Add transparent colors to 2ColorHM

This adjustment to the TwoColorHeatMap script allows the heatmap graphics to use the alpha channel value for the color sent from the GUI and display custom levels of transparency to the heatmap colors.

This is updated to mimic ThreeColorHeatMap changes (#66).

Author: owlang

src/scripts/Figure_Generation/TwoColorHeatMap.java

@@ -120,7 +120,7 @@ public static BufferedImage generateHeatMap(ArrayList<double[]> matrix) throws F
 		BufferedImage im = new BufferedImage(pixwidth, pixheight, BufferedImage.TYPE_INT_ARGB);
 		Graphics g = im.getGraphics();
 		Graphics2D g2 = (Graphics2D) g;
-		g2.setColor(new Color(255, 255, 255));
+		g2.setColor(new Color(255, 255, 255, 0));
 		g2.fillRect(0, 0, pixwidth, pixheight);
 
 		int count = 0;
@@ -134,7 +134,8 @@ public static BufferedImage generateHeatMap(ArrayList<double[]> matrix) throws F
 					int red = (int) (MAXCOLOR.getRed() * sVal + MINCOLOR.getRed() * (1 - sVal));
 					int green = (int) (MAXCOLOR.getGreen() * sVal + MINCOLOR.getGreen() * (1 - sVal));
 					int blue = (int) (MAXCOLOR.getBlue() * sVal + MINCOLOR.getBlue() * (1 - sVal));
-					g.setColor(new Color(red, green, blue));
+					int alpha = (int) (MAXCOLOR.getAlpha() * sVal + MINCOLOR.getAlpha() * (1 - sVal));
+					g.setColor(new Color(red, green, blue, alpha));
 				} else {
 					g.setColor(Color.WHITE);
 				}