src/jalview/io/HTMLOutput.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
   3  * Copyright (C) 2014 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 java.io.*;
  24
  25 import java.awt.*;
  26
  27 import jalview.datamodel.*;
  28 import jalview.gui.*;
  29 import jalview.util.MessageManager;
  30
  31 public class HTMLOutput
  32 {
  33   AlignViewport av;
  34
  35   SequenceRenderer sr;
  36
  37   FeatureRenderer fr;
  38
  39   Color color;
  40
  41   public HTMLOutput(AlignmentPanel ap, SequenceRenderer sr,
  42           FeatureRenderer fr1)
  43   {
  44     this.av = ap.av;
  45     this.sr = sr;
  46
  47     fr = new FeatureRenderer(ap);
  48     fr.transferSettings(fr1);
  49
  50     JalviewFileChooser chooser = new JalviewFileChooser(
  51             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
  52             { "html" }, new String[]
  53             { "HTML files" }, "HTML files");
  54
  55     chooser.setFileView(new JalviewFileView());
  56     chooser.setDialogTitle(MessageManager.getString("label.save_as_html"));
  57     chooser.setToolTipText(MessageManager.getString("action.save"));
  58
  59     int value = chooser.showSaveDialog(null);
  60
  61     if (value == JalviewFileChooser.APPROVE_OPTION)
  62     {
  63       String choice = chooser.getSelectedFile().getPath();
  64       jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
  65               .getSelectedFile().getParent());
  66
  67       try
  68       {
  69         PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
  70                 choice));
  71         out.println("<HTML>");
  72         out.println("<style type=\"text/css\">");
  73         out.println("<!--");
  74         out.print("td {font-family: \"" + av.getFont().getFamily()
  75                 + "\", \"" + av.getFont().getName() + "\", mono; "
  76                 + "font-size: " + av.getFont().getSize() + "px; ");
  77
  78         if (av.getFont().getStyle() == Font.BOLD)
  79         {
  80           out.print("font-weight: BOLD; ");
  81         }
  82
  83         if (av.getFont().getStyle() == Font.ITALIC)
  84         {
  85           out.print("font-style: italic; ");
  86         }
  87
  88         out.println("text-align: center; }");
  89
  90         out.println("-->");
  91         out.println("</style>");
  92         out.println("<BODY>");
  93
  94         if (av.getWrapAlignment())
  95         {
  96           drawWrappedAlignment(out);
  97         }
  98         else
  99         {
 100           drawUnwrappedAlignment(out);
 101         }
 102
 103         out.println("\n</body>\n</html>");
 104         out.close();
 105         jalview.util.BrowserLauncher.openURL("file:///" + choice);
 106       } catch (Exception ex)
 107       {
 108         ex.printStackTrace();
 109       }
 110     }
 111   }
 112
 113   void drawUnwrappedAlignment(PrintWriter out)
 114   {
 115     out.println("<table border=\"1\"><tr><td>\n");
 116     out.println("<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
 117
 118     // ////////////
 119     SequenceI seq;
 120     AlignmentI alignment = av.getAlignment();
 121
 122     // draws the top row, the measure rule
 123     out.println("<tr><td colspan=\"6\"></td>");
 124
 125     int i = 0;
 126
 127     for (i = 10; i < (alignment.getWidth() - 10); i += 10)
 128     {
 129       out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
 130     }
 131
 132     out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i
 133             + "<br>|</td>");
 134     out.println("</tr>");
 135
 136     for (i = 0; i < alignment.getHeight(); i++)
 137     {
 138       seq = alignment.getSequenceAt(i);
 139
 140       String id = seq.getDisplayId(av.getShowJVSuffix());
 141
 142       out.println("<tr><td nowrap>" + id + "&nbsp;&nbsp;</td>");
 143
 144       for (int res = 0; res < seq.getLength(); res++)
 145       {
 146         if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
 147         {
 148           color = sr.getResidueBoxColour(seq, res);
 149
 150           color = fr.findFeatureColour(color, seq, res);
 151         }
 152         else
 153         {
 154           color = Color.white;
 155         }
 156
 157         if (color.getRGB() < -1)
 158         {
 159           out.println("<td bgcolor=\"#"
 160                   + jalview.util.Format.getHexString(color) + "\">"
 161                   + seq.getCharAt(res) + "</td>");
 162         }
 163         else
 164         {
 165           out.println("<td>" + seq.getCharAt(res) + "</td>");
 166         }
 167       }
 168
 169       out.println("</tr>");
 170     }
 171
 172     // ////////////
 173     out.println("</table>");
 174     out.println("</td></tr></table>");
 175   }
 176
 177   void drawWrappedAlignment(PrintWriter out)
 178   {
 179     // //////////////////////////////////
 180     // / How many sequences and residues can we fit on a printable page?
 181     AlignmentI al = av.getAlignment();
 182     SequenceI seq;
 183     String r;
 184     String g;
 185     String b;
 186
 187     out.println("<table border=\"1\"><tr><td>\n");
 188     out.println("<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
 189
 190     for (int startRes = 0; startRes < al.getWidth(); startRes += av
 191             .getWrappedWidth())
 192     {
 193       int endRes = startRes + av.getWrappedWidth();
 194
 195       if (endRes > al.getWidth())
 196       {
 197         endRes = al.getWidth();
 198       }
 199
 200       if (av.getScaleAboveWrapped())
 201       {
 202         out.println("<tr>");
 203
 204         if (av.getScaleLeftWrapped())
 205         {
 206           out.println("<td colspan=\"7\">&nbsp;</td>");
 207         }
 208         else
 209         {
 210           out.println("<td colspan=\"6\">&nbsp;</td>");
 211         }
 212
 213         for (int i = startRes + 10; i < endRes; i += 10)
 214         {
 215           out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
 216         }
 217
 218         out.println("</tr>");
 219       }
 220
 221       int startPos, endPos;
 222       for (int s = 0; s < al.getHeight(); s++)
 223       {
 224         out.println("<tr>");
 225         seq = al.getSequenceAt(s);
 226
 227         startPos = seq.findPosition(startRes);
 228         endPos = seq.findPosition(endRes) - 1;
 229
 230         String id = seq.getDisplayId(av.getShowJVSuffix());
 231
 232         out.println("<td nowrap>" + id + "&nbsp;&nbsp;</td>");
 233
 234         if (av.getScaleLeftWrapped())
 235         {
 236           if (startPos > seq.getEnd() || endPos == 0)
 237           {
 238             out.println("<td nowrap>&nbsp;</td>");
 239           }
 240           else
 241           {
 242             out.println("<td nowrap>" + startPos + "&nbsp;&nbsp;</td>");
 243           }
 244         }
 245
 246         for (int res = startRes; res < endRes; res++)
 247         {
 248           if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
 249           {
 250             color = sr.getResidueBoxColour(seq, res);
 251
 252             color = fr.findFeatureColour(color, seq, res);
 253           }
 254           else
 255           {
 256             color = Color.white;
 257           }
 258
 259           if (color.getRGB() < -1)
 260           {
 261             out.println("<td bgcolor=\"#"
 262                     + jalview.util.Format.getHexString(color) + "\">"
 263                     + seq.getCharAt(res) + "</td>");
 264           }
 265           else
 266           {
 267             out.println("<td>" + seq.getCharAt(res) + "</td>");
 268           }
 269
 270         }
 271
 272         if (av.getScaleRightWrapped()
 273                 && endRes < startRes + av.getWrappedWidth())
 274         {
 275           out.println("<td colspan=\""
 276                   + (startRes + av.getWrappedWidth() - endRes) + "\">"
 277                   + "&nbsp;&nbsp;</td>");
 278         }
 279
 280         if (av.getScaleRightWrapped() && startPos < endPos)
 281         {
 282           out.println("<td nowrap>&nbsp;" + endPos + "&nbsp;&nbsp;</td>");
 283         }
 284
 285         out.println("</tr>");
 286       }
 287
 288       if (endRes < al.getWidth())
 289       {
 290         out.println("<tr><td height=\"5\"></td></tr>");
 291       }
 292     }
 293
 294     out.println("</table>");
 295     out.println("</table>");
 296   }
 297
 298   public static String getImageMapHTML()
 299   {
 300     return new String(
 301             "<html>\n"
 302                     + "<head>\n"
 303                     + "<script language=\"JavaScript\">\n"
 304                     + "var ns4 = document.layers;\n"
 305                     + "var ns6 = document.getElementById && !document.all;\n"
 306                     + "var ie4 = document.all;\n"
 307                     + "offsetX = 0;\n"
 308                     + "offsetY = 20;\n"
 309                     + "var toolTipSTYLE=\"\";\n"
 310                     + "function initToolTips()\n"
 311                     + "{\n"
 312                     + "  if(ns4||ns6||ie4)\n"
 313                     + "  {\n"
 314                     + "    if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
 315                     + "    else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
 316                     + "    else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
 317                     + "    if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
 318                     + "    else\n"
 319                     + "    {\n"
 320                     + "      toolTipSTYLE.visibility = \"visible\";\n"
 321                     + "      toolTipSTYLE.display = \"none\";\n"
 322                     + "    }\n"
 323                     + "    document.onmousemove = moveToMouseLoc;\n"
 324                     + "  }\n"
 325                     + "}\n"
 326                     + "function toolTip(msg, fg, bg)\n"
 327                     + "{\n"
 328                     + "  if(toolTip.arguments.length < 1) // hide\n"
 329                     + "  {\n"
 330                     + "    if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
 331                     + "    else toolTipSTYLE.display = \"none\";\n"
 332                     + "  }\n"
 333                     + "  else // show\n"
 334                     + "  {\n"
 335                     + "    if(!fg) fg = \"#555555\";\n"
 336                     + "    if(!bg) bg = \"#FFFFFF\";\n"
 337                     + "    var content =\n"
 338                     + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
 339                     + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
 340                     + "    '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
 341                     + "    '\" size=\"-2\">&nbsp;' + msg +\n"
 342                     + "    '&nbsp;</font></td></table></td></table>';\n"
 343                     + "    if(ns4)\n"
 344                     + "    {\n"
 345                     + "      toolTipSTYLE.document.write(content);\n"
 346                     + "      toolTipSTYLE.document.close();\n"
 347                     + "      toolTipSTYLE.visibility = \"visible\";\n"
 348                     + "    }\n"
 349                     + "    if(ns6)\n"
 350                     + "    {\n"
 351                     + "      document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
 352                     + "      toolTipSTYLE.display='block'\n"
 353                     + "    }\n"
 354                     + "    if(ie4)\n"
 355                     + "    {\n"
 356                     + "      document.all(\"toolTipLayer\").innerHTML=content;\n"
 357                     + "      toolTipSTYLE.display='block'\n"
 358                     + "    }\n"
 359                     + "  }\n"
 360                     + "}\n"
 361                     + "function moveToMouseLoc(e)\n"
 362                     + "{\n"
 363                     + "  if(ns4||ns6)\n"
 364                     + "  {\n"
 365                     + "    x = e.pageX;\n"
 366                     + "    y = e.pageY;\n"
 367                     + "  }\n"
 368                     + "  else\n"
 369                     + "  {\n"
 370                     + "    x = event.x + document.body.scrollLeft;\n"
 371                     + "    y = event.y + document.body.scrollTop;\n"
 372                     + "  }\n"
 373                     + "  toolTipSTYLE.left = x + offsetX;\n"
 374                     + "  toolTipSTYLE.top = y + offsetY;\n"
 375                     + "  return true;\n"
 376                     + "}\n"
 377                     + "</script>\n"
 378                     + "</head>\n"
 379                     + "<body>\n"
 380                     + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
 381                     + "<script language=\"JavaScript\"><!--\n"
 382                     + "initToolTips(); //--></script>\n");
 383
 384   }
 385 }