Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
HTMLOutput	38	61	27	72	0.2340425623.4%	Show methods

Class HTMLOutput

Class HTMLOutput	Line # 38	Total Statements 61	Complexity 27	Uncovered Elements 72	TOTAL Coverage 0.2340425623.4%
HTMLOutput(AlignmentPanel)   HTMLOutput(AlignmentPanel)	5555	2.02	1.01	2.02	0.0 0.00%
getBioJSONData() : String   getBioJSONData() : String	6868	7.07	3.03	11.011	0.0 0.00%
readFileAsString(File) : String   readFileAsString(File) : String	9696	19.019	6.06	6.06	0.7777778 0.777777877.8%
getImageMapHTML() : String   getImageMapHTML() : String	136136	1.01	1.01	1.01	0.0 0.00%
getOutputFile() : String   getOutputFile() : String	196196	10.010	2.02	12.012	0.0 0.00%
setProgressMessage(String) : void   setProgressMessage(String) : void	221221	3.03	3.03	5.05	0.0 0.00%
isHeadless() : boolean   isHeadless() : boolean	238238	1.01	1.01	1.01	0.0 0.00%
exportStarted() : void   exportStarted() : void	249249	1.01	1.01	1.01	0.0 0.00%
exportCompleted() : void   exportCompleted() : void	259259	4.04	4.04	6.06	0.0 0.00%
getExportedFile() : File   getExportedFile() : File	295295	1.01	1.01	1.01	0.0 0.00%
exportHTML(String) : void   exportHTML(String) : void	300300	12.012	4.04	16.016	0.0 0.00%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.23404256	jalview.io.BioJsHTMLOutputTest.getJalviewAlignmentAsJsonStringjalview.io.BioJsHTMLOutputTest.getJalviewAlignmentAsJsonString	1PASS

 

Source view

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 jalview.api.AlignExportSettingsI;
24		import jalview.bin.Cache;
25		import jalview.datamodel.AlignExportSettingsAdapter;
26		import jalview.datamodel.AlignmentExportData;
27		import jalview.gui.AlignmentPanel;
28		import jalview.gui.IProgressIndicator;
29		import jalview.util.MessageManager;
30
31		import java.io.BufferedReader;
32		import java.io.File;
33		import java.io.IOException;
34		import java.io.InputStreamReader;
35		import java.net.URL;
36		import java.util.Objects;
37
		23.4% Uncovered Elements: 72 (94) Complexity: 27 Complexity Density: 0.44
38		public abstract class HTMLOutput implements Runnable
39		{
40		protected AlignmentPanel ap;
41
42		protected long pSessionId;
43
44		protected IProgressIndicator pIndicator;
45
46		protected File generatedFile;
47
48		String _bioJson = null;
49
50		/**
51		* Constructor given an alignment panel (which should not be null)
52		*
53		* @param ap
54		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
55	0	public HTMLOutput(AlignmentPanel ap)...
56		{
57	0	this.ap = ap;
58	0	this.pIndicator = ap.alignFrame;
59		}
60
61		/**
62		* Gets the BioJSON data as a string, with lazy evaluation (first time called
63		* only). If the output format is configured not to embed BioJSON, returns
64		* null.
65		*
66		* @return
67		*/
		0% Uncovered Elements: 11 (11) Complexity: 3 Complexity Density: 0.43
68	0	public String getBioJSONData()...
69		{
70	0	if (!isEmbedData())
71		{
72	0	return null;
73		}
74	0	if (_bioJson == null)
75		{
76	0	AlignExportSettingsI options = new AlignExportSettingsAdapter(true);
77	0	AlignmentExportData exportData = ap.getAlignViewport()
78		.getAlignExportData(options);
79	0	_bioJson = new FormatAdapter(ap, options).formatSequences(
80		FileFormat.Json, exportData.getAlignment(),
81		exportData.getOmitHidden(), exportData.getStartEndPostions(),
82		ap.getAlignViewport().getAlignment().getHiddenColumns());
83		}
84
85	0	return _bioJson;
86		}
87
88		/**
89		* Read a template file content as string
90		*
91		* @param file
92		* - the file to be read
93		* @return File content as String
94		* @throws IOException
95		*/
		77.8% Uncovered Elements: 6 (27) Complexity: 6 Complexity Density: 0.32
96	1	public static String readFileAsString(File file) throws IOException...
97		{
98	1	InputStreamReader isReader = null;
99	1	BufferedReader buffReader = null;
100	1	StringBuilder sb = new StringBuilder();
101	1	Objects.requireNonNull(file, "File must not be null!");
102	1	@SuppressWarnings("deprecation")
103		URL url = file.toURL();
104	1	if (url != null)
105		{
106	1	try
107		{
108	1	isReader = new InputStreamReader(url.openStream());
109	1	buffReader = new BufferedReader(isReader);
110	1	String line;
111	1	String lineSeparator = System.getProperty("line.separator");
112	?	while ((line = buffReader.readLine()) != null)
113		{
114	9670	sb.append(line).append(lineSeparator);
115		}
116
117		} catch (Exception ex)
118		{
119	0	ex.printStackTrace();
120		} finally
121		{
122	1	if (isReader != null)
123		{
124	1	isReader.close();
125		}
126
127	1	if (buffReader != null)
128		{
129	1	buffReader.close();
130		}
131		}
132		}
133	1	return sb.toString();
134		}
135
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
136	0	public static String getImageMapHTML()...
137		{
138	0	return new String("<html>\n" + "<head>\n"
139		+ "<script language=\"JavaScript\">\n"
140		+ "var ns4 = document.layers;\n"
141		+ "var ns6 = document.getElementById && !document.all;\n"
142		+ "var ie4 = document.all;\n" + "offsetX = 0;\n"
143		+ "offsetY = 20;\n" + "var toolTipSTYLE=\"\";\n"
144		+ "function initToolTips()\n" + "{\n" + " if(ns4||ns6||ie4)\n"
145		+ " {\n"
146		+ " if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
147		+ " else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
148		+ " else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
149		+ " if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
150		+ " else\n" + " {\n"
151		+ " toolTipSTYLE.visibility = \"visible\";\n"
152		+ " toolTipSTYLE.display = \"none\";\n" + " }\n"
153		+ " document.onmousemove = moveToMouseLoc;\n" + " }\n"
154		+ "}\n" + "function toolTip(msg, fg, bg)\n" + "{\n"
155		+ " if(toolTip.arguments.length < 1) // hide\n" + " {\n"
156		+ " if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
157		+ " else toolTipSTYLE.display = \"none\";\n" + " }\n"
158		+ " else // show\n" + " {\n"
159		+ " if(!fg) fg = \"#555555\";\n"
160		+ " if(!bg) bg = \"#FFFFFF\";\n" + " var content =\n"
161		+ " '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
162		+ " '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
163		+ " '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
164		+ " '\" size=\"-2\">&nbsp;' + msg +\n"
165		+ " '&nbsp;</font></td></table></td></table>';\n"
166		+ " if(ns4)\n" + " {\n"
167		+ " toolTipSTYLE.document.write(content);\n"
168		+ " toolTipSTYLE.document.close();\n"
169		+ " toolTipSTYLE.visibility = \"visible\";\n" + " }\n"
170		+ " if(ns6)\n" + " {\n"
171		+ " document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
172		+ " toolTipSTYLE.display='block'\n" + " }\n"
173		+ " if(ie4)\n" + " {\n"
174		+ " document.all(\"toolTipLayer\").innerHTML=content;\n"
175		+ " toolTipSTYLE.display='block'\n" + " }\n" + " }\n"
176		+ "}\n" + "function moveToMouseLoc(e)\n" + "{\n"
177		+ " if(ns4||ns6)\n" + " {\n" + " x = e.pageX;\n"
178		+ " y = e.pageY;\n" + " }\n" + " else\n" + " {\n"
179		+ " x = event.x + document.body.scrollLeft;\n"
180		+ " y = event.y + document.body.scrollTop;\n" + " }\n"
181		+ " toolTipSTYLE.left = x + offsetX;\n"
182		+ " toolTipSTYLE.top = y + offsetY;\n" + " return true;\n"
183		+ "}\n" + "</script>\n" + "</head>\n" + "<body>\n"
184		+ "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
185		+ "<script language=\"JavaScript\"><!--\n"
186		+ "initToolTips(); //--></script>\n");
187
188		}
189
190		/**
191		* Prompts the user to choose an output file and returns the file path, or
192		* null on Cancel
193		*
194		* @return
195		*/
		0% Uncovered Elements: 12 (12) Complexity: 2 Complexity Density: 0.2
196	0	public String getOutputFile()...
197		{
198	0	String selectedFile = null;
199
200		// TODO: JAL-3048 generate html rendered view (requires SvgGraphics and/or
201		// Jalview HTML rendering system- probably not required for Jalview-JS)
202	0	JalviewFileChooser jvFileChooser = new JalviewFileChooser("html",
203		"HTML files");
204	0	jvFileChooser.setFileView(new JalviewFileView());
205
206	0	jvFileChooser
207		.setDialogTitle(MessageManager.getString("label.save_as_html"));
208	0	jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
209
210	0	int fileChooserOpt = jvFileChooser.showSaveDialog(null);
211	0	if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
212		{
213	0	Cache.setProperty("LAST_DIRECTORY",
214		jvFileChooser.getSelectedFile().getParent());
215	0	selectedFile = jvFileChooser.getSelectedFile().getPath();
216		}
217
218	0	return selectedFile;
219		}
220
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
221	0	protected void setProgressMessage(String message)...
222		{
223	0	if (pIndicator != null && !isHeadless())
224		{
225	0	pIndicator.setProgressBar(message, pSessionId);
226		}
227		else
228		{
229	0	System.out.println(message);
230		}
231		}
232
233		/**
234		* Answers true if HTML export is invoke in headless mode or false otherwise
235		*
236		* @return
237		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
238	0	protected boolean isHeadless()...
239		{
240	0	return System.getProperty("java.awt.headless") != null
241		&& System.getProperty("java.awt.headless").equals("true");
242		}
243
244		/**
245		* This method provides implementation of consistent behaviour which should
246		* occur before a HTML file export. It MUST be called at the start of the
247		* exportHTML() method implementation.
248		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
249	0	protected void exportStarted()...
250		{
251	0	pSessionId = System.currentTimeMillis();
252		}
253
254		/**
255		* This method provides implementation of consistent behaviour which should
256		* occur after a HTML file export. It MUST be called at the end of the
257		* exportHTML() method implementation.
258		*/
		0% Uncovered Elements: 6 (6) Complexity: 4 Complexity Density: 1
259	0	protected void exportCompleted()...
260		{
261	0	if (isLaunchInBrowserAfterExport() && !isHeadless())
262		{
263	0	try
264		{
265	0	jalview.util.BrowserLauncher
266		.openURL("file:///" + getExportedFile());
267		} catch (IOException e)
268		{
269	0	e.printStackTrace();
270		}
271		}
272		}
273
274		/**
275		* if this answers true then BioJSON data will be embedded to the exported
276		* HTML file otherwise it won't be embedded.
277		*
278		* @return
279		*/
280		public abstract boolean isEmbedData();
281
282		/**
283		* if this answers true then the generated HTML file is opened for viewing in
284		* a browser after its generation otherwise it won't be opened in a browser
285		*
286		* @return
287		*/
288		public abstract boolean isLaunchInBrowserAfterExport();
289
290		/**
291		* handle to the generated HTML file
292		*
293		* @return
294		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
295	0	public File getExportedFile()...
296		{
297	0	return generatedFile;
298		}
299
		0% Uncovered Elements: 16 (16) Complexity: 4 Complexity Density: 0.33
300	0	public void exportHTML(String outputFile)...
301		{
302	0	exportStarted();
303	0	try
304		{
305	0	if (outputFile == null)
306		{
307		/*
308		* prompt for output file
309		*/
310	0	outputFile = getOutputFile();
311	0	if (outputFile == null)
312		{
313	0	setProgressMessage(MessageManager.formatMessage(
314		"status.cancelled_image_export_operation",
315		getDescription()));
316	0	return;
317		}
318		}
319	0	generatedFile = new File(outputFile);
320		} catch (Exception e)
321		{
322	0	setProgressMessage(MessageManager
323		.formatMessage("info.error_creating_file", getDescription()));
324	0	e.printStackTrace();
325	0	return;
326		}
327	0	new Thread(this).start();
328
329		}
330
331		/**
332		* Answers a short description of the image format suitable for display in
333		* messages
334		*
335		* @return
336		*/
337		protected abstract String getDescription();
338		}