src/jalview/io/HTMLOutput.java

   1 package jalview.io;
   2
   3 import jalview.api.AlignExportSettingI;
   4 import jalview.bin.Cache;
   5 import jalview.datamodel.AlignmentExportData;
   6 import jalview.exceptions.NoFileSelectedException;
   7 import jalview.gui.AlignmentPanel;
   8 import jalview.gui.IProgressIndicator;
   9 import jalview.util.MessageManager;
  10
  11 import java.io.BufferedReader;
  12 import java.io.File;
  13 import java.io.IOException;
  14 import java.io.InputStreamReader;
  15 import java.net.URL;
  16 import java.util.Objects;
  17
  18 public abstract class HTMLOutput implements Runnable
  19 {
  20   protected AlignmentPanel ap;
  21
  22   protected long pSessionId;
  23
  24   protected IProgressIndicator pIndicator;
  25
  26   protected File generatedFile;
  27
  28   public HTMLOutput(AlignmentPanel ap)
  29   {
  30     if (ap != null)
  31     {
  32       this.ap = ap;
  33       this.pIndicator = ap.alignFrame;
  34     }
  35   }
  36
  37   public String getBioJSONData()
  38   {
  39     return getBioJSONData(null);
  40   }
  41
  42   public String getBioJSONData(AlignExportSettingI exportSettings)
  43   {
  44     if (!isEmbedData())
  45     {
  46       return null;
  47     }
  48     if (exportSettings == null)
  49     {
  50       exportSettings = new AlignExportSettingI()
  51       {
  52         @Override
  53         public boolean isExportHiddenSequences()
  54         {
  55           return true;
  56         }
  57
  58         @Override
  59         public boolean isExportHiddenColumns()
  60         {
  61           return true;
  62         }
  63
  64         @Override
  65         public boolean isExportAnnotations()
  66         {
  67           return true;
  68         }
  69
  70         @Override
  71         public boolean isExportFeatures()
  72         {
  73           return true;
  74         }
  75
  76         @Override
  77         public boolean isExportGroups()
  78         {
  79           return true;
  80         }
  81
  82         @Override
  83         public boolean isCancelled()
  84         {
  85           return false;
  86         }
  87       };
  88     }
  89     AlignmentExportData exportData = jalview.gui.AlignFrame
  90             .getAlignmentForExport(FileFormat.Json,
  91                     ap.getAlignViewport(), exportSettings);
  92     String bioJSON = new FormatAdapter(ap, exportData.getSettings())
  93             .formatSequences(FileFormat.Json, exportData.getAlignment(),
  94                     exportData.getOmitHidden(), exportData
  95                             .getStartEndPostions(), ap.getAlignViewport()
  96                             .getColumnSelection());
  97     return bioJSON;
  98   }
  99
 100   /**
 101    * Read a template file content as string
 102    *
 103    * @param file
 104    *          - the file to be read
 105    * @return File content as String
 106    * @throws IOException
 107    */
 108   public static String readFileAsString(File file) throws IOException
 109   {
 110     InputStreamReader isReader = null;
 111     BufferedReader buffReader = null;
 112     StringBuilder sb = new StringBuilder();
 113     Objects.requireNonNull(file, "File must not be null!");
 114     @SuppressWarnings("deprecation")
 115     URL url = file.toURL();
 116     if (url != null)
 117     {
 118       try
 119       {
 120         isReader = new InputStreamReader(url.openStream());
 121         buffReader = new BufferedReader(isReader);
 122         String line;
 123         String lineSeparator = System.getProperty("line.separator");
 124         while ((line = buffReader.readLine()) != null)
 125         {
 126           sb.append(line).append(lineSeparator);
 127         }
 128
 129       } catch (Exception ex)
 130       {
 131         ex.printStackTrace();
 132       } finally
 133       {
 134         if (isReader != null)
 135         {
 136           isReader.close();
 137         }
 138
 139         if (buffReader != null)
 140         {
 141           buffReader.close();
 142         }
 143       }
 144     }
 145     return sb.toString();
 146   }
 147
 148   public static String getImageMapHTML()
 149   {
 150     return new String(
 151             "<html>\n"
 152                     + "<head>\n"
 153                     + "<script language=\"JavaScript\">\n"
 154                     + "var ns4 = document.layers;\n"
 155                     + "var ns6 = document.getElementById && !document.all;\n"
 156                     + "var ie4 = document.all;\n"
 157                     + "offsetX = 0;\n"
 158                     + "offsetY = 20;\n"
 159                     + "var toolTipSTYLE=\"\";\n"
 160                     + "function initToolTips()\n"
 161                     + "{\n"
 162                     + "  if(ns4||ns6||ie4)\n"
 163                     + "  {\n"
 164                     + "    if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
 165                     + "    else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
 166                     + "    else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
 167                     + "    if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
 168                     + "    else\n"
 169                     + "    {\n"
 170                     + "      toolTipSTYLE.visibility = \"visible\";\n"
 171                     + "      toolTipSTYLE.display = \"none\";\n"
 172                     + "    }\n"
 173                     + "    document.onmousemove = moveToMouseLoc;\n"
 174                     + "  }\n"
 175                     + "}\n"
 176                     + "function toolTip(msg, fg, bg)\n"
 177                     + "{\n"
 178                     + "  if(toolTip.arguments.length < 1) // hide\n"
 179                     + "  {\n"
 180                     + "    if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
 181                     + "    else toolTipSTYLE.display = \"none\";\n"
 182                     + "  }\n"
 183                     + "  else // show\n"
 184                     + "  {\n"
 185                     + "    if(!fg) fg = \"#555555\";\n"
 186                     + "    if(!bg) bg = \"#FFFFFF\";\n"
 187                     + "    var content =\n"
 188                     + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
 189                     + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
 190                     + "    '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
 191                     + "    '\" size=\"-2\">&nbsp;' + msg +\n"
 192                     + "    '&nbsp;</font></td></table></td></table>';\n"
 193                     + "    if(ns4)\n"
 194                     + "    {\n"
 195                     + "      toolTipSTYLE.document.write(content);\n"
 196                     + "      toolTipSTYLE.document.close();\n"
 197                     + "      toolTipSTYLE.visibility = \"visible\";\n"
 198                     + "    }\n"
 199                     + "    if(ns6)\n"
 200                     + "    {\n"
 201                     + "      document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
 202                     + "      toolTipSTYLE.display='block'\n"
 203                     + "    }\n"
 204                     + "    if(ie4)\n"
 205                     + "    {\n"
 206                     + "      document.all(\"toolTipLayer\").innerHTML=content;\n"
 207                     + "      toolTipSTYLE.display='block'\n"
 208                     + "    }\n"
 209                     + "  }\n"
 210                     + "}\n"
 211                     + "function moveToMouseLoc(e)\n"
 212                     + "{\n"
 213                     + "  if(ns4||ns6)\n"
 214                     + "  {\n"
 215                     + "    x = e.pageX;\n"
 216                     + "    y = e.pageY;\n"
 217                     + "  }\n"
 218                     + "  else\n"
 219                     + "  {\n"
 220                     + "    x = event.x + document.body.scrollLeft;\n"
 221                     + "    y = event.y + document.body.scrollTop;\n"
 222                     + "  }\n"
 223                     + "  toolTipSTYLE.left = x + offsetX;\n"
 224                     + "  toolTipSTYLE.top = y + offsetY;\n"
 225                     + "  return true;\n"
 226                     + "}\n"
 227                     + "</script>\n"
 228                     + "</head>\n"
 229                     + "<body>\n"
 230                     + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
 231                     + "<script language=\"JavaScript\"><!--\n"
 232                     + "initToolTips(); //--></script>\n");
 233
 234   }
 235
 236   public String getOutputFile() throws NoFileSelectedException
 237   {
 238     String selectedFile = null;
 239     if (pIndicator != null && !isHeadless())
 240     {
 241       pIndicator.setProgressBar(MessageManager.formatMessage(
 242               "status.waiting_for_user_to_select_output_file", "HTML"),
 243               pSessionId);
 244     }
 245
 246     JalviewFileChooser jvFileChooser = new JalviewFileChooser(
 247             Cache.getProperty("LAST_DIRECTORY"), "html", "HTML files");
 248     jvFileChooser.setFileView(new JalviewFileView());
 249
 250     jvFileChooser.setDialogTitle(MessageManager
 251             .getString("label.save_as_html"));
 252     jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
 253
 254     int fileChooserOpt = jvFileChooser.showSaveDialog(null);
 255     if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
 256     {
 257       jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
 258               .getSelectedFile().getParent());
 259       selectedFile = jvFileChooser.getSelectedFile().getPath();
 260     }
 261     else
 262     {
 263       throw new NoFileSelectedException("No file was selected.");
 264     }
 265     return selectedFile;
 266   }
 267
 268   protected void setProgressMessage(String message)
 269   {
 270     if (pIndicator != null && !isHeadless())
 271     {
 272       pIndicator.setProgressBar(message, pSessionId);
 273     }
 274     else
 275     {
 276       System.out.println(message);
 277     }
 278   }
 279
 280   /**
 281    * Answers true if HTML export is invoke in headless mode or false otherwise
 282    *
 283    * @return
 284    */
 285   protected boolean isHeadless()
 286   {
 287     return System.getProperty("java.awt.headless") != null
 288             && System.getProperty("java.awt.headless").equals("true");
 289   }
 290
 291   /**
 292    * This method provides implementation of consistent behaviour which should
 293    * occur before a HTML file export. It MUST be called at the start of the
 294    * exportHTML() method implementation.
 295    */
 296   protected void exportStarted()
 297   {
 298     pSessionId = System.currentTimeMillis();
 299   }
 300
 301   /**
 302    * This method provides implementation of consistent behaviour which should
 303    * occur after a HTML file export. It MUST be called at the end of the
 304    * exportHTML() method implementation.
 305    */
 306   protected void exportCompleted()
 307   {
 308     if (isLaunchInBrowserAfterExport() && !isHeadless())
 309     {
 310       try
 311       {
 312         jalview.util.BrowserLauncher
 313                 .openURL("file:///" + getExportedFile());
 314       } catch (IOException e)
 315       {
 316         e.printStackTrace();
 317       }
 318     }
 319   }
 320
 321   /**
 322    * if this answers true then BioJSON data will be embedded to the exported
 323    * HTML file otherwise it won't be embedded.
 324    *
 325    * @return
 326    */
 327   public abstract boolean isEmbedData();
 328
 329   /**
 330    * if this answers true then the generated HTML file is opened for viewing in
 331    * a browser after its generation otherwise it won't be opened in a browser
 332    *
 333    * @return
 334    */
 335   public abstract boolean isLaunchInBrowserAfterExport();
 336
 337   /**
 338    * handle to the generated HTML file
 339    *
 340    * @return
 341    */
 342   public abstract File getExportedFile();
 343
 344   /**
 345    * This is the main method to handle the HTML generation.
 346    *
 347    * @param outputFile
 348    *          the file path of the generated HTML
 349    */
 350   public abstract void exportHTML(String outputFile);
 351 }