src/jalview/io/HTMLOutput.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
   3  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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(
  47             jalview.bin.Cache.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.println("<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
 113
 114     // ////////////
 115     SequenceI seq;
 116     AlignmentI alignment = av.getAlignment();
 117
 118     // draws the top row, the measure rule
 119     out.println("<tr><td colspan=\"6\"></td>");
 120
 121     int i = 0;
 122
 123     for (i = 10; i < (alignment.getWidth() - 10); i += 10)
 124     {
 125       out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
 126     }
 127
 128     out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i
 129             + "<br>|</td>");
 130     out.println("</tr>");
 131
 132     for (i = 0; i < alignment.getHeight(); i++)
 133     {
 134       seq = alignment.getSequenceAt(i);
 135
 136       String id = seq.getDisplayId(av.getShowJVSuffix());
 137
 138       out.println("<tr><td nowrap>" + id + "&nbsp;&nbsp;</td>");
 139
 140       for (int res = 0; res < seq.getLength(); res++)
 141       {
 142         if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
 143         {
 144           color = sr.getResidueBoxColour(seq, res);
 145
 146           color = fr.findFeatureColour(color, seq, res);
 147         }
 148         else
 149         {
 150           color = Color.white;
 151         }
 152
 153         if (color.getRGB() < -1)
 154         {
 155           out.println("<td bgcolor=\"#"
 156                   + jalview.util.Format.getHexString(color) + "\">"
 157                   + seq.getCharAt(res) + "</td>");
 158         }
 159         else
 160         {
 161           out.println("<td>" + seq.getCharAt(res) + "</td>");
 162         }
 163       }
 164
 165       out.println("</tr>");
 166     }
 167
 168     // ////////////
 169     out.println("</table>");
 170     out.println("</td></tr></table>");
 171   }
 172
 173   void drawWrappedAlignment(PrintWriter out)
 174   {
 175     // //////////////////////////////////
 176     // / How many sequences and residues can we fit on a printable page?
 177     AlignmentI al = av.getAlignment();
 178     SequenceI seq;
 179     String r;
 180     String g;
 181     String b;
 182
 183     out.println("<table border=\"1\"><tr><td>\n");
 184     out.println("<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
 185
 186     for (int startRes = 0; startRes < al.getWidth(); startRes += av
 187             .getWrappedWidth())
 188     {
 189       int endRes = startRes + av.getWrappedWidth();
 190
 191       if (endRes > al.getWidth())
 192       {
 193         endRes = al.getWidth();
 194       }
 195
 196       if (av.getScaleAboveWrapped())
 197       {
 198         out.println("<tr>");
 199
 200         if (av.getScaleLeftWrapped())
 201         {
 202           out.println("<td colspan=\"7\">&nbsp;</td>");
 203         }
 204         else
 205         {
 206           out.println("<td colspan=\"6\">&nbsp;</td>");
 207         }
 208
 209         for (int i = startRes + 10; i < endRes; i += 10)
 210         {
 211           out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
 212         }
 213
 214         out.println("</tr>");
 215       }
 216
 217       int startPos, endPos;
 218       for (int s = 0; s < al.getHeight(); s++)
 219       {
 220         out.println("<tr>");
 221         seq = al.getSequenceAt(s);
 222
 223         startPos = seq.findPosition(startRes);
 224         endPos = seq.findPosition(endRes) - 1;
 225
 226         String id = seq.getDisplayId(av.getShowJVSuffix());
 227
 228         out.println("<td nowrap>" + id + "&nbsp;&nbsp;</td>");
 229
 230         if (av.getScaleLeftWrapped())
 231         {
 232           if (startPos > seq.getEnd() || endPos == 0)
 233           {
 234             out.println("<td nowrap>&nbsp;</td>");
 235           }
 236           else
 237           {
 238             out.println("<td nowrap>" + startPos + "&nbsp;&nbsp;</td>");
 239           }
 240         }
 241
 242         for (int res = startRes; res < endRes; res++)
 243         {
 244           if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
 245           {
 246             color = sr.getResidueBoxColour(seq, res);
 247
 248             color = fr.findFeatureColour(color, seq, res);
 249           }
 250           else
 251           {
 252             color = Color.white;
 253           }
 254
 255           if (color.getRGB() < -1)
 256           {
 257             out.println("<td bgcolor=\"#"
 258                     + jalview.util.Format.getHexString(color) + "\">"
 259                     + seq.getCharAt(res) + "</td>");
 260           }
 261           else
 262           {
 263             out.println("<td>" + seq.getCharAt(res) + "</td>");
 264           }
 265
 266         }
 267
 268         if (av.getScaleRightWrapped()
 269                 && endRes < startRes + av.getWrappedWidth())
 270         {
 271           out.println("<td colspan=\""
 272                   + (startRes + av.getWrappedWidth() - endRes) + "\">"
 273                   + "&nbsp;&nbsp;</td>");
 274         }
 275
 276         if (av.getScaleRightWrapped() && startPos < endPos)
 277         {
 278           out.println("<td nowrap>&nbsp;" + endPos + "&nbsp;&nbsp;</td>");
 279         }
 280
 281         out.println("</tr>");
 282       }
 283
 284       if (endRes < al.getWidth())
 285       {
 286         out.println("<tr><td height=\"5\"></td></tr>");
 287       }
 288     }
 289
 290     out.println("</table>");
 291     out.println("</table>");
 292   }
 293
 294   public static String getImageMapHTML()
 295   {
 296     return new String(
 297             "<html>\n"
 298                     + "<head>\n"
 299                     + "<script language=\"JavaScript\">\n"
 300                     + "var ns4 = document.layers;\n"
 301                     + "var ns6 = document.getElementById && !document.all;\n"
 302                     + "var ie4 = document.all;\n"
 303                     + "offsetX = 0;\n"
 304                     + "offsetY = 20;\n"
 305                     + "var toolTipSTYLE=\"\";\n"
 306                     + "function initToolTips()\n"
 307                     + "{\n"
 308                     + "  if(ns4||ns6||ie4)\n"
 309                     + "  {\n"
 310                     + "    if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
 311                     + "    else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
 312                     + "    else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
 313                     + "    if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
 314                     + "    else\n"
 315                     + "    {\n"
 316                     + "      toolTipSTYLE.visibility = \"visible\";\n"
 317                     + "      toolTipSTYLE.display = \"none\";\n"
 318                     + "    }\n"
 319                     + "    document.onmousemove = moveToMouseLoc;\n"
 320                     + "  }\n"
 321                     + "}\n"
 322                     + "function toolTip(msg, fg, bg)\n"
 323                     + "{\n"
 324                     + "  if(toolTip.arguments.length < 1) // hide\n"
 325                     + "  {\n"
 326                     + "    if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
 327                     + "    else toolTipSTYLE.display = \"none\";\n"
 328                     + "  }\n"
 329                     + "  else // show\n"
 330                     + "  {\n"
 331                     + "    if(!fg) fg = \"#555555\";\n"
 332                     + "    if(!bg) bg = \"#FFFFFF\";\n"
 333                     + "    var content =\n"
 334                     + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
 335                     + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
 336                     + "    '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
 337                     + "    '\" size=\"-2\">&nbsp;' + msg +\n"
 338                     + "    '&nbsp;</font></td></table></td></table>';\n"
 339                     + "    if(ns4)\n"
 340                     + "    {\n"
 341                     + "      toolTipSTYLE.document.write(content);\n"
 342                     + "      toolTipSTYLE.document.close();\n"
 343                     + "      toolTipSTYLE.visibility = \"visible\";\n"
 344                     + "    }\n"
 345                     + "    if(ns6)\n"
 346                     + "    {\n"
 347                     + "      document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
 348                     + "      toolTipSTYLE.display='block'\n"
 349                     + "    }\n"
 350                     + "    if(ie4)\n"
 351                     + "    {\n"
 352                     + "      document.all(\"toolTipLayer\").innerHTML=content;\n"
 353                     + "      toolTipSTYLE.display='block'\n"
 354                     + "    }\n"
 355                     + "  }\n"
 356                     + "}\n"
 357                     + "function moveToMouseLoc(e)\n"
 358                     + "{\n"
 359                     + "  if(ns4||ns6)\n"
 360                     + "  {\n"
 361                     + "    x = e.pageX;\n"
 362                     + "    y = e.pageY;\n"
 363                     + "  }\n"
 364                     + "  else\n"
 365                     + "  {\n"
 366                     + "    x = event.x + document.body.scrollLeft;\n"
 367                     + "    y = event.y + document.body.scrollTop;\n"
 368                     + "  }\n"
 369                     + "  toolTipSTYLE.left = x + offsetX;\n"
 370                     + "  toolTipSTYLE.top = y + offsetY;\n"
 371                     + "  return true;\n"
 372                     + "}\n"
 373                     + "</script>\n"
 374                     + "</head>\n"
 375                     + "<body>\n"
 376                     + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
 377                     + "<script language=\"JavaScript\"><!--\n"
 378                     + "initToolTips(); //--></script>\n");
 379
 380   }
 381 }