src/jalview/io/HTMLOutput.java

   1 /*\r
   2 * Jalview - A Sequence Alignment Editor and Viewer\r
   3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4 *\r
   5 * This program is free software; you can redistribute it and/or\r
   6 * modify it under the terms of the GNU General Public License\r
   7 * as published by the Free Software Foundation; either version 2\r
   8 * of the License, or (at your option) any later version.\r
   9 *\r
  10 * This program is distributed in the hope that it will be useful,\r
  11 * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13 * GNU General Public License for more details.\r
  14 *\r
  15 * You should have received a copy of the GNU General Public License\r
  16 * along with this program; if not, write to the Free Software\r
  17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18 */\r
  19 package jalview.io;\r
  20 \r
  21 import jalview.datamodel.*;\r
  22 \r
  23 import jalview.gui.*;\r
  24 \r
  25 import jalview.schemes.*;\r
  26 \r
  27 import java.awt.*;\r
  28 \r
  29 import java.io.*;\r
  30 \r
  31 import java.util.*;\r
  32 \r
  33 import javax.swing.*;\r
  34 \r
  35 \r
  36 public class HTMLOutput {\r
  37     AlignViewport av;\r
  38     SequenceRenderer sr;\r
  39     Color color;\r
  40 \r
  41     public HTMLOutput(AlignViewport av) {\r
  42         this.av = av;\r
  43         sr = new SequenceRenderer(av);\r
  44 \r
  45         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
  46                     "LAST_DIRECTORY"), new String[] { "html" },\r
  47                 new String[] { "HTML files" }, "HTML files");\r
  48 \r
  49         chooser.setFileView(new JalviewFileView());\r
  50         chooser.setDialogTitle("Save as HTML");\r
  51         chooser.setToolTipText("Save");\r
  52 \r
  53         int value = chooser.showSaveDialog(null);\r
  54 \r
  55         if (value == JalviewFileChooser.APPROVE_OPTION) {\r
  56             String choice = chooser.getSelectedFile().getPath();\r
  57             jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
  58                 chooser.getSelectedFile().getParent());\r
  59 \r
  60             try {\r
  61                 PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(\r
  62                             choice));\r
  63                 out.println("<HTML>");\r
  64                 out.println("<style type=\"text/css\">");\r
  65                 out.println("<!--");\r
  66                 out.print("td {font-family: \"" + av.getFont().getFamily() +\r
  67                     "\", \"" + av.getFont().getName() + "\", mono; " +\r
  68                     "font-size: " + av.getFont().getSize() + "px; ");\r
  69 \r
  70                 if (av.getFont().getStyle() == Font.BOLD) {\r
  71                     out.print("font-weight: BOLD; ");\r
  72                 }\r
  73 \r
  74                 if (av.getFont().getStyle() == Font.ITALIC) {\r
  75                     out.print("font-style: italic; ");\r
  76                 }\r
  77 \r
  78                 out.println("text-align: center; }");\r
  79 \r
  80                 out.println("-->");\r
  81                 out.println("</style>");\r
  82                 out.println("<BODY>");\r
  83 \r
  84                 if (av.getWrapAlignment()) {\r
  85                     drawWrappedAlignment(out);\r
  86                 } else {\r
  87                     drawUnwrappedAlignment(out);\r
  88                 }\r
  89 \r
  90                 out.println("\n</body>\n</html>");\r
  91                 out.close();\r
  92                 jalview.util.BrowserLauncher.openURL("file:///" + choice);\r
  93             } catch (Exception ex) {\r
  94                 ex.printStackTrace();\r
  95             }\r
  96         }\r
  97     }\r
  98 \r
  99     void drawUnwrappedAlignment(PrintWriter out) {\r
 100         out.println("<table border=\"1\"><tr><td>\n");\r
 101         out.println(\r
 102             "<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");\r
 103 \r
 104         //////////////\r
 105         SequenceGroup[] groups;\r
 106         SequenceI seq;\r
 107         ColourSchemeI cs = null;\r
 108         AlignmentI alignment = av.getAlignment();\r
 109         String r;\r
 110         String g;\r
 111         String b;\r
 112 \r
 113         // draws the top row, the measure rule\r
 114         out.println("<tr><td colspan=\"6\"></td>");\r
 115 \r
 116         int i = 0;\r
 117 \r
 118         for (i = 10; i < (alignment.getWidth() - 10); i += 10)\r
 119             out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");\r
 120 \r
 121         out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +\r
 122             "<br>|</td>");\r
 123         out.println("</tr>");\r
 124 \r
 125         for (i = 0; i < alignment.getHeight(); i++) {\r
 126             seq = alignment.getSequenceAt(i);\r
 127             groups = alignment.findAllGroups(seq);\r
 128 \r
 129             if (av.getShowFullId()) {\r
 130                 out.println("<tr><td nowrap>" + seq.getDisplayId() +\r
 131                     "&nbsp;&nbsp;</td>");\r
 132             } else {\r
 133                 out.println("<tr><td nowrap>" + seq.getName() +\r
 134                     "&nbsp;&nbsp;</td>");\r
 135             }\r
 136 \r
 137             for (int res = 0; res < seq.getLength(); res++) {\r
 138                 cs = av.getGlobalColourScheme();\r
 139 \r
 140                 if (groups != null) {\r
 141                     for (int k = 0; k < groups.length; k++)\r
 142                         if ((groups[k].getStartRes() <= res) &&\r
 143                                 (groups[k].getEndRes() >= res)) {\r
 144                             cs = groups[k].cs;\r
 145 \r
 146                             break;\r
 147                         }\r
 148                 }\r
 149 \r
 150                 color = sr.getResidueBoxColour(cs, seq, res);\r
 151 \r
 152                 if (color.getRGB() < -1) {\r
 153                     out.println("<td bgcolor=\"#" +\r
 154                         jalview.util.Format.getHexString(color) + "\">" +\r
 155                         seq.getCharAt(res) + "</td>");\r
 156                 } else {\r
 157                     out.println("<td>" + seq.getCharAt(res) + "</td>");\r
 158                 }\r
 159             }\r
 160 \r
 161             out.println("</tr>");\r
 162         }\r
 163 \r
 164         //////////////\r
 165         out.println("</table>");\r
 166         out.println("</td></tr></table>");\r
 167     }\r
 168 \r
 169     void drawWrappedAlignment(PrintWriter out) {\r
 170         ////////////////////////////////////\r
 171         /// How many sequences and residues can we fit on a printable page?\r
 172         AlignmentI al = av.getAlignment();\r
 173         SequenceGroup[] groups;\r
 174         SequenceI seq;\r
 175         ColourSchemeI cs = null;\r
 176         String r;\r
 177         String g;\r
 178         String b;\r
 179 \r
 180         out.println("<table border=\"1\"><tr><td>\n");\r
 181         out.println(\r
 182             "<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");\r
 183 \r
 184         for (int startRes = 0; startRes < al.getWidth();\r
 185                 startRes += av.getChunkWidth()) {\r
 186             int endRes = startRes + av.getChunkWidth();\r
 187 \r
 188             if (endRes > al.getWidth()) {\r
 189                 endRes = al.getWidth();\r
 190             }\r
 191 \r
 192             out.println("<tr>");\r
 193             out.println("<td colspan=\"6\">&nbsp;</td>");\r
 194 \r
 195             for (int i = startRes + 10; i < endRes; i += 10)\r
 196                 out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");\r
 197 \r
 198             // out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +\r
 199             //             "<br>|</td>");\r
 200             out.println("</tr>");\r
 201 \r
 202             for (int s = 0; s < al.getHeight(); s++) {\r
 203                 out.println("<tr>");\r
 204                 seq = al.getSequenceAt(s);\r
 205                 groups = al.findAllGroups(seq);\r
 206 \r
 207                 if (av.getShowFullId()) {\r
 208                     out.println("<td nowrap>" + seq.getDisplayId() +\r
 209                         "&nbsp;&nbsp;</td>");\r
 210                 } else {\r
 211                     out.println("<td nowrap>" + seq.getName() +\r
 212                         "&nbsp;&nbsp;</td>");\r
 213                 }\r
 214 \r
 215                 for (int res = startRes; res < endRes; res++) {\r
 216                     cs = av.getGlobalColourScheme();\r
 217 \r
 218                     if (groups != null) {\r
 219                         for (int k = 0; k < groups.length; k++)\r
 220                             if ((groups[k].getStartRes() <= res) &&\r
 221                                     (groups[k].getEndRes() >= res)) {\r
 222                                 cs = groups[k].cs;\r
 223 \r
 224                                 break;\r
 225                             }\r
 226                     }\r
 227 \r
 228                     color = sr.getResidueBoxColour(cs, seq, res);\r
 229 \r
 230                     if (color.getRGB() < -1) {\r
 231                         r = Integer.toHexString(color.getRed());\r
 232 \r
 233                         if (r.length() < 2) {\r
 234                             r = "0" + r;\r
 235                         }\r
 236 \r
 237                         g = Integer.toHexString(color.getGreen());\r
 238 \r
 239                         if (g.length() < 2) {\r
 240                             g = "0" + g;\r
 241                         }\r
 242 \r
 243                         b = Integer.toHexString(color.getBlue());\r
 244 \r
 245                         if (b.length() < 2) {\r
 246                             b = "0" + b;\r
 247                         }\r
 248 \r
 249                         out.println("<td bgcolor=\"#" + r + g + b + "\">" +\r
 250                             seq.getCharAt(res) + "</td>");\r
 251                     } else {\r
 252                         out.println("<td>" + seq.getCharAt(res) + "</td>");\r
 253                     }\r
 254                 }\r
 255 \r
 256                 out.println("</tr>");\r
 257             }\r
 258 \r
 259             if (endRes < al.getWidth()) {\r
 260                 out.println("<tr><td height=\"5\"></td></tr>");\r
 261             }\r
 262         }\r
 263 \r
 264         out.println("</table>");\r
 265         out.println("</table>");\r
 266     }\r
 267 }\r