/*
 * 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.
 */

package org.broad.igv.renderer;

import org.broad.igv.feature.IGVFeature;
import org.broad.igv.track.RenderContext;
import org.broad.igv.track.Track;
import org.broad.igv.ui.FontManager;
import org.broad.igv.ui.IGV;

import java.awt.*;
import java.awt.geom.GeneralPath;
import java.util.List;

/**
 * Created by jrobinson on 9/17/15.
 */
public class ArcRenderer extends FeatureRenderer {

    @Override
    public void render(List<IGVFeature> featureList, RenderContext context, Rectangle trackRectangle, Track track) {

        double origin = context.getOrigin();
        double locScale = context.getScale();
        Color ARC_COLOR = new Color(150, 50, 50);


        double maxWidth = 1;
        if (featureList != null && featureList.size() > 0) {

            Rectangle lastRect = null;

            boolean colorOverlay = IGV.getInstance().getSession().getColorOverlay();

            // Get max feature width
            for (IGVFeature feature : featureList) {
                // Note -- don't cast these to an int until the range is checked.
                // could get an overflow.
                double pixelStart = ((feature.getStart() - origin) / locScale);
                double pixelEnd = ((feature.getEnd() - origin) / locScale);

                // If the any part of the feature fits in the
                // Track rectangle draw it
                if (pixelEnd >= trackRectangle.getX() && pixelStart <= trackRectangle.getMaxX()) {
                    if (pixelEnd - pixelStart > maxWidth) maxWidth = pixelEnd - pixelStart;
                }
            }
        }

        for (IGVFeature feature : featureList) {
            // Note -- don't cast these to an int until the range is checked.
            // could get an overflow.
            double pixelStart = ((feature.getStart() - origin) / locScale);
            double pixelEnd = ((feature.getEnd() - origin) / locScale);

            // If the any part of the feature fits in the
            // Track rectangle draw it
            if (pixelEnd >= trackRectangle.getX() && pixelStart <= trackRectangle.getMaxX()) {

                // Set color used to draw the feature

                Color color = feature.getColor();
                if(color == null) {
                    color = ARC_COLOR;
                }
                Graphics2D g = context.getGraphic2DForColor(color);
                g.setFont(FontManager.getDefaultFont());


                int w = (int) (pixelEnd - pixelStart);
                if (w < 3) {
                    w = 3;
                    pixelStart--;
                }

               // double mutHeight = 1.3 * (Math.log(w) / Math.log(maxWidth)) * trackRectangle.height;
                double mutHeight = 1.3 * (Math.log(w) / Math.log(maxWidth)) * trackRectangle.height;
                int mutY = trackRectangle.y + trackRectangle.height;

                double bezierXPad = 0; //Math.max(1, w / 30);

                GeneralPath arcPath = new GeneralPath();
                arcPath.moveTo(pixelStart, mutY);
                arcPath.curveTo(pixelStart - bezierXPad, mutY - mutHeight, //Bezier 1
                        pixelStart + w + bezierXPad, mutY - mutHeight,         //Bezier 2
                        pixelStart + w, mutY);

                //Draw the arc, to ensure outline is drawn completely (fill won't do it, necessarily). This will also
                //give the arc a darker outline
                g.draw(arcPath);

            }
        }
    }

}



@@ -1386,16 +1386,44 @@
 .awt.*;%0A
+import java.awt.geom.Arc2D;%0A
 import j
@@ -2762,32 +2762,86 @@
    %7D%0A        %7D%0A%0A
+        double f = trackRectangle.height / maxWidth;%0A%0A
         for (IGV
@@ -3500,25 +3500,32 @@
 color = 
-ARC_COLOR
+track.getColor()
 ;%0A      
@@ -3856,62 +3856,38 @@
 ble 
-mutHeight = 1.3 * (Math.log(w) / Math.log(maxWidth)) *
+f = Math.min(1, ((double) w) /
  tra
@@ -3890,38 +3890,38 @@
  trackRectangle.
-height
+width)
 ;%0A              
@@ -3933,84 +3933,17 @@
 ble 
-mutHeight = 1.3 * (Math.log(w) / Math.log(maxWidth)) * trackRectangle.height
+h = f * w
 ;%0A  
@@ -3960,16 +3960,16 @@
     
-int mutY
+double y
  = t
@@ -4011,71 +4011,12 @@
 ight
-;%0A%0A                double bezierXPad = 0; //Math.max(1, w / 30)
+ - h
 ;%0A%0A 
@@ -4030,27 +4030,28 @@
         
-GeneralPath
+Arc2D.Double
  arcPath
@@ -4061,297 +4061,67 @@
 new 
-GeneralPath();%0A                arcPath.moveTo(pixelStart, mutY);%0A                arcPath.curveTo(pixelStart - bezierXPad, mutY - mutHeight, //Bezier 1%0A                        pixelStart + w + bezierXPad, mutY - mutHeight,         //Bezier 2%0A                        pixelStart + w, mutY
+Arc2D.Double(pixelStart, y, w, 2*h, 0, 180, Arc2D.OPEN
 );%0A%0A
+%0A
     

Tweak to arc renderer