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