Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
HTMLOutput	41	64	28	0.660%	Show methods

Class HTMLOutput

Class HTMLOutput	Line # 41	Total Statements 64	Complexity 28	TOTAL Coverage 0.660%
HTMLOutput(AlignmentPanel,String)   HTMLOutput(AlignmentPanel,String)	6767	4.04	1.01	1.0 1.0100%
getBioJSONData() : String   getBioJSONData() : String	8282	7.07	3.03	0.90909094 0.9090909490.9%
readFileAsString(File) : String   readFileAsString(File) : String	110110	19.019	6.06	0.7777778 0.777777877.8%
getImageMapHTML() : String   getImageMapHTML() : String	150150	1.01	1.01	0.0 0.00%
getOutputFile() : String   getOutputFile() : String	210210	10.010	2.02	0.0 0.00%
setProgressMessage(String) : void   setProgressMessage(String) : void	235235	3.03	3.03	0.6 0.660%
isHeadless() : boolean   isHeadless() : boolean	252252	1.01	1.01	1.0 1.0100%
exportCompleted() : void   exportCompleted() : void	263263	2.02	3.03	0.5 0.550%
getExportedFile() : File   getExportedFile() : File	302302	1.01	1.01	0.0 0.00%
exportHTML(String) : void   exportHTML(String) : void	307307	1.01	1.01	1.0 1.0100%
exportHTML(String,String) : void   exportHTML(String,String) : void	312312	14.014	5.05	0.4 0.440%
getDescription() : String   getDescription() : String	358358	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.22	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 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
		60% Uncovered Elements: 40 (100) Complexity: 28 Complexity Density: 0.44
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		*/
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
67	2	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		*/
		90.9% Uncovered Elements: 1 (11) Complexity: 3 Complexity Density: 0.43
82	2	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		*/
		77.8% Uncovered Elements: 6 (27) Complexity: 6 Complexity Density: 0.32
110	2	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
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
150	0	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		*/
		0% Uncovered Elements: 12 (12) Complexity: 2 Complexity Density: 0.2
210	0	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
		60% Uncovered Elements: 2 (5) Complexity: 3 Complexity Density: 1
235	4	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		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
252	7	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		*/
		50% Uncovered Elements: 2 (4) Complexity: 3 Complexity Density: 1.5
263	2	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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
302	0	public File getExportedFile()...
303		{
304	0	return generatedFile;
305		}
306
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
307	1	public void exportHTML(String outputFile) throws ImageOutputException...
308		{
309	1	exportHTML(outputFile, null);
310		}
311
		40% Uncovered Elements: 12 (20) Complexity: 5 Complexity Density: 0.36
312	2	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		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
358	4	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		}