2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
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;
34 import java.awt.Graphics;
35 import java.awt.print.PrinterException;
37 import java.io.FileOutputStream;
38 import java.io.IOException;
40 import org.jfree.graphics2d.svg.SVGGraphics2D;
41 import org.jfree.graphics2d.svg.SVGHints;
43 public class HtmlSvgOutput
51 private IProgressIndicator pIndicator;
53 private long pSessionId;
55 private boolean headless;
57 public HtmlSvgOutput(AlignmentPanel ap)
61 fr = ap.cloneFeatureRenderer();
64 public void generateHtmlSvgOutput(File file)
66 pIndicator = ap.alignFrame;
67 pSessionId = System.currentTimeMillis();
70 headless = (System.getProperty("java.awt.headless") != null && System
71 .getProperty("java.awt.headless").equals("true"));
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);
82 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
84 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
85 .getSelectedFile().getParent());
86 file = chooser.getSelectedFile();
87 ap.alignFrame.repaint();
91 setProgressMessage(MessageManager.formatMessage(
92 "status.cancelled_image_export_operation", "HTML"));
98 pIndicator.setProgressBar(MessageManager.formatMessage(
99 "info.error_creating_file", "HTML"), pSessionId);
103 final File fileX = file;
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());
122 String renderStyle = jalview.bin.Cache.getDefault(
123 "HTML_RENDERING", "Prompt each time");
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")))
131 HTMLOptions svgOption = new HTMLOptions();
132 renderStyle = svgOption.getValue();
134 if (renderStyle == null || svgOption.cancelled)
136 setProgressMessage(MessageManager.formatMessage(
137 "status.cancelled_image_export_operation", "HTML"));
142 if (renderStyle.equalsIgnoreCase("Lineart"))
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);
150 if (av.getWrapAlignment())
152 printWrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
157 printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
158 idPanelGraphics, alignPanelGraphics);
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"));
168 AlignExportSettingI exportSettings = new AlignExportSettingI()
171 public boolean isExportHiddenSequences()
177 public boolean isExportHiddenColumns()
183 public boolean isExportAnnotations()
189 public boolean isExportFeatures()
195 public boolean isExportGroups()
201 public boolean isCancelled()
207 AlignmentExportData exportData = jalview.gui.AlignFrame
208 .getAlignmentForExport(JSONFile.FILE_DESC, av,
210 jsonData = new FormatAdapter(ap, exportData.getSettings())
211 .formatSequences(JSONFile.FILE_DESC,
212 exportData.getAlignment(),
213 exportData.getOmitHidden(),
214 exportData.getStartEndPostions(),
215 av.getColumnSelection());
217 String htmlData = getHtml(idPanelSvgData, alignPanelSvgData, jsonData,
218 av.getWrapAlignment());
219 FileOutputStream out = new FileOutputStream(fileX);
220 out.write(htmlData.getBytes());
223 if (!(System.getProperty("java.awt.headless") != null && System
224 .getProperty("java.awt.headless").equals("true")))
226 jalview.util.BrowserLauncher.openURL("file:///" + fileX);
228 } catch (OutOfMemoryError err)
230 System.out.println("########################\n"
231 + "OUT OF MEMORY " + fileX + "\n"
232 + "########################");
233 new OOMWarning("Creating Image for " + fileX, err);
234 } catch (Exception e)
237 pIndicator.setProgressBar(MessageManager.formatMessage(
238 "info.error_creating_file", "HTML"), pSessionId);
240 setProgressMessage(MessageManager.formatMessage(
241 "status.export_complete", "HTML"));
247 private void setProgressMessage(String message)
249 if (pIndicator != null && !headless)
251 pIndicator.setProgressBar(message, pSessionId);
255 System.out.println(message);
259 static JalviewFileChooser getHTMLChooser()
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");
268 public int printUnwrapped(int pwidth, int pheight, int pi, Graphics... pg)
269 throws PrinterException
271 return ap.printUnwrapped(pwidth, pheight, pi, pg);
274 public int printWrapped(int pwidth, int pheight, int pi, Graphics... pg)
275 throws PrinterException
277 return ap.printWrappedAlignment(pwidth, pheight, pi, pg[0]);
280 private String getHtml(String titleSvg, String alignmentSvg,
281 String jsonData, boolean wrapped)
283 StringBuilder htmlSvg = new StringBuilder();
284 htmlSvg.append("<html>\n");
285 if (jsonData != null)
287 htmlSvg.append("<button onclick=\"javascipt:openJalviewUsingCurrentUrl();\">Launch in Jalview</button> ");
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/> ");
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)
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; }");
321 htmlSvg.append("</style>");
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\" >");
332 "<div class=\"sub-category-container\"> <div style=\"overflow-x: scroll;\">")
333 .append(alignmentSvg).append("</div></div>").append("</div>");
334 htmlSvg.append("</div>");
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"
339 + "var subCatContainer = $(\".sub-category-container\");\n"
340 + "subCatContainer.scroll(\nfunction() {\n"
341 + "subCatContainer.scrollTop($(this).scrollTop());\n});\n");
343 htmlSvg.append("</script>\n");
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");
354 // javascript for launching file in Jalview
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");
380 // jquery facebox for displaying raw BioJSON data");
381 if (jsonData != null)
383 File faceBoxJsFile = new File("examples/javascript/facebox-1.3.js");
386 htmlSvg.append(HtmlFile.readFileAsString(faceBoxJsFile));
387 } catch (IOException e)
393 htmlSvg.append("</script>\n");
394 htmlSvg.append("</html>");
395 return htmlSvg.toString();