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.gui.AlignmentPanel;
  24 import jalview.gui.HTMLOptions;
  25 import jalview.gui.OOMWarning;
  26 import jalview.math.AlignmentDimension;
  27 import jalview.util.MessageManager;
  28
  29 import java.awt.Graphics;
  30 import java.awt.print.PrinterException;
  31 import java.io.File;
  32 import java.io.FileOutputStream;
  33 import java.io.IOException;
  34
  35 import org.jfree.graphics2d.svg.SVGGraphics2D;
  36 import org.jfree.graphics2d.svg.SVGHints;
  37
  38 public class HtmlSvgOutput extends HTMLOutput
  39 {
  40
  41   private File generatedFile;
  42
  43   public HtmlSvgOutput(AlignmentPanel ap)
  44   {
  45     super(ap);
  46   }
  47
  48   @Override
  49   public void exportHTML(String file)
  50   {
  51     exportStarted();
  52     try
  53     {
  54       if (file == null)
  55       {
  56         file = getOutputFile();
  57       }
  58       generatedFile = new File(file);
  59     } catch (Exception e)
  60     {
  61       setProgressMessage(MessageManager.formatMessage(
  62               "info.error_creating_file", "HTML"));
  63       e.printStackTrace();
  64       return;
  65     }
  66     new Thread()
  67     {
  68       @Override
  69       public void run()
  70       {
  71         try
  72         {
  73           setProgressMessage(null);
  74           setProgressMessage(MessageManager.formatMessage(
  75                   "status.exporting_alignment_as_x_file", "HTML"));
  76           AlignmentDimension aDimension = ap.getAlignmentDimension();
  77           SVGGraphics2D idPanelGraphics = new SVGGraphics2D(
  78                   aDimension.getWidth(),
  79                   aDimension.getHeight());
  80           SVGGraphics2D alignPanelGraphics = new SVGGraphics2D(
  81                   aDimension.getWidth(),
  82                   aDimension.getHeight());
  83
  84           String renderStyle = jalview.bin.Cache.getDefault(
  85                   "HTML_RENDERING", "Prompt each time");
  86
  87           // If we need to prompt, and if the GUI is visible then
  88           // Prompt for rendering style
  89           if (renderStyle.equalsIgnoreCase("Prompt each time")
  90                   && !isHeadless())
  91           {
  92             HTMLOptions svgOption = new HTMLOptions();
  93             renderStyle = svgOption.getValue();
  94
  95             if (renderStyle == null || svgOption.cancelled)
  96             {
  97               setProgressMessage(MessageManager.formatMessage(
  98                       "status.cancelled_image_export_operation", "HTML"));
  99               return;
 100             }
 101           }
 102
 103           if (renderStyle.equalsIgnoreCase("Lineart"))
 104           {
 105             idPanelGraphics.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
 106                     SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
 107             alignPanelGraphics.setRenderingHint(
 108                     SVGHints.KEY_DRAW_STRING_TYPE,
 109                     SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
 110           }
 111           if (ap.av.getWrapAlignment())
 112           {
 113             printWrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
 114                     alignPanelGraphics);
 115           }
 116           else
 117           {
 118           printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
 119  idPanelGraphics, alignPanelGraphics);
 120           }
 121
 122           String idPanelSvgData = idPanelGraphics.getSVGDocument();
 123           String alignPanelSvgData = alignPanelGraphics.getSVGDocument();
 124           String jsonData = getBioJSONData();
 125           String htmlData = getHtml(idPanelSvgData, alignPanelSvgData, jsonData,
 126  ap.av.getWrapAlignment());
 127           FileOutputStream out = new FileOutputStream(generatedFile);
 128           out.write(htmlData.getBytes());
 129           out.flush();
 130           out.close();
 131           exportCompleted();
 132         } catch (OutOfMemoryError err)
 133         {
 134           System.out.println("########################\n"
 135                   + "OUT OF MEMORY " + generatedFile + "\n"
 136                   + "########################");
 137           new OOMWarning("Creating Image for " + generatedFile, err);
 138         } catch (Exception e)
 139         {
 140           e.printStackTrace();
 141           setProgressMessage(MessageManager.formatMessage(
 142                   "info.error_creating_file", "HTML"));
 143         }
 144         setProgressMessage(MessageManager.formatMessage(
 145                 "status.export_complete", "HTML"));
 146       }
 147     }.start();
 148
 149   }
 150
 151
 152   static JalviewFileChooser getHTMLChooser()
 153   {
 154     return new jalview.io.JalviewFileChooser(
 155             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
 156             new String[] { "html" },
 157             new String[] { "Hypertext Markup Language" },
 158             "Hypertext Markup Language");
 159   }
 160
 161   public int printUnwrapped(int pwidth, int pheight, int pi, Graphics... pg)
 162           throws PrinterException
 163   {
 164     return ap.printUnwrapped(pwidth, pheight, pi, pg);
 165   }
 166
 167   public int printWrapped(int pwidth, int pheight, int pi, Graphics... pg)
 168           throws PrinterException
 169   {
 170     return ap.printWrappedAlignment(pwidth, pheight, pi, pg[0]);
 171   }
 172
 173   private String getHtml(String titleSvg, String alignmentSvg,
 174           String jsonData, boolean wrapped)
 175   {
 176     StringBuilder htmlSvg = new StringBuilder();
 177     htmlSvg.append("<html>\n");
 178     if (jsonData != null)
 179     {
 180       htmlSvg.append("<button onclick=\"javascipt:openJalviewUsingCurrentUrl();\">Launch in Jalview</button> &nbsp;");
 181       htmlSvg.append("<input type=\"submit\" value=\"View raw BioJSON Data\" onclick=\"jQuery.facebox({ div:'#seqData' }); return false;\" />");
 182       htmlSvg.append("<div style=\"display: none;\" name=\"seqData\" id=\"seqData\" >"
 183               + jsonData + "</div>");
 184       htmlSvg.append("<br/>&nbsp;");
 185     }
 186     htmlSvg.append("\n<style type=\"text/css\"> "
 187             + "div.parent{ width:100%;<!-- overflow: auto; -->}\n"
 188             + "div.titlex{ width:11%; float: left; }\n"
 189             + "div.align{ width:89%; float: right; }\n"
 190             + "div.main-container{ border: 2px solid blue; border: 2px solid blue; width: 99%;   min-height: 99%; }\n"
 191             + ".sub-category-container {overflow-y: scroll; overflow-x: hidden; width: 100%; height: 100%;}\n"
 192             + "object {pointer-events: none;}");
 193     if (jsonData != null)
 194     {
 195       // facebox style sheet for displaying raw BioJSON data
 196       htmlSvg.append("#facebox { position: absolute;  top: 0;   left: 0; z-index: 100; text-align: left; }\n"
 197               + "#facebox .popup{ position:relative; border:3px solid rgba(0,0,0,0); -webkit-border-radius:5px;"
 198               + "-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);"
 199               + "box-shadow:0 0 18px rgba(0,0,0,0.4); }\n"
 200               + "#facebox .content { display:table; width: 98%; padding: 10px; background: #fff; -webkit-border-radius:4px; -moz-border-radius:4px;"
 201               + " border-radius:4px; }\n"
 202               + "#facebox .content > p:first-child{ margin-top:0; }\n"
 203               + "#facebox .content > p:last-child{ margin-bottom:0; }\n"
 204               + "#facebox .close{ position:absolute; top:5px; right:5px; padding:2px; background:#fff; }\n"
 205               + "#facebox .close img{ opacity:0.3; }\n"
 206               + "#facebox .close:hover img{ opacity:1.0; }\n"
 207               + "#facebox .loading { text-align: center; }\n"
 208               + "#facebox .image { text-align: center;}\n"
 209               + "#facebox img { border: 0;  margin: 0; }\n"
 210               + "#facebox_overlay { position: fixed; top: 0px; left: 0px; height:100%; width:100%; }\n"
 211               + ".facebox_hide { z-index:-100; }\n"
 212               + ".facebox_overlayBG { background-color: #000;  z-index: 99;  }");
 213     }
 214     htmlSvg.append("</style>");
 215     if (!wrapped)
 216     {
 217     htmlSvg.append("<div class=\"main-container\" \n>");
 218     htmlSvg.append("<div class=\"titlex\">\n");
 219     htmlSvg.append("<div class=\"sub-category-container\"> \n");
 220     htmlSvg.append(titleSvg);
 221     htmlSvg.append("</div>");
 222     htmlSvg.append("</div>\n\n<!-- ========================================================================================== -->\n\n");
 223     htmlSvg.append("<div class=\"align\" >");
 224     htmlSvg.append(
 225             "<div class=\"sub-category-container\"> <div style=\"overflow-x: scroll;\">")
 226             .append(alignmentSvg).append("</div></div>").append("</div>");
 227     htmlSvg.append("</div>");
 228
 229     htmlSvg.append("<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
 230             + "<script language=\"JavaScript\" type=\"text/javascript\"  src=\"http://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n"
 231             + "<script>\n"
 232             + "var subCatContainer = $(\".sub-category-container\");\n"
 233             + "subCatContainer.scroll(\nfunction() {\n"
 234             + "subCatContainer.scrollTop($(this).scrollTop());\n});\n");
 235
 236     htmlSvg.append("</script>\n");
 237     }
 238     else
 239     {
 240       htmlSvg.append("<div>\n")
 241               .append(alignmentSvg).append("</div>");
 242       htmlSvg.append("<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
 243               + "<script language=\"JavaScript\" type=\"text/javascript\"  src=\"http://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n");
 244
 245     }
 246
 247     // javascript for launching file in Jalview
 248
 249     htmlSvg.append("<script language=\"JavaScript\">\n");
 250     htmlSvg.append("function openJalviewUsingCurrentUrl(){\n");
 251     htmlSvg.append("    var json = JSON.parse(document.getElementById(\"seqData\").innerHTML);\n");
 252     htmlSvg.append("    var jalviewVersion = json['appSettings'].version;\n");
 253     htmlSvg.append("    var url = json['appSettings'].webStartUrl;\n");
 254     htmlSvg.append("    var myForm = document.createElement(\"form\");\n\n");
 255     htmlSvg.append("    var heap = document.createElement(\"input\");\n");
 256     htmlSvg.append("    heap.setAttribute(\"name\", \"jvm-max-heap\") ;\n");
 257     htmlSvg.append("    heap.setAttribute(\"value\", \"2G\");\n\n");
 258     htmlSvg.append("    var target = document.createElement(\"input\");\n");
 259     htmlSvg.append("    target.setAttribute(\"name\", \"open\");\n");
 260     htmlSvg.append("    target.setAttribute(\"value\", document.URL);\n\n");
 261     htmlSvg.append("    var jvVersion = document.createElement(\"input\");\n");
 262     htmlSvg.append("    jvVersion.setAttribute(\"name\", \"version\") ;\n");
 263     htmlSvg.append("    jvVersion.setAttribute(\"value\", jalviewVersion);\n\n");
 264     htmlSvg.append("    myForm.action = url;\n");
 265     htmlSvg.append("    myForm.appendChild(heap);\n");
 266     htmlSvg.append("    myForm.appendChild(target);\n");
 267     htmlSvg.append("    myForm.appendChild(jvVersion);\n");
 268     htmlSvg.append("    document.body.appendChild(myForm);\n");
 269     htmlSvg.append("    myForm.submit() ;\n");
 270     htmlSvg.append("    document.body.removeChild(myForm);\n");
 271     htmlSvg.append("}\n");
 272
 273     // jquery facebox for displaying raw BioJSON data");
 274     if (jsonData != null)
 275     {
 276       File faceBoxJsFile = new File("examples/javascript/facebox-1.3.js");
 277       try
 278       {
 279         htmlSvg.append(HTMLOutput.readFileAsString(faceBoxJsFile));
 280       } catch (IOException e)
 281       {
 282         e.printStackTrace();
 283       }
 284     }
 285
 286     htmlSvg.append("</script>\n");
 287     htmlSvg.append("</html>");
 288     return htmlSvg.toString();
 289   }
 290
 291   @Override
 292   public boolean isEmbedData()
 293   {
 294     return Boolean.valueOf(jalview.bin.Cache.getDefault(
 295             "EXPORT_EMBBED_BIOJSON", "true"));
 296   }
 297
 298   @Override
 299   public boolean isLaunchInBrowserAfterExport()
 300   {
 301     return true;
 302   }
 303
 304   @Override
 305   public File getExportedFile()
 306   {
 307     return generatedFile;
 308   }
 309 }