src/jalview/io/HTMLOutput.java

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