\r
public class HTMLOutput\r
{\r
-\r
+ AlignViewport av;\r
+ SequenceRenderer sr;\r
+ Color color;\r
\r
public HTMLOutput(AlignViewport av)\r
{\r
- SequenceRenderer sr = new SequenceRenderer(av);\r
- Color color;\r
+ this.av = av;\r
+ sr = new SequenceRenderer(av);\r
JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);\r
chooser.setDialogTitle("Save as HTML");\r
chooser.setToolTipText("Save");\r
out.println("-->");\r
out.println("</style>");\r
out.println("<BODY>");\r
- out.println("<table border=\"1\"><tr><td>\n");\r
- out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");\r
\r
\r
- //////////////\r
- SequenceGroup [] groups;\r
- SequenceI seq;\r
- ColourSchemeI cs = null;\r
- AlignmentI alignment = av.getAlignment();\r
- String r,g,b;\r
+ if(av.getWrapAlignment())\r
+ drawWrappedAlignment(out);\r
+ else\r
+ drawUnwrappedAlignment(out);\r
\r
- // draws the top row, the measure rule\r
- out.println("<tr><td colspan=\"6\"></td>");\r
- int i=0;\r
- for(i=10; i<alignment.getWidth()-10; i+=10)\r
- out.println("<td colspan=\"9\">"+i+"<br>|</td><td></td>");\r
+ out.println("\n</body>\n</html>");\r
+ out.close();\r
+ jalview.util.BrowserLauncher.openURL( "file:///"+choice );\r
+ }\r
+ catch(Exception ex){ex.printStackTrace();}\r
+ }\r
+ }\r
\r
- out.println("<td colspan=\"3\"></td><td colspan=\"3\">"+i+"<br>|</td>");\r
- out.println("</tr>");\r
+ void drawUnwrappedAlignment(PrintWriter out)\r
+ {\r
\r
- for (i = 0; i < alignment.getHeight(); i++)\r
- {\r
- seq = alignment.getSequenceAt(i);\r
- groups = alignment.findAllGroups( seq );\r
- out.println("<tr><td nowrap>"+seq.getDisplayId()+" </td>");\r
+ out.println("<table border=\"1\"><tr><td>\n");\r
+ out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");\r
+\r
+\r
+ //////////////\r
+ SequenceGroup [] groups;\r
+ SequenceI seq;\r
+ ColourSchemeI cs = null;\r
+ AlignmentI alignment = av.getAlignment();\r
+ String r,g,b;\r
\r
+ // draws the top row, the measure rule\r
+ out.println("<tr><td colspan=\"6\"></td>");\r
+ int i=0;\r
+ for(i=10; i<alignment.getWidth()-10; i+=10)\r
+ out.println("<td colspan=\"9\">"+i+"<br>|</td><td></td>");\r
\r
- for (int res = 0; res < seq.getLength(); res++)\r
- {\r
- cs = av.getGlobalColourScheme();\r
+ out.println("<td colspan=\"3\"></td><td colspan=\"3\">"+i+"<br>|</td>");\r
+ out.println("</tr>");\r
\r
- if(groups!=null)\r
+ for (i = 0; i < alignment.getHeight(); i++)\r
+ {\r
+ seq = alignment.getSequenceAt(i);\r
+ groups = alignment.findAllGroups( seq );\r
+ out.println("<tr><td nowrap>"+seq.getDisplayId()+" </td>");\r
+\r
+\r
+ for (int res = 0; res < seq.getLength(); res++)\r
+ {\r
+ cs = av.getGlobalColourScheme();\r
+\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
- for (int k = 0; k < groups.length; k++)\r
- if (groups[k].getStartRes() <= res && groups[k].getEndRes() >= res)\r
+ cs = groups[k].cs;\r
+ break;\r
+ }\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
+ 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
+ out.println("<td nowrap>"+seq.getDisplayId()+" </td>");\r
+\r
+ for (int res = startRes; res < endRes; res++)\r
+ {\r
+ cs = av.getGlobalColourScheme();\r
+ if(groups!=null)\r
{\r
- cs = groups[k].cs;\r
- break;\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
\r
+ color = sr.getResidueBoxColour(cs, seq, res);\r
\r
- color = sr.getResidueBoxColour(cs, seq, res);\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
- 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
- out.println("</tr>");\r
- }\r
- //////////////\r
- out.println("</table>");\r
- out.println("</td></tr></table>\n</body>\n</html>");\r
\r
- out.close();\r
\r
- jalview.util.BrowserLauncher.openURL( "file:///"+choice );\r
- }\r
- catch(Exception ex){ex.printStackTrace();}\r
- }\r
}\r
\r
\r
git://source.jalview.org / jalview.git / commitdiff