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.api.AlignExportSettingI;
  24 import jalview.datamodel.AlignmentExportData;
  25 import jalview.exceptions.NoFileSelectedException;
  26 import jalview.gui.AlignmentPanel;
  27 import jalview.gui.IProgressIndicator;
  28 import jalview.util.MessageManager;
  29
  30 import java.io.BufferedReader;
  31 import java.io.File;
  32 import java.io.IOException;
  33 import java.io.InputStreamReader;
  34 import java.net.URL;
  35 import java.util.Objects;
  36
  37
  38 public abstract class HTMLOutput
  39 {
  40   protected AlignmentPanel ap;
  41
  42   protected long pSessionId;
  43
  44   protected IProgressIndicator pIndicator;
  45
  46   private boolean headless;
  47
  48   protected File generatedFile;
  49
  50   public HTMLOutput(AlignmentPanel ap)
  51   {
  52     if (ap != null)
  53     {
  54       this.ap = ap;
  55       this.pIndicator = ap.alignFrame;
  56     }
  57   }
  58
  59
  60   public String getBioJSONData()
  61   {
  62     if (!isEmbedData())
  63     {
  64       return null;
  65     }
  66     AlignExportSettingI exportSettings = new AlignExportSettingI()
  67     {
  68       @Override
  69       public boolean isExportHiddenSequences()
  70       {
  71         return true;
  72       }
  73
  74       @Override
  75       public boolean isExportHiddenColumns()
  76       {
  77         return true;
  78       }
  79
  80       @Override
  81       public boolean isExportAnnotations()
  82       {
  83         return true;
  84       }
  85
  86       @Override
  87       public boolean isExportFeatures()
  88       {
  89         return true;
  90       }
  91
  92       @Override
  93       public boolean isExportGroups()
  94       {
  95         return true;
  96       }
  97
  98       @Override
  99       public boolean isCancelled()
 100       {
 101         return false;
 102       }
 103
 104     };
 105     AlignmentExportData exportData = jalview.gui.AlignFrame
 106             .getAlignmentForExport(JSONFile.FILE_DESC,
 107                     ap.getAlignViewport(), exportSettings);
 108     String bioJSON = new FormatAdapter(ap, exportData.getSettings())
 109             .formatSequences(JSONFile.FILE_DESC, exportData.getAlignment(),
 110                     exportData.getOmitHidden(), exportData
 111                             .getStartEndPostions(), ap.getAlignViewport()
 112                             .getColumnSelection());
 113     return bioJSON;
 114   }
 115
 116   /**
 117    * Read a template file content as string
 118    *
 119    * @param file
 120    *          - the file to be read
 121    * @return File content as String
 122    * @throws IOException
 123    */
 124   public static String readFileAsString(File file) throws IOException
 125   {
 126     InputStreamReader isReader = null;
 127     BufferedReader buffReader = null;
 128     StringBuilder sb = new StringBuilder();
 129     Objects.requireNonNull(file, "File must not be null!");
 130     @SuppressWarnings("deprecation")
 131     URL url = file.toURL();
 132     if (url != null)
 133     {
 134       try
 135       {
 136         isReader = new InputStreamReader(url.openStream());
 137         buffReader = new BufferedReader(isReader);
 138         String line;
 139         String lineSeparator = System.getProperty("line.separator");
 140         while ((line = buffReader.readLine()) != null)
 141         {
 142           sb.append(line).append(lineSeparator);
 143         }
 144
 145       } catch (Exception ex)
 146       {
 147         ex.printStackTrace();
 148       } finally
 149       {
 150         if (isReader != null)
 151         {
 152           isReader.close();
 153         }
 154
 155         if (buffReader != null)
 156         {
 157           buffReader.close();
 158         }
 159       }
 160     }
 161     return sb.toString();
 162   }
 163
 164   public static String getImageMapHTML()
 165   {
 166     return new String(
 167             "<html>\n"
 168                     + "<head>\n"
 169                     + "<script language=\"JavaScript\">\n"
 170                     + "var ns4 = document.layers;\n"
 171                     + "var ns6 = document.getElementById && !document.all;\n"
 172                     + "var ie4 = document.all;\n"
 173                     + "offsetX = 0;\n"
 174                     + "offsetY = 20;\n"
 175                     + "var toolTipSTYLE=\"\";\n"
 176                     + "function initToolTips()\n"
 177                     + "{\n"
 178                     + "  if(ns4||ns6||ie4)\n"
 179                     + "  {\n"
 180                     + "    if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
 181                     + "    else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
 182                     + "    else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
 183                     + "    if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
 184                     + "    else\n"
 185                     + "    {\n"
 186                     + "      toolTipSTYLE.visibility = \"visible\";\n"
 187                     + "      toolTipSTYLE.display = \"none\";\n"
 188                     + "    }\n"
 189                     + "    document.onmousemove = moveToMouseLoc;\n"
 190                     + "  }\n"
 191                     + "}\n"
 192                     + "function toolTip(msg, fg, bg)\n"
 193                     + "{\n"
 194                     + "  if(toolTip.arguments.length < 1) // hide\n"
 195                     + "  {\n"
 196                     + "    if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
 197                     + "    else toolTipSTYLE.display = \"none\";\n"
 198                     + "  }\n"
 199                     + "  else // show\n"
 200                     + "  {\n"
 201                     + "    if(!fg) fg = \"#555555\";\n"
 202                     + "    if(!bg) bg = \"#FFFFFF\";\n"
 203                     + "    var content =\n"
 204                     + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
 205                     + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
 206                     + "    '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
 207                     + "    '\" size=\"-2\">&nbsp;' + msg +\n"
 208                     + "    '&nbsp;</font></td></table></td></table>';\n"
 209                     + "    if(ns4)\n"
 210                     + "    {\n"
 211                     + "      toolTipSTYLE.document.write(content);\n"
 212                     + "      toolTipSTYLE.document.close();\n"
 213                     + "      toolTipSTYLE.visibility = \"visible\";\n"
 214                     + "    }\n"
 215                     + "    if(ns6)\n"
 216                     + "    {\n"
 217                     + "      document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
 218                     + "      toolTipSTYLE.display='block'\n"
 219                     + "    }\n"
 220                     + "    if(ie4)\n"
 221                     + "    {\n"
 222                     + "      document.all(\"toolTipLayer\").innerHTML=content;\n"
 223                     + "      toolTipSTYLE.display='block'\n"
 224                     + "    }\n"
 225                     + "  }\n"
 226                     + "}\n"
 227                     + "function moveToMouseLoc(e)\n"
 228                     + "{\n"
 229                     + "  if(ns4||ns6)\n"
 230                     + "  {\n"
 231                     + "    x = e.pageX;\n"
 232                     + "    y = e.pageY;\n"
 233                     + "  }\n"
 234                     + "  else\n"
 235                     + "  {\n"
 236                     + "    x = event.x + document.body.scrollLeft;\n"
 237                     + "    y = event.y + document.body.scrollTop;\n"
 238                     + "  }\n"
 239                     + "  toolTipSTYLE.left = x + offsetX;\n"
 240                     + "  toolTipSTYLE.top = y + offsetY;\n"
 241                     + "  return true;\n"
 242                     + "}\n"
 243                     + "</script>\n"
 244                     + "</head>\n"
 245                     + "<body>\n"
 246                     + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
 247                     + "<script language=\"JavaScript\"><!--\n"
 248                     + "initToolTips(); //--></script>\n");
 249
 250   }
 251
 252   public String getOutputFile() throws NoFileSelectedException
 253   {
 254     String selectedFile = null;
 255     if (pIndicator != null && !headless)
 256     {
 257       pIndicator.setProgressBar(MessageManager.formatMessage(
 258               "status.waiting_for_user_to_select_output_file", "HTML"),
 259               pSessionId);
 260     }
 261
 262     JalviewFileChooser jvFileChooser = new JalviewFileChooser(
 263             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
 264             new String[] { "html" }, new String[] { "HTML files" },
 265             "HTML files");
 266     jvFileChooser.setFileView(new JalviewFileView());
 267
 268     jvFileChooser.setDialogTitle(MessageManager
 269             .getString("label.save_as_biojs_html"));
 270     jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
 271
 272     int fileChooserOpt = jvFileChooser.showSaveDialog(null);
 273     if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
 274     {
 275       jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
 276               .getSelectedFile().getParent());
 277       selectedFile = jvFileChooser.getSelectedFile().getPath();
 278     }
 279     else
 280     {
 281       pIndicator.setProgressBar(MessageManager.formatMessage(
 282               "status.cancelled_image_export_operation", "BioJS"),
 283               pSessionId);
 284       throw new NoFileSelectedException("No file was selected.");
 285     }
 286     return selectedFile;
 287   }
 288
 289   protected void setProgressMessage(String message)
 290   {
 291     if (pIndicator != null && !headless)
 292     {
 293       pIndicator.setProgressBar(message, pSessionId);
 294     }
 295     else
 296     {
 297       System.out.println(message);
 298     }
 299   }
 300
 301   /**
 302    * Answers true if HTML export is invoke in headless mode or false otherwise
 303    *
 304    * @return
 305    */
 306   protected boolean isHeadless()
 307   {
 308     return System.getProperty("java.awt.headless") != null
 309             && System.getProperty("java.awt.headless").equals("true");
 310   }
 311
 312   /**
 313    * This method provides implementation of consistent behaviour which should
 314    * occur before a HTML file export. It MUST be called at the start of the
 315    * exportHTML() method implementation.
 316    */
 317   protected void exportStarted()
 318   {
 319     pSessionId = System.currentTimeMillis();
 320   }
 321
 322   /**
 323    * This method provides implementation of consistent behaviour which should
 324    * occur after a HTML file export. It MUST be called at the end of the
 325    * exportHTML() method implementation.
 326    */
 327   protected void exportCompleted()
 328   {
 329     if (isLaunchInBrowserAfterExport() && !isHeadless())
 330     {
 331       try
 332       {
 333         jalview.util.BrowserLauncher
 334                 .openURL("file:///" + getExportedFile());
 335       } catch (IOException e)
 336       {
 337         e.printStackTrace();
 338       }
 339     }
 340   }
 341
 342   /**
 343    * if this answers true then BioJSON data will be embedded to the exported
 344    * HTML file otherwise it won't be embedded.
 345    *
 346    * @return
 347    */
 348   public abstract boolean isEmbedData();
 349
 350   /**
 351    * if this answers true then the generated HTML file is opened for viewing in
 352    * a browser after its generation otherwise it won't be opened in a browser
 353    *
 354    * @return
 355    */
 356   public abstract boolean isLaunchInBrowserAfterExport();
 357
 358   /**
 359    * handle to the generated HTML file
 360    *
 361    * @return
 362    */
 363   public abstract File getExportedFile();
 364
 365   /**
 366    * This is the main method to handle the HTML generation.
 367    *
 368    * @param outputFile
 369    *          the file path of the generated HTML
 370    */
 371   public abstract void exportHTML(String outputFile);
 372 }