Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
WebserviceInfo	65	220	95	0.00%	Show methods
WebserviceInfo.AnimatedPanel	798	48	16	0.00%	Show methods

Class WebserviceInfo

Class WebserviceInfo	Line # 65	Total Statements 220	Complexity 95	TOTAL Coverage 0.00%
setVisible(boolean) : void   setVisible(boolean) : void	103103	2.02	1.01	0.0 0.00%
isViewResultsImmediatly() : boolean   isViewResultsImmediatly() : boolean	125125	1.01	1.01	0.0 0.00%
setViewResultsImmediatly(boolean) : void   setViewResultsImmediatly(boolean) : void	137137	1.01	1.01	0.0 0.00%
getStyleSheet(HTMLEditorKit) : StyleSheet   getStyleSheet(HTMLEditorKit) : StyleSheet	142142	4.04	1.01	0.0 0.00%
addJobPane() : int   addJobPane() : int	169169	34.034	5.05	0.0 0.00%
WebserviceInfo(String,String,boolean)   WebserviceInfo(String,String,boolean)	246246	1.01	1.01	0.0 0.00%
WebserviceInfo(String,String,int,int,boolean)   WebserviceInfo(String,String,int,int,boolean)	263263	1.01	1.01	0.0 0.00%
getthisService() : jalview.ws.WSClientI   getthisService() : jalview.ws.WSClientI	275275	1.01	1.01	0.0 0.00%
setthisService(jalview.ws.WSClientI) : void   setthisService(jalview.ws.WSClientI) : void	287287	5.05	1.01	0.0 0.00%
rebuildButtonPanel() : void   rebuildButtonPanel() : void	296296	6.06	3.03	0.0 0.00%
internalFrameClosed(InternalFrameEvent) : void   internalFrameClosed(InternalFrameEvent) : void	367367	3.03	3.03	0.0 0.00%
init(String,String,int,int,boolean) : void   init(String,String,int,int,boolean) : void	325325	24.024	3.03	0.0 0.00%
setStatus(int) : void   setStatus(int) : void	388388	23.023	8.08	0.0 0.00%
setStatus(int,int) : void   setStatus(int,int) : void	429429	23.023	9.09	0.0 0.00%
getInfoText() : String   getInfoText() : String	467467	1.01	1.01	0.0 0.00%
setInfoText(String) : void   setInfoText(String) : void	478478	1.01	1.01	0.0 0.00%
appendInfoText(String) : void   appendInfoText(String) : void	489489	1.01	1.01	0.0 0.00%
getProgressText(int) : String   getProgressText(int) : String	499499	5.05	3.03	0.0 0.00%
setProgressText(int,String) : void   setProgressText(int,String) : void	523523	5.05	3.03	0.0 0.00%
getHtmlFragment(String,boolean,boolean) : String   getHtmlFragment(String,boolean,boolean) : String	551551	11.011	9.09	0.0 0.00%
ensureHtmlTagged(String) : String   ensureHtmlTagged(String) : String	581581	16.016	9.09	0.0 0.00%
appendProgressText(int,String) : void   appendProgressText(int,String) : void	623623	6.06	3.03	0.0 0.00%
setProgressText(String) : void   setProgressText(String) : void	650650	1.01	1.01	0.0 0.00%
appendProgressText(String) : void   appendProgressText(String) : void	658658	1.01	1.01	0.0 0.00%
getProgressText() : String   getProgressText() : String	666666	1.01	1.01	0.0 0.00%
getProgressName(int) : String   getProgressName(int) : String	678678	5.05	3.03	0.0 0.00%
setProgressName(String,int) : void   setProgressName(String,int) : void	703703	7.07	2.02	0.0 0.00%
cancel_actionPerformed(ActionEvent) : void   cancel_actionPerformed(ActionEvent) : void	722722	4.04	2.02	0.0 0.00%
run() : void   run() : void	754754	1.01	1.01	0.0 0.00%
warnUser(String,String) : void   warnUser(String,String) : void	750750	1.01	1.01	0.0 0.00%
setResultsReady() : void   setResultsReady() : void	768768	10.010	3.03	0.0 0.00%
setFinishedNoResults() : void   setFinishedNoResults() : void	790790	4.04	1.01	0.0 0.00%
setRenderAsHtml(boolean) : void   setRenderAsHtml(boolean) : void	918918	1.01	1.01	0.0 0.00%
hyperlinkUpdate(HyperlinkEvent) : void   hyperlinkUpdate(HyperlinkEvent) : void	923923	1.01	1.01	0.0 0.00%
setProgressBar(String,long) : void   setProgressBar(String,long) : void	934934	1.01	1.01	0.0 0.00%
addProgressBar(long,String) : void   addProgressBar(long,String) : void	940940	1.01	1.01	0.0 0.00%
removeProgressBar(long) : void   removeProgressBar(long) : void	946946	1.01	1.01	0.0 0.00%
registerHandler(long,IProgressIndicatorHandler) : void   registerHandler(long,IProgressIndicatorHandler) : void	952952	1.01	1.01	0.0 0.00%
operationInProgress() : boolean   operationInProgress() : boolean	963963	1.01	1.01	0.0 0.00%
getProgressBar(long) : JProgressBar   getProgressBar(long) : JProgressBar	969969	1.01	1.01	0.0 0.00%
getMessage(long) : String   getMessage(long) : String	975975	1.01	1.01	0.0 0.00%
setProgressBarMessage(long,String) : void   setProgressBarMessage(long,String) : void	980980	1.01	1.01	0.0 0.00%

 

Class WebserviceInfo.AnimatedPanel

Class WebserviceInfo.AnimatedPanel	Line # 798	Total Statements 48	Complexity 16	TOTAL Coverage 0.00%
run() : void   run() : void	804804	21.021	6.06	0.0 0.00%
park() : void   park() : void	848848	12.012	4.04	0.0 0.00%
drawPanel() : void   drawPanel() : void	877877	13.013	5.05	0.0 0.00%
paintComponent(Graphics) : void   paintComponent(Graphics) : void	907907	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.util.Platform;
26		import jalview.util.ChannelProperties;
27		import jalview.ws.WSClientI;
28
29		import java.awt.BorderLayout;
30		import java.awt.Color;
31		import java.awt.Dimension;
32		import java.awt.Graphics;
33		import java.awt.Graphics2D;
34		import java.awt.GridLayout;
35		import java.awt.Image;
36		import java.awt.MediaTracker;
37		import java.awt.RenderingHints;
38		import java.awt.event.ActionEvent;
39		import java.awt.image.BufferedImage;
40		import java.util.Locale;
41		import java.util.Vector;
42
43		import javax.swing.JComponent;
44		import javax.swing.JEditorPane;
45		import javax.swing.JInternalFrame;
46		import javax.swing.JPanel;
47		import javax.swing.JProgressBar;
48		import javax.swing.JScrollPane;
49		import javax.swing.JTabbedPane;
50		import javax.swing.JTextArea;
51		import javax.swing.event.HyperlinkEvent;
52		import javax.swing.event.HyperlinkListener;
53		import javax.swing.event.InternalFrameAdapter;
54		import javax.swing.event.InternalFrameEvent;
55		import javax.swing.text.html.HTMLEditorKit;
56		import javax.swing.text.html.StyleSheet;
57
58		/**
59		* Base class for web service client thread and gui TODO: create StAX parser to
60		* extract html body content reliably when preparing html formatted job statuses
61		*
62		* @author $author$
63		* @version $Revision$
64		*/
		0% Uncovered Elements: 330 (330) Complexity: 95 Complexity Density: 0.43
65		public class WebserviceInfo extends GWebserviceInfo
66		implements HyperlinkListener, IProgressIndicator
67		{
68
69		/** Job is Queued */
70		public static final int STATE_QUEUING = 0;
71
72		/** Job is Running */
73		public static final int STATE_RUNNING = 1;
74
75		/** Job has finished with no errors */
76		public static final int STATE_STOPPED_OK = 2;
77
78		/** Job has been cancelled with no errors */
79		public static final int STATE_CANCELLED_OK = 3;
80
81		/** job has stopped because of some error */
82		public static final int STATE_STOPPED_ERROR = 4;
83
84		/** job has failed because of some unavoidable service interruption */
85		public static final int STATE_STOPPED_SERVERERROR = 5;
86
87		int currentStatus = STATE_QUEUING;
88
89		Image image;
90
91		float angle = 0f;
92
93		String title = "";
94
95		jalview.ws.WSClientI thisService;
96
97		boolean serviceIsCancellable;
98
99		JInternalFrame frame;
100
101		private IProgressIndicator progressBar;
102
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
103	0	@Override...
104		public void setVisible(boolean aFlag)
105		{
106	0	super.setVisible(aFlag);
107	0	frame.setVisible(aFlag);
108		}
109
110		JTabbedPane subjobs = null;
111
112		java.util.Vector jobPanes = null;
113
114		private boolean serviceCanMergeResults = false;
115
116		private boolean viewResultsImmediatly = true;
117
118		/**
119		* Get
120		*
121		* @param flag
122		* to indicate if results will be shown in a new window as soon as
123		* they are available.
124		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
125	0	public boolean isViewResultsImmediatly()...
126		{
127	0	return viewResultsImmediatly;
128		}
129
130		/**
131		* Set
132		*
133		* @param flag
134		* to indicate if results will be shown in a new window as soon as
135		* they are available.
136		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
137	0	public void setViewResultsImmediatly(boolean viewResultsImmediatly)...
138		{
139	0	this.viewResultsImmediatly = viewResultsImmediatly;
140		}
141
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
142	0	private StyleSheet getStyleSheet(HTMLEditorKit editorKit)...
143		{
144
145		// Copied blatantly from
146		// http://www.velocityreviews.com/forums/t132265-string-into-htmldocument.html
147	0	StyleSheet myStyleSheet = new StyleSheet();
148
149	0	myStyleSheet.addStyleSheet(editorKit.getStyleSheet());
150
151	0	editorKit.setStyleSheet(myStyleSheet);
152
153		/*
154		* Set the style sheet rules here by reading them from the constants
155		* interface.
156		*/
157		/*
158		* for (int ix=0; ix<CSS_RULES.length; ix++) {
159		*
160		* myStyleSheet.addRule(CSS_RULES[ix]);
161		*
162		* }
163		*/
164	0	return myStyleSheet;
165
166		}
167
168		// tabbed or not
		0% Uncovered Elements: 42 (42) Complexity: 5 Complexity Density: 0.15
169	0	public synchronized int addJobPane()...
170		{
171	0	JScrollPane jobpane = new JScrollPane();
172	0	JComponent _progressText;
173	0	if (renderAsHtml)
174		{
175	0	JEditorPane progressText = new JEditorPane("text/html", "");
176	0	progressText.addHyperlinkListener(this);
177	0	_progressText = progressText;
178		// progressText.setFont(new java.awt.Font("Verdana", 0, 10));
179		// progressText.setBorder(null);
180	0	progressText.setEditable(false);
181		/*
182		* HTMLEditorKit myEditorKit = new HTMLEditorKit();
183		*
184		* StyleSheet myStyleSheet = getStyleSheet(myEditorKit);
185		*
186		* HTMLDocument tipDocument = (HTMLDocument)
187		* (myEditorKit.createDefaultDocument());
188		*
189		* progressText.setDocument(tipDocument);
190	0	*/progressText.setText("<html><h1>WS Job</h1></html>");
191		}
192		else
193		{
194	0	JTextArea progressText = new JTextArea();
195	0	_progressText = progressText;
196
197	0	progressText.setFont(new java.awt.Font("Verdana", 0, 10));
198	0	progressText.setBorder(null);
199	0	progressText.setEditable(false);
200	0	progressText.setText("WS Job");
201	0	progressText.setLineWrap(true);
202	0	progressText.setWrapStyleWord(true);
203		}
204	0	jobpane.setName("JobPane");
205	0	jobpane.getViewport().add(_progressText, null);
206	0	jobpane.setBorder(null);
207	0	if (jobPanes == null)
208		{
209	0	jobPanes = new Vector();
210		}
211	0	int newpane = jobPanes.size();
212	0	jobPanes.add(jobpane);
213
214	0	if (newpane == 0)
215		{
216	0	this.add(jobpane, BorderLayout.CENTER);
217		}
218		else
219		{
220	0	if (newpane == 1)
221		{
222		// revert to a tabbed pane.
223	0	JScrollPane firstpane;
224	0	this.remove(firstpane = (JScrollPane) jobPanes.get(0));
225	0	subjobs = new JTabbedPane();
226	0	this.add(subjobs, BorderLayout.CENTER);
227	0	subjobs.add(firstpane);
228	0	subjobs.setTitleAt(0, firstpane.getName());
229		}
230	0	subjobs.add(jobpane);
231		}
232	0	return newpane; // index for accessor methods below
233		}
234
235		/**
236		* Creates a new WebserviceInfo object.
237		*
238		* @param title
239		* short name and job type
240		* @param info
241		* reference or other human readable description
242		* @param makeVisible
243		* true to display the webservices window immediatly (otherwise need
244		* to call setVisible(true))
245		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
246	0	public WebserviceInfo(String title, String info, boolean makeVisible)...
247		{
248	0	init(title, info, 520, 500, makeVisible);
249		}
250
251		/**
252		* Creates a new WebserviceInfo object.
253		*
254		* @param title
255		* DOCUMENT ME!
256		* @param info
257		* DOCUMENT ME!
258		* @param width
259		* DOCUMENT ME!
260		* @param height
261		* DOCUMENT ME!
262		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
263	0	public WebserviceInfo(String title, String info, int width, int height,...
264		boolean makeVisible)
265		{
266		// no references
267	0	init(title, info, width, height, makeVisible);
268		}
269
270		/**
271		* DOCUMENT ME!
272		*
273		* @return DOCUMENT ME!
274		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
275	0	public jalview.ws.WSClientI getthisService()...
276		{
277	0	return thisService;
278		}
279
280		/**
281		* Update state of GUI based on client capabilities (like whether the job is
282		* cancellable, whether the 'merge results' button is shown.
283		*
284		* @param newservice
285		* service client to query for capabilities
286		*/
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
287	0	public void setthisService(jalview.ws.WSClientI newservice)...
288		{
289	0	thisService = newservice;
290	0	serviceIsCancellable = newservice.isCancellable();
291	0	frame.setClosable(!serviceIsCancellable);
292	0	serviceCanMergeResults = newservice.canMergeResults();
293	0	rebuildButtonPanel();
294		}
295
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
296	0	private void rebuildButtonPanel()...
297		{
298	0	if (buttonPanel != null)
299		{
300	0	buttonPanel.removeAll();
301	0	if (serviceIsCancellable)
302		{
303	0	buttonPanel.add(cancel);
304	0	frame.setClosable(false);
305		}
306		else
307		{
308	0	frame.setClosable(true);
309		}
310		}
311		}
312
313		/**
314		* DOCUMENT ME!
315		*
316		* @param title
317		* DOCUMENT ME!
318		* @param info
319		* DOCUMENT ME!
320		* @param width
321		* DOCUMENT ME!
322		* @param height
323		* DOCUMENT ME!
324		*/
		0% Uncovered Elements: 26 (26) Complexity: 3 Complexity Density: 0.12
325	0	void init(String title, String info, int width, int height,...
326		boolean makeVisible)
327		{
328	0	frame = new JInternalFrame();
329	0	frame.setFrameIcon(null);
330	0	frame.setContentPane(this);
331	0	Desktop.addInternalFrame(frame, title, makeVisible, width, height, Desktop.FRAME_ALLOW_RESIZE, Desktop.FRAME_SET_MIN_SIZE_300);
332	0	frame.setClosable(false);
333
334	0	progressBar = new ProgressBar(statusPanel, statusBar);
335
336	0	this.title = title;
337	0	setInfoText(info);
338
339	0	image = ChannelProperties.getImage("rotatable_logo.48");
340
341	0	MediaTracker mt = new MediaTracker(this);
342	0	mt.addImage(image, 0);
343
344	0	try
345		{
346	0	mt.waitForID(0);
347		} catch (Exception ex)
348		{
349		}
350
351	0	AnimatedPanel ap = new AnimatedPanel();
352	0	ap.setPreferredSize(new Dimension(60, 60));
353	0	titlePanel.add(ap, BorderLayout.WEST);
354	0	titlePanel.add(titleText, BorderLayout.CENTER);
355	0	setStatus(currentStatus);
356
357	0	if (!Platform.isJS())
358		{
359		// No animation for the moment//
360	0	Thread thread = new Thread(ap);
361	0	thread.start();
362		}
363	0	final WebserviceInfo thisinfo = this;
364	0	frame.addInternalFrameListener(
365		new InternalFrameAdapter()
366		{
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
367	0	@Override...
368		public void internalFrameClosed(InternalFrameEvent evt)
369		{
370		// jalview.bin.Console.outPrintln("Shutting down webservice client");
371	0	WSClientI service = thisinfo.getthisService();
372	0	if (service != null && service.isCancellable())
373		{
374	0	service.cancelJob();
375		}
376		}
377		});
378	0	frame.validate();
379
380		}
381
382		/**
383		* DOCUMENT ME!
384		*
385		* @param status
386		* integer status from state constants
387		*/
		0% Uncovered Elements: 25 (25) Complexity: 8 Complexity Density: 0.35
388	0	public void setStatus(int status)...
389		{
390	0	currentStatus = status;
391
392	0	String message = null;
393	0	switch (currentStatus)
394		{
395	0	case STATE_QUEUING:
396	0	message = MessageManager.getString("label.state_queueing");
397	0	break;
398
399	0	case STATE_RUNNING:
400	0	message = MessageManager.getString("label.state_running");
401	0	break;
402
403	0	case STATE_STOPPED_OK:
404	0	message = MessageManager.getString("label.state_completed");
405	0	break;
406
407	0	case STATE_CANCELLED_OK:
408	0	message = MessageManager.getString("label.state_job_cancelled");
409	0	break;
410
411	0	case STATE_STOPPED_ERROR:
412	0	message = MessageManager.getString("label.state_job_error");
413	0	break;
414
415	0	case STATE_STOPPED_SERVERERROR:
416	0	message = MessageManager.getString("label.server_error_try_later");
417	0	break;
418		}
419	0	titleText.setText(title + (message == null ? "" : " - " + message));
420	0	titleText.repaint();
421		}
422
423		/**
424		* subjob status indicator
425		*
426		* @param jobpane
427		* @param status
428		*/
		0% Uncovered Elements: 25 (25) Complexity: 9 Complexity Density: 0.39
429	0	public void setStatus(int jobpane, int status)...
430		{
431	0	if (jobpane < 0 || jobpane >= jobPanes.size())
432		{
433	0	throw new Error(MessageManager.formatMessage(
434		"error.setstatus_called_non_existent_job_pane", new String[]
435		{ Integer.valueOf(jobpane).toString() }));
436		}
437	0	switch (status)
438		{
439	0	case STATE_QUEUING:
440	0	setProgressName(jobpane + " - QUEUED", jobpane);
441	0	break;
442	0	case STATE_RUNNING:
443	0	setProgressName(jobpane + " - RUNNING", jobpane);
444	0	break;
445	0	case STATE_STOPPED_OK:
446	0	setProgressName(jobpane + " - FINISHED", jobpane);
447	0	break;
448	0	case STATE_CANCELLED_OK:
449	0	setProgressName(jobpane + " - CANCELLED", jobpane);
450	0	break;
451	0	case STATE_STOPPED_ERROR:
452	0	setProgressName(jobpane + " - BROKEN", jobpane);
453	0	break;
454	0	case STATE_STOPPED_SERVERERROR:
455	0	setProgressName(jobpane + " - ALERT", jobpane);
456	0	break;
457	0	default:
458	0	setProgressName(jobpane + " - UNKNOWN STATE", jobpane);
459		}
460		}
461
462		/**
463		* DOCUMENT ME!
464		*
465		* @return DOCUMENT ME!
466		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
467	0	public String getInfoText()...
468		{
469	0	return infoText.getText();
470		}
471
472		/**
473		* DOCUMENT ME!
474		*
475		* @param text
476		* DOCUMENT ME!
477		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
478	0	public void setInfoText(String text)...
479		{
480	0	infoText.setText(text);
481		}
482
483		/**
484		* DOCUMENT ME!
485		*
486		* @param text
487		* DOCUMENT ME!
488		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
489	0	public void appendInfoText(String text)...
490		{
491	0	infoText.append(text);
492		}
493
494		/**
495		* DOCUMENT ME!
496		*
497		* @return DOCUMENT ME!
498		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
499	0	public String getProgressText(int which)...
500		{
501	0	if (jobPanes == null)
502		{
503	0	addJobPane();
504		}
505	0	if (renderAsHtml)
506		{
507	0	return ((JEditorPane) ((JScrollPane) jobPanes.get(which))
508		.getViewport().getComponent(0)).getText();
509		}
510		else
511		{
512	0	return ((JTextArea) ((JScrollPane) jobPanes.get(which)).getViewport()
513		.getComponent(0)).getText();
514		}
515		}
516
517		/**
518		* DOCUMENT ME!
519		*
520		* @param text
521		* DOCUMENT ME!
522		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
523	0	public void setProgressText(int which, String text)...
524		{
525	0	if (jobPanes == null)
526		{
527	0	addJobPane();
528		}
529	0	if (renderAsHtml)
530		{
531	0	((JEditorPane) ((JScrollPane) jobPanes.get(which)).getViewport()
532		.getComponent(0)).setText(ensureHtmlTagged(text));
533		}
534		else
535		{
536	0	((JTextArea) ((JScrollPane) jobPanes.get(which)).getViewport()
537		.getComponent(0)).setText(text);
538		}
539		}
540
541		/**
542		* extract content from &lt;body&gt; content &lt;/body&gt;
543		*
544		* @param text
545		* @param leaveFirst
546		* - set to leave the initial html tag intact
547		* @param leaveLast
548		* - set to leave the final html tag intact
549		* @return
550		*/
		0% Uncovered Elements: 25 (25) Complexity: 9 Complexity Density: 0.82
551	0	private String getHtmlFragment(String text, boolean leaveFirst,...
552		boolean leaveLast)
553		{
554	0	if (text == null)
555		{
556	0	return null;
557		}
558	0	String lowertxt = text.toLowerCase(Locale.ROOT);
559	0	int htmlpos = leaveFirst ? -1 : lowertxt.indexOf("<body");
560
561	0	int htmlend = leaveLast ? -1 : lowertxt.indexOf("</body");
562	0	int htmlpose = lowertxt.indexOf(">", htmlpos),
563		htmlende = lowertxt.indexOf(">", htmlend);
564	0	if (htmlend == -1 && htmlpos == -1)
565		{
566	0	return text;
567		}
568	0	if (htmlend > -1)
569		{
570	0	return text.substring((htmlpos == -1 ? 0 : htmlpose + 1), htmlend);
571		}
572	0	return text.substring(htmlpos == -1 ? 0 : htmlpose + 1);
573		}
574
575		/**
576		* very simple routine for adding/ensuring html tags are present in text.
577		*
578		* @param text
579		* @return properly html tag enclosed text
580		*/
		0% Uncovered Elements: 26 (26) Complexity: 9 Complexity Density: 0.56
581	0	private String ensureHtmlTagged(String text)...
582		{
583	0	if (text == null)
584		{
585	0	return "";
586		}
587	0	String lowertxt = text.toLowerCase(Locale.ROOT);
588	0	int htmlpos = lowertxt.indexOf("<body");
589	0	int htmlend = lowertxt.indexOf("</body");
590	0	int doctype = lowertxt.indexOf("<!doctype");
591	0	int xmltype = lowertxt.indexOf("<?xml");
592	0	if (htmlend == -1)
593		{
594	0	text = text + "</body></html>";
595		}
596	0	if (htmlpos > -1)
597		{
598	0	if ((doctype > -1 && htmlpos > doctype)
599		|| (xmltype > -1 && htmlpos > xmltype))
600		{
601	0	text = "<html><head></head><body>\n" + text.substring(htmlpos - 1);
602		}
603		}
604		else
605		{
606	0	text = "<html><head></head><body>\n" + text;
607		}
608	0	if (text.indexOf("<meta") > -1)
609		{
610	0	System.err
611		.println("HTML COntent: \n" + text + "<< END HTML CONTENT\n");
612
613		}
614	0	return text;
615		}
616
617		/**
618		* DOCUMENT ME!
619		*
620		* @param text
621		* DOCUMENT ME!
622		*/
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
623	0	public void appendProgressText(int which, String text)...
624		{
625	0	if (jobPanes == null)
626		{
627	0	addJobPane();
628		}
629	0	if (renderAsHtml)
630		{
631	0	String txt = getHtmlFragment(
632		((JEditorPane) ((JScrollPane) jobPanes.get(which))
633		.getViewport().getComponent(0)).getText(),
634		true, false);
635	0	((JEditorPane) ((JScrollPane) jobPanes.get(which)).getViewport()
636		.getComponent(0))
637		.setText(ensureHtmlTagged(
638		txt + getHtmlFragment(text, false, true)));
639		}
640		else
641		{
642	0	((JTextArea) ((JScrollPane) jobPanes.get(which)).getViewport()
643		.getComponent(0)).append(text);
644		}
645		}
646
647		/**
648		* setProgressText(0, text)
649		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
650	0	public void setProgressText(String text)...
651		{
652	0	setProgressText(0, text);
653		}
654
655		/**
656		* appendProgressText(0, text)
657		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
658	0	public void appendProgressText(String text)...
659		{
660	0	appendProgressText(0, text);
661		}
662
663		/**
664		* getProgressText(0)
665		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
666	0	public String getProgressText()...
667		{
668	0	return getProgressText(0);
669		}
670
671		/**
672		* get the tab title for a subjob
673		*
674		* @param which
675		* int
676		* @return String
677		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
678	0	public String getProgressName(int which)...
679		{
680	0	if (jobPanes == null)
681		{
682	0	addJobPane();
683		}
684	0	if (subjobs != null)
685		{
686	0	return subjobs.getTitleAt(which);
687		}
688		else
689		{
690	0	return ((JScrollPane) jobPanes.get(which)).getViewport()
691		.getComponent(0).getName();
692		}
693		}
694
695		/**
696		* set the tab title for a subjob
697		*
698		* @param name
699		* String
700		* @param which
701		* int
702		*/
		0% Uncovered Elements: 9 (9) Complexity: 2 Complexity Density: 0.29
703	0	public void setProgressName(String name, int which)...
704		{
705	0	if (subjobs != null)
706		{
707	0	subjobs.setTitleAt(which, name);
708	0	subjobs.revalidate();
709	0	subjobs.repaint();
710		}
711	0	JScrollPane c = (JScrollPane) jobPanes.get(which);
712	0	c.getViewport().getComponent(0).setName(name);
713	0	c.repaint();
714		}
715
716		/**
717		* Gui action for cancelling the current job, if possible.
718		*
719		* @param e
720		* DOCUMENT ME!
721		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
722	0	@Override...
723		protected void cancel_actionPerformed(ActionEvent e)
724		{
725	0	if (!serviceIsCancellable)
726		{
727		// JBPNote : TODO: We should REALLY just tell the WSClientI to cancel
728		// anyhow - it has to stop threads and clean up
729		// JBPNote : TODO: Instead of a warning, we should have an optional 'Are
730		// you sure?' prompt
731	0	warnUser(
732		MessageManager.getString(
733		"warn.job_cannot_be_cancelled_close_window"),
734		MessageManager.getString("action.cancel_job"));
735		}
736		else
737		{
738	0	thisService.cancelJob();
739		}
740	0	frame.setClosable(true);
741		}
742
743		/**
744		* Spawns a thread that pops up a warning dialog box with the given message
745		* and title.
746		*
747		* @param message
748		* @param title
749		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
750	0	public void warnUser(final String message, final String title)...
751		{
752	0	javax.swing.SwingUtilities.invokeLater(new Runnable()
753		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
754	0	@Override...
755		public void run()
756		{
757	0	JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), message,
758		title, JvOptionPane.WARNING_MESSAGE);
759
760		}
761		});
762		}
763
764		/**
765		* Set up GUI for user to get at results - and possibly automatically display
766		* them if viewResultsImmediatly is set.
767		*/
		0% Uncovered Elements: 14 (14) Complexity: 3 Complexity Density: 0.3
768	0	public void setResultsReady()...
769		{
770	0	frame.setClosable(true);
771	0	buttonPanel.remove(cancel);
772	0	buttonPanel.add(showResultsNewFrame);
773	0	if (serviceCanMergeResults)
774		{
775	0	buttonPanel.add(mergeResults);
776	0	buttonPanel.setLayout(new GridLayout(2, 1, 5, 5));
777		}
778	0	buttonPanel.validate();
779	0	validate();
780	0	if (viewResultsImmediatly)
781		{
782	0	showResultsNewFrame.doClick();
783		}
784		}
785
786		/**
787		* called when job has finished but no result objects can be passed back to
788		* user
789		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
790	0	public void setFinishedNoResults()...
791		{
792	0	frame.setClosable(true);
793	0	buttonPanel.remove(cancel);
794	0	buttonPanel.validate();
795	0	validate();
796		}
797
		0% Uncovered Elements: 68 (68) Complexity: 16 Complexity Density: 0.33
798		class AnimatedPanel extends JPanel implements Runnable
799		{
800		long startTime = 0;
801
802		BufferedImage offscreen;
803
		0% Uncovered Elements: 29 (29) Complexity: 6 Complexity Density: 0.29
804	0	@Override...
805		public void run()
806		{
807	0	startTime = System.currentTimeMillis();
808
809	0	float invSpeed = 15f;
810	0	float factor = 1f;
811	0	while (currentStatus < STATE_STOPPED_OK)
812		{
813	0	if (currentStatus == STATE_QUEUING)
814		{
815	0	invSpeed = 25f;
816	0	factor = 1f;
817		}
818	0	else if (currentStatus == STATE_RUNNING)
819		{
820	0	invSpeed = 10f;
821	0	factor = (float) (0.5 + 1.5
822		* (0.5 - (0.5 * Math.sin(3.14159 / 180 * (angle + 45)))));
823		}
824	0	try
825		{
826	0	Thread.sleep(50);
827
828	0	float delta = (System.currentTimeMillis() - startTime) / invSpeed;
829	0	angle += delta * factor;
830	0	angle %= 360;
831	0	startTime = System.currentTimeMillis();
832
833	0	if (currentStatus >= STATE_STOPPED_OK)
834		{
835	0	park();
836	0	angle = 0;
837		}
838
839	0	repaint();
840		} catch (Exception ex)
841		{
842		}
843		}
844
845	0	cancel.setEnabled(false);
846		}
847
		0% Uncovered Elements: 16 (16) Complexity: 4 Complexity Density: 0.33
848	0	public void park()...
849		{
850	0	startTime = System.currentTimeMillis();
851
852	0	while (angle < 360)
853		{
854	0	float invSpeed = 5f;
855	0	float factor = 1f;
856	0	try
857		{
858	0	Thread.sleep(25);
859
860	0	float delta = (System.currentTimeMillis() - startTime) / invSpeed;
861	0	angle += delta * factor;
862	0	startTime = System.currentTimeMillis();
863
864	0	if (angle >= 360)
865		{
866	0	angle = 360;
867		}
868
869	0	repaint();
870		} catch (Exception ex)
871		{
872		}
873		}
874
875		}
876
		0% Uncovered Elements: 17 (17) Complexity: 5 Complexity Density: 0.38
877	0	void drawPanel()...
878		{
879	0	if (offscreen == null || offscreen.getWidth(this) != getWidth()
880		|| offscreen.getHeight(this) != getHeight())
881		{
882	0	offscreen = new BufferedImage(getWidth(), getHeight(),
883		BufferedImage.TYPE_INT_RGB);
884		}
885
886	0	Graphics2D g = (Graphics2D) offscreen.getGraphics();
887
888	0	g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
889		RenderingHints.VALUE_ANTIALIAS_ON);
890	0	g.setRenderingHint(RenderingHints.KEY_INTERPOLATION,
891		RenderingHints.VALUE_INTERPOLATION_BICUBIC);
892	0	g.setRenderingHint(RenderingHints.KEY_RENDERING,
893		RenderingHints.VALUE_RENDER_QUALITY);
894
895	0	g.setColor(Color.white);
896	0	g.fillRect(0, 0, getWidth(), getHeight());
897
898	0	if (image != null)
899		{
900	0	int x = image.getWidth(this) / 2, y = image.getHeight(this) / 2;
901	0	g.rotate(3.14159 / 180 * (angle), x, y);
902	0	g.drawImage(image, 0, 0, this);
903	0	g.rotate(-3.14159 / 180 * (angle), x, y);
904		}
905		}
906
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
907	0	@Override...
908		public void paintComponent(Graphics g1)
909		{
910	0	drawPanel();
911
912	0	g1.drawImage(offscreen, 0, 0, this);
913		}
914		}
915
916		boolean renderAsHtml = false;
917
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
918	0	public void setRenderAsHtml(boolean b)...
919		{
920	0	renderAsHtml = b;
921		}
922
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
923	0	@Override...
924		public void hyperlinkUpdate(HyperlinkEvent e)
925		{
926	0	Desktop.hyperlinkUpdate(e);
927		}
928
929		/*
930		* (non-Javadoc)
931		*
932		* @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
933		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
934	0	@Override...
935		public void setProgressBar(String message, long id)
936		{
937	0	progressBar.setProgressBar(message, id);
938		}
939
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
940	0	@Override...
941		public void addProgressBar(long id, String message)
942		{
943	0	progressBar.addProgressBar(id, message);
944		}
945
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
946	0	@Override...
947		public void removeProgressBar(long id)
948		{
949	0	progressBar.removeProgressBar(id);
950		}
951
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
952	0	@Override...
953		public void registerHandler(final long id,
954		final IProgressIndicatorHandler handler)
955		{
956	0	progressBar.registerHandler(id, handler);
957		}
958
959		/**
960		*
961		* @return true if any progress bars are still active
962		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
963	0	@Override...
964		public boolean operationInProgress()
965		{
966	0	return progressBar.operationInProgress();
967		}
968
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
969	0	@Override...
970		public JProgressBar getProgressBar(long id)
971		{
972	0	return progressBar.getProgressBar(id);
973		}
974
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
975	0	public String getMessage(long id)...
976		{
977	0	return progressBar.getMessage(id);
978		}
979
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
980	0	public void setProgressBarMessage(long id, String message)...
981		{
982	0	progressBar.setProgressBarMessage(id, message);
983		}
984		}