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