- //////////////\r
- out.println("</table>");\r
- out.println("</td></tr></table>");\r
- }\r
-\r
- void drawWrappedAlignment(PrintWriter out) {\r
- ////////////////////////////////////\r
- /// How many sequences and residues can we fit on a printable page?\r
- AlignmentI al = av.getAlignment();\r
- SequenceGroup[] groups;\r
- SequenceI seq;\r
- ColourSchemeI cs = null;\r
- String r;\r
- String g;\r
- String b;\r
-\r
- out.println("<table border=\"1\"><tr><td>\n");\r
- out.println(\r
- "<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");\r
-\r
- for (int startRes = 0; startRes < al.getWidth();\r
- startRes += av.getChunkWidth()) {\r
- int endRes = startRes + av.getChunkWidth();\r
-\r
- if (endRes > al.getWidth()) {\r
- endRes = al.getWidth();\r
- }\r
-\r
- out.println("<tr>");\r
- out.println("<td colspan=\"6\"> </td>");\r
-\r
- for (int i = startRes + 10; i < endRes; i += 10)\r
- out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");\r
-\r
- // out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +\r
- // "<br>|</td>");\r
- out.println("</tr>");\r
-\r
- for (int s = 0; s < al.getHeight(); s++) {\r
- out.println("<tr>");\r
- seq = al.getSequenceAt(s);\r
- groups = al.findAllGroups(seq);\r
-\r
- if (av.getShowFullId()) {\r
- out.println("<td nowrap>" + seq.getDisplayId() +\r
- " </td>");\r
- } else {\r
- out.println("<td nowrap>" + seq.getName() +\r
- " </td>");\r
- }\r
-\r
- for (int res = startRes; res < endRes; res++) {\r
- cs = av.getGlobalColourScheme();\r
-\r
- if (groups != null) {\r
- for (int k = 0; k < groups.length; k++)\r
- if ((groups[k].getStartRes() <= res) &&\r
- (groups[k].getEndRes() >= res)) {\r
- cs = groups[k].cs;\r
-\r
- break;\r
- }\r
- }\r
-\r
- color = sr.getResidueBoxColour(cs, seq, res);\r
-\r
- if (color.getRGB() < -1) {\r
- r = Integer.toHexString(color.getRed());\r
-\r
- if (r.length() < 2) {\r
- r = "0" + r;\r
- }\r
-\r
- g = Integer.toHexString(color.getGreen());\r
-\r
- if (g.length() < 2) {\r
- g = "0" + g;\r
- }\r
-\r
- b = Integer.toHexString(color.getBlue());\r
-\r
- if (b.length() < 2) {\r
- b = "0" + b;\r
- }\r
-\r
- out.println("<td bgcolor=\"#" + r + g + b + "\">" +\r
- seq.getCharAt(res) + "</td>");\r
- } else {\r
- out.println("<td>" + seq.getCharAt(res) + "</td>");\r
- }\r
- }\r
-\r
- out.println("</tr>");\r
- }\r