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 java.awt.Graphics;
  24 import java.awt.print.PrinterException;
  25 import java.io.File;
  26 import java.io.FileOutputStream;
  27 import java.io.IOException;
  28 import java.util.Locale;
  29 import java.util.concurrent.Callable;
  30 import java.util.concurrent.atomic.AtomicBoolean;
  31
  32 import org.jfree.graphics2d.svg.SVGGraphics2D;
  33 import org.jfree.graphics2d.svg.SVGHints;
  34
  35 import jalview.bin.Cache;
  36 import jalview.gui.AlignmentPanel;
  37 import jalview.gui.LineartOptions;
  38 import jalview.gui.OOMWarning;
  39 import jalview.math.AlignmentDimension;
  40 import jalview.util.MessageManager;
  41
  42 public class HtmlSvgOutput extends HTMLOutput
  43 {
  44   public HtmlSvgOutput(AlignmentPanel ap)
  45   {
  46     super(ap, "HTML");
  47   }
  48
  49   public int printUnwrapped(int pwidth, int pheight, int pi,
  50           Graphics idGraphics, Graphics alignmentGraphics)
  51           throws PrinterException
  52   {
  53     return ap.printUnwrapped(pwidth, pheight, pi, idGraphics,
  54             alignmentGraphics);
  55   }
  56
  57   public int printWrapped(int pwidth, int pheight, int pi, Graphics... pg)
  58           throws PrinterException
  59   {
  60     return ap.printWrappedAlignment(pwidth, pheight, pi, pg[0]);
  61   }
  62
  63   String getHtml(String titleSvg, String alignmentSvg, String jsonData,
  64           boolean wrapped)
  65   {
  66     StringBuilder htmlSvg = new StringBuilder();
  67     htmlSvg.append("<html>\n");
  68     if (jsonData != null)
  69     {
  70       htmlSvg.append(
  71               "<button onclick=\"javascipt:openJalviewUsingCurrentUrl();\">Launch in Jalview</button> &nbsp;");
  72       htmlSvg.append(
  73               "<input type=\"submit\" value=\"View raw BioJSON Data\" onclick=\"jQuery.facebox({ div:'#seqData' }); return false;\" />");
  74       htmlSvg.append(
  75               "<div style=\"display: none;\" name=\"seqData\" id=\"seqData\" >"
  76                       + jsonData + "</div>");
  77       htmlSvg.append("<br/>&nbsp;");
  78     }
  79     htmlSvg.append("\n<style type=\"text/css\"> "
  80             + "div.parent{ width:100%;<!-- overflow: auto; -->}\n"
  81             + "div.titlex{ width:11%; float: left; }\n"
  82             + "div.align{ width:89%; float: right; }\n"
  83             + "div.main-container{ border: 2px solid blue; border: 2px solid blue; width: 99%;   min-height: 99%; }\n"
  84             + ".sub-category-container {overflow-y: scroll; overflow-x: hidden; width: 100%; height: 100%;}\n"
  85             + "object {pointer-events: none;}");
  86     if (jsonData != null)
  87     {
  88       // facebox style sheet for displaying raw BioJSON data
  89       htmlSvg.append(
  90               "#facebox { position: absolute;  top: 0;   left: 0; z-index: 100; text-align: left; }\n"
  91                       + "#facebox .popup{ position:relative; border:3px solid rgba(0,0,0,0); -webkit-border-radius:5px;"
  92                       + "-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);"
  93                       + "box-shadow:0 0 18px rgba(0,0,0,0.4); }\n"
  94                       + "#facebox .content { display:table; width: 98%; padding: 10px; background: #fff; -webkit-border-radius:4px; -moz-border-radius:4px;"
  95                       + " border-radius:4px; }\n"
  96                       + "#facebox .content > p:first-child{ margin-top:0; }\n"
  97                       + "#facebox .content > p:last-child{ margin-bottom:0; }\n"
  98                       + "#facebox .close{ position:absolute; top:5px; right:5px; padding:2px; background:#fff; }\n"
  99                       + "#facebox .close img{ opacity:0.3; }\n"
 100                       + "#facebox .close:hover img{ opacity:1.0; }\n"
 101                       + "#facebox .loading { text-align: center; }\n"
 102                       + "#facebox .image { text-align: center;}\n"
 103                       + "#facebox img { border: 0;  margin: 0; }\n"
 104                       + "#facebox_overlay { position: fixed; top: 0px; left: 0px; height:100%; width:100%; }\n"
 105                       + ".facebox_hide { z-index:-100; }\n"
 106                       + ".facebox_overlayBG { background-color: #000;  z-index: 99;  }");
 107     }
 108     htmlSvg.append("</style>");
 109     if (!wrapped)
 110     {
 111       htmlSvg.append("<div class=\"main-container\" \n>");
 112       htmlSvg.append("<div class=\"titlex\">\n");
 113       htmlSvg.append("<div class=\"sub-category-container\"> \n");
 114       htmlSvg.append(titleSvg);
 115       htmlSvg.append("</div>");
 116       htmlSvg.append(
 117               "</div>\n\n<!-- ========================================================================================== -->\n\n");
 118       htmlSvg.append("<div class=\"align\" >");
 119       htmlSvg.append(
 120               "<div class=\"sub-category-container\"> <div style=\"overflow-x: scroll;\">")
 121               .append(alignmentSvg).append("</div></div>").append("</div>");
 122       htmlSvg.append("</div>");
 123
 124       htmlSvg.append(
 125               "<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
 126                       + "<script language=\"JavaScript\" type=\"text/javascript\"  src=\"http://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n"
 127                       + "<script>\n"
 128                       + "var subCatContainer = $(\".sub-category-container\");\n"
 129                       + "subCatContainer.scroll(\nfunction() {\n"
 130                       + "subCatContainer.scrollTop($(this).scrollTop());\n});\n");
 131
 132       htmlSvg.append("</script>\n");
 133     }
 134     else
 135     {
 136       htmlSvg.append("<div>\n").append(alignmentSvg).append("</div>");
 137       htmlSvg.append(
 138               "<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
 139                       + "<script language=\"JavaScript\" type=\"text/javascript\"  src=\"http://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n");
 140     }
 141
 142     // javascript for launching file in Jalview
 143     htmlSvg.append("<script language=\"JavaScript\">\n");
 144     htmlSvg.append("function openJalviewUsingCurrentUrl(){\n");
 145     htmlSvg.append(
 146             "    var json = JSON.parse(document.getElementById(\"seqData\").innerHTML);\n");
 147     htmlSvg.append(
 148             "    var jalviewVersion = json['appSettings'].version;\n");
 149     htmlSvg.append("    var url = json['appSettings'].webStartUrl;\n");
 150     htmlSvg.append(
 151             "    var myForm = document.createElement(\"form\");\n\n");
 152     htmlSvg.append("    var heap = document.createElement(\"input\");\n");
 153     htmlSvg.append("    heap.setAttribute(\"name\", \"jvm-max-heap\") ;\n");
 154     htmlSvg.append("    heap.setAttribute(\"value\", \"2G\");\n\n");
 155     htmlSvg.append("    var target = document.createElement(\"input\");\n");
 156     htmlSvg.append("    target.setAttribute(\"name\", \"open\");\n");
 157     htmlSvg.append("    target.setAttribute(\"value\", document.URL);\n\n");
 158     htmlSvg.append(
 159             "    var jvVersion = document.createElement(\"input\");\n");
 160     htmlSvg.append("    jvVersion.setAttribute(\"name\", \"version\") ;\n");
 161     htmlSvg.append(
 162             "    jvVersion.setAttribute(\"value\", jalviewVersion);\n\n");
 163     htmlSvg.append("    myForm.action = url;\n");
 164     htmlSvg.append("    myForm.appendChild(heap);\n");
 165     htmlSvg.append("    myForm.appendChild(target);\n");
 166     htmlSvg.append("    myForm.appendChild(jvVersion);\n");
 167     htmlSvg.append("    document.body.appendChild(myForm);\n");
 168     htmlSvg.append("    myForm.submit() ;\n");
 169     htmlSvg.append("    document.body.removeChild(myForm);\n");
 170     htmlSvg.append("}\n");
 171
 172     if (jsonData != null)
 173     {
 174       // JQuery FaceBox for displaying raw BioJSON data");
 175       File faceBoxJsFile = new File("examples/javascript/facebox-1.3.js");
 176       try
 177       {
 178         htmlSvg.append(HTMLOutput.readFileAsString(faceBoxJsFile));
 179       } catch (IOException e)
 180       {
 181         e.printStackTrace();
 182       }
 183     }
 184
 185     htmlSvg.append("</script>\n");
 186     htmlSvg.append("</html>");
 187     return htmlSvg.toString();
 188   }
 189
 190   @Override
 191   public boolean isEmbedData()
 192   {
 193     return Boolean
 194             .valueOf(Cache.getDefault("EXPORT_EMBBED_BIOJSON", "true"));
 195   }
 196
 197   @Override
 198   public boolean isLaunchInBrowserAfterExport()
 199   {
 200     return true;
 201   }
 202
 203   @Override
 204   public void run()
 205   {
 206     run(null);
 207   }
 208
 209   @Override
 210   public void run(String renderer)
 211   {
 212     try
 213     {
 214       String renderStyle = renderer == null
 215               ? Cache.getDefault("HTML_RENDERING",
 216                       LineartOptions.PROMPT_EACH_TIME)
 217               : renderer;
 218       AtomicBoolean textOption = new AtomicBoolean(
 219               !"lineart".equals(renderStyle.toLowerCase(Locale.ROOT)));
 220
 221       /*
 222        * configure the action to run on OK in the dialog
 223        */
 224       Callable<Void> okAction = () -> {
 225         doOutput(textOption.get());
 226         return null;
 227       };
 228
 229       /*
 230        * Prompt for character rendering style if preference is not set
 231        */
 232       if (renderStyle.equalsIgnoreCase(LineartOptions.PROMPT_EACH_TIME)
 233               && !isHeadless())
 234       {
 235         LineartOptions svgOption = new LineartOptions("HTML", textOption);
 236         svgOption.setResponseAction(1, () -> {
 237           setProgressMessage(MessageManager.formatMessage(
 238                   "status.cancelled_image_export_operation",
 239                   getDescription()));
 240           return null;
 241         });
 242         svgOption.setResponseAction(0, okAction);
 243         svgOption.showDialog();
 244         /* no code here - JalviewJS cannot execute it */
 245       }
 246       else
 247       {
 248         /*
 249          * else (if preference set) just do the export action
 250          */
 251         doOutput(textOption.get());
 252       }
 253     } catch (OutOfMemoryError err)
 254     {
 255       System.out.println("########################\n" + "OUT OF MEMORY "
 256               + generatedFile + "\n" + "########################");
 257       new OOMWarning("Creating Image for " + generatedFile, err);
 258     } catch (Exception e)
 259     {
 260       e.printStackTrace();
 261       setProgressMessage(MessageManager
 262               .formatMessage("info.error_creating_file", getDescription()));
 263     }
 264   }
 265
 266   /**
 267    * Builds and writes the image to the file specified by field
 268    * <code>generatedFile</code>
 269    *
 270    * @param textCharacters
 271    *          true for Text character rendering, false for Lineart
 272    */
 273   protected void doOutput(boolean textCharacters)
 274   {
 275     try
 276     {
 277       AlignmentDimension aDimension = ap.getAlignmentDimension();
 278       SVGGraphics2D idPanelGraphics = new SVGGraphics2D(
 279               aDimension.getWidth(), aDimension.getHeight());
 280       SVGGraphics2D alignPanelGraphics = new SVGGraphics2D(
 281               aDimension.getWidth(), aDimension.getHeight());
 282       if (!textCharacters) // Lineart selected
 283       {
 284         idPanelGraphics.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
 285                 SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
 286         alignPanelGraphics.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
 287                 SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
 288       }
 289       if (ap.av.getWrapAlignment())
 290       {
 291         printWrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
 292                 alignPanelGraphics);
 293       }
 294       else
 295       {
 296         printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
 297                 idPanelGraphics, alignPanelGraphics);
 298       }
 299
 300       String idPanelSvgData = idPanelGraphics.getSVGDocument();
 301       String alignPanelSvgData = alignPanelGraphics.getSVGDocument();
 302       String jsonData = getBioJSONData();
 303       String htmlData = getHtml(idPanelSvgData, alignPanelSvgData, jsonData,
 304               ap.av.getWrapAlignment());
 305       FileOutputStream out = new FileOutputStream(generatedFile);
 306       out.write(htmlData.getBytes());
 307       out.flush();
 308       out.close();
 309       setProgressMessage(MessageManager
 310               .formatMessage("status.export_complete", getDescription()));
 311       exportCompleted();
 312     } catch (Exception e)
 313     {
 314       e.printStackTrace();
 315       setProgressMessage(MessageManager
 316               .formatMessage("info.error_creating_file", getDescription()));
 317     }
 318   }
 319 }