fix color encoding for 2013a schema

Author: mkutmon

org.pathvisio.lib/src/main/java/org/pathvisio/libgpml/model/GPML2013aWriter.java

@@ -376,7 +376,7 @@ protected void writeStates(List<DataNode> dataNodes, Element root) throws Conver
 				setAttr("State.Graphics", "Height", gfx, Double.toString(state.getHeight()));
 				// state does not have custom font properties in GPML2013a
 				// z-order for state is not written to GPML2013a
-				setAttr("State.Graphics", "FillColor", gfx, ColorUtils.colorToHex(state.getFillColor(), false));
+				setAttr("State.Graphics", "FillColor", gfx, ColorUtils.colorToHex2013(state.getFillColor(), false));
 				writeShapeStyleProperty(state, gfx);
 				writeColor(state, gfx);
 				// writes xref (write even if empty)
@@ -620,7 +620,6 @@ protected void writeShapes(List<Shape> shapes, Element root) throws ConverterExc
 			writeShapedElement(shape, shp);
 			writeGroupRef(shape.getGroupRef(), shp);
 			Element gfx = shp.getChild("Graphics", shp.getNamespace());
-			setAttr("Shape.Graphics", "FillColor", gfx, ColorUtils.colorToHex(shape.getFillColor(), false));
 			setAttr("Shape.Graphics", "Rotation", gfx, Double.toString(shape.getRotation()));
 			if (shp != null) {
 				root.addContent(shp);
@@ -900,7 +899,7 @@ protected void writeShapedElement(ShapedElement shapedElement, Element se) throw
 		writeRectProperty(shapedElement, gfx);
 		// writes z-order and fill color (separately to preserve GPML2013 order)
 		setAttr(base + ".Graphics", "ZOrder", gfx, String.valueOf(shapedElement.getZOrder()));
-		setAttr(base + ".Graphics", "FillColor", gfx, ColorUtils.colorToHex(shapedElement.getFillColor(), false));
+		setAttr(base + ".Graphics", "FillColor", gfx, ColorUtils.colorToHex2013(shapedElement.getFillColor(), false));
 		// writes font properties
 		writeFontProperty(shapedElement, gfx);
 		// writes rest of shape style properties
@@ -1060,8 +1059,7 @@ protected void writeRectProperty(ShapedElement shapedElement, Element gfx) throw
 	 */
 	protected void writeColor(ShapedElement shapedElement, Element gfx) throws ConverterException {
 		String base = ((Element) gfx.getParent()).getName();
-		setAttr(base + ".Graphics", "Color", gfx, ColorUtils.colorToHex(shapedElement.getTextColor(), false));
-
+		setAttr(base + ".Graphics", "Color", gfx, ColorUtils.colorToHex2013(shapedElement.getTextColor(), false));
 	}
 
 	/**
@@ -1148,7 +1146,6 @@ protected void writeLineStyleProperty(LineElement lineElement, Element gfx) thro
 			setAttr(base + ".Graphics", "LineStyle", gfx, lineStyleStr);
 		}
 		setAttr(base + ".Graphics", "LineThickness", gfx, String.valueOf(lineElement.getLineWidth()));
-		setAttr(base + ".Graphics", "Color", gfx, ColorUtils.colorToHex(lineElement.getLineColor(), false));
+		setAttr(base + ".Graphics", "Color", gfx, ColorUtils.colorToHex2013(lineElement.getLineColor(), false));
 	}
-
 }

org.pathvisio.lib/src/main/java/org/pathvisio/libgpml/util/ColorUtils.java

@@ -58,6 +58,31 @@ public static String colorToHex(Color color, boolean appendHash) {
 			}
 		}
 	}
+	
+	/**
+	 * Converts a {@link Color} object to a hexBinary string for 2013a.
+	 * 
+	 * @param color      the color object.
+	 * @param appendHash the boolean, if true appends "#" to beginning of hex
+	 *                   string.
+	 * @return the resulting hex string.
+	 */
+	public static String colorToHex2013(Color color, boolean appendHash) {
+		int a = color.getAlpha();
+		int r = color.getRed();
+		int g = color.getGreen();
+		int b = color.getBlue();
+		
+		if(a == 0 && r == 0 && g == 0 && b == 0) {
+			return "Transparent";
+		} else {
+			if (appendHash) {
+				return String.format("#%02x%02x%02x", r, g, b);
+			} else {
+				return String.format("%02x%02x%02x", r, g, b);
+			}
+		}
+	}
 
 	/**
 	 * Converts a hexBinary string to {@link Color} (r,g,b) or (r,g,b,a). If it