src/jalview/io/HTMLOutput.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
   3  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
   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 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.io;
  19
  20 import java.io.*;
  21
  22 import java.awt.*;
  23
  24 import jalview.datamodel.*;
  25 import jalview.gui.*;
  26
  27 public class HTMLOutput
  28 {
  29   AlignViewport av;
  30
  31   SequenceRenderer sr;
  32
  33   FeatureRenderer fr;
  34
  35   Color color;
  36
  37   public HTMLOutput(AlignmentPanel ap, SequenceRenderer sr,
  38           FeatureRenderer fr1)
  39   {
  40     this.av = ap.av;
  41     this.sr = sr;
  42
  43     fr = new FeatureRenderer(ap);
  44     fr.transferSettings(fr1);
  45
  46     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
  47             .getProperty("LAST_DIRECTORY"), new String[]
  48     { "html" }, new String[]
  49     { "HTML files" }, "HTML files");
  50
  51     chooser.setFileView(new JalviewFileView());
  52     chooser.setDialogTitle("Save as HTML");
  53     chooser.setToolTipText("Save");
  54
  55     int value = chooser.showSaveDialog(null);
  56
  57     if (value == JalviewFileChooser.APPROVE_OPTION)
  58     {
  59       String choice = chooser.getSelectedFile().getPath();
  60       jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
  61               .getSelectedFile().getParent());
  62
  63       try
  64       {
  65         PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
  66                 choice));
  67         out.println("<HTML>");
  68         out.println("<style type=\"text/css\">");
  69         out.println("<!--");
  70         out.print("td {font-family: \"" + av.getFont().getFamily()
  71                 + "\", \"" + av.getFont().getName() + "\", mono; "
  72                 + "font-size: " + av.getFont().getSize() + "px; ");
  73
  74         if (av.getFont().getStyle() == Font.BOLD)
  75         {
  76           out.print("font-weight: BOLD; ");
  77         }
  78
  79         if (av.getFont().getStyle() == Font.ITALIC)
  80         {
  81           out.print("font-style: italic; ");
  82         }
  83
  84         out.println("text-align: center; }");
  85
  86         out.println("-->");
  87         out.println("</style>");
  88         out.println("<BODY>");
  89
  90         if (av.getWrapAlignment())
  91         {
  92           drawWrappedAlignment(out);
  93         }
  94         else
  95         {
  96           drawUnwrappedAlignment(out);
  97         }
  98
  99         out.println("\n</body>\n</html>");
 100         out.close();
 101         jalview.util.BrowserLauncher.openURL("file:///" + choice);
 102       } catch (Exception ex)
 103       {
 104         ex.printStackTrace();
 105       }
 106     }
 107   }
 108
 109   void drawUnwrappedAlignment(PrintWriter out)
 110   {
 111     out.println("<table border=\"1\"><tr><td>\n");
 112     out
 113             .println("<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
 114
 115     // ////////////
 116     SequenceI seq;
 117     AlignmentI alignment = av.getAlignment();
 118
 119     // draws the top row, the measure rule
 120     out.println("<tr><td colspan=\"6\"></td>");
 121
 122     int i = 0;
 123
 124     for (i = 10; i < (alignment.getWidth() - 10); i += 10)
 125     {
 126       out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
 127     }
 128
 129     out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i
 130             + "<br>|</td>");
 131     out.println("</tr>");
 132
 133     for (i = 0; i < alignment.getHeight(); i++)
 134     {
 135       seq = alignment.getSequenceAt(i);
 136
 137       String id = seq.getDisplayId(av.getShowJVSuffix());
 138
 139       out.println("<tr><td nowrap>" + id + "&nbsp;&nbsp;</td>");
 140
 141       for (int res = 0; res < seq.getLength(); res++)
 142       {
 143         if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
 144         {
 145           color = sr.getResidueBoxColour(seq, res);
 146
 147           color = fr.findFeatureColour(color, seq, res);
 148         }
 149         else
 150         {
 151           color = Color.white;
 152         }
 153
 154         if (color.getRGB() < -1)
 155         {
 156           out.println("<td bgcolor=\"#"
 157                   + jalview.util.Format.getHexString(color) + "\">"
 158                   + seq.getCharAt(res) + "</td>");
 159         }
 160         else
 161         {
 162           out.println("<td>" + seq.getCharAt(res) + "</td>");
 163         }
 164       }
 165
 166       out.println("</tr>");
 167     }
 168
 169     // ////////////
 170     out.println("</table>");
 171     out.println("</td></tr></table>");
 172   }
 173
 174   void drawWrappedAlignment(PrintWriter out)
 175   {
 176     // //////////////////////////////////
 177     // / How many sequences and residues can we fit on a printable page?
 178     AlignmentI al = av.getAlignment();
 179     SequenceI seq;
 180     String r;
 181     String g;
 182     String b;
 183
 184     out.println("<table border=\"1\"><tr><td>\n");
 185     out
 186             .println("<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
 187
 188     for (int startRes = 0; startRes < al.getWidth(); startRes += av
 189             .getWrappedWidth())
 190     {
 191       int endRes = startRes + av.getWrappedWidth();
 192
 193       if (endRes > al.getWidth())
 194       {
 195         endRes = al.getWidth();
 196       }
 197
 198       if (av.getScaleAboveWrapped())
 199       {
 200         out.println("<tr>");
 201
 202         if (av.getScaleLeftWrapped())
 203         {
 204           out.println("<td colspan=\"7\">&nbsp;</td>");
 205         }
 206         else
 207         {
 208           out.println("<td colspan=\"6\">&nbsp;</td>");
 209         }
 210
 211         for (int i = startRes + 10; i < endRes; i += 10)
 212         {
 213           out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
 214         }
 215
 216         out.println("</tr>");
 217       }
 218
 219       int startPos, endPos;
 220       for (int s = 0; s < al.getHeight(); s++)
 221       {
 222         out.println("<tr>");
 223         seq = al.getSequenceAt(s);
 224
 225         startPos = seq.findPosition(startRes);
 226         endPos = seq.findPosition(endRes) - 1;
 227
 228         String id = seq.getDisplayId(av.getShowJVSuffix());
 229
 230         out.println("<td nowrap>" + id + "&nbsp;&nbsp;</td>");
 231
 232         if (av.getScaleLeftWrapped())
 233         {
 234           if (startPos > seq.getEnd() || endPos == 0)
 235           {
 236             out.println("<td nowrap>&nbsp;</td>");
 237           }
 238           else
 239           {
 240             out.println("<td nowrap>" + startPos + "&nbsp;&nbsp;</td>");
 241           }
 242         }
 243
 244         for (int res = startRes; res < endRes; res++)
 245         {
 246           if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
 247           {
 248             color = sr.getResidueBoxColour(seq, res);
 249
 250             color = fr.findFeatureColour(color, seq, res);
 251           }
 252           else
 253           {
 254             color = Color.white;
 255           }
 256
 257           if (color.getRGB() < -1)
 258           {
 259             out.println("<td bgcolor=\"#"
 260                     + jalview.util.Format.getHexString(color) + "\">"
 261                     + seq.getCharAt(res) + "</td>");
 262           }
 263           else
 264           {
 265             out.println("<td>" + seq.getCharAt(res) + "</td>");
 266           }
 267
 268         }
 269
 270         if (av.getScaleRightWrapped()
 271                 && endRes < startRes + av.getWrappedWidth())
 272         {
 273           out.println("<td colspan=\""
 274                   + (startRes + av.getWrappedWidth() - endRes) + "\">"
 275                   + "&nbsp;&nbsp;</td>");
 276         }
 277
 278         if (av.getScaleRightWrapped() && startPos < endPos)
 279         {
 280           out.println("<td nowrap>&nbsp;" + endPos + "&nbsp;&nbsp;</td>");
 281         }
 282
 283         out.println("</tr>");
 284       }
 285
 286       if (endRes < al.getWidth())
 287       {
 288         out.println("<tr><td height=\"5\"></td></tr>");
 289       }
 290     }
 291
 292     out.println("</table>");
 293     out.println("</table>");
 294   }
 295
 296   public static String getImageMapHTML()
 297   {
 298     return new String(
 299             "<html>\n"
 300                     + "<head>\n"
 301                     + "<script language=\"JavaScript\">\n"
 302                     + "var ns4 = document.layers;\n"
 303                     + "var ns6 = document.getElementById && !document.all;\n"
 304                     + "var ie4 = document.all;\n"
 305                     + "offsetX = 0;\n"
 306                     + "offsetY = 20;\n"
 307                     + "var toolTipSTYLE=\"\";\n"
 308                     + "function initToolTips()\n"
 309                     + "{\n"
 310                     + "  if(ns4||ns6||ie4)\n"
 311                     + "  {\n"
 312                     + "    if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
 313                     + "    else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
 314                     + "    else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
 315                     + "    if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
 316                     + "    else\n"
 317                     + "    {\n"
 318                     + "      toolTipSTYLE.visibility = \"visible\";\n"
 319                     + "      toolTipSTYLE.display = \"none\";\n"
 320                     + "    }\n"
 321                     + "    document.onmousemove = moveToMouseLoc;\n"
 322                     + "  }\n"
 323                     + "}\n"
 324                     + "function toolTip(msg, fg, bg)\n"
 325                     + "{\n"
 326                     + "  if(toolTip.arguments.length < 1) // hide\n"
 327                     + "  {\n"
 328                     + "    if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
 329                     + "    else toolTipSTYLE.display = \"none\";\n"
 330                     + "  }\n"
 331                     + "  else // show\n"
 332                     + "  {\n"
 333                     + "    if(!fg) fg = \"#555555\";\n"
 334                     + "    if(!bg) bg = \"#FFFFFF\";\n"
 335                     + "    var content =\n"
 336                     + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
 337                     + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
 338                     + "    '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
 339                     + "    '\" size=\"-2\">&nbsp;' + msg +\n"
 340                     + "    '&nbsp;</font></td></table></td></table>';\n"
 341                     + "    if(ns4)\n"
 342                     + "    {\n"
 343                     + "      toolTipSTYLE.document.write(content);\n"
 344                     + "      toolTipSTYLE.document.close();\n"
 345                     + "      toolTipSTYLE.visibility = \"visible\";\n"
 346                     + "    }\n"
 347                     + "    if(ns6)\n"
 348                     + "    {\n"
 349                     + "      document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
 350                     + "      toolTipSTYLE.display='block'\n"
 351                     + "    }\n"
 352                     + "    if(ie4)\n"
 353                     + "    {\n"
 354                     + "      document.all(\"toolTipLayer\").innerHTML=content;\n"
 355                     + "      toolTipSTYLE.display='block'\n"
 356                     + "    }\n"
 357                     + "  }\n"
 358                     + "}\n"
 359                     + "function moveToMouseLoc(e)\n"
 360                     + "{\n"
 361                     + "  if(ns4||ns6)\n"
 362                     + "  {\n"
 363                     + "    x = e.pageX;\n"
 364                     + "    y = e.pageY;\n"
 365                     + "  }\n"
 366                     + "  else\n"
 367                     + "  {\n"
 368                     + "    x = event.x + document.body.scrollLeft;\n"
 369                     + "    y = event.y + document.body.scrollTop;\n"
 370                     + "  }\n"
 371                     + "  toolTipSTYLE.left = x + offsetX;\n"
 372                     + "  toolTipSTYLE.top = y + offsetY;\n"
 373                     + "  return true;\n"
 374                     + "}\n"
 375                     + "</script>\n"
 376                     + "</head>\n"
 377                     + "<body>\n"
 378                     + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
 379                     + "<script language=\"JavaScript\"><!--\n"
 380                     + "initToolTips(); //--></script>\n");
 381
 382   }
 383 }