+ //////////////\r
+ out.println("</table>");\r
+ out.println("</td></tr></table>");\r
+\r
+ }\r
+\r
+ void drawWrappedAlignment(PrintWriter out)\r
+ {\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,g,b;\r
+\r
+ out.println("<table border=\"1\"><tr><td>\n");\r
+ out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");\r
+\r
+ for(int startRes=0; startRes<al.getWidth(); startRes+=av.getChunkWidth())\r
+ {\r
+\r
+ int endRes = startRes+av.getChunkWidth();\r
+ if(endRes>al.getWidth())\r
+ endRes = al.getWidth();\r
+\r
+ out.println("<tr>");\r
+ out.println("<td colspan=\"6\"> </td>");\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
+\r
+\r
+ for (int s = 0; s < al.getHeight(); s++)\r
+ {\r
+ out.println("<tr>");\r
+ seq = al.getSequenceAt(s);\r
+ groups = al.findAllGroups( seq );\r
+ if(av.getShowFullId())\r
+ out.println("<td nowrap>"+seq.getDisplayId()+" </td>");\r
+ else\r
+ out.println("<td nowrap>"+seq.getName()+" </td>");\r
+\r
+ for (int res = startRes; res < endRes; res++)\r
+ {\r
+ cs = av.getGlobalColourScheme();\r
+ if(groups!=null)\r
+ {\r
+ for (int k = 0; k < groups.length; k++)\r
+ if (groups[k].getStartRes() <= res && groups[k].getEndRes() >= res)\r
+ {\r
+ cs = groups[k].cs;\r
+ break;\r
+ }\r
+ }\r
+\r
+ color = sr.getResidueBoxColour(cs, seq, res);\r
+\r
+ if(color.getRGB()<-1)\r
+ {\r
+ r = Integer.toHexString(color.getRed());\r
+ if(r.length()<2)\r
+ r = "0"+r;\r
+ g = Integer.toHexString(color.getGreen());\r
+ if(g.length()<2)\r
+ g = "0"+g;\r
+ b = Integer.toHexString(color.getBlue());\r
+ if(b.length()<2)\r
+ b = "0"+b;\r
+ out.println("<td bgcolor=\"#"+ r + g + b + "\">"+seq.getCharAt(res)+"</td>");\r
+ }\r
+ else\r
+ out.println("<td>"+seq.getCharAt(res)+"</td>");\r
+\r
+ }\r
+\r
+ out.println("</tr>");\r
+\r
+ }\r
+ if(endRes<al.getWidth())\r
+ out.println("<tr><td height=\"5\"></td></tr>");\r
+\r
+\r
+\r
+ }\r
+\r
+ out.println("</table>");\r
+ out.println("</table>");\r
+\r
+\r
+\r