1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.io

File HTMLOutput.java

 

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Classes

Class
Line #
Actions
HTMLOutput 41 64 28
0.660%
 

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This file is covered by 1 test. .

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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.io.BufferedReader;
24    import java.io.File;
25    import java.io.IOException;
26    import java.io.InputStreamReader;
27    import java.net.URL;
28    import java.util.Objects;
29   
30    import jalview.api.AlignExportSettingsI;
31    import jalview.bin.Cache;
32    import jalview.bin.Jalview;
33    import jalview.datamodel.AlignExportSettingsAdapter;
34    import jalview.datamodel.AlignmentExportData;
35    import jalview.gui.AlignmentPanel;
36    import jalview.gui.IProgressIndicator;
37    import jalview.io.exceptions.ImageOutputException;
38    import jalview.util.HttpUtils;
39    import jalview.util.MessageManager;
40   
 
41    public abstract class HTMLOutput implements Runnable
42    {
43    protected AlignmentPanel ap;
44   
45    /*
46    * key for progress or status messages
47    */
48    protected long pSessionId;
49   
50    /*
51    * (optional) place to write progress messages to
52    */
53    protected IProgressIndicator pIndicator;
54   
55    protected File generatedFile;
56   
57    String _bioJson = null;
58   
59    private String description;
60   
61    /**
62    * Constructor given an alignment panel (which should not be null)
63    *
64    * @param ap
65    * @param desc
66    */
 
67  2 toggle public HTMLOutput(AlignmentPanel ap, String desc)
68    {
69  2 this.ap = ap;
70  2 this.pIndicator = ap.alignFrame;
71  2 this.description = desc;
72  2 this.pSessionId = System.currentTimeMillis();
73    }
74   
75    /**
76    * Gets the BioJSON data as a string, with lazy evaluation (first time called
77    * only). If the output format is configured not to embed BioJSON, returns
78    * null.
79    *
80    * @return
81    */
 
82  2 toggle public String getBioJSONData()
83    {
84  2 if (!isEmbedData())
85    {
86  1 return null;
87    }
88  1 if (_bioJson == null)
89    {
90  1 AlignExportSettingsI options = new AlignExportSettingsAdapter(true);
91  1 AlignmentExportData exportData = ap.getAlignViewport()
92    .getAlignExportData(options);
93  1 _bioJson = new FormatAdapter(ap, options).formatSequences(
94    FileFormat.Json, exportData.getAlignment(),
95    exportData.getOmitHidden(), exportData.getStartEndPostions(),
96    ap.getAlignViewport().getAlignment().getHiddenColumns());
97    }
98   
99  1 return _bioJson;
100    }
101   
102    /**
103    * Read a template file content as string
104    *
105    * @param file
106    * - the file to be read
107    * @return File content as String
108    * @throws IOException
109    */
 
110  2 toggle public static String readFileAsString(File file) throws IOException
111    {
112  2 InputStreamReader isReader = null;
113  2 BufferedReader buffReader = null;
114  2 StringBuilder sb = new StringBuilder();
115  2 Objects.requireNonNull(file, "File must not be null!");
116  2 @SuppressWarnings("deprecation")
117    URL url = file.toURL();
118  2 if (url != null)
119    {
120  2 try
121    {
122  2 isReader = new InputStreamReader(HttpUtils.openStream(url));
123  2 buffReader = new BufferedReader(isReader);
124  2 String line;
125  2 String lineSeparator = System.getProperty("line.separator");
126  ? while ((line = buffReader.readLine()) != null)
127    {
128  9979 sb.append(line).append(lineSeparator);
129    }
130   
131    } catch (Exception ex)
132    {
133  0 ex.printStackTrace();
134    } finally
135    {
136  2 if (isReader != null)
137    {
138  2 isReader.close();
139    }
140   
141  2 if (buffReader != null)
142    {
143  2 buffReader.close();
144    }
145    }
146    }
147  2 return sb.toString();
148    }
149   
 
150  0 toggle public static String getImageMapHTML()
151    {
152  0 return new String("<html>\n" + "<head>\n"
153    + "<script language=\"JavaScript\">\n"
154    + "var ns4 = document.layers;\n"
155    + "var ns6 = document.getElementById && !document.all;\n"
156    + "var ie4 = document.all;\n" + "offsetX = 0;\n"
157    + "offsetY = 20;\n" + "var toolTipSTYLE=\"\";\n"
158    + "function initToolTips()\n" + "{\n" + " if(ns4||ns6||ie4)\n"
159    + " {\n"
160    + " if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
161    + " else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
162    + " else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
163    + " if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
164    + " else\n" + " {\n"
165    + " toolTipSTYLE.visibility = \"visible\";\n"
166    + " toolTipSTYLE.display = \"none\";\n" + " }\n"
167    + " document.onmousemove = moveToMouseLoc;\n" + " }\n"
168    + "}\n" + "function toolTip(msg, fg, bg)\n" + "{\n"
169    + " if(toolTip.arguments.length < 1) // hide\n" + " {\n"
170    + " if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
171    + " else toolTipSTYLE.display = \"none\";\n" + " }\n"
172    + " else // show\n" + " {\n"
173    + " if(!fg) fg = \"#555555\";\n"
174    + " if(!bg) bg = \"#FFFFFF\";\n" + " var content =\n"
175    + " '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
176    + " '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
177    + " '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
178    + " '\" size=\"-2\">&nbsp;' + msg +\n"
179    + " '&nbsp;</font></td></table></td></table>';\n"
180    + " if(ns4)\n" + " {\n"
181    + " toolTipSTYLE.document.write(content);\n"
182    + " toolTipSTYLE.document.close();\n"
183    + " toolTipSTYLE.visibility = \"visible\";\n" + " }\n"
184    + " if(ns6)\n" + " {\n"
185    + " document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
186    + " toolTipSTYLE.display='block'\n" + " }\n"
187    + " if(ie4)\n" + " {\n"
188    + " document.all(\"toolTipLayer\").innerHTML=content;\n"
189    + " toolTipSTYLE.display='block'\n" + " }\n" + " }\n"
190    + "}\n" + "function moveToMouseLoc(e)\n" + "{\n"
191    + " if(ns4||ns6)\n" + " {\n" + " x = e.pageX;\n"
192    + " y = e.pageY;\n" + " }\n" + " else\n" + " {\n"
193    + " x = event.x + document.body.scrollLeft;\n"
194    + " y = event.y + document.body.scrollTop;\n" + " }\n"
195    + " toolTipSTYLE.left = x + offsetX;\n"
196    + " toolTipSTYLE.top = y + offsetY;\n" + " return true;\n"
197    + "}\n" + "</script>\n" + "</head>\n" + "<body>\n"
198    + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
199    + "<script language=\"JavaScript\"><!--\n"
200    + "initToolTips(); //--></script>\n");
201   
202    }
203   
204    /**
205    * Prompts the user to choose an output file and returns the file path, or
206    * null on Cancel
207    *
208    * @return
209    */
 
210  0 toggle public String getOutputFile()
211    {
212  0 String selectedFile = null;
213   
214    // TODO: JAL-3048 generate html rendered view (requires SvgGraphics and/or
215    // Jalview HTML rendering system- probably not required for Jalview-JS)
216  0 JalviewFileChooser jvFileChooser = new JalviewFileChooser("html",
217    "HTML files");
218  0 jvFileChooser.setFileView(new JalviewFileView());
219   
220  0 jvFileChooser
221    .setDialogTitle(MessageManager.getString("label.save_as_html"));
222  0 jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
223   
224  0 int fileChooserOpt = jvFileChooser.showSaveDialog(null);
225  0 if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
226    {
227  0 Cache.setProperty("LAST_DIRECTORY",
228    jvFileChooser.getSelectedFile().getParent());
229  0 selectedFile = jvFileChooser.getSelectedFile().getPath();
230    }
231   
232  0 return selectedFile;
233    }
234   
 
235  4 toggle protected void setProgressMessage(String message)
236    {
237  4 if (pIndicator != null && !isHeadless())
238    {
239  0 pIndicator.setProgressBar(message, pSessionId);
240    }
241    else
242    {
243  4 jalview.bin.Console.outPrintln(message);
244    }
245    }
246   
247    /**
248    * Answers true if HTML export is invoke in headless mode or false otherwise
249    *
250    * @return
251    */
 
252  7 toggle protected boolean isHeadless()
253    {
254  7 return System.getProperty("java.awt.headless") != null
255    && System.getProperty("java.awt.headless").equals("true");
256    }
257   
258    /**
259    * This method provides implementation of consistent behaviour which should
260    * occur after a HTML file export. It MUST be called at the end of the
261    * exportHTML() method implementation.
262    */
 
263  2 toggle protected void exportCompleted()
264    {
265  2 if (isLaunchInBrowserAfterExport() && !isHeadless())
266    {
267    /*
268    try
269    {
270    */
271  0 jalview.util.BrowserLauncher.openURL("file:///" + getExportedFile());
272    /*
273    } catch (IOException e)
274    {
275    e.printStackTrace();
276    }
277    */
278    }
279    }
280   
281    /**
282    * if this answers true then BioJSON data will be embedded to the exported
283    * HTML file otherwise it won't be embedded.
284    *
285    * @return
286    */
287    public abstract boolean isEmbedData();
288   
289    /**
290    * if this answers true then the generated HTML file is opened for viewing in
291    * a browser after its generation otherwise it won't be opened in a browser
292    *
293    * @return
294    */
295    public abstract boolean isLaunchInBrowserAfterExport();
296   
297    /**
298    * handle to the generated HTML file
299    *
300    * @return
301    */
 
302  0 toggle public File getExportedFile()
303    {
304  0 return generatedFile;
305    }
306   
 
307  1 toggle public void exportHTML(String outputFile) throws ImageOutputException
308    {
309  1 exportHTML(outputFile, null);
310    }
311   
 
312  2 toggle public void exportHTML(String outputFile, String renderer)
313    throws ImageOutputException
314    {
315  2 setProgressMessage(MessageManager.formatMessage(
316    "status.exporting_alignment_as_x_file", getDescription()));
317  2 try
318    {
319  2 if (outputFile == null)
320    {
321    /*
322    * prompt for output file
323    */
324  0 outputFile = getOutputFile();
325  0 if (outputFile == null)
326    {
327  0 setProgressMessage(MessageManager.formatMessage(
328    "status.cancelled_image_export_operation",
329    getDescription()));
330  0 return;
331    }
332    }
333  2 generatedFile = new File(outputFile);
334    } catch (Exception e)
335    {
336  0 setProgressMessage(MessageManager
337    .formatMessage("info.error_creating_file", getDescription()));
338  0 e.printStackTrace();
339  0 return;
340    }
341  2 if (Jalview.isHeadlessMode())
342    {
343  2 this.run(renderer);
344    }
345    else
346    {
347  0 new Thread(this).start();
348    }
349   
350    }
351   
352    /**
353    * Answers a short description of the image format suitable for display in
354    * messages
355    *
356    * @return
357    */
 
358  4 toggle protected final String getDescription()
359    {
360  4 return description;
361    }
362   
363    // used to pass an option such as render to run
364    public abstract void run(String string) throws ImageOutputException;
365    }