- 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 +\r
+ AlignmentUtil.getPixelHeight(starty, i, av.charHeight);\r
+ ex = ( ( (group.getEndRes() + 1) - group.getStartRes()) *\r
+ av.charWidth) -\r
+ 1;\r
+\r
+ if ( (sx < getWidth()) && (ex > 0) &&\r
+ group.sequences.contains(av.alignment.getSequenceAt(\r
+ i)))\r
+ {\r
+ if ( (bottom == -1) &&\r
+ !group.sequences.contains(\r
+ av.alignment.getSequenceAt(i + 1)))\r
+ {\r
+ bottom = sy + av.charHeight;\r
+ }\r
+\r
+ if (!inGroup)\r
+ {\r
+ if ( ( (top == -1) && (i == 0)) ||\r
+ !group.sequences.contains(\r
+ av.alignment.getSequenceAt(i - 1)))\r
+ {\r
+ top = sy;\r
+ }\r
+\r
+ oldY = sy;\r
+ inGroup = true;\r
+\r
+ if (group == av.getSelectionGroup())\r
+ {\r
+ g.setStroke(new BasicStroke(1,\r
+ BasicStroke.CAP_BUTT,\r
+ BasicStroke.JOIN_ROUND, 3f,\r
+ new float[]\r
+ {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
+\r
+ if (bottom != -1)\r
+ {\r
+ g.drawLine(sx, bottom, sx + ex, bottom);\r
+ bottom = -1;\r
+ }\r
+\r
+ inGroup = false;\r
+ }\r
+ }\r