src/jalview/io/HTMLOutput.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
   3  * Copyright (C) 2015 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.datamodel.AlignmentI;
  24 import jalview.datamodel.SequenceI;
  25 import jalview.gui.AlignViewport;
  26 import jalview.gui.AlignmentPanel;
  27 import jalview.gui.FeatureRenderer;
  28 import jalview.gui.SequenceRenderer;
  29 import jalview.util.MessageManager;
  30
  31 import java.awt.Color;
  32 import java.awt.Font;
  33 import java.io.PrintWriter;
  34
  35 public class HTMLOutput
  36 {
  37   AlignViewport av;
  38
  39   SequenceRenderer sr;
  40
  41   jalview.renderer.seqfeatures.FeatureRenderer fr;
  42
  43   Color color;
  44
  45   public HTMLOutput(AlignmentPanel ap, SequenceRenderer sr,
  46           FeatureRenderer fr1)
  47   {
  48     this.av = ap.av;
  49     this.sr = sr;
  50
  51     fr = new FeatureRenderer(ap);
  52     fr.transferSettings(fr1);
  53
  54     JalviewFileChooser chooser = new JalviewFileChooser(
  55             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
  56             new String[] { "html" }, new String[] { "HTML files" },
  57             "HTML files");
  58
  59     chooser.setFileView(new JalviewFileView());
  60     chooser.setDialogTitle(MessageManager.getString("label.save_as_html"));
  61     chooser.setToolTipText(MessageManager.getString("action.save"));
  62
  63     int value = chooser.showSaveDialog(null);
  64
  65     if (value == JalviewFileChooser.APPROVE_OPTION)
  66     {
  67       String choice = chooser.getSelectedFile().getPath();
  68       jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
  69               .getSelectedFile().getParent());
  70
  71       try
  72       {
  73         PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
  74                 choice));
  75         out.println("<HTML>");
  76         out.println("<style type=\"text/css\">");
  77         out.println("<!--");
  78         out.print("td {font-family: \"" + av.getFont().getFamily()
  79                 + "\", \"" + av.getFont().getName() + "\", mono; "
  80                 + "font-size: " + av.getFont().getSize() + "px; ");
  81
  82         if (av.getFont().getStyle() == Font.BOLD)
  83         {
  84           out.print("font-weight: BOLD; ");
  85         }
  86
  87         if (av.getFont().getStyle() == Font.ITALIC)
  88         {
  89           out.print("font-style: italic; ");
  90         }
  91
  92         out.println("text-align: center; }");
  93
  94         out.println("-->");
  95         out.println("</style>");
  96         out.println("<BODY>");
  97
  98         if (av.getWrapAlignment())
  99         {
 100           drawWrappedAlignment(out);
 101         }
 102         else
 103         {
 104           drawUnwrappedAlignment(out);
 105         }
 106
 107         out.println("\n</body>\n</html>");
 108         out.close();
 109         jalview.util.BrowserLauncher.openURL("file:///" + choice);
 110       } catch (Exception ex)
 111       {
 112         ex.printStackTrace();
 113       }
 114     }
 115   }
 116
 117   void drawUnwrappedAlignment(PrintWriter out)
 118   {
 119     out.println("<table border=\"1\"><tr><td>\n");
 120     out.println("<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
 121
 122     // ////////////
 123     SequenceI seq;
 124     AlignmentI alignment = av.getAlignment();
 125
 126     // draws the top row, the measure rule
 127     out.println("<tr><td colspan=\"6\"></td>");
 128
 129     int i = 0;
 130
 131     for (i = 10; i < (alignment.getWidth() - 10); i += 10)
 132     {
 133       out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
 134     }
 135
 136     out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i
 137             + "<br>|</td>");
 138     out.println("</tr>");
 139
 140     for (i = 0; i < alignment.getHeight(); i++)
 141     {
 142       seq = alignment.getSequenceAt(i);
 143
 144       String id = seq.getDisplayId(av.getShowJVSuffix());
 145
 146       out.println("<tr><td nowrap>" + id + "&nbsp;&nbsp;</td>");
 147
 148       for (int res = 0; res < seq.getLength(); res++)
 149       {
 150         if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
 151         {
 152           color = sr.getResidueBoxColour(seq, res);
 153
 154           color = fr.findFeatureColour(color, seq, res);
 155         }
 156         else
 157         {
 158           color = Color.white;
 159         }
 160
 161         if (color.getRGB() < -1)
 162         {
 163           out.println("<td bgcolor=\"#"
 164                   + jalview.util.Format.getHexString(color) + "\">"
 165                   + seq.getCharAt(res) + "</td>");
 166         }
 167         else
 168         {
 169           out.println("<td>" + seq.getCharAt(res) + "</td>");
 170         }
 171       }
 172
 173       out.println("</tr>");
 174     }
 175
 176     // ////////////
 177     out.println("</table>");
 178     out.println("</td></tr></table>");
 179   }
 180
 181   void drawWrappedAlignment(PrintWriter out)
 182   {
 183     // //////////////////////////////////
 184     // / How many sequences and residues can we fit on a printable page?
 185     AlignmentI al = av.getAlignment();
 186     SequenceI seq;
 187     String r;
 188     String g;
 189     String b;
 190
 191     out.println("<table border=\"1\"><tr><td>\n");
 192     out.println("<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
 193
 194     for (int startRes = 0; startRes < al.getWidth(); startRes += av
 195             .getWrappedWidth())
 196     {
 197       int endRes = startRes + av.getWrappedWidth();
 198
 199       if (endRes > al.getWidth())
 200       {
 201         endRes = al.getWidth();
 202       }
 203
 204       if (av.getScaleAboveWrapped())
 205       {
 206         out.println("<tr>");
 207
 208         if (av.getScaleLeftWrapped())
 209         {
 210           out.println("<td colspan=\"7\">&nbsp;</td>");
 211         }
 212         else
 213         {
 214           out.println("<td colspan=\"6\">&nbsp;</td>");
 215         }
 216
 217         for (int i = startRes + 10; i < endRes; i += 10)
 218         {
 219           out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
 220         }
 221
 222         out.println("</tr>");
 223       }
 224
 225       int startPos, endPos;
 226       for (int s = 0; s < al.getHeight(); s++)
 227       {
 228         out.println("<tr>");
 229         seq = al.getSequenceAt(s);
 230
 231         startPos = seq.findPosition(startRes);
 232         endPos = seq.findPosition(endRes) - 1;
 233
 234         String id = seq.getDisplayId(av.getShowJVSuffix());
 235
 236         out.println("<td nowrap>" + id + "&nbsp;&nbsp;</td>");
 237
 238         if (av.getScaleLeftWrapped())
 239         {
 240           if (startPos > seq.getEnd() || endPos == 0)
 241           {
 242             out.println("<td nowrap>&nbsp;</td>");
 243           }
 244           else
 245           {
 246             out.println("<td nowrap>" + startPos + "&nbsp;&nbsp;</td>");
 247           }
 248         }
 249
 250         for (int res = startRes; res < endRes; res++)
 251         {
 252           if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
 253           {
 254             color = sr.getResidueBoxColour(seq, res);
 255
 256             color = fr.findFeatureColour(color, seq, res);
 257           }
 258           else
 259           {
 260             color = Color.white;
 261           }
 262
 263           if (color.getRGB() < -1)
 264           {
 265             out.println("<td bgcolor=\"#"
 266                     + jalview.util.Format.getHexString(color) + "\">"
 267                     + seq.getCharAt(res) + "</td>");
 268           }
 269           else
 270           {
 271             out.println("<td>" + seq.getCharAt(res) + "</td>");
 272           }
 273
 274         }
 275
 276         if (av.getScaleRightWrapped()
 277                 && endRes < startRes + av.getWrappedWidth())
 278         {
 279           out.println("<td colspan=\""
 280                   + (startRes + av.getWrappedWidth() - endRes) + "\">"
 281                   + "&nbsp;&nbsp;</td>");
 282         }
 283
 284         if (av.getScaleRightWrapped() && startPos < endPos)
 285         {
 286           out.println("<td nowrap>&nbsp;" + endPos + "&nbsp;&nbsp;</td>");
 287         }
 288
 289         out.println("</tr>");
 290       }
 291
 292       if (endRes < al.getWidth())
 293       {
 294         out.println("<tr><td height=\"5\"></td></tr>");
 295       }
 296     }
 297
 298     out.println("</table>");
 299     out.println("</table>");
 300   }
 301
 302   public static String getImageMapHTML()
 303   {
 304     return new String(
 305             "<html>\n"
 306                     + "<head>\n"
 307                     + "<script language=\"JavaScript\">\n"
 308                     + "var ns4 = document.layers;\n"
 309                     + "var ns6 = document.getElementById && !document.all;\n"
 310                     + "var ie4 = document.all;\n"
 311                     + "offsetX = 0;\n"
 312                     + "offsetY = 20;\n"
 313                     + "var toolTipSTYLE=\"\";\n"
 314                     + "function initToolTips()\n"
 315                     + "{\n"
 316                     + "  if(ns4||ns6||ie4)\n"
 317                     + "  {\n"
 318                     + "    if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
 319                     + "    else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
 320                     + "    else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
 321                     + "    if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
 322                     + "    else\n"
 323                     + "    {\n"
 324                     + "      toolTipSTYLE.visibility = \"visible\";\n"
 325                     + "      toolTipSTYLE.display = \"none\";\n"
 326                     + "    }\n"
 327                     + "    document.onmousemove = moveToMouseLoc;\n"
 328                     + "  }\n"
 329                     + "}\n"
 330                     + "function toolTip(msg, fg, bg)\n"
 331                     + "{\n"
 332                     + "  if(toolTip.arguments.length < 1) // hide\n"
 333                     + "  {\n"
 334                     + "    if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
 335                     + "    else toolTipSTYLE.display = \"none\";\n"
 336                     + "  }\n"
 337                     + "  else // show\n"
 338                     + "  {\n"
 339                     + "    if(!fg) fg = \"#555555\";\n"
 340                     + "    if(!bg) bg = \"#FFFFFF\";\n"
 341                     + "    var content =\n"
 342                     + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
 343                     + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
 344                     + "    '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
 345                     + "    '\" size=\"-2\">&nbsp;' + msg +\n"
 346                     + "    '&nbsp;</font></td></table></td></table>';\n"
 347                     + "    if(ns4)\n"
 348                     + "    {\n"
 349                     + "      toolTipSTYLE.document.write(content);\n"
 350                     + "      toolTipSTYLE.document.close();\n"
 351                     + "      toolTipSTYLE.visibility = \"visible\";\n"
 352                     + "    }\n"
 353                     + "    if(ns6)\n"
 354                     + "    {\n"
 355                     + "      document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
 356                     + "      toolTipSTYLE.display='block'\n"
 357                     + "    }\n"
 358                     + "    if(ie4)\n"
 359                     + "    {\n"
 360                     + "      document.all(\"toolTipLayer\").innerHTML=content;\n"
 361                     + "      toolTipSTYLE.display='block'\n"
 362                     + "    }\n"
 363                     + "  }\n"
 364                     + "}\n"
 365                     + "function moveToMouseLoc(e)\n"
 366                     + "{\n"
 367                     + "  if(ns4||ns6)\n"
 368                     + "  {\n"
 369                     + "    x = e.pageX;\n"
 370                     + "    y = e.pageY;\n"
 371                     + "  }\n"
 372                     + "  else\n"
 373                     + "  {\n"
 374                     + "    x = event.x + document.body.scrollLeft;\n"
 375                     + "    y = event.y + document.body.scrollTop;\n"
 376                     + "  }\n"
 377                     + "  toolTipSTYLE.left = x + offsetX;\n"
 378                     + "  toolTipSTYLE.top = y + offsetY;\n"
 379                     + "  return true;\n"
 380                     + "}\n"
 381                     + "</script>\n"
 382                     + "</head>\n"
 383                     + "<body>\n"
 384                     + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
 385                     + "<script language=\"JavaScript\"><!--\n"
 386                     + "initToolTips(); //--></script>\n");
 387
 388   }
 389 }