/*
 * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard.  All Rights Reserved.
 *
 * 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.
 *
 * THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR
 * WARRANTES OF ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING,
 * WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
 * PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER
 * OR NOT DISCOVERABLE.  IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR RESPECTIVE
 * TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES
 * OF ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES,
 * ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER
 * THE BROAD OR MIT SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT
 * SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
 */

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

import org.broad.igv.Globals;
import org.broad.igv.feature.LocusScore;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.renderer.DataRange;
import org.broad.igv.renderer.Renderer;
import org.broad.igv.tdf.TDFDataSource;
import org.broad.igv.tdf.TDFReader;
import org.broad.igv.track.*;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.panel.IGVPopupMenu;
import org.broad.igv.util.ResourceLocator;

import javax.swing.*;
import java.awt.*;
import java.awt.event.MouseEvent;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

/**
 * Developmental track to explore display of conservation scores.
 *
 * @author jrobinso
 */
public class EWigTrack extends AbstractTrack {

    //    double dataMax;
    char[] nucleotides = {'A', 'C', 'G', 'T'};
    public static Color grey1 = new Color(230, 230, 230);
    Map<Character, TDFDataSource> baseSources;
    TDFDataSource scoreSource;

    public EWigTrack(ResourceLocator locator, Genome genome) {
        super(locator);

        TDFReader reader = TDFReader.getReader(locator.getPath());
        scoreSource = new TDFDataSource(reader, 4, "Pi", genome);
        scoreSource.setAggregateLikeBins(false);

        setDataRange(new DataRange(0, 0, 10));
        baseSources = new HashMap();
        for (int i = 0; i < 4; i++) {
            TDFDataSource src = new TDFDataSource(reader, i, Character.toString(nucleotides[i]), genome);
            src.setAggregateLikeBins(false);
            baseSources.put(nucleotides[i], src);
        }
    }

    public void render(RenderContext context, Rectangle rect) {
        paint(context, rect);
    }

    public void setWindowFunction(WindowFunction type) {
    }

    public WindowFunction getWindowFunction() {
        return null;
    }

    public void setRendererClass(Class rc) {
    }

    public Renderer getRenderer() {
        return null;
    }

    public boolean isLogNormalized() {
        return false;
    }

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

    private void paint(RenderContext context, Rectangle rect) {

        // The total score
        List<LocusScore> scores = scoreSource.getSummaryScoresForRange(context.getChr(),
                (int) context.getOrigin(),
                (int) context.getEndLocation(),
                context.getZoom());
        Map<Character, List<LocusScore>> nScores = new HashMap();
        for (Character c : nucleotides) {
            nScores.put(c, baseSources.get(c).getSummaryScoresForRange(context.getChr(),
                    (int) context.getOrigin(),
                    (int) context.getEndLocation(),
                    context.getZoom()));
        }

        for (int idx = 0; idx < scores.size(); idx++) {

            LocusScore score = scores.get(idx);
            int startPosition = score.getStart();
            int endPosition = score.getEnd();

            int pX = (int) (rect.getX() + (startPosition - context.getOrigin()) / context.getScale());
            int dX = Math.max(1,
                    (int) (rect.getX() + (endPosition - context.getOrigin()) / context.getScale()) - pX);
            if (dX > 4) {
                dX -= 2;
                pX++;
            }

            if (pX + dX < 0) {
                continue;
            } else if (pX > context.getVisibleRect().getMaxX()) {
                break;
            }


            float totalCount = score.getScore();
            int pY = (int) rect.getMaxY() - 1;

            float dataMax = getDataRange().getMaximum();

            double height = (totalCount * rect.getHeight() / dataMax);
            height = Math.min(height, rect.height - 1);

            for (char c : nucleotides) {
                try {
                    LocusScore ns = nScores.get(c).get(idx);
                    float count = ns.getScore() * totalCount;

                    //pY = drawBar(context, idx, rect, dataMax, pY, pX, dX, c, count);
                    Graphics2D tGraphics = context.getGraphic2DForColor(Globals.nucleotideColors.get(c));

                    int h = (int) Math.round(count * height / totalCount);
                    h = Math.min(pY - rect.y, h);
                    int baseY = (int) (pY - h);

                    if (h > 0) {
                        tGraphics.fillRect(pX, baseY, dX, h);
                    }
                    pY = baseY;
                } catch (Exception e) {
                    e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
                }
            }

        }

        // Draw border
        context.getGraphic2DForColor(Color.gray).drawLine(
                rect.x, rect.y + rect.height,
                rect.x + rect.width, rect.y + rect.height);

        // Draw scale
        /*
        DataRange range = getDataRange();
        if (range != null) {
            Graphics2D g = context.getGraphic2DForColor(Color.black);
            Font font = g.getFont();
            Font smallFont = FontManager.getScalableFont(8);
            try {
                g.setFont(smallFont);
                String scale = "Scale: " + (int) range.getMinimum() + " - " +
                        (int) range.getMaximum();
                g.drawString(scale, rect.x + 10, rect.y + 10);

            } finally {
                g.setFont(font);
            }
        }*/

    }

    public JPopupMenu getPopupMenu(
            final MouseEvent evt) {

        JPopupMenu 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();

        // addSortMenuItem(popupMenu);
        // addPackMenuItem(popupMenu);
        // addShadeBaseMenuItem(popupMenu);
        // addCopyToClipboardItem(popupMenu, evt);
        // addGoToMate(popupMenu, evt);
        // popupMenu.addSeparator();


        //JLabel trackSettingsHeading = new JLabel("  Track Settings",
        //        JLabel.LEFT);
        //trackSettingsHeading.setFont(newFont);

        //popupMenu.add(trackSettingsHeading);

        ArrayList<Track> tmp = new ArrayList();
        tmp.add(this);
        popupMenu.add(TrackMenuUtils.getTrackRenameItem(tmp));
        popupMenu.add(TrackMenuUtils.getChangeTrackHeightItem(tmp));
        popupMenu.add(TrackMenuUtils.getDataRangeItem(tmp));


        return popupMenu;
    }

//    public String getValueStringAt(String chr, double position, int y, ReferenceFrame frame) {
//        return null;
//    }
}
