- g.drawLine(oldStartX, oldY, oldEndX, oldY); // Horizontal, bottom of old box\r
- g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box\r
+ sx = (group.getStartRes() - startx) * av.charWidth;\r
+ sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);\r
+ ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth -1;\r
+\r
+ if (sx < getWidth()\r
+ && ex > 0\r
+ && group.sequences.contains(av.alignment.getSequenceAt(i)))\r
+ {\r
+ if (bottom == -1 &&\r
+ !group.sequences.contains(av.alignment.getSequenceAt(i + 1)))\r
+ bottom = sy + av.charHeight ;\r
+\r
+ if (!inGroup)\r
+ {\r
+ if (top == -1 && i==0 ||\r
+ !group.sequences.contains(av.alignment.getSequenceAt(i - 1)))\r
+ top = sy;\r
+\r
+\r
+ oldY = sy;\r
+ inGroup = true;\r
+ if (group == av.getSelectionGroup())\r
+ {\r
+ g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND, 3f, new float[]{5f,3f}, 0f ));\r
+ g.setColor(Color.RED);\r
+ }\r
+ else\r
+ {\r
+ g.setStroke(new BasicStroke());\r
+ g.setColor(group.getOutlineColour());\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ if (inGroup)\r
+ {\r
+ g.drawLine(sx, oldY, sx, sy );\r
+ g.drawLine(sx+ex, oldY, sx+ex, sy );\r
+\r
+ if (top != -1)\r
+ {\r
+ g.drawLine(sx, top, sx + ex, top);\r
+ top =-1;\r
+ }\r
+ if (bottom != -1)\r
+ {\r
+ g.drawLine(sx, bottom, sx + ex, bottom);\r
+ bottom = -1;\r
+ }\r
+\r
+\r
+ inGroup = false;\r
+ }\r
+ }\r