src/jalview/io/HTMLOutput.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.io;
  22
  23 import jalview.api.ColorI;
  24 import jalview.datamodel.AlignmentI;
  25 import jalview.datamodel.SequenceI;
  26 import jalview.gui.AlignViewport;
  27 import jalview.gui.AlignmentPanel;
  28 import jalview.gui.FeatureRenderer;
  29 import jalview.gui.SequenceRenderer;
  30 import jalview.schemes.Colour;
  31 import jalview.util.MessageManager;
  32
  33 import java.awt.Font;
  34 import java.io.PrintWriter;
  35
  36 public class HTMLOutput
  37 {
  38   AlignViewport av;
  39
  40   SequenceRenderer sr;
  41
  42   jalview.renderer.seqfeatures.FeatureRenderer fr;
  43
  44   ColorI color;
  45
  46   public HTMLOutput(AlignmentPanel ap, SequenceRenderer sr,
  47           FeatureRenderer fr1)
  48   {
  49     this.av = ap.av;
  50     this.sr = sr;
  51
  52     fr = new FeatureRenderer(ap);
  53     fr.transferSettings(fr1);
  54
  55     JalviewFileChooser chooser = new JalviewFileChooser(
  56             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
  57             new String[] { "html" }, new String[] { "HTML files" },
  58             "HTML files");
  59
  60     chooser.setFileView(new JalviewFileView());
  61     chooser.setDialogTitle(MessageManager.getString("label.save_as_html"));
  62     chooser.setToolTipText(MessageManager.getString("action.save"));
  63
  64     int value = chooser.showSaveDialog(null);
  65
  66     if (value == JalviewFileChooser.APPROVE_OPTION)
  67     {
  68       String choice = chooser.getSelectedFile().getPath();
  69       jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
  70               .getSelectedFile().getParent());
  71
  72       try
  73       {
  74         PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
  75                 choice));
  76         out.println("<HTML>");
  77         out.println("<style type=\"text/css\">");
  78         out.println("<!--");
  79         out.print("td {font-family: \"" + av.getFont().getFamily()
  80                 + "\", \"" + av.getFont().getName() + "\", mono; "
  81                 + "font-size: " + av.getFont().getSize() + "px; ");
  82
  83         if (av.getFont().getStyle() == Font.BOLD)
  84         {
  85           out.print("font-weight: BOLD; ");
  86         }
  87
  88         if (av.getFont().getStyle() == Font.ITALIC)
  89         {
  90           out.print("font-style: italic; ");
  91         }
  92
  93         out.println("text-align: center; }");
  94
  95         out.println("-->");
  96         out.println("</style>");
  97         out.println("<BODY>");
  98
  99         if (av.getWrapAlignment())
 100         {
 101           drawWrappedAlignment(out);
 102         }
 103         else
 104         {
 105           drawUnwrappedAlignment(out);
 106         }
 107
 108         out.println("\n</body>\n</html>");
 109         out.close();
 110         jalview.util.BrowserLauncher.openURL("file:///" + choice);
 111       } catch (Exception ex)
 112       {
 113         ex.printStackTrace();
 114       }
 115     }
 116   }
 117
 118   void drawUnwrappedAlignment(PrintWriter out)
 119   {
 120     out.println("<table border=\"1\"><tr><td>\n");
 121     out.println("<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
 122
 123     // ////////////
 124     SequenceI seq;
 125     AlignmentI alignment = av.getAlignment();
 126
 127     // draws the top row, the measure rule
 128     out.println("<tr><td colspan=\"6\"></td>");
 129
 130     int i = 0;
 131
 132     for (i = 10; i < (alignment.getWidth() - 10); i += 10)
 133     {
 134       out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
 135     }
 136
 137     out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i
 138             + "<br>|</td>");
 139     out.println("</tr>");
 140
 141     for (i = 0; i < alignment.getHeight(); i++)
 142     {
 143       seq = alignment.getSequenceAt(i);
 144
 145       String id = seq.getDisplayId(av.getShowJVSuffix());
 146
 147       out.println("<tr><td nowrap>" + id + "&nbsp;&nbsp;</td>");
 148
 149       for (int res = 0; res < seq.getLength(); res++)
 150       {
 151         if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
 152         {
 153           color = sr.getResidueBoxColour(seq, res);
 154
 155           color = fr.findFeatureColour(color, seq, res);
 156         }
 157         else
 158         {
 159           color = Colour.white;
 160         }
 161
 162         if (color.getRGB() < -1)
 163         {
 164           out.println("<td bgcolor=\"#"
 165                   + jalview.util.Format.getHexString(color) + "\">"
 166                   + seq.getCharAt(res) + "</td>");
 167         }
 168         else
 169         {
 170           out.println("<td>" + seq.getCharAt(res) + "</td>");
 171         }
 172       }
 173
 174       out.println("</tr>");
 175     }
 176
 177     // ////////////
 178     out.println("</table>");
 179     out.println("</td></tr></table>");
 180   }
 181
 182   void drawWrappedAlignment(PrintWriter out)
 183   {
 184     // //////////////////////////////////
 185     // / How many sequences and residues can we fit on a printable page?
 186     AlignmentI al = av.getAlignment();
 187     SequenceI seq;
 188     String r;
 189     String g;
 190     String b;
 191
 192     out.println("<table border=\"1\"><tr><td>\n");
 193     out.println("<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
 194
 195     for (int startRes = 0; startRes < al.getWidth(); startRes += av
 196             .getWrappedWidth())
 197     {
 198       int endRes = startRes + av.getWrappedWidth();
 199
 200       if (endRes > al.getWidth())
 201       {
 202         endRes = al.getWidth();
 203       }
 204
 205       if (av.getScaleAboveWrapped())
 206       {
 207         out.println("<tr>");
 208
 209         if (av.getScaleLeftWrapped())
 210         {
 211           out.println("<td colspan=\"7\">&nbsp;</td>");
 212         }
 213         else
 214         {
 215           out.println("<td colspan=\"6\">&nbsp;</td>");
 216         }
 217
 218         for (int i = startRes + 10; i < endRes; i += 10)
 219         {
 220           out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
 221         }
 222
 223         out.println("</tr>");
 224       }
 225
 226       int startPos, endPos;
 227       for (int s = 0; s < al.getHeight(); s++)
 228       {
 229         out.println("<tr>");
 230         seq = al.getSequenceAt(s);
 231
 232         startPos = seq.findPosition(startRes);
 233         endPos = seq.findPosition(endRes) - 1;
 234
 235         String id = seq.getDisplayId(av.getShowJVSuffix());
 236
 237         out.println("<td nowrap>" + id + "&nbsp;&nbsp;</td>");
 238
 239         if (av.getScaleLeftWrapped())
 240         {
 241           if (startPos > seq.getEnd() || endPos == 0)
 242           {
 243             out.println("<td nowrap>&nbsp;</td>");
 244           }
 245           else
 246           {
 247             out.println("<td nowrap>" + startPos + "&nbsp;&nbsp;</td>");
 248           }
 249         }
 250
 251         for (int res = startRes; res < endRes; res++)
 252         {
 253           if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
 254           {
 255             color = sr.getResidueBoxColour(seq, res);
 256
 257             color = fr.findFeatureColour(color, seq, res);
 258           }
 259           else
 260           {
 261             color = Colour.white;
 262           }
 263
 264           if (color.getRGB() < -1)
 265           {
 266             out.println("<td bgcolor=\"#"
 267                     + jalview.util.Format.getHexString(color) + "\">"
 268                     + seq.getCharAt(res) + "</td>");
 269           }
 270           else
 271           {
 272             out.println("<td>" + seq.getCharAt(res) + "</td>");
 273           }
 274
 275         }
 276
 277         if (av.getScaleRightWrapped()
 278                 && endRes < startRes + av.getWrappedWidth())
 279         {
 280           out.println("<td colspan=\""
 281                   + (startRes + av.getWrappedWidth() - endRes) + "\">"
 282                   + "&nbsp;&nbsp;</td>");
 283         }
 284
 285         if (av.getScaleRightWrapped() && startPos < endPos)
 286         {
 287           out.println("<td nowrap>&nbsp;" + endPos + "&nbsp;&nbsp;</td>");
 288         }
 289
 290         out.println("</tr>");
 291       }
 292
 293       if (endRes < al.getWidth())
 294       {
 295         out.println("<tr><td height=\"5\"></td></tr>");
 296       }
 297     }
 298
 299     out.println("</table>");
 300     out.println("</table>");
 301   }
 302
 303   public static String getImageMapHTML()
 304   {
 305     return new String(
 306             "<html>\n"
 307                     + "<head>\n"
 308                     + "<script language=\"JavaScript\">\n"
 309                     + "var ns4 = document.layers;\n"
 310                     + "var ns6 = document.getElementById && !document.all;\n"
 311                     + "var ie4 = document.all;\n"
 312                     + "offsetX = 0;\n"
 313                     + "offsetY = 20;\n"
 314                     + "var toolTipSTYLE=\"\";\n"
 315                     + "function initToolTips()\n"
 316                     + "{\n"
 317                     + "  if(ns4||ns6||ie4)\n"
 318                     + "  {\n"
 319                     + "    if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
 320                     + "    else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
 321                     + "    else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
 322                     + "    if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
 323                     + "    else\n"
 324                     + "    {\n"
 325                     + "      toolTipSTYLE.visibility = \"visible\";\n"
 326                     + "      toolTipSTYLE.display = \"none\";\n"
 327                     + "    }\n"
 328                     + "    document.onmousemove = moveToMouseLoc;\n"
 329                     + "  }\n"
 330                     + "}\n"
 331                     + "function toolTip(msg, fg, bg)\n"
 332                     + "{\n"
 333                     + "  if(toolTip.arguments.length < 1) // hide\n"
 334                     + "  {\n"
 335                     + "    if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
 336                     + "    else toolTipSTYLE.display = \"none\";\n"
 337                     + "  }\n"
 338                     + "  else // show\n"
 339                     + "  {\n"
 340                     + "    if(!fg) fg = \"#555555\";\n"
 341                     + "    if(!bg) bg = \"#FFFFFF\";\n"
 342                     + "    var content =\n"
 343                     + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
 344                     + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
 345                     + "    '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
 346                     + "    '\" size=\"-2\">&nbsp;' + msg +\n"
 347                     + "    '&nbsp;</font></td></table></td></table>';\n"
 348                     + "    if(ns4)\n"
 349                     + "    {\n"
 350                     + "      toolTipSTYLE.document.write(content);\n"
 351                     + "      toolTipSTYLE.document.close();\n"
 352                     + "      toolTipSTYLE.visibility = \"visible\";\n"
 353                     + "    }\n"
 354                     + "    if(ns6)\n"
 355                     + "    {\n"
 356                     + "      document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
 357                     + "      toolTipSTYLE.display='block'\n"
 358                     + "    }\n"
 359                     + "    if(ie4)\n"
 360                     + "    {\n"
 361                     + "      document.all(\"toolTipLayer\").innerHTML=content;\n"
 362                     + "      toolTipSTYLE.display='block'\n"
 363                     + "    }\n"
 364                     + "  }\n"
 365                     + "}\n"
 366                     + "function moveToMouseLoc(e)\n"
 367                     + "{\n"
 368                     + "  if(ns4||ns6)\n"
 369                     + "  {\n"
 370                     + "    x = e.pageX;\n"
 371                     + "    y = e.pageY;\n"
 372                     + "  }\n"
 373                     + "  else\n"
 374                     + "  {\n"
 375                     + "    x = event.x + document.body.scrollLeft;\n"
 376                     + "    y = event.y + document.body.scrollTop;\n"
 377                     + "  }\n"
 378                     + "  toolTipSTYLE.left = x + offsetX;\n"
 379                     + "  toolTipSTYLE.top = y + offsetY;\n"
 380                     + "  return true;\n"
 381                     + "}\n"
 382                     + "</script>\n"
 383                     + "</head>\n"
 384                     + "<body>\n"
 385                     + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
 386                     + "<script language=\"JavaScript\"><!--\n"
 387                     + "initToolTips(); //--></script>\n");
 388
 389   }
 390 }