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.datamodel.AlignmentExportData;
25 import jalview.exceptions.NoFileSelectedException;
26 import jalview.gui.AlignmentPanel;
27 import jalview.gui.IProgressIndicator;
28 import jalview.util.MessageManager;
30 import java.io.BufferedReader;
32 import java.io.IOException;
33 import java.io.InputStreamReader;
35 import java.util.Objects;
38 public abstract class HTMLOutput implements Runnable
40 protected AlignmentPanel ap;
42 protected long pSessionId;
44 protected IProgressIndicator pIndicator;
46 protected File generatedFile;
48 public HTMLOutput(AlignmentPanel ap)
53 this.pIndicator = ap.alignFrame;
57 public String getBioJSONData()
59 return getBioJSONData(null);
62 public String getBioJSONData(AlignExportSettingI exportSettings)
68 if (exportSettings == null)
70 exportSettings = new AlignExportSettingI()
73 public boolean isExportHiddenSequences()
79 public boolean isExportHiddenColumns()
85 public boolean isExportAnnotations()
91 public boolean isExportFeatures()
97 public boolean isExportGroups()
103 public boolean isCancelled()
109 AlignmentExportData exportData = jalview.gui.AlignFrame
110 .getAlignmentForExport(JSONFile.FILE_DESC,
111 ap.getAlignViewport(), exportSettings);
112 String bioJSON = new FormatAdapter(ap, exportData.getSettings())
113 .formatSequences(JSONFile.FILE_DESC, exportData.getAlignment(),
114 exportData.getOmitHidden(), exportData
115 .getStartEndPostions(), ap.getAlignViewport()
116 .getColumnSelection());
121 * Read a template file content as string
124 * - the file to be read
125 * @return File content as String
126 * @throws IOException
128 public static String readFileAsString(File file) throws IOException
130 InputStreamReader isReader = null;
131 BufferedReader buffReader = null;
132 StringBuilder sb = new StringBuilder();
133 Objects.requireNonNull(file, "File must not be null!");
134 @SuppressWarnings("deprecation")
135 URL url = file.toURL();
140 isReader = new InputStreamReader(url.openStream());
141 buffReader = new BufferedReader(isReader);
143 String lineSeparator = System.getProperty("line.separator");
144 while ((line = buffReader.readLine()) != null)
146 sb.append(line).append(lineSeparator);
149 } catch (Exception ex)
151 ex.printStackTrace();
154 if (isReader != null)
159 if (buffReader != null)
165 return sb.toString();
168 public static String getImageMapHTML()
173 + "<script language=\"JavaScript\">\n"
174 + "var ns4 = document.layers;\n"
175 + "var ns6 = document.getElementById && !document.all;\n"
176 + "var ie4 = document.all;\n"
179 + "var toolTipSTYLE=\"\";\n"
180 + "function initToolTips()\n"
182 + " if(ns4||ns6||ie4)\n"
184 + " if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
185 + " else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
186 + " else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
187 + " if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
190 + " toolTipSTYLE.visibility = \"visible\";\n"
191 + " toolTipSTYLE.display = \"none\";\n"
193 + " document.onmousemove = moveToMouseLoc;\n"
196 + "function toolTip(msg, fg, bg)\n"
198 + " if(toolTip.arguments.length < 1) // hide\n"
200 + " if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
201 + " else toolTipSTYLE.display = \"none\";\n"
205 + " if(!fg) fg = \"#555555\";\n"
206 + " if(!bg) bg = \"#FFFFFF\";\n"
208 + " '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
209 + " '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
210 + " '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
211 + " '\" size=\"-2\"> ' + msg +\n"
212 + " ' </font></td></table></td></table>';\n"
215 + " toolTipSTYLE.document.write(content);\n"
216 + " toolTipSTYLE.document.close();\n"
217 + " toolTipSTYLE.visibility = \"visible\";\n"
221 + " document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
222 + " toolTipSTYLE.display='block'\n"
226 + " document.all(\"toolTipLayer\").innerHTML=content;\n"
227 + " toolTipSTYLE.display='block'\n"
231 + "function moveToMouseLoc(e)\n"
240 + " x = event.x + document.body.scrollLeft;\n"
241 + " y = event.y + document.body.scrollTop;\n"
243 + " toolTipSTYLE.left = x + offsetX;\n"
244 + " toolTipSTYLE.top = y + offsetY;\n"
250 + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
251 + "<script language=\"JavaScript\"><!--\n"
252 + "initToolTips(); //--></script>\n");
256 public String getOutputFile() throws NoFileSelectedException
258 String selectedFile = null;
259 if (pIndicator != null && !isHeadless())
261 pIndicator.setProgressBar(MessageManager.formatMessage(
262 "status.waiting_for_user_to_select_output_file", "HTML"),
266 JalviewFileChooser jvFileChooser = new JalviewFileChooser(
267 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
268 new String[] { "html" }, new String[] { "HTML files" },
270 jvFileChooser.setFileView(new JalviewFileView());
272 jvFileChooser.setDialogTitle(MessageManager
273 .getString("label.save_as_html"));
274 jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
276 int fileChooserOpt = jvFileChooser.showSaveDialog(null);
277 if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
279 jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
280 .getSelectedFile().getParent());
281 selectedFile = jvFileChooser.getSelectedFile().getPath();
285 throw new NoFileSelectedException("No file was selected.");
290 protected void setProgressMessage(String message)
292 if (pIndicator != null && !isHeadless())
294 pIndicator.setProgressBar(message, pSessionId);
298 System.out.println(message);
303 * Answers true if HTML export is invoke in headless mode or false otherwise
307 protected boolean isHeadless()
309 return System.getProperty("java.awt.headless") != null
310 && System.getProperty("java.awt.headless").equals("true");
314 * This method provides implementation of consistent behaviour which should
315 * occur before a HTML file export. It MUST be called at the start of the
316 * exportHTML() method implementation.
318 protected void exportStarted()
320 pSessionId = System.currentTimeMillis();
324 * This method provides implementation of consistent behaviour which should
325 * occur after a HTML file export. It MUST be called at the end of the
326 * exportHTML() method implementation.
328 protected void exportCompleted()
330 if (isLaunchInBrowserAfterExport() && !isHeadless())
334 jalview.util.BrowserLauncher
335 .openURL("file:///" + getExportedFile());
336 } catch (IOException e)
344 * if this answers true then BioJSON data will be embedded to the exported
345 * HTML file otherwise it won't be embedded.
349 public abstract boolean isEmbedData();
352 * if this answers true then the generated HTML file is opened for viewing in
353 * a browser after its generation otherwise it won't be opened in a browser
357 public abstract boolean isLaunchInBrowserAfterExport();
360 * handle to the generated HTML file
364 public abstract File getExportedFile();
367 * This is the main method to handle the HTML generation.
370 * the file path of the generated HTML
372 public abstract void exportHTML(String outputFile);