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.bin.Cache;
  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.util.BrowserLauncher;
  31 import jalview.util.Comparison;
  32 import jalview.util.Format;
  33 import jalview.util.MessageManager;
  34
  35 import java.awt.Color;
  36 import java.awt.Font;
  37 import java.io.PrintWriter;
  38
  39 public class HTMLOutput
  40 {
  41   AlignViewport av;
  42
  43   SequenceRenderer sr;
  44
  45   jalview.renderer.seqfeatures.FeatureRenderer fr;
  46
  47   Color color;
  48
  49   public HTMLOutput(AlignmentPanel ap, SequenceRenderer sr,
  50           FeatureRenderer fr1)
  51   {
  52     this.av = ap.av;
  53     this.sr = sr;
  54
  55     fr = new FeatureRenderer(ap);
  56     fr.transferSettings(fr1);
  57
  58     JalviewFileChooser chooser = new JalviewFileChooser(
  59             Cache.getProperty("LAST_DIRECTORY"), new String[]
  60             { "html" }, new String[]
  61             { "HTML files" }, "HTML files");
  62
  63     chooser.setFileView(new JalviewFileView());
  64     chooser.setDialogTitle(MessageManager.getString("label.save_as_html"));
  65     chooser.setToolTipText(MessageManager.getString("action.save"));
  66
  67     int value = chooser.showSaveDialog(null);
  68
  69     if (value == JalviewFileChooser.APPROVE_OPTION)
  70     {
  71       String choice = chooser.getSelectedFile().getPath();
  72       Cache.setProperty("LAST_DIRECTORY", chooser
  73               .getSelectedFile().getParent());
  74
  75       try
  76       {
  77         PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
  78                 choice));
  79         out.println("<HTML>");
  80         out.println("<style type=\"text/css\">");
  81         out.println("<!--");
  82         out.print("td {font-family: \"" + av.getFont().getFamily()
  83                 + "\", \"" + av.getFont().getName() + "\", mono; "
  84                 + "font-size: " + av.getFont().getSize() + "px; ");
  85
  86         if (av.getFont().getStyle() == Font.BOLD)
  87         {
  88           out.print("font-weight: BOLD; ");
  89         }
  90
  91         if (av.getFont().getStyle() == Font.ITALIC)
  92         {
  93           out.print("font-style: italic; ");
  94         }
  95
  96         out.println("text-align: center; }");
  97
  98         out.println("-->");
  99         out.println("</style>");
 100         out.println("<BODY>");
 101
 102         if (av.getWrapAlignment())
 103         {
 104           drawWrappedAlignment(out);
 105         }
 106         else
 107         {
 108           drawUnwrappedAlignment(out);
 109         }
 110
 111         out.println("\n</body>\n</html>");
 112         out.close();
 113         BrowserLauncher.openURL("file:///" + choice);
 114       } catch (Exception ex)
 115       {
 116         ex.printStackTrace();
 117       }
 118     }
 119   }
 120
 121   void drawUnwrappedAlignment(PrintWriter out)
 122   {
 123     out.println("<table border=\"1\"><tr><td>\n");
 124     out.println("<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
 125
 126     // ////////////
 127     SequenceI seq;
 128     AlignmentI alignment = av.getAlignment();
 129
 130     // draws the top row, the measure rule
 131     out.println("<tr><td colspan=\"6\"></td>");
 132
 133     int i = 0;
 134
 135     for (i = 10; i < (alignment.getWidth() - 10); i += 10)
 136     {
 137       out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
 138     }
 139
 140     out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i
 141             + "<br>|</td>");
 142     out.println("</tr>");
 143
 144     for (i = 0; i < alignment.getHeight(); i++)
 145     {
 146       seq = alignment.getSequenceAt(i);
 147
 148       String id = seq.getDisplayId(av.getShowJVSuffix());
 149
 150       out.println("<tr><td nowrap>" + id + "&nbsp;&nbsp;</td>");
 151
 152       for (int res = 0; res < seq.getLength(); res++)
 153       {
 154         if (!Comparison.isGap(seq.getCharAt(res)))
 155         {
 156           color = sr.getResidueBoxColour(seq, res);
 157
 158           color = fr.findFeatureColour(color, seq, res);
 159         }
 160         else
 161         {
 162           color = Color.white;
 163         }
 164
 165         if (color.getRGB() < -1)
 166         {
 167           out.println("<td bgcolor=\"#" + Format.getHexString(color)
 168                   + "\">" + seq.getCharAt(res) + "</td>");
 169         }
 170         else
 171         {
 172           out.println("<td>" + seq.getCharAt(res) + "</td>");
 173         }
 174       }
 175
 176       out.println("</tr>");
 177     }
 178
 179     // ////////////
 180     out.println("</table>");
 181     out.println("</td></tr></table>");
 182   }
 183
 184   void drawWrappedAlignment(PrintWriter out)
 185   {
 186     // //////////////////////////////////
 187     // / How many sequences and residues can we fit on a printable page?
 188     AlignmentI al = av.getAlignment();
 189     SequenceI seq;
 190     String r;
 191     String g;
 192     String b;
 193
 194     out.println("<table border=\"1\"><tr><td>\n");
 195     out.println("<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
 196
 197     for (int startRes = 0; startRes < al.getWidth(); startRes += av
 198             .getWrappedWidth())
 199     {
 200       int endRes = startRes + av.getWrappedWidth();
 201
 202       if (endRes > al.getWidth())
 203       {
 204         endRes = al.getWidth();
 205       }
 206
 207       if (av.getScaleAboveWrapped())
 208       {
 209         out.println("<tr>");
 210
 211         if (av.getScaleLeftWrapped())
 212         {
 213           out.println("<td colspan=\"7\">&nbsp;</td>");
 214         }
 215         else
 216         {
 217           out.println("<td colspan=\"6\">&nbsp;</td>");
 218         }
 219
 220         for (int i = startRes + 10; i < endRes; i += 10)
 221         {
 222           out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
 223         }
 224
 225         out.println("</tr>");
 226       }
 227
 228       int startPos, endPos;
 229       for (int s = 0; s < al.getHeight(); s++)
 230       {
 231         out.println("<tr>");
 232         seq = al.getSequenceAt(s);
 233
 234         startPos = seq.findPosition(startRes);
 235         endPos = seq.findPosition(endRes) - 1;
 236
 237         String id = seq.getDisplayId(av.getShowJVSuffix());
 238
 239         out.println("<td nowrap>" + id + "&nbsp;&nbsp;</td>");
 240
 241         if (av.getScaleLeftWrapped())
 242         {
 243           if (startPos > seq.getEnd() || endPos == 0)
 244           {
 245             out.println("<td nowrap>&nbsp;</td>");
 246           }
 247           else
 248           {
 249             out.println("<td nowrap>" + startPos + "&nbsp;&nbsp;</td>");
 250           }
 251         }
 252
 253         for (int res = startRes; res < endRes; res++)
 254         {
 255           if (!Comparison.isGap(seq.getCharAt(res)))
 256           {
 257             color = sr.getResidueBoxColour(seq, res);
 258
 259             color = fr.findFeatureColour(color, seq, res);
 260           }
 261           else
 262           {
 263             color = Color.white;
 264           }
 265
 266           if (color.getRGB() < -1)
 267           {
 268             out.println("<td bgcolor=\"#" + Format.getHexString(color)
 269                     + "\">" + seq.getCharAt(res) + "</td>");
 270           }
 271           else
 272           {
 273             out.println("<td>" + seq.getCharAt(res) + "</td>");
 274           }
 275
 276         }
 277
 278         if (av.getScaleRightWrapped()
 279                 && endRes < startRes + av.getWrappedWidth())
 280         {
 281           out.println("<td colspan=\""
 282                   + (startRes + av.getWrappedWidth() - endRes) + "\">"
 283                   + "&nbsp;&nbsp;</td>");
 284         }
 285
 286         if (av.getScaleRightWrapped() && startPos < endPos)
 287         {
 288           out.println("<td nowrap>&nbsp;" + endPos + "&nbsp;&nbsp;</td>");
 289         }
 290
 291         out.println("</tr>");
 292       }
 293
 294       if (endRes < al.getWidth())
 295       {
 296         out.println("<tr><td height=\"5\"></td></tr>");
 297       }
 298     }
 299
 300     out.println("</table>");
 301     out.println("</table>");
 302   }
 303
 304   public static String getImageMapHTML()
 305   {
 306     return new String(
 307             "<html>\n"
 308                     + "<head>\n"
 309                     + "<script language=\"JavaScript\">\n"
 310                     + "var ns4 = document.layers;\n"
 311                     + "var ns6 = document.getElementById && !document.all;\n"
 312                     + "var ie4 = document.all;\n"
 313                     + "offsetX = 0;\n"
 314                     + "offsetY = 20;\n"
 315                     + "var toolTipSTYLE=\"\";\n"
 316                     + "function initToolTips()\n"
 317                     + "{\n"
 318                     + "  if(ns4||ns6||ie4)\n"
 319                     + "  {\n"
 320                     + "    if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
 321                     + "    else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
 322                     + "    else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
 323                     + "    if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
 324                     + "    else\n"
 325                     + "    {\n"
 326                     + "      toolTipSTYLE.visibility = \"visible\";\n"
 327                     + "      toolTipSTYLE.display = \"none\";\n"
 328                     + "    }\n"
 329                     + "    document.onmousemove = moveToMouseLoc;\n"
 330                     + "  }\n"
 331                     + "}\n"
 332                     + "function toolTip(msg, fg, bg)\n"
 333                     + "{\n"
 334                     + "  if(toolTip.arguments.length < 1) // hide\n"
 335                     + "  {\n"
 336                     + "    if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
 337                     + "    else toolTipSTYLE.display = \"none\";\n"
 338                     + "  }\n"
 339                     + "  else // show\n"
 340                     + "  {\n"
 341                     + "    if(!fg) fg = \"#555555\";\n"
 342                     + "    if(!bg) bg = \"#FFFFFF\";\n"
 343                     + "    var content =\n"
 344                     + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
 345                     + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
 346                     + "    '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
 347                     + "    '\" size=\"-2\">&nbsp;' + msg +\n"
 348                     + "    '&nbsp;</font></td></table></td></table>';\n"
 349                     + "    if(ns4)\n"
 350                     + "    {\n"
 351                     + "      toolTipSTYLE.document.write(content);\n"
 352                     + "      toolTipSTYLE.document.close();\n"
 353                     + "      toolTipSTYLE.visibility = \"visible\";\n"
 354                     + "    }\n"
 355                     + "    if(ns6)\n"
 356                     + "    {\n"
 357                     + "      document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
 358                     + "      toolTipSTYLE.display='block'\n"
 359                     + "    }\n"
 360                     + "    if(ie4)\n"
 361                     + "    {\n"
 362                     + "      document.all(\"toolTipLayer\").innerHTML=content;\n"
 363                     + "      toolTipSTYLE.display='block'\n"
 364                     + "    }\n"
 365                     + "  }\n"
 366                     + "}\n"
 367                     + "function moveToMouseLoc(e)\n"
 368                     + "{\n"
 369                     + "  if(ns4||ns6)\n"
 370                     + "  {\n"
 371                     + "    x = e.pageX;\n"
 372                     + "    y = e.pageY;\n"
 373                     + "  }\n"
 374                     + "  else\n"
 375                     + "  {\n"
 376                     + "    x = event.x + document.body.scrollLeft;\n"
 377                     + "    y = event.y + document.body.scrollTop;\n"
 378                     + "  }\n"
 379                     + "  toolTipSTYLE.left = x + offsetX;\n"
 380                     + "  toolTipSTYLE.top = y + offsetY;\n"
 381                     + "  return true;\n"
 382                     + "}\n"
 383                     + "</script>\n"
 384                     + "</head>\n"
 385                     + "<body>\n"
 386                     + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
 387                     + "<script language=\"JavaScript\"><!--\n"
 388                     + "initToolTips(); //--></script>\n");
 389
 390   }
 391 }