+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ * @param col DOCUMENT ME!\r
+ */\r
+ public void drawBackground(Graphics g, Color col)\r
+ {\r
+ g.setColor(col);\r
+ g.fillRect(0, 0, prefsize.width, prefsize.height);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ */\r
+ public void drawScene(Graphics g1)\r
+ {\r
+\r
+ Graphics2D g = (Graphics2D) g1;\r
+\r
+ g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+ RenderingHints.VALUE_ANTIALIAS_ON);\r
+\r
+\r
+ int halfwidth = getWidth() / 2;\r
+ int halfheight = getHeight() / 2;\r
+\r
+ for (int i = 0; i < npoint; i++)\r
+ {\r
+ SequencePoint sp = (SequencePoint) points.elementAt(i);\r
+ int x = (int) ((float) (sp.coord[0] - centre[0]) * scale) +\r
+ halfwidth;\r
+ int y = (int) ((float) (sp.coord[1] - centre[1]) * scale) +\r
+ halfheight;\r
+ float z = sp.coord[1] - centre[2];\r
+\r
+ if (sp.sequence.getColor() == Color.black)\r
+ {\r
+ g.setColor(Color.white);\r
+ }\r
+ else\r
+ {\r
+ g.setColor(sp.sequence.getColor());\r
+ }\r
+\r
+ if (av.getSelectionGroup() != null)\r
+ {\r
+ if (av.getSelectionGroup().getSequences(false).contains(\r
+ ((SequencePoint) points.elementAt(i)).sequence))\r
+ {\r
+ g.setColor(Color.gray);\r
+ }\r
+ }\r
+\r
+ if (z < 0)\r
+ {\r
+ g.setColor(g.getColor().darker());\r
+ }\r
+\r
+ g.fillRect(x - 3, y - 3, 6, 6);\r
+ if(showLabels)\r
+ {\r
+ g.setColor(Color.red);\r
+ g.drawString( ( (SequencePoint) points.elementAt(i)).sequence.\r
+ getName(),\r
+ x - 3, y - 4);\r
+ }\r