPixelFromChromosomeLocation(exon.getChr(), cdStart, theOrigin,
                        locationScale);
                aaRect.width = getPixelFromChromosomeLocation(exon.getChr(),
                        aaSeqStartPosition, theOrigin, locationScale) - aaRect.x;

                if (trackRectangle.intersects(aaRect)) {
                    //use opposite color from first AA color
                    Graphics2D bgGraphics = context.getGraphic2DForColor(!odd ? AA_COLOR_1 : AA_COLOR_2);
                    bgGraphics.fill(aaRect);
                }
            }


            for (AminoAcid acid : aaSequence.getSequence()) {
                if (acid != null) {

                    int px = getPixelFromChromosomeLocation(exon.getChr(), aaSeqStartPosition, theOrigin, locationScale);
                    int px2 = getPixelFromChromosomeLocation(exon.getChr(), aaSeqStartPosition + 3, theOrigin, locationScale);

                    if ((px <= trackRectangle.getMaxX()) && (px2 >= trackRectangle.getX())) {

                        // {

                        aaRect.x = px;
                        aaRect.width = px2 - px;


                        Graphics2D bgGraphics = context.getGraphic2DForColor(odd ? AA_COLOR_1 : AA_COLOR_2);
                        if (((acid.getSymbol() == 'M') && (((gene.getStrand() == Strand.POSITIVE) &&
                                (aaSeqStartPosition == exon.getCdStart())) || ((gene.getStrand() == Strand.NEGATIVE) &&
                                (aaSeqStartPosition == exon.getCdEnd() - 3))))) {
                            bgGraphics = context.getGraphic2DForColor(Color.green);
                        } else if (acid.getSymbol() == '*') {
                            bgGraphics = context.getGraphic2DForColor(Color.RED);
                        }

                        bgGraphics.fill(aaRect);

                        String tmp = new String(new char[]{acid.getSymbol()});
                        GraphicUtils.drawCenteredText(tmp, aaRect, fontGraphics);
                    }
                    odd = !odd;
                    aaSeqStartPosition += 3;

                }
            }

            if (aaSeqStartPosition < exon.getEnd()) {

                // The last codon is not complete (continues on next exon).
                // TODO -- get base from previous exon and compute aaSequence
                int cdEnd = Math.min(exon.getCdEnd(), exon.getEnd());
                aaRect.x = getPixelFromChromosomeLocation(exon.getChr(), aaSeqStartPosition, theOrigin, locationScale);
                aaRect.width = getPixelFromChromosomeLocation(exon.getChr(), cdEnd, theOrigin, locationScale) - aaRect.x;
                Graphics2D bgGraphics = context.getGraphic2DForColor(odd ? AA_COLOR_1 : AA_COLOR_2);
                odd = !odd;
                bgGraphics.fill(aaRect);
            }
        }
    }

    /**
     * Method description
     *
     * @return
     */
    public String getDisplayName() {
        return "Basic Feature";
    }

    protected Color getFeatureColor(IGVFeature feature, Track track) {
        // Set color used to draw the feature

        Color color = null;
        if (track.isItemRGB()) {
            color = feature.getColor();
        }

        if (color == null) {
            // TODO -- hack, generalize this
            if (track.getTrackType() == TrackType.CNV) {
                color = feature.getName().equals("gain") ? DULL_RED : DULL_BLUE;
            } else {
                // Only used if feature color is not set
                color = track.getColor();
            }

        }

        if (track.isUseScore()) {
            float min = getViewLimitMin(track);
            float max = getViewLimitMax(track);

            float score = feature.getScore();
            float alpha = Float.isNaN(score) ? 1 : getAlpha(min, max, feature.getScore());
            color = ColorUtilities.getCompositeColor(color, alpha);
        }

        return color;
    }

    float getViewLimitMin(Track track) {
        if (Float.isNaN(viewLimitMin)) {
            viewLimitMin = Float.isNaN(track.getViewLimitMin()) ? 0 : track.getViewLimitMin();
        }
        return viewLimitMin;
    }

    float getViewLimitMax(Track track) {
        if (Float.isNaN(viewLimitMax)) {
            viewLimitMax = Float.isNaN(track.getViewLimitMax()) ? 1000 : track.getViewLimitMax();
        }
        return viewLimitMax;
    }

    private float getAlpha(float minRange, float maxRange, float value) {
        float binWidth = (maxRange - minRange) / 9;
        int binNumber = (int) ((value - minRange) / binWidth);
        return Math.min(1.0f, 0.2f + (binNumber * 0.8f) / 9);
    }


    private int getLastLargestMaxY() {

        double largestY = Math.max(lastFeatureLineMaxY,
                Math.max(lastFeatureBoundsMaxY, lastRegionMaxY));

        return (int) Math.ceil(largestY);
    }

    protected int getPixelFromChromosomeLocation(String chr, int chromosomeLocation, double origin,
                                                 double locationScale) {
        return (int) Math.round((chromosomeLocation - origin) / locationScale);
    }

    public void reset() {
        exonMap.clear();
    }
}
