- SequenceI nextSeq;\r
- SequenceGroup group;\r
- for (int i = y1 ; i < y2 ;i++)\r
- {\r
- /* if (av.getSelection().contains(av.getAlignment().getSequenceAt(i))) {\r
- r = fr;\r
- System.out.println("use feature renderer");\r
- } else if ( i == 0) {\r
- // r = br;\r
- } else if (av.getAlignment().getSequenceAt(i).getName().equals("CpG")) {\r
- r = cgr;\r
- System.out.println("cg renderer");\r
- }\r
-*/\r
- nextSeq = av.getAlignment().getSequenceAt(i);\r
- group = av.alignment.findGroup( nextSeq );\r
- if( group!=null )\r
- {\r
- sr.drawSequence(g, group.cs, nextSeq,\r
- x1,\r
- x2,\r
- (int) ( (x1 - startx) * charWidth),\r
- offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()),\r
- charWidth, charHeight,\r
- false, group.getDisplayBoxes(), group.getDisplayText(), group.getColourText(),\r
- null, i);\r
- }\r
- else\r
- {\r
- sr.drawSequence(g, cs, nextSeq,\r
- x1,\r
- x2,\r
- (int) ( (x1 - startx) * charWidth),\r
- offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()),\r
- charWidth,charHeight,\r
- showScores, av.getShowBoxes(), av.getShowText(), av.getColourText(),\r
- null, i);\r
+ if (group != null)\r
+ do\r
+ {\r
+ int oldY = -1;\r
+ int i = 0;\r
+ boolean inGroup = false;\r
+ int top=-1, bottom =-1;\r
+ for (i = y1; i < y2; i++)\r
+ {\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
+ }\r