Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
WebserviceInfo	64	217	92	0.00%	Show methods
WebserviceInfo.AnimatedPanel	791	48	16	0.00%	Show methods

Class WebserviceInfo

Class WebserviceInfo	Line # 64	Total Statements 217	Complexity 92	TOTAL Coverage 0.00%
setVisible(boolean) : void   setVisible(boolean) : void	102102	2.02	1.01	0.0 0.00%
isViewResultsImmediatly() : boolean   isViewResultsImmediatly() : boolean	124124	1.01	1.01	0.0 0.00%
setViewResultsImmediatly(boolean) : void   setViewResultsImmediatly(boolean) : void	136136	1.01	1.01	0.0 0.00%
getStyleSheet(HTMLEditorKit) : StyleSheet   getStyleSheet(HTMLEditorKit) : StyleSheet	141141	4.04	1.01	0.0 0.00%
addJobPane() : int   addJobPane() : int	168168	34.034	5.05	0.0 0.00%
WebserviceInfo(String,String,boolean)   WebserviceInfo(String,String,boolean)	245245	1.01	1.01	0.0 0.00%
WebserviceInfo(String,String,int,int,boolean)   WebserviceInfo(String,String,int,int,boolean)	262262	1.01	1.01	0.0 0.00%
getthisService() : jalview.ws.WSClientI   getthisService() : jalview.ws.WSClientI	273273	1.01	1.01	0.0 0.00%
setthisService(jalview.ws.WSClientI) : void   setthisService(jalview.ws.WSClientI) : void	285285	5.05	1.01	0.0 0.00%
rebuildButtonPanel() : void   rebuildButtonPanel() : void	294294	6.06	3.03	0.0 0.00%
internalFrameClosed(InternalFrameEvent) : void   internalFrameClosed(InternalFrameEvent) : void	360360	3.03	3.03	0.0 0.00%
init(String,String,int,int,boolean) : void   init(String,String,int,int,boolean) : void	323323	23.023	2.02	0.0 0.00%
setStatus(int) : void   setStatus(int) : void	381381	23.023	8.08	0.0 0.00%
setStatus(int,int) : void   setStatus(int,int) : void	422422	23.023	9.09	0.0 0.00%
getInfoText() : String   getInfoText() : String	460460	1.01	1.01	0.0 0.00%
setInfoText(String) : void   setInfoText(String) : void	471471	1.01	1.01	0.0 0.00%
appendInfoText(String) : void   appendInfoText(String) : void	482482	1.01	1.01	0.0 0.00%
getProgressText(int) : String   getProgressText(int) : String	492492	5.05	3.03	0.0 0.00%
setProgressText(int,String) : void   setProgressText(int,String) : void	516516	5.05	3.03	0.0 0.00%
getHtmlFragment(String,boolean,boolean) : String   getHtmlFragment(String,boolean,boolean) : String	544544	11.011	9.09	0.0 0.00%
ensureHtmlTagged(String) : String   ensureHtmlTagged(String) : String	574574	16.016	9.09	0.0 0.00%
appendProgressText(int,String) : void   appendProgressText(int,String) : void	616616	6.06	3.03	0.0 0.00%
setProgressText(String) : void   setProgressText(String) : void	643643	1.01	1.01	0.0 0.00%
appendProgressText(String) : void   appendProgressText(String) : void	651651	1.01	1.01	0.0 0.00%
getProgressText() : String   getProgressText() : String	659659	1.01	1.01	0.0 0.00%
getProgressName(int) : String   getProgressName(int) : String	671671	5.05	3.03	0.0 0.00%
setProgressName(String,int) : void   setProgressName(String,int) : void	696696	7.07	2.02	0.0 0.00%
cancel_actionPerformed(ActionEvent) : void   cancel_actionPerformed(ActionEvent) : void	715715	4.04	2.02	0.0 0.00%
run() : void   run() : void	747747	1.01	1.01	0.0 0.00%
warnUser(String,String) : void   warnUser(String,String) : void	743743	1.01	1.01	0.0 0.00%
setResultsReady() : void   setResultsReady() : void	761761	10.010	3.03	0.0 0.00%
setFinishedNoResults() : void   setFinishedNoResults() : void	783783	4.04	1.01	0.0 0.00%
setRenderAsHtml(boolean) : void   setRenderAsHtml(boolean) : void	911911	1.01	1.01	0.0 0.00%
hyperlinkUpdate(HyperlinkEvent) : void   hyperlinkUpdate(HyperlinkEvent) : void	916916	1.01	1.01	0.0 0.00%
setProgressBar(String,long) : void   setProgressBar(String,long) : void	927927	1.01	1.01	0.0 0.00%
registerHandler(long,IProgressIndicatorHandler) : void   registerHandler(long,IProgressIndicatorHandler) : void	933933	1.01	1.01	0.0 0.00%
operationInProgress() : boolean   operationInProgress() : boolean	944944	1.01	1.01	0.0 0.00%
getProgressBar(long) : JProgressBar   getProgressBar(long) : JProgressBar	950950	1.01	1.01	0.0 0.00%
getMessage(long) : String   getMessage(long) : String	956956	1.01	1.01	0.0 0.00%
setProgressBarMessage(long,String) : void   setProgressBarMessage(long,String) : void	961961	1.01	1.01	0.0 0.00%

 

Class WebserviceInfo.AnimatedPanel

Class WebserviceInfo.AnimatedPanel	Line # 791	Total Statements 48	Complexity 16	TOTAL Coverage 0.00%
run() : void   run() : void	797797	21.021	6.06	0.0 0.00%
park() : void   park() : void	841841	12.012	4.04	0.0 0.00%
drawPanel() : void   drawPanel() : void	870870	13.013	5.05	0.0 0.00%
paintComponent(Graphics) : void   paintComponent(Graphics) : void	900900	2.02	1.01	0.0 0.00%

 

Contributing tests

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.gui;
22
23		import java.awt.BorderLayout;
24		import java.awt.Color;
25		import java.awt.Dimension;
26		import java.awt.Graphics;
27		import java.awt.Graphics2D;
28		import java.awt.GridLayout;
29		import java.awt.Image;
30		import java.awt.MediaTracker;
31		import java.awt.RenderingHints;
32		import java.awt.event.ActionEvent;
33		import java.awt.image.BufferedImage;
34		import java.util.Locale;
35		import java.util.Vector;
36
37		import javax.swing.JComponent;
38		import javax.swing.JEditorPane;
39		import javax.swing.JInternalFrame;
40		import javax.swing.JPanel;
41		import javax.swing.JProgressBar;
42		import javax.swing.JScrollPane;
43		import javax.swing.JTabbedPane;
44		import javax.swing.JTextArea;
45		import javax.swing.event.HyperlinkEvent;
46		import javax.swing.event.HyperlinkListener;
47		import javax.swing.event.InternalFrameAdapter;
48		import javax.swing.event.InternalFrameEvent;
49		import javax.swing.text.html.HTMLEditorKit;
50		import javax.swing.text.html.StyleSheet;
51
52		import jalview.jbgui.GWebserviceInfo;
53		import jalview.util.ChannelProperties;
54		import jalview.util.MessageManager;
55		import jalview.ws.WSClientI;
56
57		/**
58		* Base class for web service client thread and gui TODO: create StAX parser to
59		* extract html body content reliably when preparing html formatted job statuses
60		*
61		* @author $author$
62		* @version $Revision$
63		*/
		0% Uncovered Elements: 323 (323) Complexity: 92 Complexity Density: 0.42
64		public class WebserviceInfo extends GWebserviceInfo
65		implements HyperlinkListener, IProgressIndicator
66		{
67
68		/** Job is Queued */
69		public static final int STATE_QUEUING = 0;
70
71		/** Job is Running */
72		public static final int STATE_RUNNING = 1;
73
74		/** Job has finished with no errors */
75		public static final int STATE_STOPPED_OK = 2;
76
77		/** Job has been cancelled with no errors */
78		public static final int STATE_CANCELLED_OK = 3;
79
80		/** job has stopped because of some error */
81		public static final int STATE_STOPPED_ERROR = 4;
82
83		/** job has failed because of some unavoidable service interruption */
84		public static final int STATE_STOPPED_SERVERERROR = 5;
85
86		int currentStatus = STATE_QUEUING;
87
88		Image image;
89
90		float angle = 0f;
91
92		String title = "";
93
94		jalview.ws.WSClientI thisService;
95
96		boolean serviceIsCancellable;
97
98		JInternalFrame frame;
99
100		private IProgressIndicator progressBar;
101
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
102	0	@Override...
103		public void setVisible(boolean aFlag)
104		{
105	0	super.setVisible(aFlag);
106	0	frame.setVisible(aFlag);
107		}
108
109		JTabbedPane subjobs = null;
110
111		java.util.Vector jobPanes = null;
112
113		private boolean serviceCanMergeResults = false;
114
115		private boolean viewResultsImmediatly = true;
116
117		/**
118		* Get
119		*
120		* @param flag
121		* to indicate if results will be shown in a new window as soon as
122		* they are available.
123		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
124	0	public boolean isViewResultsImmediatly()...
125		{
126	0	return viewResultsImmediatly;
127		}
128
129		/**
130		* Set
131		*
132		* @param flag
133		* to indicate if results will be shown in a new window as soon as
134		* they are available.
135		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
136	0	public void setViewResultsImmediatly(boolean viewResultsImmediatly)...
137		{
138	0	this.viewResultsImmediatly = viewResultsImmediatly;
139		}
140
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
141	0	private StyleSheet getStyleSheet(HTMLEditorKit editorKit)...
142		{
143
144		// Copied blatantly from
145		// http://www.velocityreviews.com/forums/t132265-string-into-htmldocument.html
146	0	StyleSheet myStyleSheet = new StyleSheet();
147
148	0	myStyleSheet.addStyleSheet(editorKit.getStyleSheet());
149
150	0	editorKit.setStyleSheet(myStyleSheet);
151
152		/*
153		* Set the style sheet rules here by reading them from the constants
154		* interface.
155		*/
156		/*
157		* for (int ix=0; ix<CSS_RULES.length; ix++) {
158		*
159		* myStyleSheet.addRule(CSS_RULES[ix]);
160		*
161		* }
162		*/
163	0	return myStyleSheet;
164
165		}
166
167		// tabbed or not
		0% Uncovered Elements: 42 (42) Complexity: 5 Complexity Density: 0.15
168	0	public synchronized int addJobPane()...
169		{
170	0	JScrollPane jobpane = new JScrollPane();
171	0	JComponent _progressText;
172	0	if (renderAsHtml)
173		{
174	0	JEditorPane progressText = new JEditorPane("text/html", "");
175	0	progressText.addHyperlinkListener(this);
176	0	_progressText = progressText;
177		// progressText.setFont(new java.awt.Font("Verdana", 0, 10));
178		// progressText.setBorder(null);
179	0	progressText.setEditable(false);
180		/*
181		* HTMLEditorKit myEditorKit = new HTMLEditorKit();
182		*
183		* StyleSheet myStyleSheet = getStyleSheet(myEditorKit);
184		*
185		* HTMLDocument tipDocument = (HTMLDocument)
186		* (myEditorKit.createDefaultDocument());
187		*
188		* progressText.setDocument(tipDocument);
189	0	*/progressText.setText("<html><h1>WS Job</h1></html>");
190		}
191		else
192		{
193	0	JTextArea progressText = new JTextArea();
194	0	_progressText = progressText;
195
196	0	progressText.setFont(new java.awt.Font("Verdana", 0, 10));
197	0	progressText.setBorder(null);
198	0	progressText.setEditable(false);
199	0	progressText.setText("WS Job");
200	0	progressText.setLineWrap(true);
201	0	progressText.setWrapStyleWord(true);
202		}
203	0	jobpane.setName("JobPane");
204	0	jobpane.getViewport().add(_progressText, null);
205	0	jobpane.setBorder(null);
206	0	if (jobPanes == null)
207		{
208	0	jobPanes = new Vector();
209		}
210	0	int newpane = jobPanes.size();
211	0	jobPanes.add(jobpane);
212
213	0	if (newpane == 0)
214		{
215	0	this.add(jobpane, BorderLayout.CENTER);
216		}
217		else
218		{
219	0	if (newpane == 1)
220		{
221		// revert to a tabbed pane.
222	0	JScrollPane firstpane;
223	0	this.remove(firstpane = (JScrollPane) jobPanes.get(0));
224	0	subjobs = new JTabbedPane();
225	0	this.add(subjobs, BorderLayout.CENTER);
226	0	subjobs.add(firstpane);
227	0	subjobs.setTitleAt(0, firstpane.getName());
228		}
229	0	subjobs.add(jobpane);
230		}
231	0	return newpane; // index for accessor methods below
232		}
233
234		/**
235		* Creates a new WebserviceInfo object.
236		*
237		* @param title
238		* short name and job type
239		* @param info
240		* reference or other human readable description
241		* @param makeVisible
242		* true to display the webservices window immediatly (otherwise need
243		* to call setVisible(true))
244		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
245	0	public WebserviceInfo(String title, String info, boolean makeVisible)...
246		{
247	0	init(title, info, 520, 500, makeVisible);
248		}
249
250		/**
251		* Creates a new WebserviceInfo object.
252		*
253		* @param title
254		* DOCUMENT ME!
255		* @param info
256		* DOCUMENT ME!
257		* @param width
258		* DOCUMENT ME!
259		* @param height
260		* DOCUMENT ME!
261		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
262	0	public WebserviceInfo(String title, String info, int width, int height,...
263		boolean makeVisible)
264		{
265	0	init(title, info, width, height, makeVisible);
266		}
267
268		/**
269		* DOCUMENT ME!
270		*
271		* @return DOCUMENT ME!
272		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
273	0	public jalview.ws.WSClientI getthisService()...
274		{
275	0	return thisService;
276		}
277
278		/**
279		* Update state of GUI based on client capabilities (like whether the job is
280		* cancellable, whether the 'merge results' button is shown.
281		*
282		* @param newservice
283		* service client to query for capabilities
284		*/
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
285	0	public void setthisService(jalview.ws.WSClientI newservice)...
286		{
287	0	thisService = newservice;
288	0	serviceIsCancellable = newservice.isCancellable();
289	0	frame.setClosable(!serviceIsCancellable);
290	0	serviceCanMergeResults = newservice.canMergeResults();
291	0	rebuildButtonPanel();
292		}
293
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
294	0	private void rebuildButtonPanel()...
295		{
296	0	if (buttonPanel != null)
297		{
298	0	buttonPanel.removeAll();
299	0	if (serviceIsCancellable)
300		{
301	0	buttonPanel.add(cancel);
302	0	frame.setClosable(false);
303		}
304		else
305		{
306	0	frame.setClosable(true);
307		}
308		}
309		}
310
311		/**
312		* DOCUMENT ME!
313		*
314		* @param title
315		* DOCUMENT ME!
316		* @param info
317		* DOCUMENT ME!
318		* @param width
319		* DOCUMENT ME!
320		* @param height
321		* DOCUMENT ME!
322		*/
		0% Uncovered Elements: 23 (23) Complexity: 2 Complexity Density: 0.09
323	0	void init(String title, String info, int width, int height,...
324		boolean makeVisible)
325		{
326	0	frame = new JInternalFrame();
327	0	frame.setFrameIcon(null);
328	0	frame.setContentPane(this);
329	0	Desktop.addInternalFrame(frame, title, makeVisible, width, height);
330	0	frame.setClosable(false);
331
332	0	progressBar = new ProgressBar(statusPanel, statusBar);
333
334	0	this.title = title;
335	0	setInfoText(info);
336
337	0	image = ChannelProperties.getImage("rotatable_logo.48");
338
339	0	MediaTracker mt = new MediaTracker(this);
340	0	mt.addImage(image, 0);
341
342	0	try
343		{
344	0	mt.waitForID(0);
345		} catch (Exception ex)
346		{
347		}
348
349	0	AnimatedPanel ap = new AnimatedPanel();
350	0	ap.setPreferredSize(new Dimension(60, 60));
351	0	titlePanel.add(ap, BorderLayout.WEST);
352	0	titlePanel.add(titleText, BorderLayout.CENTER);
353	0	setStatus(currentStatus);
354
355	0	Thread thread = new Thread(ap);
356	0	thread.start();
357	0	final WebserviceInfo thisinfo = this;
358	0	frame.addInternalFrameListener(new InternalFrameAdapter()
359		{
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
360	0	@Override...
361		public void internalFrameClosed(InternalFrameEvent evt)
362		{
363		// jalview.bin.Console.outPrintln("Shutting down webservice client");
364	0	WSClientI service = thisinfo.getthisService();
365	0	if (service != null && service.isCancellable())
366		{
367	0	service.cancelJob();
368		}
369		}
370		});
371	0	frame.validate();
372
373		}
374
375		/**
376		* DOCUMENT ME!
377		*
378		* @param status
379		* integer status from state constants
380		*/
		0% Uncovered Elements: 25 (25) Complexity: 8 Complexity Density: 0.35
381	0	public void setStatus(int status)...
382		{
383	0	currentStatus = status;
384
385	0	String message = null;
386	0	switch (currentStatus)
387		{
388	0	case STATE_QUEUING:
389	0	message = MessageManager.getString("label.state_queueing");
390	0	break;
391
392	0	case STATE_RUNNING:
393	0	message = MessageManager.getString("label.state_running");
394	0	break;
395
396	0	case STATE_STOPPED_OK:
397	0	message = MessageManager.getString("label.state_completed");
398	0	break;
399
400	0	case STATE_CANCELLED_OK:
401	0	message = MessageManager.getString("label.state_job_cancelled");
402	0	break;
403
404	0	case STATE_STOPPED_ERROR:
405	0	message = MessageManager.getString("label.state_job_error");
406	0	break;
407
408	0	case STATE_STOPPED_SERVERERROR:
409	0	message = MessageManager.getString("label.server_error_try_later");
410	0	break;
411		}
412	0	titleText.setText(title + (message == null ? "" : " - " + message));
413	0	titleText.repaint();
414		}
415
416		/**
417		* subjob status indicator
418		*
419		* @param jobpane
420		* @param status
421		*/
		0% Uncovered Elements: 25 (25) Complexity: 9 Complexity Density: 0.39
422	0	public void setStatus(int jobpane, int status)...
423		{
424	0	if (jobpane < 0 || jobpane >= jobPanes.size())
425		{
426	0	throw new Error(MessageManager.formatMessage(
427		"error.setstatus_called_non_existent_job_pane", new String[]
428		{ Integer.valueOf(jobpane).toString() }));
429		}
430	0	switch (status)
431		{
432	0	case STATE_QUEUING:
433	0	setProgressName(jobpane + " - QUEUED", jobpane);
434	0	break;
435	0	case STATE_RUNNING:
436	0	setProgressName(jobpane + " - RUNNING", jobpane);
437	0	break;
438	0	case STATE_STOPPED_OK:
439	0	setProgressName(jobpane + " - FINISHED", jobpane);
440	0	break;
441	0	case STATE_CANCELLED_OK:
442	0	setProgressName(jobpane + " - CANCELLED", jobpane);
443	0	break;
444	0	case STATE_STOPPED_ERROR:
445	0	setProgressName(jobpane + " - BROKEN", jobpane);
446	0	break;
447	0	case STATE_STOPPED_SERVERERROR:
448	0	setProgressName(jobpane + " - ALERT", jobpane);
449	0	break;
450	0	default:
451	0	setProgressName(jobpane + " - UNKNOWN STATE", jobpane);
452		}
453		}
454
455		/**
456		* DOCUMENT ME!
457		*
458		* @return DOCUMENT ME!
459		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
460	0	public String getInfoText()...
461		{
462	0	return infoText.getText();
463		}
464
465		/**
466		* DOCUMENT ME!
467		*
468		* @param text
469		* DOCUMENT ME!
470		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
471	0	public void setInfoText(String text)...
472		{
473	0	infoText.setText(text);
474		}
475
476		/**
477		* DOCUMENT ME!
478		*
479		* @param text
480		* DOCUMENT ME!
481		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
482	0	public void appendInfoText(String text)...
483		{
484	0	infoText.append(text);
485		}
486
487		/**
488		* DOCUMENT ME!
489		*
490		* @return DOCUMENT ME!
491		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
492	0	public String getProgressText(int which)...
493		{
494	0	if (jobPanes == null)
495		{
496	0	addJobPane();
497		}
498	0	if (renderAsHtml)
499		{
500	0	return ((JEditorPane) ((JScrollPane) jobPanes.get(which))
501		.getViewport().getComponent(0)).getText();
502		}
503		else
504		{
505	0	return ((JTextArea) ((JScrollPane) jobPanes.get(which)).getViewport()
506		.getComponent(0)).getText();
507		}
508		}
509
510		/**
511		* DOCUMENT ME!
512		*
513		* @param text
514		* DOCUMENT ME!
515		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
516	0	public void setProgressText(int which, String text)...
517		{
518	0	if (jobPanes == null)
519		{
520	0	addJobPane();
521		}
522	0	if (renderAsHtml)
523		{
524	0	((JEditorPane) ((JScrollPane) jobPanes.get(which)).getViewport()
525		.getComponent(0)).setText(ensureHtmlTagged(text));
526		}
527		else
528		{
529	0	((JTextArea) ((JScrollPane) jobPanes.get(which)).getViewport()
530		.getComponent(0)).setText(text);
531		}
532		}
533
534		/**
535		* extract content from &lt;body&gt; content &lt;/body&gt;
536		*
537		* @param text
538		* @param leaveFirst
539		* - set to leave the initial html tag intact
540		* @param leaveLast
541		* - set to leave the final html tag intact
542		* @return
543		*/
		0% Uncovered Elements: 25 (25) Complexity: 9 Complexity Density: 0.82
544	0	private String getHtmlFragment(String text, boolean leaveFirst,...
545		boolean leaveLast)
546		{
547	0	if (text == null)
548		{
549	0	return null;
550		}
551	0	String lowertxt = text.toLowerCase(Locale.ROOT);
552	0	int htmlpos = leaveFirst ? -1 : lowertxt.indexOf("<body");
553
554	0	int htmlend = leaveLast ? -1 : lowertxt.indexOf("</body");
555	0	int htmlpose = lowertxt.indexOf(">", htmlpos),
556		htmlende = lowertxt.indexOf(">", htmlend);
557	0	if (htmlend == -1 && htmlpos == -1)
558		{
559	0	return text;
560		}
561	0	if (htmlend > -1)
562		{
563	0	return text.substring((htmlpos == -1 ? 0 : htmlpose + 1), htmlend);
564		}
565	0	return text.substring(htmlpos == -1 ? 0 : htmlpose + 1);
566		}
567
568		/**
569		* very simple routine for adding/ensuring html tags are present in text.
570		*
571		* @param text
572		* @return properly html tag enclosed text
573		*/
		0% Uncovered Elements: 26 (26) Complexity: 9 Complexity Density: 0.56
574	0	private String ensureHtmlTagged(String text)...
575		{
576	0	if (text == null)
577		{
578	0	return "";
579		}
580	0	String lowertxt = text.toLowerCase(Locale.ROOT);
581	0	int htmlpos = lowertxt.indexOf("<body");
582	0	int htmlend = lowertxt.indexOf("</body");
583	0	int doctype = lowertxt.indexOf("<!doctype");
584	0	int xmltype = lowertxt.indexOf("<?xml");
585	0	if (htmlend == -1)
586		{
587	0	text = text + "</body></html>";
588		}
589	0	if (htmlpos > -1)
590		{
591	0	if ((doctype > -1 && htmlpos > doctype)
592		|| (xmltype > -1 && htmlpos > xmltype))
593		{
594	0	text = "<html><head></head><body>\n" + text.substring(htmlpos - 1);
595		}
596		}
597		else
598		{
599	0	text = "<html><head></head><body>\n" + text;
600		}
601	0	if (text.indexOf("<meta") > -1)
602		{
603	0	System.err
604		.println("HTML COntent: \n" + text + "<< END HTML CONTENT\n");
605
606		}
607	0	return text;
608		}
609
610		/**
611		* DOCUMENT ME!
612		*
613		* @param text
614		* DOCUMENT ME!
615		*/
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
616	0	public void appendProgressText(int which, String text)...
617		{
618	0	if (jobPanes == null)
619		{
620	0	addJobPane();
621		}
622	0	if (renderAsHtml)
623		{
624	0	String txt = getHtmlFragment(
625		((JEditorPane) ((JScrollPane) jobPanes.get(which))
626		.getViewport().getComponent(0)).getText(),
627		true, false);
628	0	((JEditorPane) ((JScrollPane) jobPanes.get(which)).getViewport()
629		.getComponent(0))
630		.setText(ensureHtmlTagged(
631		txt + getHtmlFragment(text, false, true)));
632		}
633		else
634		{
635	0	((JTextArea) ((JScrollPane) jobPanes.get(which)).getViewport()
636		.getComponent(0)).append(text);
637		}
638		}
639
640		/**
641		* setProgressText(0, text)
642		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
643	0	public void setProgressText(String text)...
644		{
645	0	setProgressText(0, text);
646		}
647
648		/**
649		* appendProgressText(0, text)
650		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
651	0	public void appendProgressText(String text)...
652		{
653	0	appendProgressText(0, text);
654		}
655
656		/**
657		* getProgressText(0)
658		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
659	0	public String getProgressText()...
660		{
661	0	return getProgressText(0);
662		}
663
664		/**
665		* get the tab title for a subjob
666		*
667		* @param which
668		* int
669		* @return String
670		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
671	0	public String getProgressName(int which)...
672		{
673	0	if (jobPanes == null)
674		{
675	0	addJobPane();
676		}
677	0	if (subjobs != null)
678		{
679	0	return subjobs.getTitleAt(which);
680		}
681		else
682		{
683	0	return ((JScrollPane) jobPanes.get(which)).getViewport()
684		.getComponent(0).getName();
685		}
686		}
687
688		/**
689		* set the tab title for a subjob
690		*
691		* @param name
692		* String
693		* @param which
694		* int
695		*/
		0% Uncovered Elements: 9 (9) Complexity: 2 Complexity Density: 0.29
696	0	public void setProgressName(String name, int which)...
697		{
698	0	if (subjobs != null)
699		{
700	0	subjobs.setTitleAt(which, name);
701	0	subjobs.revalidate();
702	0	subjobs.repaint();
703		}
704	0	JScrollPane c = (JScrollPane) jobPanes.get(which);
705	0	c.getViewport().getComponent(0).setName(name);
706	0	c.repaint();
707		}
708
709		/**
710		* Gui action for cancelling the current job, if possible.
711		*
712		* @param e
713		* DOCUMENT ME!
714		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
715	0	@Override...
716		protected void cancel_actionPerformed(ActionEvent e)
717		{
718	0	if (!serviceIsCancellable)
719		{
720		// JBPNote : TODO: We should REALLY just tell the WSClientI to cancel
721		// anyhow - it has to stop threads and clean up
722		// JBPNote : TODO: Instead of a warning, we should have an optional 'Are
723		// you sure?' prompt
724	0	warnUser(
725		MessageManager.getString(
726		"warn.job_cannot_be_cancelled_close_window"),
727		MessageManager.getString("action.cancel_job"));
728		}
729		else
730		{
731	0	thisService.cancelJob();
732		}
733	0	frame.setClosable(true);
734		}
735
736		/**
737		* Spawns a thread that pops up a warning dialog box with the given message
738		* and title.
739		*
740		* @param message
741		* @param title
742		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
743	0	public void warnUser(final String message, final String title)...
744		{
745	0	javax.swing.SwingUtilities.invokeLater(new Runnable()
746		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
747	0	@Override...
748		public void run()
749		{
750	0	JvOptionPane.showInternalMessageDialog(Desktop.desktop, message,
751		title, JvOptionPane.WARNING_MESSAGE);
752
753		}
754		});
755		}
756
757		/**
758		* Set up GUI for user to get at results - and possibly automatically display
759		* them if viewResultsImmediatly is set.
760		*/
		0% Uncovered Elements: 14 (14) Complexity: 3 Complexity Density: 0.3
761	0	public void setResultsReady()...
762		{
763	0	frame.setClosable(true);
764	0	buttonPanel.remove(cancel);
765	0	buttonPanel.add(showResultsNewFrame);
766	0	if (serviceCanMergeResults)
767		{
768	0	buttonPanel.add(mergeResults);
769	0	buttonPanel.setLayout(new GridLayout(2, 1, 5, 5));
770		}
771	0	buttonPanel.validate();
772	0	validate();
773	0	if (viewResultsImmediatly)
774		{
775	0	showResultsNewFrame.doClick();
776		}
777		}
778
779		/**
780		* called when job has finished but no result objects can be passed back to
781		* user
782		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
783	0	public void setFinishedNoResults()...
784		{
785	0	frame.setClosable(true);
786	0	buttonPanel.remove(cancel);
787	0	buttonPanel.validate();
788	0	validate();
789		}
790
		0% Uncovered Elements: 68 (68) Complexity: 16 Complexity Density: 0.33
791		class AnimatedPanel extends JPanel implements Runnable
792		{
793		long startTime = 0;
794
795		BufferedImage offscreen;
796
		0% Uncovered Elements: 29 (29) Complexity: 6 Complexity Density: 0.29
797	0	@Override...
798		public void run()
799		{
800	0	startTime = System.currentTimeMillis();
801
802	0	float invSpeed = 15f;
803	0	float factor = 1f;
804	0	while (currentStatus < STATE_STOPPED_OK)
805		{
806	0	if (currentStatus == STATE_QUEUING)
807		{
808	0	invSpeed = 25f;
809	0	factor = 1f;
810		}
811	0	else if (currentStatus == STATE_RUNNING)
812		{
813	0	invSpeed = 10f;
814	0	factor = (float) (0.5 + 1.5
815		* (0.5 - (0.5 * Math.sin(3.14159 / 180 * (angle + 45)))));
816		}
817	0	try
818		{
819	0	Thread.sleep(50);
820
821	0	float delta = (System.currentTimeMillis() - startTime) / invSpeed;
822	0	angle += delta * factor;
823	0	angle %= 360;
824	0	startTime = System.currentTimeMillis();
825
826	0	if (currentStatus >= STATE_STOPPED_OK)
827		{
828	0	park();
829	0	angle = 0;
830		}
831
832	0	repaint();
833		} catch (Exception ex)
834		{
835		}
836		}
837
838	0	cancel.setEnabled(false);
839		}
840
		0% Uncovered Elements: 16 (16) Complexity: 4 Complexity Density: 0.33
841	0	public void park()...
842		{
843	0	startTime = System.currentTimeMillis();
844
845	0	while (angle < 360)
846		{
847	0	float invSpeed = 5f;
848	0	float factor = 1f;
849	0	try
850		{
851	0	Thread.sleep(25);
852
853	0	float delta = (System.currentTimeMillis() - startTime) / invSpeed;
854	0	angle += delta * factor;
855	0	startTime = System.currentTimeMillis();
856
857	0	if (angle >= 360)
858		{
859	0	angle = 360;
860		}
861
862	0	repaint();
863		} catch (Exception ex)
864		{
865		}
866		}
867
868		}
869
		0% Uncovered Elements: 17 (17) Complexity: 5 Complexity Density: 0.38
870	0	void drawPanel()...
871		{
872	0	if (offscreen == null || offscreen.getWidth(this) != getWidth()
873		|| offscreen.getHeight(this) != getHeight())
874		{
875	0	offscreen = new BufferedImage(getWidth(), getHeight(),
876		BufferedImage.TYPE_INT_RGB);
877		}
878
879	0	Graphics2D g = (Graphics2D) offscreen.getGraphics();
880
881	0	g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
882		RenderingHints.VALUE_ANTIALIAS_ON);
883	0	g.setRenderingHint(RenderingHints.KEY_INTERPOLATION,
884		RenderingHints.VALUE_INTERPOLATION_BICUBIC);
885	0	g.setRenderingHint(RenderingHints.KEY_RENDERING,
886		RenderingHints.VALUE_RENDER_QUALITY);
887
888	0	g.setColor(Color.white);
889	0	g.fillRect(0, 0, getWidth(), getHeight());
890
891	0	if (image != null)
892		{
893	0	int x = image.getWidth(this) / 2, y = image.getHeight(this) / 2;
894	0	g.rotate(3.14159 / 180 * (angle), x, y);
895	0	g.drawImage(image, 0, 0, this);
896	0	g.rotate(-3.14159 / 180 * (angle), x, y);
897		}
898		}
899
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
900	0	@Override...
901		public void paintComponent(Graphics g1)
902		{
903	0	drawPanel();
904
905	0	g1.drawImage(offscreen, 0, 0, this);
906		}
907		}
908
909		boolean renderAsHtml = false;
910
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
911	0	public void setRenderAsHtml(boolean b)...
912		{
913	0	renderAsHtml = b;
914		}
915
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
916	0	@Override...
917		public void hyperlinkUpdate(HyperlinkEvent e)
918		{
919	0	Desktop.hyperlinkUpdate(e);
920		}
921
922		/*
923		* (non-Javadoc)
924		*
925		* @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
926		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
927	0	@Override...
928		public void setProgressBar(String message, long id)
929		{
930	0	progressBar.setProgressBar(message, id);
931		}
932
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
933	0	@Override...
934		public void registerHandler(final long id,
935		final IProgressIndicatorHandler handler)
936		{
937	0	progressBar.registerHandler(id, handler);
938		}
939
940		/**
941		*
942		* @return true if any progress bars are still active
943		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
944	0	@Override...
945		public boolean operationInProgress()
946		{
947	0	return progressBar.operationInProgress();
948		}
949
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
950	0	@Override...
951		public JProgressBar getProgressBar(long id)
952		{
953	0	return progressBar.getProgressBar(id);
954		}
955
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
956	0	public String getMessage(long id)...
957		{
958	0	return progressBar.getMessage(id);
959		}
960
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
961	0	public void setProgressBarMessage(long id, String message)...
962		{
963	0	progressBar.setProgressBarMessage(id, message);
964		}
965		}