src/jalview/io/HtmlSvgOutput.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.api.FeatureRenderer;
  25 import jalview.datamodel.AlignmentExportData;
  26 import jalview.gui.AlignViewport;
  27 import jalview.gui.AlignmentPanel;
  28 import jalview.gui.HTMLOptions;
  29 import jalview.gui.IProgressIndicator;
  30 import jalview.gui.OOMWarning;
  31 import jalview.math.AlignmentDimension;
  32 import jalview.util.MessageManager;
  33
  34 import java.awt.Graphics;
  35 import java.awt.print.PrinterException;
  36 import java.io.File;
  37 import java.io.FileOutputStream;
  38 import java.io.IOException;
  39
  40 import org.jfree.graphics2d.svg.SVGGraphics2D;
  41 import org.jfree.graphics2d.svg.SVGHints;
  42
  43 public class HtmlSvgOutput
  44 {
  45   AlignViewport av;
  46
  47   FeatureRenderer fr;
  48
  49   AlignmentPanel ap;
  50
  51   private IProgressIndicator pIndicator;
  52
  53   private long pSessionId;
  54
  55   private boolean headless;
  56
  57   public HtmlSvgOutput(AlignmentPanel ap)
  58   {
  59     this.av = ap.av;
  60     this.ap = ap;
  61     fr = ap.cloneFeatureRenderer();
  62   }
  63
  64   public void generateHtmlSvgOutput(File file)
  65   {
  66     pIndicator = ap.alignFrame;
  67     pSessionId = System.currentTimeMillis();
  68     try
  69     {
  70       headless = (System.getProperty("java.awt.headless") != null && System
  71               .getProperty("java.awt.headless").equals("true"));
  72       if (file == null)
  73       {
  74         setProgressMessage(MessageManager.formatMessage(
  75                 "status.waiting_for_user_to_select_output_file", "HTML"));
  76         JalviewFileChooser chooser = getHTMLChooser();
  77         chooser.setFileView(new jalview.io.JalviewFileView());
  78         chooser.setDialogTitle(ap.alignFrame.getTitle());
  79         chooser.setToolTipText(MessageManager.getString("action.save"));
  80         int value = chooser.showSaveDialog(ap.alignFrame);
  81
  82         if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
  83         {
  84           jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
  85                   .getSelectedFile().getParent());
  86           file = chooser.getSelectedFile();
  87           ap.alignFrame.repaint();
  88         }
  89         else
  90         {
  91           setProgressMessage(MessageManager.formatMessage(
  92                   "status.cancelled_image_export_operation", "HTML"));
  93           return;
  94         }
  95       }
  96     } catch (Exception e)
  97     {
  98       pIndicator.setProgressBar(MessageManager.formatMessage(
  99               "info.error_creating_file", "HTML"), pSessionId);
 100       e.printStackTrace();
 101       return;
 102     }
 103     final File fileX = file;
 104     new Thread()
 105     {
 106       @Override
 107       public void run()
 108       {
 109         try
 110         {
 111           setProgressMessage(null);
 112           setProgressMessage(MessageManager.formatMessage(
 113                   "status.exporting_alignment_as_x_file", "HTML"));
 114           AlignmentDimension aDimension = ap.getAlignmentDimension();
 115           SVGGraphics2D idPanelGraphics = new SVGGraphics2D(
 116                   aDimension.getWidth(),
 117                   aDimension.getHeight());
 118           SVGGraphics2D alignPanelGraphics = new SVGGraphics2D(
 119                   aDimension.getWidth(),
 120                   aDimension.getHeight());
 121
 122           String renderStyle = jalview.bin.Cache.getDefault(
 123                   "HTML_RENDERING", "Prompt each time");
 124
 125           // If we need to prompt, and if the GUI is visible then
 126           // Prompt for rendering style
 127           if (renderStyle.equalsIgnoreCase("Prompt each time")
 128                   && !(System.getProperty("java.awt.headless") != null && System
 129                           .getProperty("java.awt.headless").equals("true")))
 130           {
 131             HTMLOptions svgOption = new HTMLOptions();
 132             renderStyle = svgOption.getValue();
 133
 134             if (renderStyle == null || svgOption.cancelled)
 135             {
 136               setProgressMessage(MessageManager.formatMessage(
 137                       "status.cancelled_image_export_operation", "HTML"));
 138               return;
 139             }
 140           }
 141
 142           if (renderStyle.equalsIgnoreCase("Lineart"))
 143           {
 144             idPanelGraphics.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
 145                     SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
 146             alignPanelGraphics.setRenderingHint(
 147                     SVGHints.KEY_DRAW_STRING_TYPE,
 148                     SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
 149           }
 150           if (av.getWrapAlignment())
 151           {
 152             printWrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
 153                     alignPanelGraphics);
 154           }
 155           else
 156           {
 157           printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
 158  idPanelGraphics, alignPanelGraphics);
 159           }
 160
 161           String idPanelSvgData = idPanelGraphics.getSVGDocument();
 162           String alignPanelSvgData = alignPanelGraphics.getSVGDocument();
 163           String jsonData = null;
 164           boolean isEmbbedBioJSON = Boolean.valueOf(jalview.bin.Cache
 165                   .getDefault("EXPORT_EMBBED_BIOJSON", "true"));
 166           if (isEmbbedBioJSON)
 167           {
 168             AlignExportSettingI exportSettings = new AlignExportSettingI()
 169             {
 170               @Override
 171               public boolean isExportHiddenSequences()
 172               {
 173                 return true;
 174               }
 175
 176               @Override
 177               public boolean isExportHiddenColumns()
 178               {
 179                 return true;
 180               }
 181
 182               @Override
 183               public boolean isExportAnnotations()
 184               {
 185                 return true;
 186               }
 187
 188               @Override
 189               public boolean isExportFeatures()
 190               {
 191                 return true;
 192               }
 193
 194               @Override
 195               public boolean isExportGroups()
 196               {
 197                 return true;
 198               }
 199
 200               @Override
 201               public boolean isCancelled()
 202               {
 203                 return false;
 204               }
 205
 206             };
 207             AlignmentExportData exportData = jalview.gui.AlignFrame
 208                     .getAlignmentForExport(JSONFile.FILE_DESC, av,
 209                             exportSettings);
 210             jsonData = new FormatAdapter(ap, exportData.getSettings())
 211                     .formatSequences(JSONFile.FILE_DESC,
 212                             exportData.getAlignment(),
 213                             exportData.getOmitHidden(),
 214                             exportData.getStartEndPostions(),
 215                             av.getColumnSelection());
 216           }
 217           String htmlData = getHtml(idPanelSvgData, alignPanelSvgData, jsonData,
 218                   av.getWrapAlignment());
 219           FileOutputStream out = new FileOutputStream(fileX);
 220           out.write(htmlData.getBytes());
 221           out.flush();
 222           out.close();
 223           if (!(System.getProperty("java.awt.headless") != null && System
 224                   .getProperty("java.awt.headless").equals("true")))
 225           {
 226             jalview.util.BrowserLauncher.openURL("file:///" + fileX);
 227           }
 228         } catch (OutOfMemoryError err)
 229         {
 230           System.out.println("########################\n"
 231                   + "OUT OF MEMORY " + fileX + "\n"
 232                   + "########################");
 233           new OOMWarning("Creating Image for " + fileX, err);
 234         } catch (Exception e)
 235         {
 236           e.printStackTrace();
 237           pIndicator.setProgressBar(MessageManager.formatMessage(
 238                   "info.error_creating_file", "HTML"), pSessionId);
 239         }
 240         setProgressMessage(MessageManager.formatMessage(
 241                 "status.export_complete", "HTML"));
 242       }
 243     }.start();
 244
 245   }
 246
 247   private void setProgressMessage(String message)
 248   {
 249     if (pIndicator != null && !headless)
 250     {
 251       pIndicator.setProgressBar(message, pSessionId);
 252     }
 253     else
 254     {
 255       System.out.println(message);
 256     }
 257   }
 258
 259   static JalviewFileChooser getHTMLChooser()
 260   {
 261     return new jalview.io.JalviewFileChooser(
 262             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
 263             new String[] { "html" },
 264             new String[] { "Hypertext Markup Language" },
 265             "Hypertext Markup Language");
 266   }
 267
 268   public int printUnwrapped(int pwidth, int pheight, int pi, Graphics... pg)
 269           throws PrinterException
 270   {
 271     return ap.printUnwrapped(pwidth, pheight, pi, pg);
 272   }
 273
 274   public int printWrapped(int pwidth, int pheight, int pi, Graphics... pg)
 275           throws PrinterException
 276   {
 277     return ap.printWrappedAlignment(pwidth, pheight, pi, pg[0]);
 278   }
 279
 280   private String getHtml(String titleSvg, String alignmentSvg,
 281           String jsonData, boolean wrapped)
 282   {
 283     StringBuilder htmlSvg = new StringBuilder();
 284     htmlSvg.append("<html>\n");
 285     if (jsonData != null)
 286     {
 287       htmlSvg.append("<button onclick=\"javascipt:openJalviewUsingCurrentUrl();\">Launch in Jalview</button> &nbsp;");
 288       htmlSvg.append("<input type=\"submit\" value=\"View raw BioJSON Data\" onclick=\"jQuery.facebox({ div:'#seqData' }); return false;\" />");
 289       htmlSvg.append("<div style=\"display: none;\" name=\"seqData\" id=\"seqData\" >"
 290               + jsonData + "</div>");
 291       htmlSvg.append("<br/>&nbsp;");
 292     }
 293     htmlSvg.append("\n<style type=\"text/css\"> "
 294             + "div.parent{ width:100%;<!-- overflow: auto; -->}\n"
 295             + "div.titlex{ width:11%; float: left; }\n"
 296             + "div.align{ width:89%; float: right; }\n"
 297             + "div.main-container{ border: 2px solid blue; border: 2px solid blue; width: 99%;   min-height: 99%; }\n"
 298             + ".sub-category-container {overflow-y: scroll; overflow-x: hidden; width: 100%; height: 100%;}\n"
 299             + "object {pointer-events: none;}");
 300     if (jsonData != null)
 301     {
 302       // facebox style sheet for displaying raw BioJSON data
 303       htmlSvg.append("#facebox { position: absolute;  top: 0;   left: 0; z-index: 100; text-align: left; }\n"
 304               + "#facebox .popup{ position:relative; border:3px solid rgba(0,0,0,0); -webkit-border-radius:5px;"
 305               + "-moz-border-radius:5px; border-radius:5px; -webkit-box-shadow:0 0 18px rgba(0,0,0,0.4); -moz-box-shadow:0 0 18px rgba(0,0,0,0.4);"
 306               + "box-shadow:0 0 18px rgba(0,0,0,0.4); }\n"
 307               + "#facebox .content { display:table; width: 98%; padding: 10px; background: #fff; -webkit-border-radius:4px; -moz-border-radius:4px;"
 308               + " border-radius:4px; }\n"
 309               + "#facebox .content > p:first-child{ margin-top:0; }\n"
 310               + "#facebox .content > p:last-child{ margin-bottom:0; }\n"
 311               + "#facebox .close{ position:absolute; top:5px; right:5px; padding:2px; background:#fff; }\n"
 312               + "#facebox .close img{ opacity:0.3; }\n"
 313               + "#facebox .close:hover img{ opacity:1.0; }\n"
 314               + "#facebox .loading { text-align: center; }\n"
 315               + "#facebox .image { text-align: center;}\n"
 316               + "#facebox img { border: 0;  margin: 0; }\n"
 317               + "#facebox_overlay { position: fixed; top: 0px; left: 0px; height:100%; width:100%; }\n"
 318               + ".facebox_hide { z-index:-100; }\n"
 319               + ".facebox_overlayBG { background-color: #000;  z-index: 99;  }");
 320     }
 321     htmlSvg.append("</style>");
 322     if (!wrapped)
 323     {
 324     htmlSvg.append("<div class=\"main-container\" \n>");
 325     htmlSvg.append("<div class=\"titlex\">\n");
 326     htmlSvg.append("<div class=\"sub-category-container\"> \n");
 327     htmlSvg.append(titleSvg);
 328     htmlSvg.append("</div>");
 329     htmlSvg.append("</div>\n\n<!-- ========================================================================================== -->\n\n");
 330     htmlSvg.append("<div class=\"align\" >");
 331     htmlSvg.append(
 332             "<div class=\"sub-category-container\"> <div style=\"overflow-x: scroll;\">")
 333             .append(alignmentSvg).append("</div></div>").append("</div>");
 334     htmlSvg.append("</div>");
 335
 336     htmlSvg.append("<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
 337             + "<script language=\"JavaScript\" type=\"text/javascript\"  src=\"http://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n"
 338             + "<script>\n"
 339             + "var subCatContainer = $(\".sub-category-container\");\n"
 340             + "subCatContainer.scroll(\nfunction() {\n"
 341             + "subCatContainer.scrollTop($(this).scrollTop());\n});\n");
 342
 343     htmlSvg.append("</script>\n");
 344     }
 345     else
 346     {
 347       htmlSvg.append("<div>\n")
 348               .append(alignmentSvg).append("</div>");
 349       htmlSvg.append("<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
 350               + "<script language=\"JavaScript\" type=\"text/javascript\"  src=\"http://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n");
 351
 352     }
 353
 354     // javascript for launching file in Jalview
 355
 356     htmlSvg.append("<script language=\"JavaScript\">\n");
 357     htmlSvg.append("function openJalviewUsingCurrentUrl(){\n");
 358     htmlSvg.append("    var json = JSON.parse(document.getElementById(\"seqData\").innerHTML);\n");
 359     htmlSvg.append("    var jalviewVersion = json['appSettings'].version;\n");
 360     htmlSvg.append("    var url = json['appSettings'].webStartUrl;\n");
 361     htmlSvg.append("    var myForm = document.createElement(\"form\");\n\n");
 362     htmlSvg.append("    var heap = document.createElement(\"input\");\n");
 363     htmlSvg.append("    heap.setAttribute(\"name\", \"jvm-max-heap\") ;\n");
 364     htmlSvg.append("    heap.setAttribute(\"value\", \"2G\");\n\n");
 365     htmlSvg.append("    var target = document.createElement(\"input\");\n");
 366     htmlSvg.append("    target.setAttribute(\"name\", \"open\");\n");
 367     htmlSvg.append("    target.setAttribute(\"value\", document.URL);\n\n");
 368     htmlSvg.append("    var jvVersion = document.createElement(\"input\");\n");
 369     htmlSvg.append("    jvVersion.setAttribute(\"name\", \"version\") ;\n");
 370     htmlSvg.append("    jvVersion.setAttribute(\"value\", jalviewVersion);\n\n");
 371     htmlSvg.append("    myForm.action = url;\n");
 372     htmlSvg.append("    myForm.appendChild(heap);\n");
 373     htmlSvg.append("    myForm.appendChild(target);\n");
 374     htmlSvg.append("    myForm.appendChild(jvVersion);\n");
 375     htmlSvg.append("    document.body.appendChild(myForm);\n");
 376     htmlSvg.append("    myForm.submit() ;\n");
 377     htmlSvg.append("    document.body.removeChild(myForm);\n");
 378     htmlSvg.append("}\n");
 379
 380     // jquery facebox for displaying raw BioJSON data");
 381     if (jsonData != null)
 382     {
 383       File faceBoxJsFile = new File("examples/javascript/facebox-1.3.js");
 384       try
 385       {
 386         htmlSvg.append(HtmlFile.readFileAsString(faceBoxJsFile));
 387       } catch (IOException e)
 388       {
 389         e.printStackTrace();
 390       }
 391     }
 392
 393     htmlSvg.append("</script>\n");
 394     htmlSvg.append("</html>");
 395     return htmlSvg.toString();
 396   }
 397 }