Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
WebserviceInfo	61	214	89	0.00%	Show methods
WebserviceInfo.AnimatedPanel	790	48	16	0.00%	Show methods

Class WebserviceInfo

Class WebserviceInfo	Line # 61	Total Statements 214	Complexity 89	TOTAL Coverage 0.00%
setVisible(boolean) : void   setVisible(boolean) : void	9999	2.02	1.01	0.0 0.00%
isViewResultsImmediatly() : boolean   isViewResultsImmediatly() : boolean	121121	1.01	1.01	0.0 0.00%
setViewResultsImmediatly(boolean) : void   setViewResultsImmediatly(boolean) : void	133133	1.01	1.01	0.0 0.00%
getStyleSheet(HTMLEditorKit) : StyleSheet   getStyleSheet(HTMLEditorKit) : StyleSheet	138138	4.04	1.01	0.0 0.00%
addJobPane() : int   addJobPane() : int	165165	34.034	5.05	0.0 0.00%
WebserviceInfo(String,String,boolean)   WebserviceInfo(String,String,boolean)	242242	1.01	1.01	0.0 0.00%
WebserviceInfo(String,String,int,int,boolean)   WebserviceInfo(String,String,int,int,boolean)	259259	1.01	1.01	0.0 0.00%
getthisService() : jalview.ws.WSClientI   getthisService() : jalview.ws.WSClientI	270270	1.01	1.01	0.0 0.00%
setthisService(jalview.ws.WSClientI) : void   setthisService(jalview.ws.WSClientI) : void	282282	5.05	1.01	0.0 0.00%
rebuildButtonPanel() : void   rebuildButtonPanel() : void	291291	6.06	3.03	0.0 0.00%
internalFrameClosed(InternalFrameEvent) : void   internalFrameClosed(InternalFrameEvent) : void	359359	3.03	3.03	0.0 0.00%
init(String,String,int,int,boolean) : void   init(String,String,int,int,boolean) : void	320320	23.023	2.02	0.0 0.00%
setStatus(int) : void   setStatus(int) : void	380380	23.023	8.08	0.0 0.00%
setStatus(int,int) : void   setStatus(int,int) : void	421421	23.023	9.09	0.0 0.00%
getInfoText() : String   getInfoText() : String	459459	1.01	1.01	0.0 0.00%
setInfoText(String) : void   setInfoText(String) : void	470470	1.01	1.01	0.0 0.00%
appendInfoText(String) : void   appendInfoText(String) : void	481481	1.01	1.01	0.0 0.00%
getProgressText(int) : String   getProgressText(int) : String	491491	5.05	3.03	0.0 0.00%
setProgressText(int,String) : void   setProgressText(int,String) : void	515515	5.05	3.03	0.0 0.00%
getHtmlFragment(String,boolean,boolean) : String   getHtmlFragment(String,boolean,boolean) : String	543543	11.011	9.09	0.0 0.00%
ensureHtmlTagged(String) : String   ensureHtmlTagged(String) : String	573573	16.016	9.09	0.0 0.00%
appendProgressText(int,String) : void   appendProgressText(int,String) : void	615615	6.06	3.03	0.0 0.00%
setProgressText(String) : void   setProgressText(String) : void	642642	1.01	1.01	0.0 0.00%
appendProgressText(String) : void   appendProgressText(String) : void	650650	1.01	1.01	0.0 0.00%
getProgressText() : String   getProgressText() : String	658658	1.01	1.01	0.0 0.00%
getProgressName(int) : String   getProgressName(int) : String	670670	5.05	3.03	0.0 0.00%
setProgressName(String,int) : void   setProgressName(String,int) : void	695695	7.07	2.02	0.0 0.00%
cancel_actionPerformed(ActionEvent) : void   cancel_actionPerformed(ActionEvent) : void	714714	4.04	2.02	0.0 0.00%
run() : void   run() : void	746746	1.01	1.01	0.0 0.00%
warnUser(String,String) : void   warnUser(String,String) : void	742742	1.01	1.01	0.0 0.00%
setResultsReady() : void   setResultsReady() : void	760760	10.010	3.03	0.0 0.00%
setFinishedNoResults() : void   setFinishedNoResults() : void	782782	4.04	1.01	0.0 0.00%
setRenderAsHtml(boolean) : void   setRenderAsHtml(boolean) : void	910910	1.01	1.01	0.0 0.00%
hyperlinkUpdate(HyperlinkEvent) : void   hyperlinkUpdate(HyperlinkEvent) : void	915915	1.01	1.01	0.0 0.00%
setProgressBar(String,long) : void   setProgressBar(String,long) : void	926926	1.01	1.01	0.0 0.00%
registerHandler(long,IProgressIndicatorHandler) : void   registerHandler(long,IProgressIndicatorHandler) : void	932932	1.01	1.01	0.0 0.00%
operationInProgress() : boolean   operationInProgress() : boolean	943943	1.01	1.01	0.0 0.00%

 

Class WebserviceInfo.AnimatedPanel

Class WebserviceInfo.AnimatedPanel	Line # 790	Total Statements 48	Complexity 16	TOTAL Coverage 0.00%
run() : void   run() : void	796796	21.021	6.06	0.0 0.00%
park() : void   park() : void	840840	12.012	4.04	0.0 0.00%
drawPanel() : void   drawPanel() : void	869869	13.013	5.05	0.0 0.00%
paintComponent(Graphics) : void   paintComponent(Graphics) : void	899899	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 jalview.jbgui.GWebserviceInfo;
24		import jalview.util.MessageManager;
25		import jalview.ws.WSClientI;
26
27		import java.awt.BorderLayout;
28		import java.awt.Color;
29		import java.awt.Dimension;
30		import java.awt.Graphics;
31		import java.awt.Graphics2D;
32		import java.awt.GridLayout;
33		import java.awt.Image;
34		import java.awt.MediaTracker;
35		import java.awt.RenderingHints;
36		import java.awt.event.ActionEvent;
37		import java.awt.image.BufferedImage;
38		import java.util.Vector;
39
40		import javax.swing.JComponent;
41		import javax.swing.JEditorPane;
42		import javax.swing.JInternalFrame;
43		import javax.swing.JPanel;
44		import javax.swing.JScrollPane;
45		import javax.swing.JTabbedPane;
46		import javax.swing.JTextArea;
47		import javax.swing.event.HyperlinkEvent;
48		import javax.swing.event.HyperlinkListener;
49		import javax.swing.event.InternalFrameAdapter;
50		import javax.swing.event.InternalFrameEvent;
51		import javax.swing.text.html.HTMLEditorKit;
52		import javax.swing.text.html.StyleSheet;
53
54		/**
55		* Base class for web service client thread and gui TODO: create StAX parser to
56		* extract html body content reliably when preparing html formatted job statuses
57		*
58		* @author $author$
59		* @version $Revision$
60		*/
		0% Uncovered Elements: 317 (317) Complexity: 89 Complexity Density: 0.42
61		public class WebserviceInfo extends GWebserviceInfo
62		implements HyperlinkListener, IProgressIndicator
63		{
64
65		/** Job is Queued */
66		public static final int STATE_QUEUING = 0;
67
68		/** Job is Running */
69		public static final int STATE_RUNNING = 1;
70
71		/** Job has finished with no errors */
72		public static final int STATE_STOPPED_OK = 2;
73
74		/** Job has been cancelled with no errors */
75		public static final int STATE_CANCELLED_OK = 3;
76
77		/** job has stopped because of some error */
78		public static final int STATE_STOPPED_ERROR = 4;
79
80		/** job has failed because of some unavoidable service interruption */
81		public static final int STATE_STOPPED_SERVERERROR = 5;
82
83		int currentStatus = STATE_QUEUING;
84
85		Image image;
86
87		float angle = 0f;
88
89		String title = "";
90
91		jalview.ws.WSClientI thisService;
92
93		boolean serviceIsCancellable;
94
95		JInternalFrame frame;
96
97		private IProgressIndicator progressBar;
98
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
99	0	@Override...
100		public void setVisible(boolean aFlag)
101		{
102	0	super.setVisible(aFlag);
103	0	frame.setVisible(aFlag);
104		}
105
106		JTabbedPane subjobs = null;
107
108		java.util.Vector jobPanes = null;
109
110		private boolean serviceCanMergeResults = false;
111
112		private boolean viewResultsImmediatly = true;
113
114		/**
115		* Get
116		*
117		* @param flag
118		* to indicate if results will be shown in a new window as soon as
119		* they are available.
120		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
121	0	public boolean isViewResultsImmediatly()...
122		{
123	0	return viewResultsImmediatly;
124		}
125
126		/**
127		* Set
128		*
129		* @param flag
130		* to indicate if results will be shown in a new window as soon as
131		* they are available.
132		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
133	0	public void setViewResultsImmediatly(boolean viewResultsImmediatly)...
134		{
135	0	this.viewResultsImmediatly = viewResultsImmediatly;
136		}
137
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
138	0	private StyleSheet getStyleSheet(HTMLEditorKit editorKit)...
139		{
140
141		// Copied blatantly from
142		// http://www.velocityreviews.com/forums/t132265-string-into-htmldocument.html
143	0	StyleSheet myStyleSheet = new StyleSheet();
144
145	0	myStyleSheet.addStyleSheet(editorKit.getStyleSheet());
146
147	0	editorKit.setStyleSheet(myStyleSheet);
148
149		/*
150		* Set the style sheet rules here by reading them from the constants
151		* interface.
152		*/
153		/*
154		* for (int ix=0; ix<CSS_RULES.length; ix++) {
155		*
156		* myStyleSheet.addRule(CSS_RULES[ix]);
157		*
158		* }
159		*/
160	0	return myStyleSheet;
161
162		}
163
164		// tabbed or not
		0% Uncovered Elements: 42 (42) Complexity: 5 Complexity Density: 0.15
165	0	public synchronized int addJobPane()...
166		{
167	0	JScrollPane jobpane = new JScrollPane();
168	0	JComponent _progressText;
169	0	if (renderAsHtml)
170		{
171	0	JEditorPane progressText = new JEditorPane("text/html", "");
172	0	progressText.addHyperlinkListener(this);
173	0	_progressText = progressText;
174		// progressText.setFont(new java.awt.Font("Verdana", 0, 10));
175		// progressText.setBorder(null);
176	0	progressText.setEditable(false);
177		/*
178		* HTMLEditorKit myEditorKit = new HTMLEditorKit();
179		*
180		* StyleSheet myStyleSheet = getStyleSheet(myEditorKit);
181		*
182		* HTMLDocument tipDocument = (HTMLDocument)
183		* (myEditorKit.createDefaultDocument());
184		*
185		* progressText.setDocument(tipDocument);
186	0	*/progressText.setText("<html><h1>WS Job</h1></html>");
187		}
188		else
189		{
190	0	JTextArea progressText = new JTextArea();
191	0	_progressText = progressText;
192
193	0	progressText.setFont(new java.awt.Font("Verdana", 0, 10));
194	0	progressText.setBorder(null);
195	0	progressText.setEditable(false);
196	0	progressText.setText("WS Job");
197	0	progressText.setLineWrap(true);
198	0	progressText.setWrapStyleWord(true);
199		}
200	0	jobpane.setName("JobPane");
201	0	jobpane.getViewport().add(_progressText, null);
202	0	jobpane.setBorder(null);
203	0	if (jobPanes == null)
204		{
205	0	jobPanes = new Vector();
206		}
207	0	int newpane = jobPanes.size();
208	0	jobPanes.add(jobpane);
209
210	0	if (newpane == 0)
211		{
212	0	this.add(jobpane, BorderLayout.CENTER);
213		}
214		else
215		{
216	0	if (newpane == 1)
217		{
218		// revert to a tabbed pane.
219	0	JScrollPane firstpane;
220	0	this.remove(firstpane = (JScrollPane) jobPanes.get(0));
221	0	subjobs = new JTabbedPane();
222	0	this.add(subjobs, BorderLayout.CENTER);
223	0	subjobs.add(firstpane);
224	0	subjobs.setTitleAt(0, firstpane.getName());
225		}
226	0	subjobs.add(jobpane);
227		}
228	0	return newpane; // index for accessor methods below
229		}
230
231		/**
232		* Creates a new WebserviceInfo object.
233		*
234		* @param title
235		* short name and job type
236		* @param info
237		* reference or other human readable description
238		* @param makeVisible
239		* true to display the webservices window immediatly (otherwise need
240		* to call setVisible(true))
241		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
242	0	public WebserviceInfo(String title, String info, boolean makeVisible)...
243		{
244	0	init(title, info, 520, 500, makeVisible);
245		}
246
247		/**
248		* Creates a new WebserviceInfo object.
249		*
250		* @param title
251		* DOCUMENT ME!
252		* @param info
253		* DOCUMENT ME!
254		* @param width
255		* DOCUMENT ME!
256		* @param height
257		* DOCUMENT ME!
258		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
259	0	public WebserviceInfo(String title, String info, int width, int height,...
260		boolean makeVisible)
261		{
262	0	init(title, info, width, height, makeVisible);
263		}
264
265		/**
266		* DOCUMENT ME!
267		*
268		* @return DOCUMENT ME!
269		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
270	0	public jalview.ws.WSClientI getthisService()...
271		{
272	0	return thisService;
273		}
274
275		/**
276		* Update state of GUI based on client capabilities (like whether the job is
277		* cancellable, whether the 'merge results' button is shown.
278		*
279		* @param newservice
280		* service client to query for capabilities
281		*/
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
282	0	public void setthisService(jalview.ws.WSClientI newservice)...
283		{
284	0	thisService = newservice;
285	0	serviceIsCancellable = newservice.isCancellable();
286	0	frame.setClosable(!serviceIsCancellable);
287	0	serviceCanMergeResults = newservice.canMergeResults();
288	0	rebuildButtonPanel();
289		}
290
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
291	0	private void rebuildButtonPanel()...
292		{
293	0	if (buttonPanel != null)
294		{
295	0	buttonPanel.removeAll();
296	0	if (serviceIsCancellable)
297		{
298	0	buttonPanel.add(cancel);
299	0	frame.setClosable(false);
300		}
301		else
302		{
303	0	frame.setClosable(true);
304		}
305		}
306		}
307
308		/**
309		* DOCUMENT ME!
310		*
311		* @param title
312		* DOCUMENT ME!
313		* @param info
314		* DOCUMENT ME!
315		* @param width
316		* DOCUMENT ME!
317		* @param height
318		* DOCUMENT ME!
319		*/
		0% Uncovered Elements: 23 (23) Complexity: 2 Complexity Density: 0.09
320	0	void init(String title, String info, int width, int height,...
321		boolean makeVisible)
322		{
323	0	frame = new JInternalFrame();
324	0	frame.setContentPane(this);
325	0	Desktop.addInternalFrame(frame, title, makeVisible, width, height);
326	0	frame.setClosable(false);
327
328	0	progressBar = new ProgressBar(statusPanel, statusBar);
329
330	0	this.title = title;
331	0	setInfoText(info);
332
333	0	java.net.URL url = getClass()
334		.getResource("/images/Jalview_Logo_small_with_border.png");
335	0	image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
336
337	0	MediaTracker mt = new MediaTracker(this);
338	0	mt.addImage(image, 0);
339
340	0	try
341		{
342	0	mt.waitForID(0);
343		} catch (Exception ex)
344		{
345		}
346
347	0	AnimatedPanel ap = new AnimatedPanel();
348	0	ap.setPreferredSize(new Dimension(60, 60));
349	0	titlePanel.add(ap, BorderLayout.WEST);
350	0	titlePanel.add(titleText, BorderLayout.CENTER);
351	0	setStatus(currentStatus);
352
353	0	Thread thread = new Thread(ap);
354	0	thread.start();
355	0	final WebserviceInfo thisinfo = this;
356	0	frame.addInternalFrameListener(
357		new InternalFrameAdapter()
358		{
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
359	0	@Override...
360		public void internalFrameClosed(InternalFrameEvent evt)
361		{
362		// System.out.println("Shutting down webservice client");
363	0	WSClientI service = thisinfo.getthisService();
364	0	if (service != null && service.isCancellable())
365		{
366	0	service.cancelJob();
367		}
368		}
369		});
370	0	frame.validate();
371
372		}
373
374		/**
375		* DOCUMENT ME!
376		*
377		* @param status
378		* integer status from state constants
379		*/
		0% Uncovered Elements: 25 (25) Complexity: 8 Complexity Density: 0.35
380	0	public void setStatus(int status)...
381		{
382	0	currentStatus = status;
383
384	0	String message = null;
385	0	switch (currentStatus)
386		{
387	0	case STATE_QUEUING:
388	0	message = MessageManager.getString("label.state_queueing");
389	0	break;
390
391	0	case STATE_RUNNING:
392	0	message = MessageManager.getString("label.state_running");
393	0	break;
394
395	0	case STATE_STOPPED_OK:
396	0	message = MessageManager.getString("label.state_completed");
397	0	break;
398
399	0	case STATE_CANCELLED_OK:
400	0	message = MessageManager.getString("label.state_job_cancelled");
401	0	break;
402
403	0	case STATE_STOPPED_ERROR:
404	0	message = MessageManager.getString("label.state_job_error");
405	0	break;
406
407	0	case STATE_STOPPED_SERVERERROR:
408	0	message = MessageManager.getString("label.server_error_try_later");
409	0	break;
410		}
411	0	titleText.setText(title + (message == null ? "" : " - " + message));
412	0	titleText.repaint();
413		}
414
415		/**
416		* subjob status indicator
417		*
418		* @param jobpane
419		* @param status
420		*/
		0% Uncovered Elements: 25 (25) Complexity: 9 Complexity Density: 0.39
421	0	public void setStatus(int jobpane, int status)...
422		{
423	0	if (jobpane < 0 || jobpane >= jobPanes.size())
424		{
425	0	throw new Error(MessageManager.formatMessage(
426		"error.setstatus_called_non_existent_job_pane", new String[]
427		{ Integer.valueOf(jobpane).toString() }));
428		}
429	0	switch (status)
430		{
431	0	case STATE_QUEUING:
432	0	setProgressName(jobpane + " - QUEUED", jobpane);
433	0	break;
434	0	case STATE_RUNNING:
435	0	setProgressName(jobpane + " - RUNNING", jobpane);
436	0	break;
437	0	case STATE_STOPPED_OK:
438	0	setProgressName(jobpane + " - FINISHED", jobpane);
439	0	break;
440	0	case STATE_CANCELLED_OK:
441	0	setProgressName(jobpane + " - CANCELLED", jobpane);
442	0	break;
443	0	case STATE_STOPPED_ERROR:
444	0	setProgressName(jobpane + " - BROKEN", jobpane);
445	0	break;
446	0	case STATE_STOPPED_SERVERERROR:
447	0	setProgressName(jobpane + " - ALERT", jobpane);
448	0	break;
449	0	default:
450	0	setProgressName(jobpane + " - UNKNOWN STATE", jobpane);
451		}
452		}
453
454		/**
455		* DOCUMENT ME!
456		*
457		* @return DOCUMENT ME!
458		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
459	0	public String getInfoText()...
460		{
461	0	return infoText.getText();
462		}
463
464		/**
465		* DOCUMENT ME!
466		*
467		* @param text
468		* DOCUMENT ME!
469		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
470	0	public void setInfoText(String text)...
471		{
472	0	infoText.setText(text);
473		}
474
475		/**
476		* DOCUMENT ME!
477		*
478		* @param text
479		* DOCUMENT ME!
480		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
481	0	public void appendInfoText(String text)...
482		{
483	0	infoText.append(text);
484		}
485
486		/**
487		* DOCUMENT ME!
488		*
489		* @return DOCUMENT ME!
490		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
491	0	public String getProgressText(int which)...
492		{
493	0	if (jobPanes == null)
494		{
495	0	addJobPane();
496		}
497	0	if (renderAsHtml)
498		{
499	0	return ((JEditorPane) ((JScrollPane) jobPanes.get(which))
500		.getViewport().getComponent(0)).getText();
501		}
502		else
503		{
504	0	return ((JTextArea) ((JScrollPane) jobPanes.get(which)).getViewport()
505		.getComponent(0)).getText();
506		}
507		}
508
509		/**
510		* DOCUMENT ME!
511		*
512		* @param text
513		* DOCUMENT ME!
514		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
515	0	public void setProgressText(int which, String text)...
516		{
517	0	if (jobPanes == null)
518		{
519	0	addJobPane();
520		}
521	0	if (renderAsHtml)
522		{
523	0	((JEditorPane) ((JScrollPane) jobPanes.get(which)).getViewport()
524		.getComponent(0)).setText(ensureHtmlTagged(text));
525		}
526		else
527		{
528	0	((JTextArea) ((JScrollPane) jobPanes.get(which)).getViewport()
529		.getComponent(0)).setText(text);
530		}
531		}
532
533		/**
534		* extract content from &lt;body&gt; content &lt;/body&gt;
535		*
536		* @param text
537		* @param leaveFirst
538		* - set to leave the initial html tag intact
539		* @param leaveLast
540		* - set to leave the final html tag intact
541		* @return
542		*/
		0% Uncovered Elements: 25 (25) Complexity: 9 Complexity Density: 0.82
543	0	private String getHtmlFragment(String text, boolean leaveFirst,...
544		boolean leaveLast)
545		{
546	0	if (text == null)
547		{
548	0	return null;
549		}
550	0	String lowertxt = text.toLowerCase();
551	0	int htmlpos = leaveFirst ? -1 : lowertxt.indexOf("<body");
552
553	0	int htmlend = leaveLast ? -1 : lowertxt.indexOf("</body");
554	0	int htmlpose = lowertxt.indexOf(">", htmlpos),
555		htmlende = lowertxt.indexOf(">", htmlend);
556	0	if (htmlend == -1 && htmlpos == -1)
557		{
558	0	return text;
559		}
560	0	if (htmlend > -1)
561		{
562	0	return text.substring((htmlpos == -1 ? 0 : htmlpose + 1), htmlend);
563		}
564	0	return text.substring(htmlpos == -1 ? 0 : htmlpose + 1);
565		}
566
567		/**
568		* very simple routine for adding/ensuring html tags are present in text.
569		*
570		* @param text
571		* @return properly html tag enclosed text
572		*/
		0% Uncovered Elements: 26 (26) Complexity: 9 Complexity Density: 0.56
573	0	private String ensureHtmlTagged(String text)...
574		{
575	0	if (text == null)
576		{
577	0	return "";
578		}
579	0	String lowertxt = text.toLowerCase();
580	0	int htmlpos = lowertxt.indexOf("<body");
581	0	int htmlend = lowertxt.indexOf("</body");
582	0	int doctype = lowertxt.indexOf("<!doctype");
583	0	int xmltype = lowertxt.indexOf("<?xml");
584	0	if (htmlend == -1)
585		{
586	0	text = text + "</body></html>";
587		}
588	0	if (htmlpos > -1)
589		{
590	0	if ((doctype > -1 && htmlpos > doctype)
591		|| (xmltype > -1 && htmlpos > xmltype))
592		{
593	0	text = "<html><head></head><body>\n" + text.substring(htmlpos - 1);
594		}
595		}
596		else
597		{
598	0	text = "<html><head></head><body>\n" + text;
599		}
600	0	if (text.indexOf("<meta") > -1)
601		{
602	0	System.err
603		.println("HTML COntent: \n" + text + "<< END HTML CONTENT\n");
604
605		}
606	0	return text;
607		}
608
609		/**
610		* DOCUMENT ME!
611		*
612		* @param text
613		* DOCUMENT ME!
614		*/
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
615	0	public void appendProgressText(int which, String text)...
616		{
617	0	if (jobPanes == null)
618		{
619	0	addJobPane();
620		}
621	0	if (renderAsHtml)
622		{
623	0	String txt = getHtmlFragment(
624		((JEditorPane) ((JScrollPane) jobPanes.get(which))
625		.getViewport().getComponent(0)).getText(),
626		true, false);
627	0	((JEditorPane) ((JScrollPane) jobPanes.get(which)).getViewport()
628		.getComponent(0))
629		.setText(ensureHtmlTagged(
630		txt + getHtmlFragment(text, false, true)));
631		}
632		else
633		{
634	0	((JTextArea) ((JScrollPane) jobPanes.get(which)).getViewport()
635		.getComponent(0)).append(text);
636		}
637		}
638
639		/**
640		* setProgressText(0, text)
641		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
642	0	public void setProgressText(String text)...
643		{
644	0	setProgressText(0, text);
645		}
646
647		/**
648		* appendProgressText(0, text)
649		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
650	0	public void appendProgressText(String text)...
651		{
652	0	appendProgressText(0, text);
653		}
654
655		/**
656		* getProgressText(0)
657		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
658	0	public String getProgressText()...
659		{
660	0	return getProgressText(0);
661		}
662
663		/**
664		* get the tab title for a subjob
665		*
666		* @param which
667		* int
668		* @return String
669		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
670	0	public String getProgressName(int which)...
671		{
672	0	if (jobPanes == null)
673		{
674	0	addJobPane();
675		}
676	0	if (subjobs != null)
677		{
678	0	return subjobs.getTitleAt(which);
679		}
680		else
681		{
682	0	return ((JScrollPane) jobPanes.get(which)).getViewport()
683		.getComponent(0).getName();
684		}
685		}
686
687		/**
688		* set the tab title for a subjob
689		*
690		* @param name
691		* String
692		* @param which
693		* int
694		*/
		0% Uncovered Elements: 9 (9) Complexity: 2 Complexity Density: 0.29
695	0	public void setProgressName(String name, int which)...
696		{
697	0	if (subjobs != null)
698		{
699	0	subjobs.setTitleAt(which, name);
700	0	subjobs.revalidate();
701	0	subjobs.repaint();
702		}
703	0	JScrollPane c = (JScrollPane) jobPanes.get(which);
704	0	c.getViewport().getComponent(0).setName(name);
705	0	c.repaint();
706		}
707
708		/**
709		* Gui action for cancelling the current job, if possible.
710		*
711		* @param e
712		* DOCUMENT ME!
713		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
714	0	@Override...
715		protected void cancel_actionPerformed(ActionEvent e)
716		{
717	0	if (!serviceIsCancellable)
718		{
719		// JBPNote : TODO: We should REALLY just tell the WSClientI to cancel
720		// anyhow - it has to stop threads and clean up
721		// JBPNote : TODO: Instead of a warning, we should have an optional 'Are
722		// you sure?' prompt
723	0	warnUser(
724		MessageManager.getString(
725		"warn.job_cannot_be_cancelled_close_window"),
726		MessageManager.getString("action.cancel_job"));
727		}
728		else
729		{
730	0	thisService.cancelJob();
731		}
732	0	frame.setClosable(true);
733		}
734
735		/**
736		* Spawns a thread that pops up a warning dialog box with the given message
737		* and title.
738		*
739		* @param message
740		* @param title
741		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
742	0	public void warnUser(final String message, final String title)...
743		{
744	0	javax.swing.SwingUtilities.invokeLater(new Runnable()
745		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
746	0	@Override...
747		public void run()
748		{
749	0	JvOptionPane.showInternalMessageDialog(Desktop.desktop, message,
750		title, JvOptionPane.WARNING_MESSAGE);
751
752		}
753		});
754		}
755
756		/**
757		* Set up GUI for user to get at results - and possibly automatically display
758		* them if viewResultsImmediatly is set.
759		*/
		0% Uncovered Elements: 14 (14) Complexity: 3 Complexity Density: 0.3
760	0	public void setResultsReady()...
761		{
762	0	frame.setClosable(true);
763	0	buttonPanel.remove(cancel);
764	0	buttonPanel.add(showResultsNewFrame);
765	0	if (serviceCanMergeResults)
766		{
767	0	buttonPanel.add(mergeResults);
768	0	buttonPanel.setLayout(new GridLayout(2, 1, 5, 5));
769		}
770	0	buttonPanel.validate();
771	0	validate();
772	0	if (viewResultsImmediatly)
773		{
774	0	showResultsNewFrame.doClick();
775		}
776		}
777
778		/**
779		* called when job has finished but no result objects can be passed back to
780		* user
781		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
782	0	public void setFinishedNoResults()...
783		{
784	0	frame.setClosable(true);
785	0	buttonPanel.remove(cancel);
786	0	buttonPanel.validate();
787	0	validate();
788		}
789
		0% Uncovered Elements: 68 (68) Complexity: 16 Complexity Density: 0.33
790		class AnimatedPanel extends JPanel implements Runnable
791		{
792		long startTime = 0;
793
794		BufferedImage offscreen;
795
		0% Uncovered Elements: 29 (29) Complexity: 6 Complexity Density: 0.29
796	0	@Override...
797		public void run()
798		{
799	0	startTime = System.currentTimeMillis();
800
801	0	float invSpeed = 15f;
802	0	float factor = 1f;
803	0	while (currentStatus < STATE_STOPPED_OK)
804		{
805	0	if (currentStatus == STATE_QUEUING)
806		{
807	0	invSpeed = 25f;
808	0	factor = 1f;
809		}
810	0	else if (currentStatus == STATE_RUNNING)
811		{
812	0	invSpeed = 10f;
813	0	factor = (float) (0.5 + 1.5
814		* (0.5 - (0.5 * Math.sin(3.14159 / 180 * (angle + 45)))));
815		}
816	0	try
817		{
818	0	Thread.sleep(50);
819
820	0	float delta = (System.currentTimeMillis() - startTime) / invSpeed;
821	0	angle += delta * factor;
822	0	angle %= 360;
823	0	startTime = System.currentTimeMillis();
824
825	0	if (currentStatus >= STATE_STOPPED_OK)
826		{
827	0	park();
828	0	angle = 0;
829		}
830
831	0	repaint();
832		} catch (Exception ex)
833		{
834		}
835		}
836
837	0	cancel.setEnabled(false);
838		}
839
		0% Uncovered Elements: 16 (16) Complexity: 4 Complexity Density: 0.33
840	0	public void park()...
841		{
842	0	startTime = System.currentTimeMillis();
843
844	0	while (angle < 360)
845		{
846	0	float invSpeed = 5f;
847	0	float factor = 1f;
848	0	try
849		{
850	0	Thread.sleep(25);
851
852	0	float delta = (System.currentTimeMillis() - startTime) / invSpeed;
853	0	angle += delta * factor;
854	0	startTime = System.currentTimeMillis();
855
856	0	if (angle >= 360)
857		{
858	0	angle = 360;
859		}
860
861	0	repaint();
862		} catch (Exception ex)
863		{
864		}
865		}
866
867		}
868
		0% Uncovered Elements: 17 (17) Complexity: 5 Complexity Density: 0.38
869	0	void drawPanel()...
870		{
871	0	if (offscreen == null || offscreen.getWidth(this) != getWidth()
872		|| offscreen.getHeight(this) != getHeight())
873		{
874	0	offscreen = new BufferedImage(getWidth(), getHeight(),
875		BufferedImage.TYPE_INT_RGB);
876		}
877
878	0	Graphics2D g = (Graphics2D) offscreen.getGraphics();
879
880	0	g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
881		RenderingHints.VALUE_ANTIALIAS_ON);
882	0	g.setRenderingHint(RenderingHints.KEY_INTERPOLATION,
883		RenderingHints.VALUE_INTERPOLATION_BICUBIC);
884	0	g.setRenderingHint(RenderingHints.KEY_RENDERING,
885		RenderingHints.VALUE_RENDER_QUALITY);
886
887	0	g.setColor(Color.white);
888	0	g.fillRect(0, 0, getWidth(), getHeight());
889
890	0	if (image != null)
891		{
892	0	int x = image.getWidth(this) / 2, y = image.getHeight(this) / 2;
893	0	g.rotate(3.14159 / 180 * (angle), x, y);
894	0	g.drawImage(image, 0, 0, this);
895	0	g.rotate(-3.14159 / 180 * (angle), x, y);
896		}
897		}
898
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
899	0	@Override...
900		public void paintComponent(Graphics g1)
901		{
902	0	drawPanel();
903
904	0	g1.drawImage(offscreen, 0, 0, this);
905		}
906		}
907
908		boolean renderAsHtml = false;
909
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
910	0	public void setRenderAsHtml(boolean b)...
911		{
912	0	renderAsHtml = b;
913		}
914
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
915	0	@Override...
916		public void hyperlinkUpdate(HyperlinkEvent e)
917		{
918	0	Desktop.hyperlinkUpdate(e);
919		}
920
921		/*
922		* (non-Javadoc)
923		*
924		* @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
925		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
926	0	@Override...
927		public void setProgressBar(String message, long id)
928		{
929	0	progressBar.setProgressBar(message, id);
930		}
931
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
932	0	@Override...
933		public void registerHandler(final long id,
934		final IProgressIndicatorHandler handler)
935		{
936	0	progressBar.registerHandler(id, handler);
937		}
938
939		/**
940		*
941		* @return true if any progress bars are still active
942		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
943	0	@Override...
944		public boolean operationInProgress()
945		{
946	0	return progressBar.operationInProgress();
947		}
948		}