Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JalviewLite	89	612	293	0.0237388722.4%	Show methods
JalviewLite.LoadJmolThread	1793	16	9	0.00%	Show methods
JalviewLite.LoadingThread	1842	231	81	0.00%	Show methods

Class JalviewLite

Class JalviewLite	Line # 89	Total Statements 612	Complexity 293	TOTAL Coverage 0.0237388722.4%
getStructureSelectionManager() : StructureSelectionManager   getStructureSelectionManager() : StructureSelectionManager	9797	1.01	1.01	0.0 0.00%
getSelectedSequences() : String   getSelectedSequences() : String	110110	1.01	1.01	0.0 0.00%
getSelectedSequences(String) : String   getSelectedSequences(String) : String	121121	1.01	1.01	0.0 0.00%
getSelectedSequencesFrom(AlignFrame) : String   getSelectedSequencesFrom(AlignFrame) : String	134134	1.01	1.01	0.0 0.00%
getSelectedSequencesFrom(AlignFrame,String) : String   getSelectedSequencesFrom(AlignFrame,String) : String	147147	9.09	5.05	0.0 0.00%
highlight(String,String,String) : void   highlight(String,String,String) : void	176176	1.01	1.01	0.0 0.00%
run() : void   run() : void	218218	1.01	1.01	0.0 0.00%
run() : void   run() : void	230230	1.01	1.01	0.0 0.00%
highlightIn(AlignFrame,String,String,String) : void   highlightIn(AlignFrame,String,String,String) : void	190190	13.013	6.06	0.0 0.00%
select(String,String) : void   select(String,String) : void	247247	1.01	1.01	0.0 0.00%
select(String,String,String) : void   select(String,String,String) : void	259259	1.01	1.01	0.0 0.00%
selectIn(AlignFrame,String,String) : void   selectIn(AlignFrame,String,String) : void	271271	1.01	1.01	0.0 0.00%
run() : void   run() : void	489489	1.01	1.01	0.0 0.00%
selectIn(AlignFrame,String,String,String) : void   selectIn(AlignFrame,String,String,String) : void	283283	93.093	37.037	0.0 0.00%
getSelectedSequencesAsAlignment(String,String) : String   getSelectedSequencesAsAlignment(String,String) : String	506506	1.01	1.01	0.0 0.00%
getSelectedSequencesAsAlignmentFrom(AlignFrame,String,String) : String   getSelectedSequencesAsAlignmentFrom(AlignFrame,String,String) : String	521521	9.09	3.03	0.0 0.00%
getAlignmentOrder() : String   getAlignmentOrder() : String	553553	1.01	1.01	0.0 0.00%
getAlignmentOrderFrom(AlignFrame) : String   getAlignmentOrderFrom(AlignFrame) : String	566566	1.01	1.01	0.0 0.00%
getAlignmentOrderFrom(AlignFrame,String) : String   getAlignmentOrderFrom(AlignFrame,String) : String	579579	5.05	2.02	0.0 0.00%
orderBy(String,String) : String   orderBy(String,String) : String	597597	1.01	1.01	0.0 0.00%
orderBy(String,String,String) : String   orderBy(String,String,String) : String	609609	1.01	1.01	0.0 0.00%
orderAlignmentBy(AlignFrame,String,String,String) : String   orderAlignmentBy(AlignFrame,String,String,String) : String	622622	25.025	11.011	0.0 0.00%
getAlignment(String) : String   getAlignment(String) : String	679679	1.01	1.01	0.0 0.00%
getAlignmentFrom(AlignFrame,String) : String   getAlignmentFrom(AlignFrame,String) : String	692692	1.01	1.01	0.0 0.00%
getAlignment(String,String) : String   getAlignment(String,String) : String	704704	1.01	1.01	0.0 0.00%
getAlignmentFrom(AlignFrame,String,String) : String   getAlignmentFrom(AlignFrame,String,String) : String	717717	7.07	2.02	0.0 0.00%
loadAnnotation(String) : void   loadAnnotation(String) : void	742742	1.01	1.01	0.0 0.00%
loadAnnotationFrom(AlignFrame,String) : void   loadAnnotationFrom(AlignFrame,String) : void	755755	4.04	2.02	0.0 0.00%
loadFeatures(String,boolean) : void   loadFeatures(String,boolean) : void	775775	1.01	1.01	0.0 0.00%
loadFeaturesFrom(AlignFrame,String,boolean) : boolean   loadFeaturesFrom(AlignFrame,String,boolean) : boolean	788788	1.01	1.01	0.0 0.00%
getFeatures(String) : String   getFeatures(String) : String	801801	1.01	1.01	0.0 0.00%
getFeaturesFrom(AlignFrame,String) : String   getFeaturesFrom(AlignFrame,String) : String	814814	1.01	1.01	0.0 0.00%
getAnnotation() : String   getAnnotation() : String	825825	1.01	1.01	0.0 0.00%
getAnnotationFrom(AlignFrame) : String   getAnnotationFrom(AlignFrame) : String	838838	1.01	1.01	0.0 0.00%
newView() : AlignFrame   newView() : AlignFrame	849849	1.01	1.01	0.0 0.00%
newView(String) : AlignFrame   newView(String) : AlignFrame	860860	1.01	1.01	0.0 0.00%
newViewFrom(AlignFrame) : AlignFrame   newViewFrom(AlignFrame) : AlignFrame	871871	1.01	1.01	0.0 0.00%
newViewFrom(AlignFrame,String) : AlignFrame   newViewFrom(AlignFrame,String) : AlignFrame	883883	1.01	1.01	0.0 0.00%
loadAlignment(String,String) : AlignFrame   loadAlignment(String,String) : AlignFrame	895895	8.08	3.03	0.0 0.00%
setMouseoverListener(String) : void   setMouseoverListener(String) : void	922922	1.01	1.01	0.0 0.00%
setMouseoverListener(AlignFrame,String) : void   setMouseoverListener(AlignFrame,String) : void	937937	11.011	5.05	0.0 0.00%
setSelectionListener(String) : void   setSelectionListener(String) : void	971971	1.01	1.01	0.0 0.00%
setSelectionListener(AlignFrame,String) : void   setSelectionListener(AlignFrame,String) : void	984984	11.011	5.05	0.0 0.00%
setStructureListener(String,String) : void   setStructureListener(String,String) : void	10241024	11.011	4.04	0.0 0.00%
removeJavascriptListener(AlignFrame,String) : void   removeJavascriptListener(AlignFrame,String) : void	10591059	20.020	11.011	0.0 0.00%
stop() : void   stop() : void	11091109	2.02	1.01	0.0 0.00%
destroy() : void   destroy() : void	11161116	2.02	1.01	0.0 0.00%
tidyUp() : void   tidyUp() : void	11231123	21.021	8.08	0.0 0.00%
run() : void   run() : void	11801180	5.05	3.03	0.0 0.00%
mouseOverStructure(String,String,String) : void   mouseOverStructure(String,String,String) : void	11731173	2.02	1.01	0.0 0.00%
run() : void   run() : void	12181218	4.04	2.02	0.0 0.00%
scrollViewToIn(AlignFrame,String,String) : void   scrollViewToIn(AlignFrame,String,String) : void	12121212	1.01	1.01	0.0 0.00%
run() : void   run() : void	12511251	4.04	2.02	0.0 0.00%
scrollViewToRowIn(AlignFrame,String) : void   scrollViewToRowIn(AlignFrame,String) : void	12451245	1.01	1.01	0.0 0.00%
run() : void   run() : void	12841284	4.04	2.02	0.0 0.00%
scrollViewToColumnIn(AlignFrame,String) : void   scrollViewToColumnIn(AlignFrame,String) : void	12771277	1.01	1.01	0.0 0.00%
initBuildDetails() : void   initBuildDetails() : void	13551355	17.017	8.08	0.0 0.00%
getBuildDate() : String   getBuildDate() : String	13941394	2.02	1.01	0.0 0.00%
getInstallation() : String   getInstallation() : String	14001400	2.02	1.01	0.0 0.00%
getVersion() : String   getVersion() : String	14061406	2.02	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	15561556	2.02	1.01	0.0 0.00%
init() : void   init() : void	14171417	67.067	22.022	0.0 0.00%
initLiveConnect() : void   initLiveConnect() : void	15761576	15.015	8.08	0.0 0.00%
callInitCallback() : void   callInitCallback() : void	16151615	16.016	6.06	0.0 0.00%
windowClosing(WindowEvent) : void   windowClosing(WindowEvent) : void	16821682	13.013	4.04	0.0 0.00%
windowActivated(WindowEvent) : void   windowActivated(WindowEvent) : void	17071707	5.05	3.03	0.0 0.00%
addFrame(Frame,String,int,int) : void   addFrame(Frame,String,int,int) : void	16721672	7.07	1.01	0.0 0.00%
paint(Graphics) : void   paint(Graphics) : void	17451745	12.012	3.03	0.0 0.00%
getAppletWindow(Class) : Vector   getAppletWindow(Class) : Vector	17761776	7.07	4.04	0.0 0.00%
getDefaultTargetFrame() : AlignFrame   getDefaultTargetFrame() : AlignFrame	25022502	6.06	3.03	0.0 0.00%
separatorListToArray(String) : String[]   separatorListToArray(String) : String[]	25352535	1.01	1.01	0.0 0.00%
separatorListToArray(String,String) : String[]   separatorListToArray(String,String) : String[]	25472547	25.025	12.012	0.53488374 0.5348837453.5%
arrayToSeparatorList(String[]) : String   arrayToSeparatorList(String[]) : String	26032603	1.01	1.01	0.0 0.00%
arrayToSeparatorList(String[],String) : String   arrayToSeparatorList(String[],String) : String	26152615	14.014	8.08	0.0 0.00%
getFeatureGroups() : String   getFeatureGroups() : String	26532653	2.02	1.01	0.0 0.00%
getFeatureGroupsOn(AlignFrame) : String   getFeatureGroupsOn(AlignFrame) : String	26682668	2.02	1.01	0.0 0.00%
getFeatureGroupsOfState(boolean) : String   getFeatureGroupsOfState(boolean) : String	26802680	1.01	1.01	0.0 0.00%
getFeatureGroupsOfStateOn(AlignFrame,boolean) : String   getFeatureGroupsOfStateOn(AlignFrame,boolean) : String	26942694	1.01	1.01	0.0 0.00%
run() : void   run() : void	27142714	1.01	1.01	0.0 0.00%
setFeatureGroupStateOn(AlignFrame,String,boolean) : void   setFeatureGroupStateOn(AlignFrame,String,boolean) : void	27062706	2.02	1.01	0.0 0.00%
setFeatureGroupState(String,boolean) : void   setFeatureGroupState(String,boolean) : void	27282728	1.01	1.01	0.0 0.00%
getSeparator() : String   getSeparator() : String	27392739	1.01	1.01	0.0 0.00%
setSeparator(String) : void   setSeparator(String) : void	27502750	5.05	4.04	0.0 0.00%
getDefaultParameter(String,boolean) : boolean   getDefaultParameter(String,boolean) : boolean	27762776	6.06	3.03	0.0 0.00%
addPdbFile(AlignFrame,String,String,String) : boolean   addPdbFile(AlignFrame,String,String,String) : boolean	27962796	1.01	1.01	0.0 0.00%
setAlignPdbStructures(boolean) : void   setAlignPdbStructures(boolean) : void	28032803	1.01	1.01	0.0 0.00%
isAlignPdbStructures() : boolean   isAlignPdbStructures() : boolean	28082808	1.01	1.01	0.0 0.00%
start() : void   start() : void	28132813	0.00	1.01	-1.0 -1.0 -
setJsMessageSet(String,String,String[]) : void   setJsMessageSet(String,String,String[]) : void	28232823	9.09	3.03	0.0 0.00%
getJsMessage(String,String) : String   getJsMessage(String,String) : String	28472847	10.010	5.05	0.0 0.00%
isJsMessageSetChanged(String,String,String[]) : boolean   isJsMessageSetChanged(String,String,String[]) : boolean	28702870	7.07	5.05	0.0 0.00%
getJsExecQueue() : Vector   getJsExecQueue() : Vector	28902890	1.01	1.01	0.0 0.00%
setExecutor(JSFunctionExec) : void   setExecutor(JSFunctionExec) : void	28952895	1.01	1.01	0.0 0.00%
getDefaultColourParameter(String,Color) : Color   getDefaultColourParameter(String,Color) : Color	29082908	7.07	5.05	0.0 0.00%
openJalviewHelpUrl() : void   openJalviewHelpUrl() : void	29242924	4.04	3.03	0.0 0.00%
resolveUrlForLocalOrAbsolute(String,URL) : String   resolveUrlForLocalOrAbsolute(String,URL) : String	29452945	17.017	5.05	0.0 0.00%
showURL(String,String) : void   showURL(String,String) : void	30013001	12.012	7.07	0.0 0.00%

 

Class JalviewLite.LoadJmolThread

Class JalviewLite.LoadJmolThread	Line # 1793	Total Statements 16	Complexity 9	TOTAL Coverage 0.00%
run() : void   run() : void	17971797	15.015	8.08	0.0 0.00%
notFinished() : boolean   notFinished() : boolean	18361836	1.01	1.01	0.0 0.00%

 

Class JalviewLite.LoadingThread

Class JalviewLite.LoadingThread	Line # 1842	Total Statements 231	Complexity 81	TOTAL Coverage 0.00%
dbgMsg(String) : void   dbgMsg(String) : void	18551855	2.02	2.02	0.0 0.00%
resolveFileProtocol(String) : String   resolveFileProtocol(String) : String	18701870	23.023	9.09	0.0 0.00%
LoadingThread(String,String,JalviewLite)   LoadingThread(String,String,JalviewLite)	19351935	3.03	1.01	0.0 0.00%
run() : void   run() : void	19421942	6.06	3.03	0.0 0.00%
startLoading() : void   startLoading() : void	19651965	16.016	2.02	0.0 0.00%
addToDisplay(AlignFrame,AlignFrame) : void   addToDisplay(AlignFrame,AlignFrame) : void	20042004	13.013	6.06	0.0 0.00%
readAlignment(String) : AlignFrame   readAlignment(String) : AlignFrame	20382038	33.033	10.010	0.0 0.00%
loadPdbFiles(AlignFrame) : boolean   loadPdbFiles(AlignFrame) : boolean	21152115	60.060	20.020	0.0 0.00%
loadJnetFile(AlignFrame) : boolean   loadJnetFile(AlignFrame) : boolean	22792279	15.015	4.04	0.0 0.00%
loadAnnotations(AlignFrame) : boolean   loadAnnotations(AlignFrame) : boolean	23182318	10.010	3.03	0.0 0.00%
loadFeatures(AlignFrame) : boolean   loadFeatures(AlignFrame) : boolean	23502350	16.016	6.06	0.0 0.00%
loadScoreFile(AlignFrame) : boolean   loadScoreFile(AlignFrame) : boolean	23972397	11.011	6.06	0.0 0.00%
loadTree(AlignFrame) : boolean   loadTree(AlignFrame) : boolean	24332433	16.016	5.05	0.0 0.00%
inArchive(String) : boolean   inArchive(String) : boolean	24752475	7.07	4.04	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.017216643	jalview.bin.JalviewLiteTest.testSeparatorListToArrayjalview.bin.JalviewLiteTest.testSeparatorListToArray	1PASS

 

Source view

1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
7		* Jalview is free software: you can redistribute it and/or
8		* modify it under the terms of the GNU General Public License
9		* as published by the Free Software Foundation, either version 3
10		* of the License, or (at your option) any later version.
11		*
12		* Jalview is distributed in the hope that it will be useful, but
13		* WITHOUT ANY WARRANTY; without even the implied warranty
14		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15		* PURPOSE. See the GNU General Public License for more details.
16		*
17		* You should have received a copy of the GNU General Public License
18		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19		* The Jalview Authors are detailed in the 'AUTHORS' file.
20		*/
21		package jalview.bin;
22
23		import java.applet.Applet;
24		import java.awt.Button;
25		import java.awt.Color;
26		import java.awt.Component;
27		import java.awt.EventQueue;
28		import java.awt.Font;
29		import java.awt.Frame;
30		import java.awt.Graphics;
31		import java.awt.event.ActionEvent;
32		import java.awt.event.WindowAdapter;
33		import java.awt.event.WindowEvent;
34		import java.io.BufferedReader;
35		import java.io.IOException;
36		import java.io.InputStreamReader;
37		import java.net.URL;
38		import java.util.ArrayList;
39		import java.util.Hashtable;
40		import java.util.List;
41		import java.util.Locale;
42		import java.util.StringTokenizer;
43		import java.util.Vector;
44
45		import jalview.analysis.AlignmentUtils;
46		import jalview.api.StructureSelectionManagerProvider;
47		import jalview.appletgui.AlignFrame;
48		import jalview.appletgui.AlignViewport;
49		import jalview.appletgui.EmbmenuFrame;
50		import jalview.appletgui.FeatureSettings;
51		import jalview.appletgui.SplitFrame;
52		import jalview.datamodel.Alignment;
53		import jalview.datamodel.AlignmentI;
54		import jalview.datamodel.AlignmentOrder;
55		import jalview.datamodel.ColumnSelection;
56		import jalview.datamodel.PDBEntry;
57		import jalview.datamodel.Sequence;
58		import jalview.datamodel.SequenceGroup;
59		import jalview.datamodel.SequenceI;
60		import jalview.io.AnnotationFile;
61		import jalview.io.AppletFormatAdapter;
62		import jalview.io.DataSourceType;
63		import jalview.io.FileFormatI;
64		import jalview.io.FileFormats;
65		import jalview.io.FileParse;
66		import jalview.io.IdentifyFile;
67		import jalview.io.JPredFile;
68		import jalview.io.JnetAnnotationMaker;
69		import jalview.io.NewickFile;
70		import jalview.appletgui.js.JSFunctionExec;
71		import jalview.appletgui.js.JalviewLiteJsApi;
72		import jalview.appletgui.js.JsCallBack;
73		import jalview.appletgui.js.JsSelectionSender;
74		import jalview.appletgui.js.MouseOverListener;
75		import jalview.appletgui.js.MouseOverStructureListener;
76		import jalview.structure.SelectionListener;
77		import jalview.structure.StructureSelectionManager;
78		import jalview.util.ColorUtils;
79		import jalview.util.HttpUtils;
80		import jalview.util.MessageManager;
81		import netscape.javascript.JSObject;
82
83		/**
84		* Jalview Applet. Runs in Java 1.18 runtime
85		*
86		* @author $author$
87		* @version $Revision: 1.92 $
88		*/
		2.4% Uncovered Elements: 987 (1,011) Complexity: 293 Complexity Density: 0.48
89		public class JalviewLite extends Applet
90		implements StructureSelectionManagerProvider, JalviewLiteJsApi
91		{
92
93		private static final String TRUE = "true";
94
95		private static final String FALSE = "false";
96
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
97	0	public StructureSelectionManager getStructureSelectionManager()...
98		{
99	0	return StructureSelectionManager.getStructureSelectionManager(this);
100		}
101
102		// /////////////////////////////////////////
103		// The following public methods may be called
104		// externally, eg via javascript in HTML page
105		/*
106		* (non-Javadoc)
107		*
108		* @see jalview.bin.JalviewLiteJsApi#getSelectedSequences()
109		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
110	0	@Override...
111		public String getSelectedSequences()
112		{
113	0	return getSelectedSequencesFrom(getDefaultTargetFrame());
114		}
115
116		/*
117		* (non-Javadoc)
118		*
119		* @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
120		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
121	0	@Override...
122		public String getSelectedSequences(String sep)
123		{
124	0	return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
125		}
126
127		/*
128		* (non-Javadoc)
129		*
130		* @see
131		* jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
132		* .AlignFrame)
133		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
134	0	@Override...
135		public String getSelectedSequencesFrom(AlignFrame alf)
136		{
137	0	return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);
138		}
139
140		/*
141		* (non-Javadoc)
142		*
143		* @see
144		* jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
145		* .AlignFrame, java.lang.String)
146		*/
		0% Uncovered Elements: 15 (15) Complexity: 5 Complexity Density: 0.56
147	0	@Override...
148		public String getSelectedSequencesFrom(AlignFrame alf, String sep)
149		{
150	0	StringBuffer result = new StringBuffer("");
151	0	if (sep == null || sep.length() == 0)
152		{
153	0	sep = separator; // "+0x00AC;
154		}
155	0	if (alf.viewport.getSelectionGroup() != null)
156		{
157	0	SequenceI[] seqs = alf.viewport.getSelectionGroup()
158		.getSequencesInOrder(alf.viewport.getAlignment());
159
160	0	for (int i = 0; i < seqs.length; i++)
161		{
162	0	result.append(seqs[i].getName());
163	0	result.append(sep);
164		}
165		}
166
167	0	return result.toString();
168		}
169
170		/*
171		* (non-Javadoc)
172		*
173		* @see jalview.bin.JalviewLiteJsApi#highlight(java.lang.String,
174		* java.lang.String, java.lang.String)
175		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
176	0	@Override...
177		public void highlight(String sequenceId, String position,
178		String alignedPosition)
179		{
180	0	highlightIn(getDefaultTargetFrame(), sequenceId, position,
181		alignedPosition);
182		}
183
184		/*
185		* (non-Javadoc)
186		*
187		* @see jalview.bin.JalviewLiteJsApi#highlightIn(jalview.appletgui.AlignFrame,
188		* java.lang.String, java.lang.String, java.lang.String)
189		*/
		0% Uncovered Elements: 17 (17) Complexity: 6 Complexity Density: 0.46
190	0	@Override...
191		public void highlightIn(final AlignFrame alf, final String sequenceId,
192		final String position, final String alignedPosition)
193		{
194		// TODO: could try to highlight in all alignments if alf==null
195	0	jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
196		alf.viewport.getAlignment().getSequencesArray());
197	0	final SequenceI sq = matcher.findIdMatch(sequenceId);
198	0	if (sq != null)
199		{
200	0	int apos = -1;
201	0	try
202		{
203	0	apos = Integer.valueOf(position).intValue();
204	0	apos--;
205		} catch (NumberFormatException ex)
206		{
207	0	return;
208		}
209	0	final StructureSelectionManagerProvider me = this;
210	0	final int pos = apos;
211		// use vamsas listener to broadcast to all listeners in scope
212	0	if (alignedPosition != null
213		&& (alignedPosition.trim().length() == 0 || alignedPosition
214		.toLowerCase(Locale.ROOT).indexOf("false") > -1))
215		{
216	0	java.awt.EventQueue.invokeLater(new Runnable()
217		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
218	0	@Override...
219		public void run()
220		{
221	0	StructureSelectionManager.getStructureSelectionManager(me)
222		.mouseOverVamsasSequence(sq, sq.findIndex(pos), null);
223		}
224		});
225		}
226		else
227		{
228	0	java.awt.EventQueue.invokeLater(new Runnable()
229		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
230	0	@Override...
231		public void run()
232		{
233	0	StructureSelectionManager.getStructureSelectionManager(me)
234		.mouseOverVamsasSequence(sq, pos, null);
235		}
236		});
237		}
238		}
239		}
240
241		/*
242		* (non-Javadoc)
243		*
244		* @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
245		* java.lang.String)
246		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
247	0	@Override...
248		public void select(String sequenceIds, String columns)
249		{
250	0	selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator);
251		}
252
253		/*
254		* (non-Javadoc)
255		*
256		* @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
257		* java.lang.String, java.lang.String)
258		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
259	0	@Override...
260		public void select(String sequenceIds, String columns, String sep)
261		{
262	0	selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep);
263		}
264
265		/*
266		* (non-Javadoc)
267		*
268		* @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
269		* java.lang.String, java.lang.String)
270		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
271	0	@Override...
272		public void selectIn(AlignFrame alf, String sequenceIds, String columns)
273		{
274	0	selectIn(alf, sequenceIds, columns, separator);
275		}
276
277		/*
278		* (non-Javadoc)
279		*
280		* @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
281		* java.lang.String, java.lang.String, java.lang.String)
282		*/
		0% Uncovered Elements: 145 (145) Complexity: 37 Complexity Density: 0.4
283	0	@Override...
284		public void selectIn(final AlignFrame alf, String sequenceIds,
285		String columns, String sep)
286		{
287	0	if (sep == null || sep.length() == 0)
288		{
289	0	sep = separator;
290		}
291		else
292		{
293	0	if (debug)
294		{
295	0	jalview.bin.Console
296		.errPrintln("Selecting region using separator string '"
297		+ separator + "'");
298		}
299		}
300		// deparse fields
301	0	String[] ids = separatorListToArray(sequenceIds, sep);
302	0	String[] cols = separatorListToArray(columns, sep);
303	0	final SequenceGroup sel = new SequenceGroup();
304	0	final ColumnSelection csel = new ColumnSelection();
305	0	AlignmentI al = alf.viewport.getAlignment();
306	0	jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
307		alf.viewport.getAlignment().getSequencesArray());
308	0	int start = 0, end = al.getWidth(), alw = al.getWidth();
309	0	boolean seqsfound = true;
310	0	if (ids != null && ids.length > 0)
311		{
312	0	seqsfound = false;
313	0	for (int i = 0; i < ids.length; i++)
314		{
315	0	if (ids[i].trim().length() == 0)
316		{
317	0	continue;
318		}
319	0	SequenceI sq = matcher.findIdMatch(ids[i]);
320	0	if (sq != null)
321		{
322	0	seqsfound = true;
323	0	sel.addSequence(sq, false);
324		}
325		}
326		}
327	0	boolean inseqpos = false;
328	0	if (cols != null && cols.length > 0)
329		{
330	0	boolean seset = false;
331	0	for (int i = 0; i < cols.length; i++)
332		{
333	0	String cl = cols[i].trim();
334	0	if (cl.length() == 0)
335		{
336	0	continue;
337		}
338	0	int p;
339	0	if ((p = cl.indexOf("-")) > -1)
340		{
341	0	int from = -1, to = -1;
342	0	try
343		{
344	0	from = Integer.valueOf(cl.substring(0, p)).intValue();
345	0	from--;
346		} catch (NumberFormatException ex)
347		{
348	0	jalview.bin.Console.errPrintln(
349		"ERROR: Couldn't parse first integer in range element column selection string '"
350		+ cl + "' - format is 'from-to'");
351	0	return;
352		}
353	0	try
354		{
355	0	to = Integer.valueOf(cl.substring(p + 1)).intValue();
356	0	to--;
357		} catch (NumberFormatException ex)
358		{
359	0	jalview.bin.Console.errPrintln(
360		"ERROR: Couldn't parse second integer in range element column selection string '"
361		+ cl + "' - format is 'from-to'");
362	0	return;
363		}
364	0	if (from >= 0 && to >= 0)
365		{
366		// valid range
367	0	if (from < to)
368		{
369	0	int t = to;
370	0	to = from;
371	0	to = t;
372		}
373	0	if (!seset)
374		{
375	0	start = from;
376	0	end = to;
377	0	seset = true;
378		}
379		else
380		{
381		// comment to prevent range extension
382	0	if (start > from)
383		{
384	0	start = from;
385		}
386	0	if (end < to)
387		{
388	0	end = to;
389		}
390		}
391	0	for (int r = from; r <= to; r++)
392		{
393	0	if (r >= 0 && r < alw)
394		{
395	0	csel.addElement(r);
396		}
397		}
398	0	if (debug)
399		{
400	0	jalview.bin.Console.errPrintln("Range '" + cl
401		+ "' deparsed as [" + from + "," + to + "]");
402		}
403		}
404		else
405		{
406	0	jalview.bin.Console.errPrintln("ERROR: Invalid Range '" + cl
407		+ "' deparsed as [" + from + "," + to + "]");
408		}
409		}
410		else
411		{
412	0	int r = -1;
413	0	try
414		{
415	0	r = Integer.valueOf(cl).intValue();
416	0	r--;
417		} catch (NumberFormatException ex)
418		{
419	0	if (cl.toLowerCase(Locale.ROOT).equals("sequence"))
420		{
421		// we are in the dataset sequence's coordinate frame.
422	0	inseqpos = true;
423		}
424		else
425		{
426	0	jalview.bin.Console.errPrintln(
427		"ERROR: Couldn't parse integer from point selection element of column selection string '"
428		+ cl + "'");
429	0	return;
430		}
431		}
432	0	if (r >= 0 && r <= alw)
433		{
434	0	if (!seset)
435		{
436	0	start = r;
437	0	end = r;
438	0	seset = true;
439		}
440		else
441		{
442		// comment to prevent range extension
443	0	if (start > r)
444		{
445	0	start = r;
446		}
447	0	if (end < r)
448		{
449	0	end = r;
450		}
451		}
452	0	csel.addElement(r);
453	0	if (debug)
454		{
455	0	jalview.bin.Console.errPrintln("Point selection '" + cl
456		+ "' deparsed as [" + r + "]");
457		}
458		}
459		else
460		{
461	0	jalview.bin.Console
462		.errPrintln("ERROR: Invalid Point selection '" + cl
463		+ "' deparsed as [" + r + "]");
464		}
465		}
466		}
467		}
468	0	if (seqsfound)
469		{
470		// we only propagate the selection when it was the null selection, or the
471		// given sequences were found in the alignment.
472	0	if (inseqpos && sel.getSize() > 0)
473		{
474		// assume first sequence provides reference frame ?
475	0	SequenceI rs = sel.getSequenceAt(0);
476	0	start = rs.findIndex(start);
477	0	end = rs.findIndex(end);
478	0	List<Integer> cs = new ArrayList<>(csel.getSelected());
479	0	csel.clear();
480	0	for (Integer selectedCol : cs)
481		{
482	0	csel.addElement(rs.findIndex(selectedCol));
483		}
484		}
485	0	sel.setStartRes(start);
486	0	sel.setEndRes(end);
487	0	EventQueue.invokeLater(new Runnable()
488		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
489	0	@Override...
490		public void run()
491		{
492	0	alf.select(sel, csel,
493		alf.getAlignViewport().getAlignment().getHiddenColumns());
494		}
495		});
496		}
497		}
498
499		/*
500		* (non-Javadoc)
501		*
502		* @see
503		* jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang.
504		* String, java.lang.String)
505		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
506	0	@Override...
507		public String getSelectedSequencesAsAlignment(String format,
508		String suffix)
509		{
510	0	return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(),
511		format, suffix);
512		}
513
514		/*
515		* (non-Javadoc)
516		*
517		* @see
518		* jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignmentFrom(jalview
519		* .appletgui.AlignFrame, java.lang.String, java.lang.String)
520		*/
		0% Uncovered Elements: 11 (11) Complexity: 3 Complexity Density: 0.33
521	0	@Override...
522		public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
523		String format, String suffix)
524		{
525	0	try
526		{
527	0	FileFormatI theFormat = FileFormats.getInstance().forName(format);
528	0	boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
529	0	if (alf.viewport.getSelectionGroup() != null)
530		{
531		// JBPNote: getSelectionAsNewSequence behaviour has changed - this
532		// method now returns a full copy of sequence data
533		// TODO consider using getSequenceSelection instead here
534	0	String reply = new AppletFormatAdapter().formatSequences(theFormat,
535		new Alignment(alf.viewport.getSelectionAsNewSequence()),
536		seqlimits);
537	0	return reply;
538		}
539		} catch (IllegalArgumentException ex)
540		{
541	0	ex.printStackTrace();
542	0	return "Error retrieving alignment, possibly invalid format specifier: "
543		+ format;
544		}
545	0	return "";
546		}
547
548		/*
549		* (non-Javadoc)
550		*
551		* @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder()
552		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
553	0	@Override...
554		public String getAlignmentOrder()
555		{
556	0	return getAlignmentOrderFrom(getDefaultTargetFrame());
557		}
558
559		/*
560		* (non-Javadoc)
561		*
562		* @see
563		* jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
564		* )
565		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
566	0	@Override...
567		public String getAlignmentOrderFrom(AlignFrame alf)
568		{
569	0	return getAlignmentOrderFrom(alf, separator);
570		}
571
572		/*
573		* (non-Javadoc)
574		*
575		* @see
576		* jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
577		* , java.lang.String)
578		*/
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
579	0	@Override...
580		public String getAlignmentOrderFrom(AlignFrame alf, String sep)
581		{
582	0	AlignmentI alorder = alf.getAlignViewport().getAlignment();
583	0	String[] order = new String[alorder.getHeight()];
584	0	for (int i = 0; i < order.length; i++)
585		{
586	0	order[i] = alorder.getSequenceAt(i).getName();
587		}
588	0	return arrayToSeparatorList(order);
589		}
590
591		/*
592		* (non-Javadoc)
593		*
594		* @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
595		* java.lang.String)
596		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
597	0	@Override...
598		public String orderBy(String order, String undoName)
599		{
600	0	return orderBy(order, undoName, separator);
601		}
602
603		/*
604		* (non-Javadoc)
605		*
606		* @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
607		* java.lang.String, java.lang.String)
608		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
609	0	@Override...
610		public String orderBy(String order, String undoName, String sep)
611		{
612	0	return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep);
613		}
614
615		/*
616		* (non-Javadoc)
617		*
618		* @see
619		* jalview.bin.JalviewLiteJsApi#orderAlignmentBy(jalview.appletgui.AlignFrame,
620		* java.lang.String, java.lang.String, java.lang.String)
621		*/
		0% Uncovered Elements: 41 (41) Complexity: 11 Complexity Density: 0.44
622	0	@Override...
623		public String orderAlignmentBy(AlignFrame alf, String order,
624		String undoName, String sep)
625		{
626	0	String[] ids = separatorListToArray(order, sep);
627	0	SequenceI[] sqs = null;
628	0	if (ids != null && ids.length > 0)
629		{
630	0	jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
631		alf.viewport.getAlignment().getSequencesArray());
632	0	int s = 0;
633	0	sqs = new SequenceI[ids.length];
634	0	for (int i = 0; i < ids.length; i++)
635		{
636	0	if (ids[i].trim().length() == 0)
637		{
638	0	continue;
639		}
640	0	SequenceI sq = matcher.findIdMatch(ids[i]);
641	0	if (sq != null)
642		{
643	0	sqs[s++] = sq;
644		}
645		}
646	0	if (s > 0)
647		{
648	0	SequenceI[] sqq = new SequenceI[s];
649	0	System.arraycopy(sqs, 0, sqq, 0, s);
650	0	sqs = sqq;
651		}
652		else
653		{
654	0	sqs = null;
655		}
656		}
657	0	if (sqs == null)
658		{
659	0	return "";
660		}
661	0	;
662	0	final AlignmentOrder aorder = new AlignmentOrder(sqs);
663
664	0	if (undoName != null && undoName.trim().length() == 0)
665		{
666	0	undoName = null;
667		}
668	0	final String _undoName = undoName;
669		// TODO: deal with synchronization here: cannot raise any events until after
670		// this has returned.
671	0	return alf.sortBy(aorder, _undoName) ? TRUE : "";
672		}
673
674		/*
675		* (non-Javadoc)
676		*
677		* @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String)
678		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
679	0	@Override...
680		public String getAlignment(String format)
681		{
682	0	return getAlignmentFrom(getDefaultTargetFrame(), format, TRUE);
683		}
684
685		/*
686		* (non-Javadoc)
687		*
688		* @see
689		* jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
690		* java.lang.String)
691		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
692	0	@Override...
693		public String getAlignmentFrom(AlignFrame alf, String format)
694		{
695	0	return getAlignmentFrom(alf, format, TRUE);
696		}
697
698		/*
699		* (non-Javadoc)
700		*
701		* @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String,
702		* java.lang.String)
703		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
704	0	@Override...
705		public String getAlignment(String format, String suffix)
706		{
707	0	return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);
708		}
709
710		/*
711		* (non-Javadoc)
712		*
713		* @see
714		* jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
715		* java.lang.String, java.lang.String)
716		*/
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.29
717	0	@Override...
718		public String getAlignmentFrom(AlignFrame alf, String format,
719		String suffix)
720		{
721	0	try
722		{
723	0	boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
724
725	0	FileFormatI theFormat = FileFormats.getInstance().forName(format);
726	0	String reply = new AppletFormatAdapter().formatSequences(theFormat,
727		alf.viewport.getAlignment(), seqlimits);
728	0	return reply;
729		} catch (IllegalArgumentException ex)
730		{
731	0	ex.printStackTrace();
732	0	return "Error retrieving alignment, possibly invalid format specifier: "
733		+ format;
734		}
735		}
736
737		/*
738		* (non-Javadoc)
739		*
740		* @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
741		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
742	0	@Override...
743		public void loadAnnotation(String annotation)
744		{
745	0	loadAnnotationFrom(getDefaultTargetFrame(), annotation);
746		}
747
748		/*
749		* (non-Javadoc)
750		*
751		* @see
752		* jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
753		* , java.lang.String)
754		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
755	0	@Override...
756		public void loadAnnotationFrom(AlignFrame alf, String annotation)
757		{
758	0	if (new AnnotationFile().annotateAlignmentView(alf.getAlignViewport(),
759		annotation, DataSourceType.PASTE))
760		{
761	0	alf.alignPanel.fontChanged();
762	0	alf.alignPanel.setScrollValues(0, 0);
763		}
764		else
765		{
766	0	alf.parseFeaturesFile(annotation, DataSourceType.PASTE);
767		}
768		}
769
770		/*
771		* (non-Javadoc)
772		*
773		* @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
774		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
775	0	@Override...
776		public void loadFeatures(String features, boolean autoenabledisplay)
777		{
778	0	loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay);
779		}
780
781		/*
782		* (non-Javadoc)
783		*
784		* @see
785		* jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
786		* , java.lang.String)
787		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
788	0	@Override...
789		public boolean loadFeaturesFrom(AlignFrame alf, String features,
790		boolean autoenabledisplay)
791		{
792	0	return alf.parseFeaturesFile(features, DataSourceType.PASTE,
793		autoenabledisplay);
794		}
795
796		/*
797		* (non-Javadoc)
798		*
799		* @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String)
800		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
801	0	@Override...
802		public String getFeatures(String format)
803		{
804	0	return getFeaturesFrom(getDefaultTargetFrame(), format);
805		}
806
807		/*
808		* (non-Javadoc)
809		*
810		* @see
811		* jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame,
812		* java.lang.String)
813		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
814	0	@Override...
815		public String getFeaturesFrom(AlignFrame alf, String format)
816		{
817	0	return alf.outputFeatures(false, format);
818		}
819
820		/*
821		* (non-Javadoc)
822		*
823		* @see jalview.bin.JalviewLiteJsApi#getAnnotation()
824		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
825	0	@Override...
826		public String getAnnotation()
827		{
828	0	return getAnnotationFrom(getDefaultTargetFrame());
829		}
830
831		/*
832		* (non-Javadoc)
833		*
834		* @see
835		* jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame
836		* )
837		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
838	0	@Override...
839		public String getAnnotationFrom(AlignFrame alf)
840		{
841	0	return alf.outputAnnotations(false);
842		}
843
844		/*
845		* (non-Javadoc)
846		*
847		* @see jalview.bin.JalviewLiteJsApi#newView()
848		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
849	0	@Override...
850		public AlignFrame newView()
851		{
852	0	return newViewFrom(getDefaultTargetFrame());
853		}
854
855		/*
856		* (non-Javadoc)
857		*
858		* @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String)
859		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
860	0	@Override...
861		public AlignFrame newView(String name)
862		{
863	0	return newViewFrom(getDefaultTargetFrame(), name);
864		}
865
866		/*
867		* (non-Javadoc)
868		*
869		* @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame)
870		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
871	0	@Override...
872		public AlignFrame newViewFrom(AlignFrame alf)
873		{
874	0	return alf.newView(null);
875		}
876
877		/*
878		* (non-Javadoc)
879		*
880		* @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame,
881		* java.lang.String)
882		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
883	0	@Override...
884		public AlignFrame newViewFrom(AlignFrame alf, String name)
885		{
886	0	return alf.newView(name);
887		}
888
889		/*
890		* (non-Javadoc)
891		*
892		* @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String,
893		* java.lang.String)
894		*/
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.38
895	0	@Override...
896		public AlignFrame loadAlignment(String text, String title)
897		{
898	0	AlignmentI al = null;
899
900	0	try
901		{
902	0	FileFormatI format = new IdentifyFile().identify(text,
903		DataSourceType.PASTE);
904	0	al = new AppletFormatAdapter().readFile(text, DataSourceType.PASTE,
905		format);
906	0	if (al.getHeight() > 0)
907		{
908	0	return new AlignFrame(al, this, title, false);
909		}
910		} catch (IOException ex)
911		{
912	0	ex.printStackTrace();
913		}
914	0	return null;
915		}
916
917		/*
918		* (non-Javadoc)
919		*
920		* @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String)
921		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
922	0	@Override...
923		public void setMouseoverListener(String listener)
924		{
925	0	setMouseoverListener(currentAlignFrame, listener);
926		}
927
928		private Vector<JSFunctionExec> javascriptListeners = new Vector<>();
929
930		/*
931		* (non-Javadoc)
932		*
933		* @see
934		* jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame
935		* , java.lang.String)
936		*/
		0% Uncovered Elements: 19 (19) Complexity: 5 Complexity Density: 0.45
937	0	@Override...
938		public void setMouseoverListener(AlignFrame af, String listener)
939		{
940	0	if (listener != null)
941		{
942	0	listener = listener.trim();
943	0	if (listener.length() == 0)
944		{
945	0	jalview.bin.Console.errPrintln(
946		"jalview Javascript error: Ignoring empty function for mouseover listener.");
947	0	return;
948		}
949		}
950	0	MouseOverListener mol = new MouseOverListener(
951		this, af, listener);
952	0	javascriptListeners.addElement(mol);
953	0	StructureSelectionManager.getStructureSelectionManager(this)
954		.addStructureViewerListener(mol);
955	0	if (debug)
956		{
957	0	jalview.bin.Console.errPrintln("Added a mouseover listener for "
958	0	+ ((af == null) ? "All frames"
959		: "Just views for "
960		+ af.getAlignViewport().getSequenceSetId()));
961	0	jalview.bin.Console.errPrintln("There are now "
962		+ javascriptListeners.size() + " listeners in total.");
963		}
964		}
965
966		/*
967		* (non-Javadoc)
968		*
969		* @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String)
970		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
971	0	@Override...
972		public void setSelectionListener(String listener)
973		{
974	0	setSelectionListener(null, listener);
975		}
976
977		/*
978		* (non-Javadoc)
979		*
980		* @see
981		* jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame
982		* , java.lang.String)
983		*/
		0% Uncovered Elements: 19 (19) Complexity: 5 Complexity Density: 0.45
984	0	@Override...
985		public void setSelectionListener(AlignFrame af, String listener)
986		{
987	0	if (listener != null)
988		{
989	0	listener = listener.trim();
990	0	if (listener.length() == 0)
991		{
992	0	jalview.bin.Console.errPrintln(
993		"jalview Javascript error: Ignoring empty function for selection listener.");
994	0	return;
995		}
996		}
997	0	JsSelectionSender mol = new JsSelectionSender(
998		this, af, listener);
999	0	javascriptListeners.addElement(mol);
1000	0	StructureSelectionManager.getStructureSelectionManager(this)
1001		.addSelectionListener(mol);
1002	0	if (debug)
1003		{
1004	0	jalview.bin.Console.errPrintln("Added a selection listener for "
1005	0	+ ((af == null) ? "All frames"
1006		: "Just views for "
1007		+ af.getAlignViewport().getSequenceSetId()));
1008	0	jalview.bin.Console.errPrintln("There are now "
1009		+ javascriptListeners.size() + " listeners in total.");
1010		}
1011		}
1012
1013		/**
1014		* Callable from javascript to register a javascript function to pass events
1015		* to a structure viewer.
1016		*
1017		* @param listener
1018		* the name of a javascript function
1019		* @param modelSet
1020		* a token separated list of PDB file names listened for
1021		* @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String,
1022		* java.lang.String)
1023		*/
		0% Uncovered Elements: 17 (17) Complexity: 4 Complexity Density: 0.36
1024	0	@Override...
1025		public void setStructureListener(String listener, String modelSet)
1026		{
1027	0	if (listener != null)
1028		{
1029	0	listener = listener.trim();
1030	0	if (listener.length() == 0)
1031		{
1032	0	jalview.bin.Console.errPrintln(
1033		"jalview Javascript error: Ignoring empty function for selection listener.");
1034	0	return;
1035		}
1036		}
1037	0	MouseOverStructureListener mol = new MouseOverStructureListener(this,
1038		listener, separatorListToArray(modelSet));
1039	0	javascriptListeners.addElement(mol);
1040	0	StructureSelectionManager.getStructureSelectionManager(this)
1041		.addStructureViewerListener(mol);
1042	0	if (debug)
1043		{
1044	0	jalview.bin.Console
1045		.errPrintln("Added a javascript structure viewer listener '"
1046		+ listener + "'");
1047	0	jalview.bin.Console.errPrintln("There are now "
1048		+ javascriptListeners.size() + " listeners in total.");
1049		}
1050		}
1051
1052		/*
1053		* (non-Javadoc)
1054		*
1055		* @see
1056		* jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui
1057		* .AlignFrame, java.lang.String)
1058		*/
		0% Uncovered Elements: 34 (34) Complexity: 11 Complexity Density: 0.55
1059	0	@Override...
1060		public void removeJavascriptListener(AlignFrame af, String listener)
1061		{
1062	0	if (listener != null)
1063		{
1064	0	listener = listener.trim();
1065	0	if (listener.length() == 0)
1066		{
1067	0	listener = null;
1068		}
1069		}
1070	0	boolean rprt = false;
1071	0	for (int ms = 0, msSize = javascriptListeners.size(); ms < msSize;)
1072		{
1073	0	Object lstn = javascriptListeners.elementAt(ms);
1074	0	JsCallBack lstner = (JsCallBack) lstn;
1075	0	if ((af == null || lstner.getAlignFrame() == af) && (listener == null
1076		|| lstner.getListenerFunction().equals(listener)))
1077		{
1078	0	javascriptListeners.removeElement(lstner);
1079	0	msSize--;
1080	0	if (lstner instanceof SelectionListener)
1081		{
1082	0	StructureSelectionManager.getStructureSelectionManager(this)
1083		.removeSelectionListener((SelectionListener) lstner);
1084		}
1085		else
1086		{
1087	0	StructureSelectionManager.getStructureSelectionManager(this)
1088		.removeStructureViewerListener(lstner, null);
1089		}
1090	0	rprt = debug;
1091	0	if (debug)
1092		{
1093	0	jalview.bin.Console
1094		.errPrintln("Removed listener '" + listener + "'");
1095		}
1096		}
1097		else
1098		{
1099	0	ms++;
1100		}
1101		}
1102	0	if (rprt)
1103		{
1104	0	jalview.bin.Console.errPrintln("There are now "
1105		+ javascriptListeners.size() + " listeners in total.");
1106		}
1107		}
1108
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
1109	0	@Override...
1110		public void stop()
1111		{
1112	0	jalview.bin.Console.errPrintln("Applet " + getName() + " stop().");
1113	0	tidyUp();
1114		}
1115
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
1116	0	@Override...
1117		public void destroy()
1118		{
1119	0	jalview.bin.Console.errPrintln("Applet " + getName() + " destroy().");
1120	0	tidyUp();
1121		}
1122
		0% Uncovered Elements: 31 (31) Complexity: 8 Complexity Density: 0.38
1123	0	private void tidyUp()...
1124		{
1125	0	removeAll();
1126	0	if (currentAlignFrame != null && currentAlignFrame.viewport != null
1127		&& currentAlignFrame.viewport.applet != null)
1128		{
1129	0	AlignViewport av = currentAlignFrame.viewport;
1130	0	currentAlignFrame.closeMenuItem_actionPerformed();
1131	0	av.applet = null;
1132	0	currentAlignFrame = null;
1133		}
1134	0	if (javascriptListeners != null)
1135		{
1136	0	while (javascriptListeners.size() > 0)
1137		{
1138	0	JSFunctionExec mol = javascriptListeners
1139		.elementAt(0);
1140	0	javascriptListeners.removeElement(mol);
1141	0	if (mol instanceof SelectionListener)
1142		{
1143	0	StructureSelectionManager.getStructureSelectionManager(this)
1144		.removeSelectionListener((SelectionListener) mol);
1145		}
1146		else
1147		{
1148	0	StructureSelectionManager.getStructureSelectionManager(this)
1149		.removeStructureViewerListener(mol, null);
1150		}
1151	0	mol.jvlite = null;
1152		}
1153		}
1154	0	if (jsFunctionExec != null)
1155		{
1156	0	jsFunctionExec.stopQueue();
1157	0	jsFunctionExec.jvlite = null;
1158		}
1159	0	initialAlignFrame = null;
1160	0	jsFunctionExec = null;
1161	0	javascriptListeners = null;
1162	0	StructureSelectionManager.release(this);
1163		}
1164
1165		private JSFunctionExec jsFunctionExec;
1166
1167		/*
1168		* (non-Javadoc)
1169		*
1170		* @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String,
1171		* java.lang.String, java.lang.String)
1172		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
1173	0	@Override...
1174		public void mouseOverStructure(final String pdbResNum, final String chain,
1175		final String pdbfile)
1176		{
1177	0	final StructureSelectionManagerProvider me = this;
1178	0	java.awt.EventQueue.invokeLater(new Runnable()
1179		{
		0% Uncovered Elements: 7 (7) Complexity: 3 Complexity Density: 0.6
1180	0	@Override...
1181		public void run()
1182		{
1183	0	try
1184		{
1185	0	StructureSelectionManager.getStructureSelectionManager(me)
1186		.mouseOverStructure(Integer.valueOf(pdbResNum).intValue(),
1187		chain, pdbfile);
1188	0	if (debug)
1189		{
1190	0	System.err
1191		.println("mouseOver for '" + pdbResNum + "' in chain '"
1192		+ chain + "' in structure '" + pdbfile + "'");
1193		}
1194		} catch (NumberFormatException e)
1195		{
1196	0	jalview.bin.Console
1197		.errPrintln("Ignoring invalid residue number string '"
1198		+ pdbResNum + "'");
1199		}
1200
1201		}
1202		});
1203		}
1204
1205		/*
1206		* (non-Javadoc)
1207		*
1208		* @see
1209		* jalview.bin.JalviewLiteJsApi#scrollViewToIn(jalview.appletgui.AlignFrame,
1210		* java.lang.String, java.lang.String)
1211		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1212	0	@Override...
1213		public void scrollViewToIn(final AlignFrame alf, final String topRow,
1214		final String leftHandColumn)
1215		{
1216	0	java.awt.EventQueue.invokeLater(new Runnable()
1217		{
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 0.5
1218	0	@Override...
1219		public void run()
1220		{
1221	0	try
1222		{
1223	0	alf.scrollTo(Integer.valueOf(topRow).intValue(),
1224		Integer.valueOf(leftHandColumn).intValue());
1225
1226		} catch (Exception ex)
1227		{
1228	0	jalview.bin.Console
1229		.errPrintln("Couldn't parse integer arguments (topRow='"
1230		+ topRow + "' and leftHandColumn='"
1231		+ leftHandColumn + "')");
1232	0	ex.printStackTrace();
1233		}
1234		}
1235		});
1236		}
1237
1238		/*
1239		* (non-Javadoc)
1240		*
1241		* @see
1242		* JalviewLiteJsApi#scrollViewToRowIn(jalview.appletgui
1243		* .AlignFrame, java.lang.String)
1244		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1245	0	@Override...
1246		public void scrollViewToRowIn(final AlignFrame alf, final String topRow)
1247		{
1248
1249	0	java.awt.EventQueue.invokeLater(new Runnable()
1250		{
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 0.5
1251	0	@Override...
1252		public void run()
1253		{
1254	0	try
1255		{
1256	0	alf.scrollToRow(Integer.valueOf(topRow).intValue());
1257
1258		} catch (Exception ex)
1259		{
1260	0	jalview.bin.Console
1261		.errPrintln("Couldn't parse integer arguments (topRow='"
1262		+ topRow + "')");
1263	0	ex.printStackTrace();
1264		}
1265
1266		}
1267		});
1268		}
1269
1270		/*
1271		* (non-Javadoc)
1272		*
1273		* @see
1274		* JalviewLiteJsApi#scrollViewToColumnIn(jalview.appletgui
1275		* .AlignFrame, java.lang.String)
1276		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1277	0	@Override...
1278		public void scrollViewToColumnIn(final AlignFrame alf,
1279		final String leftHandColumn)
1280		{
1281	0	java.awt.EventQueue.invokeLater(new Runnable()
1282		{
1283
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 0.5
1284	0	@Override...
1285		public void run()
1286		{
1287	0	try
1288		{
1289	0	alf.scrollToColumn(Integer.valueOf(leftHandColumn).intValue());
1290
1291		} catch (Exception ex)
1292		{
1293	0	jalview.bin.Console.errPrintln(
1294		"Couldn't parse integer arguments (leftHandColumn='"
1295		+ leftHandColumn + "')");
1296	0	ex.printStackTrace();
1297		}
1298		}
1299		});
1300
1301		}
1302
1303		// //////////////////////////////////////////////
1304		// //////////////////////////////////////////////
1305
1306		public static int lastFrameX = 200;
1307
1308		public static int lastFrameY = 200;
1309
1310		boolean fileFound = true;
1311
1312		String file = "No file";
1313
1314		String file2 = null;
1315
1316		Button launcher = new Button(
1317		MessageManager.getString("label.start_jalview"));
1318
1319		/**
1320		* The currentAlignFrame is static, it will change if and when the user
1321		* selects a new window. Note that it will *never* point back to the embedded
1322		* AlignFrame if the applet is started as embedded on the page and then
1323		* afterwards a new view is created.
1324		*/
1325		public AlignFrame currentAlignFrame = null;
1326
1327		/**
1328		* This is the first frame to be displayed, and does not change. API calls
1329		* will default to this instance if currentAlignFrame is null.
1330		*/
1331		AlignFrame initialAlignFrame = null;
1332
1333		boolean embedded = false;
1334
1335		private boolean checkForJmol = true;
1336
1337		private boolean checkedForJmol = false; // ensure we don't check for jmol
1338
1339		// every time the app is re-inited
1340
1341		public boolean jmolAvailable = false;
1342
1343		private boolean alignPdbStructures = false;
1344
1345		/**
1346		* use an external structure viewer exclusively (no jmols or mc_views will be
1347		* opened by JalviewLite itself)
1348		*/
1349		public boolean useXtrnalSviewer = false;
1350
1351		public static boolean debug = false;
1352
1353		static String builddate = null, version = null, installation = null;
1354
		0% Uncovered Elements: 29 (29) Complexity: 8 Complexity Density: 0.47
1355	0	private static void initBuildDetails()...
1356		{
1357	0	if (builddate == null)
1358		{
1359	0	builddate = "unknown";
1360	0	version = "test";
1361	0	installation = "applet";
1362	0	java.net.URL url = JalviewLite.class
1363		.getResource("/.build_properties");
1364	0	if (url != null)
1365		{
1366	0	try
1367		{
1368	0	BufferedReader reader = new BufferedReader(
1369		new InputStreamReader(HttpUtils.openStream(url)));
1370	0	String line;
1371	0	while ((line = reader.readLine()) != null)
1372		{
1373	0	if (line.indexOf("VERSION") > -1)
1374		{
1375	0	version = line.substring(line.indexOf("=") + 1);
1376		}
1377	0	if (line.indexOf("BUILD_DATE") > -1)
1378		{
1379	0	builddate = line.substring(line.indexOf("=") + 1);
1380		}
1381	0	if (line.indexOf("INSTALLATION") > -1)
1382		{
1383	0	installation = line.substring(line.indexOf("=") + 1);
1384		}
1385		}
1386		} catch (Exception ex)
1387		{
1388	0	ex.printStackTrace();
1389		}
1390		}
1391		}
1392		}
1393
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
1394	0	public static String getBuildDate()...
1395		{
1396	0	initBuildDetails();
1397	0	return builddate;
1398		}
1399
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
1400	0	public static String getInstallation()...
1401		{
1402	0	initBuildDetails();
1403	0	return installation;
1404		}
1405
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
1406	0	public static String getVersion()...
1407		{
1408	0	initBuildDetails();
1409	0	return version;
1410		}
1411
1412		// public JSObject scriptObject = null;
1413
1414		/**
1415		* init method for Jalview Applet
1416		*/
		0% Uncovered Elements: 103 (103) Complexity: 22 Complexity Density: 0.33
1417	0	@Override...
1418		public void init()
1419		{
1420	0	debug = TRUE.equalsIgnoreCase(getParameter("debug"));
1421	0	try
1422		{
1423	0	if (debug)
1424		{
1425	0	jalview.bin.Console.errPrintln("Applet context is '"
1426		+ getAppletContext().getClass().toString() + "'");
1427		}
1428	0	JSObject scriptObject = JSObject.getWindow(this);
1429	0	if (debug && scriptObject != null)
1430		{
1431	0	jalview.bin.Console
1432		.errPrintln("Applet has Javascript callback support.");
1433		}
1434
1435		} catch (Exception ex)
1436		{
1437	0	jalview.bin.Console.errPrintln(
1438		"Warning: No JalviewLite javascript callbacks available.");
1439	0	if (debug)
1440		{
1441	0	ex.printStackTrace();
1442		}
1443		}
1444
1445	0	if (debug)
1446		{
1447	0	jalview.bin.Console.errPrintln("JalviewLite Version " + getVersion());
1448	0	jalview.bin.Console.errPrintln("Build Date : " + getBuildDate());
1449	0	jalview.bin.Console.errPrintln("Installation : " + getInstallation());
1450		}
1451	0	String externalsviewer = getParameter("externalstructureviewer");
1452	0	if (externalsviewer != null)
1453		{
1454	0	useXtrnalSviewer = externalsviewer.trim().toLowerCase(Locale.ROOT)
1455		.equals(TRUE);
1456		}
1457		/**
1458		* if true disable the check for jmol
1459		*/
1460	0	String chkforJmol = getParameter("nojmol");
1461	0	if (chkforJmol != null)
1462		{
1463	0	checkForJmol = !chkforJmol.equals(TRUE);
1464		}
1465		/**
1466		* get the separator parameter if present
1467		*/
1468	0	String sep = getParameter("separator");
1469	0	if (sep != null)
1470		{
1471	0	if (sep.length() > 0)
1472		{
1473	0	separator = sep;
1474	0	if (debug)
1475		{
1476	0	jalview.bin.Console
1477		.errPrintln("Separator set to '" + separator + "'");
1478		}
1479		}
1480		else
1481		{
1482	0	throw new Error(MessageManager
1483		.getString("error.invalid_separator_parameter"));
1484		}
1485		}
1486	0	int r = 255;
1487	0	int g = 255;
1488	0	int b = 255;
1489	0	String param = getParameter("RGB");
1490
1491	0	if (param != null)
1492		{
1493	0	try
1494		{
1495	0	r = Integer.parseInt(param.substring(0, 2), 16);
1496	0	g = Integer.parseInt(param.substring(2, 4), 16);
1497	0	b = Integer.parseInt(param.substring(4, 6), 16);
1498		} catch (Exception ex)
1499		{
1500	0	r = 255;
1501	0	g = 255;
1502	0	b = 255;
1503		}
1504		}
1505	0	param = getParameter("label");
1506	0	if (param != null)
1507		{
1508	0	launcher.setLabel(param);
1509		}
1510
1511	0	setBackground(new Color(r, g, b));
1512
1513	0	file = getParameter("file");
1514
1515	0	if (file == null)
1516		{
1517		// Maybe the sequences are added as parameters
1518	0	StringBuffer data = new StringBuffer("PASTE");
1519	0	int i = 1;
1520	0	while ((file = getParameter("sequence" + i)) != null)
1521		{
1522	0	data.append(file.toString() + "\n");
1523	0	i++;
1524		}
1525	0	if (data.length() > 5)
1526		{
1527	0	file = data.toString();
1528		}
1529		}
1530	0	if (getDefaultParameter("enableSplitFrame", true))
1531		{
1532	0	file2 = getParameter("file2");
1533		}
1534
1535	0	embedded = TRUE.equalsIgnoreCase(getParameter("embedded"));
1536	0	if (embedded)
1537		{
1538	0	LoadingThread loader = new LoadingThread(file, file2, this);
1539	0	loader.start();
1540		}
1541	0	else if (file != null)
1542		{
1543		/*
1544		* Start the applet immediately or show a button to start it
1545		*/
1546	0	if (FALSE.equalsIgnoreCase(getParameter("showbutton")))
1547		{
1548	0	LoadingThread loader = new LoadingThread(file, file2, this);
1549	0	loader.start();
1550		}
1551		else
1552		{
1553	0	add(launcher);
1554	0	launcher.addActionListener(new java.awt.event.ActionListener()
1555		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
1556	0	@Override...
1557		public void actionPerformed(ActionEvent e)
1558		{
1559	0	LoadingThread loader = new LoadingThread(file, file2,
1560		JalviewLite.this);
1561	0	loader.start();
1562		}
1563		});
1564		}
1565		}
1566		else
1567		{
1568		// jalview initialisation with no alignment. loadAlignment() method can
1569		// still be called to open new alignments.
1570	0	file = "NO FILE";
1571	0	fileFound = false;
1572	0	callInitCallback();
1573		}
1574		}
1575
		0% Uncovered Elements: 23 (23) Complexity: 8 Complexity Density: 0.53
1576	0	private void initLiveConnect()...
1577		{
1578		// try really hard to get the liveConnect thing working
1579	0	boolean notFailed = false;
1580	0	int tries = 0;
1581	0	while (!notFailed && tries < 10)
1582		{
1583	0	if (tries > 0)
1584		{
1585	0	jalview.bin.Console
1586		.errPrintln("LiveConnect request thread going to sleep.");
1587		}
1588	0	try
1589		{
1590	0	Thread.sleep(700 * (1 + tries));
1591		} catch (InterruptedException q)
1592		{
1593		}
1594	0	;
1595	0	if (tries++ > 0)
1596		{
1597	0	jalview.bin.Console
1598		.errPrintln("LiveConnect request thread woken up.");
1599		}
1600	0	try
1601		{
1602	0	JSObject scriptObject = JSObject.getWindow(this);
1603	0	if (scriptObject.eval("navigator") != null)
1604		{
1605	0	notFailed = true;
1606		}
1607		} catch (Exception jsex)
1608		{
1609	0	jalview.bin.Console.errPrintln("Attempt " + tries
1610		+ " to access LiveConnect javascript failed.");
1611		}
1612		}
1613		}
1614
		0% Uncovered Elements: 22 (22) Complexity: 6 Complexity Density: 0.38
1615	0	private void callInitCallback()...
1616		{
1617	0	String initjscallback = getParameter("oninit");
1618	0	if (initjscallback == null)
1619		{
1620	0	return;
1621		}
1622	0	initjscallback = initjscallback.trim();
1623	0	if (initjscallback.length() > 0)
1624		{
1625	0	JSObject scriptObject = null;
1626	0	try
1627		{
1628	0	scriptObject = JSObject.getWindow(this);
1629		} catch (Exception ex)
1630		{
1631		}
1632	0	;
1633		// try really hard to let the browser plugin know we want liveconnect
1634	0	initLiveConnect();
1635
1636	0	if (scriptObject != null)
1637		{
1638	0	try
1639		{
1640		// do onInit with the JS executor thread
1641	0	new JSFunctionExec(this).executeJavascriptFunction(true,
1642		initjscallback, null,
1643		"Calling oninit callback '" + initjscallback + "'.");
1644		} catch (Exception e)
1645		{
1646	0	jalview.bin.Console
1647		.errPrintln("Exception when executing _oninit callback '"
1648		+ initjscallback + "'.");
1649	0	e.printStackTrace();
1650		}
1651		}
1652		else
1653		{
1654	0	jalview.bin.Console.errPrintln("Not executing _oninit callback '"
1655		+ initjscallback + "' - no scripting allowed.");
1656		}
1657		}
1658		}
1659
1660		/**
1661		* Initialises and displays a new java.awt.Frame
1662		*
1663		* @param frame
1664		* java.awt.Frame to be displayed
1665		* @param title
1666		* title of new frame
1667		* @param width
1668		* width if new frame
1669		* @param height
1670		* height of new frame
1671		*/
		0% Uncovered Elements: 7 (7) Complexity: 1 Complexity Density: 0.14
1672	0	public static void addFrame(final Frame frame, String title, int width,...
1673		int height)
1674		{
1675	0	frame.setLocation(lastFrameX, lastFrameY);
1676	0	lastFrameX += 40;
1677	0	lastFrameY += 40;
1678	0	frame.setSize(width, height);
1679	0	frame.setTitle(title);
1680	0	frame.addWindowListener(new WindowAdapter()
1681		{
		0% Uncovered Elements: 19 (19) Complexity: 4 Complexity Density: 0.31
1682	0	@Override...
1683		public void windowClosing(WindowEvent e)
1684		{
1685	0	if (frame instanceof AlignFrame)
1686		{
1687	0	AlignViewport vp = ((AlignFrame) frame).viewport;
1688	0	((AlignFrame) frame).closeMenuItem_actionPerformed();
1689	0	if (vp.applet.currentAlignFrame == frame)
1690		{
1691	0	vp.applet.currentAlignFrame = null;
1692		}
1693	0	vp.applet = null;
1694	0	vp = null;
1695
1696		}
1697	0	lastFrameX -= 40;
1698	0	lastFrameY -= 40;
1699	0	if (frame instanceof EmbmenuFrame)
1700		{
1701	0	((EmbmenuFrame) frame).destroyMenus();
1702		}
1703	0	frame.setMenuBar(null);
1704	0	frame.dispose();
1705		}
1706
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
1707	0	@Override...
1708		public void windowActivated(WindowEvent e)
1709		{
1710	0	if (frame instanceof AlignFrame)
1711		{
1712	0	((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame;
1713	0	if (debug)
1714		{
1715	0	jalview.bin.Console.errPrintln("Activated window " + frame);
1716		}
1717		}
1718		// be good.
1719	0	super.windowActivated(e);
1720		}
1721		/*
1722		* Probably not necessary to do this - see TODO above. (non-Javadoc)
1723		*
1724		* @see
1725		* java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent
1726		* )
1727		*
1728		* public void windowDeactivated(WindowEvent e) { if (currentAlignFrame ==
1729		* frame) { currentAlignFrame = null; if (debug) {
1730		* jalview.bin.Console.errPrintln("Deactivated window "+frame); } }
1731		* super.windowDeactivated(e); }
1732		*/
1733		});
1734	0	frame.setVisible(true);
1735		}
1736
1737		/**
1738		* This paints the background surrounding the "Launch Jalview button" <br>
1739		* <br>
1740		* If file given in parameter not found, displays error message
1741		*
1742		* @param g
1743		* graphics context
1744		*/
		0% Uncovered Elements: 16 (16) Complexity: 3 Complexity Density: 0.25
1745	0	@Override...
1746		public void paint(Graphics g)
1747		{
1748	0	if (!fileFound)
1749		{
1750	0	g.setColor(new Color(200, 200, 200));
1751	0	g.setColor(Color.cyan);
1752	0	g.fillRect(0, 0, getSize().width, getSize().height);
1753	0	g.setColor(Color.red);
1754	0	g.drawString(
1755		MessageManager.getString("label.jalview_cannot_open_file"), 5,
1756		15);
1757	0	g.drawString("\"" + file + "\"", 5, 30);
1758		}
1759	0	else if (embedded)
1760		{
1761	0	g.setColor(Color.black);
1762	0	g.setFont(new Font("Arial", Font.BOLD, 24));
1763	0	g.drawString(MessageManager.getString("label.jalview_applet"), 50,
1764		getSize().height / 2 - 30);
1765	0	g.drawString(MessageManager.getString("label.loading_data") + "...",
1766		50, getSize().height / 2);
1767		}
1768		}
1769
1770		/**
1771		* get all components associated with the applet of the given type
1772		*
1773		* @param class1
1774		* @return
1775		*/
		0% Uncovered Elements: 13 (13) Complexity: 4 Complexity Density: 0.57
1776	0	public Vector getAppletWindow(Class class1)...
1777		{
1778	0	Vector wnds = new Vector();
1779	0	Component[] cmp = getComponents();
1780	0	if (cmp != null)
1781		{
1782	0	for (int i = 0; i < cmp.length; i++)
1783		{
1784	0	if (class1.isAssignableFrom(cmp[i].getClass()))
1785		{
1786	0	wnds.addElement(cmp);
1787		}
1788		}
1789		}
1790	0	return wnds;
1791		}
1792
		0% Uncovered Elements: 28 (28) Complexity: 9 Complexity Density: 0.56
1793		class LoadJmolThread extends Thread
1794		{
1795		private boolean running = false;
1796
		0% Uncovered Elements: 25 (25) Complexity: 8 Complexity Density: 0.53
1797	0	@Override...
1798		public void run()
1799		{
1800	0	if (running || checkedForJmol)
1801		{
1802	0	return;
1803		}
1804	0	running = true;
1805	0	if (checkForJmol)
1806		{
1807	0	try
1808		{
1809	0	if (!System.getProperty("java.version").startsWith("1.1"))
1810		{
1811	0	Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
1812	0	jmolAvailable = true;
1813		}
1814	0	if (!jmolAvailable)
1815		{
1816	0	jalview.bin.Console.outPrintln(
1817		"Jmol not available - Using mc_view for structures");
1818		}
1819		} catch (java.lang.ClassNotFoundException ex)
1820		{
1821		}
1822		}
1823		else
1824		{
1825	0	jmolAvailable = false;
1826	0	if (debug)
1827		{
1828	0	jalview.bin.Console.errPrintln(
1829		"Skipping Jmol check. Will use mc_view (probably)");
1830		}
1831		}
1832	0	checkedForJmol = true;
1833	0	running = false;
1834		}
1835
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1836	0	public boolean notFinished()...
1837		{
1838	0	return running || !checkedForJmol;
1839		}
1840		}
1841
		0% Uncovered Elements: 355 (355) Complexity: 81 Complexity Density: 0.35
1842		class LoadingThread extends Thread
1843		{
1844		/**
1845		* State variable: protocol for access to file source
1846		*/
1847		DataSourceType protocol;
1848
1849		String _file; // alignment file or URL spec
1850
1851		String _file2; // second alignment file or URL spec
1852
1853		JalviewLite applet;
1854
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
1855	0	private void dbgMsg(String msg)...
1856		{
1857	0	if (JalviewLite.debug)
1858		{
1859	0	jalview.bin.Console.errPrintln(msg);
1860		}
1861		}
1862
1863		/**
1864		* update the protocol state variable for accessing the datasource located
1865		* by file.
1866		*
1867		* @param path
1868		* @return possibly updated datasource string
1869		*/
		0% Uncovered Elements: 37 (37) Complexity: 9 Complexity Density: 0.39
1870	0	public String resolveFileProtocol(String path)...
1871		{
1872		/*
1873		* is it paste data?
1874		*/
1875	0	if (path.startsWith("PASTE"))
1876		{
1877	0	protocol = DataSourceType.PASTE;
1878	0	return path.substring(5);
1879		}
1880
1881		/*
1882		* is it a URL?
1883		*/
1884	0	if (path.indexOf("://") != -1)
1885		{
1886	0	protocol = DataSourceType.URL;
1887	0	return path;
1888		}
1889
1890		/*
1891		* try relative to document root
1892		*/
1893	0	URL documentBase = getDocumentBase();
1894	0	String withDocBase = resolveUrlForLocalOrAbsolute(path, documentBase);
1895	0	if (HttpUtils.isValidUrl(withDocBase))
1896		{
1897	0	if (debug)
1898		{
1899	0	jalview.bin.Console.errPrintln("Prepended document base '"
1900		+ documentBase + "' to make: '" + withDocBase + "'");
1901		}
1902	0	protocol = DataSourceType.URL;
1903	0	return withDocBase;
1904		}
1905
1906		/*
1907		* try relative to codebase (if different to document base)
1908		*/
1909	0	URL codeBase = getCodeBase();
1910	0	String withCodeBase = applet.resolveUrlForLocalOrAbsolute(path,
1911		codeBase);
1912	0	if (!withCodeBase.equals(withDocBase)
1913		&& HttpUtils.isValidUrl(withCodeBase))
1914		{
1915	0	protocol = DataSourceType.URL;
1916	0	if (debug)
1917		{
1918	0	jalview.bin.Console.errPrintln("Prepended codebase '" + codeBase
1919		+ "' to make: '" + withCodeBase + "'");
1920		}
1921	0	return withCodeBase;
1922		}
1923
1924		/*
1925		* try locating by classloader; try this last so files in the directory
1926		* are resolved using document base
1927		*/
1928	0	if (inArchive(path))
1929		{
1930	0	protocol = DataSourceType.CLASSLOADER;
1931		}
1932	0	return path;
1933		}
1934
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
1935	0	public LoadingThread(String file, String file2, JalviewLite _applet)...
1936		{
1937	0	this._file = file;
1938	0	this._file2 = file2;
1939	0	applet = _applet;
1940		}
1941
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.5
1942	0	@Override...
1943		public void run()
1944		{
1945	0	LoadJmolThread jmolchecker = new LoadJmolThread();
1946	0	jmolchecker.start();
1947	0	while (jmolchecker.notFinished())
1948		{
1949		// wait around until the Jmol check is complete.
1950	0	try
1951		{
1952	0	Thread.sleep(2);
1953		} catch (Exception e)
1954		{
1955		}
1956		}
1957	0	startLoading();
1958		// applet.callInitCallback();
1959		}
1960
1961		/**
1962		* Load the alignment and any related files as specified by applet
1963		* parameters
1964		*/
		0% Uncovered Elements: 18 (18) Complexity: 2 Complexity Density: 0.12
1965	0	private void startLoading()...
1966		{
1967	0	dbgMsg("Loading thread started with:\n>>file\n" + _file
1968		+ ">>endfile");
1969
1970	0	dbgMsg("Loading started.");
1971
1972	0	AlignFrame newAlignFrame = readAlignment(_file);
1973	0	AlignFrame newAlignFrame2 = readAlignment(_file2);
1974	0	if (newAlignFrame != null)
1975		{
1976	0	addToDisplay(newAlignFrame, newAlignFrame2);
1977	0	loadTree(newAlignFrame);
1978
1979	0	loadScoreFile(newAlignFrame);
1980
1981	0	loadFeatures(newAlignFrame);
1982
1983	0	loadAnnotations(newAlignFrame);
1984
1985	0	loadJnetFile(newAlignFrame);
1986
1987	0	loadPdbFiles(newAlignFrame);
1988		}
1989		else
1990		{
1991	0	fileFound = false;
1992	0	applet.remove(launcher);
1993	0	applet.repaint();
1994		}
1995	0	callInitCallback();
1996		}
1997
1998		/**
1999		* Add an AlignFrame to the display; or if two are provided, a SplitFrame.
2000		*
2001		* @param af
2002		* @param af2
2003		*/
		0% Uncovered Elements: 23 (23) Complexity: 6 Complexity Density: 0.46
2004	0	public void addToDisplay(AlignFrame af, AlignFrame af2)...
2005		{
2006	0	if (af2 != null)
2007		{
2008	0	AlignmentI al1 = af.viewport.getAlignment();
2009	0	AlignmentI al2 = af2.viewport.getAlignment();
2010	0	AlignmentI cdna = al1.isNucleotide() ? al1 : al2;
2011	0	AlignmentI prot = al1.isNucleotide() ? al2 : al1;
2012	0	if (AlignmentUtils.mapProteinAlignmentToCdna(prot, cdna))
2013		{
2014	0	al2.alignAs(al1);
2015	0	SplitFrame sf = new SplitFrame(af, af2);
2016	0	sf.addToDisplay(embedded, JalviewLite.this);
2017	0	return;
2018		}
2019		else
2020		{
2021	0	String msg = "Could not map any sequence in " + af2.getTitle()
2022		+ " as "
2023	0	+ (al1.isNucleotide() ? "protein product" : "cDNA")
2024		+ " for " + af.getTitle();
2025	0	jalview.bin.Console.errPrintln(msg);
2026		}
2027		}
2028
2029	0	af.addToDisplay(embedded);
2030		}
2031
2032		/**
2033		* Read the alignment file (from URL, text 'paste', or archive by
2034		* classloader).
2035		*
2036		* @return
2037		*/
		0% Uncovered Elements: 45 (45) Complexity: 10 Complexity Density: 0.3
2038	0	protected AlignFrame readAlignment(String fileParam)...
2039		{
2040	0	if (fileParam == null)
2041		{
2042	0	return null;
2043		}
2044	0	String resolvedFile = resolveFileProtocol(fileParam);
2045	0	AlignmentI al = null;
2046	0	try
2047		{
2048	0	FileFormatI format = new IdentifyFile().identify(resolvedFile,
2049		protocol);
2050	0	dbgMsg("File identified as '" + format + "'");
2051	0	al = new AppletFormatAdapter().readFile(resolvedFile, protocol,
2052		format);
2053	0	if ((al != null) && (al.getHeight() > 0))
2054		{
2055	0	dbgMsg("Successfully loaded file.");
2056	0	al.setDataset(null);
2057	0	AlignFrame newAlignFrame = new AlignFrame(al, applet,
2058		resolvedFile, embedded, false);
2059	0	newAlignFrame.setTitle(resolvedFile);
2060	0	if (initialAlignFrame == null)
2061		{
2062	0	initialAlignFrame = newAlignFrame;
2063		}
2064		// update the focus.
2065	0	currentAlignFrame = newAlignFrame;
2066
2067	0	if (protocol == DataSourceType.PASTE)
2068		{
2069	0	newAlignFrame.setTitle(MessageManager
2070		.formatMessage("label.sequences_from", new Object[]
2071		{ applet.getDocumentBase().toString() }));
2072		}
2073
2074	0	newAlignFrame.statusBar.setText(MessageManager.formatMessage(
2075		"label.successfully_loaded_file", new Object[]
2076		{ resolvedFile }));
2077
2078	0	return newAlignFrame;
2079		}
2080		} catch (java.io.IOException ex)
2081		{
2082	0	dbgMsg("File load exception.");
2083	0	ex.printStackTrace();
2084	0	if (debug)
2085		{
2086	0	try
2087		{
2088	0	FileParse fp = new FileParse(resolvedFile, protocol);
2089	0	String ln = null;
2090	0	dbgMsg(">>>Dumping contents of '" + resolvedFile + "' " + "("
2091		+ protocol + ")");
2092	0	while ((ln = fp.nextLine()) != null)
2093		{
2094	0	dbgMsg(ln);
2095		}
2096	0	dbgMsg(">>>Dump finished.");
2097		} catch (Exception e)
2098		{
2099	0	jalview.bin.Console.errPrintln(
2100		"Exception when trying to dump the content of the file parameter.");
2101	0	e.printStackTrace();
2102		}
2103		}
2104		}
2105	0	return null;
2106		}
2107
2108		/**
2109		* Load PDBFiles if any specified by parameter(s). Returns true if loaded,
2110		* else false.
2111		*
2112		* @param alignFrame
2113		* @return
2114		*/
		0% Uncovered Elements: 96 (96) Complexity: 20 Complexity Density: 0.33
2115	0	protected boolean loadPdbFiles(AlignFrame alignFrame)...
2116		{
2117	0	boolean result = false;
2118		/*
2119		* <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6 -
2120		* related to JAL-434
2121		*/
2122
2123	0	applet.setAlignPdbStructures(
2124		getDefaultParameter("alignpdbfiles", false));
2125		/*
2126		* <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
2127		* PDB|1GAQ|1GAQ|C">
2128		*
2129		* <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
2130		*
2131		* <param name="PDBfile3" value="1q0o Q45135_9MICO">
2132		*/
2133
2134	0	int pdbFileCount = 0;
2135		// Accumulate pdbs here if they are heading for the same view (if
2136		// alignPdbStructures is true)
2137	0	Vector pdbs = new Vector();
2138		// create a lazy matcher if we're asked to
2139	0	jalview.analysis.SequenceIdMatcher matcher = (applet
2140		.getDefaultParameter("relaxedidmatch", false))
2141		? new jalview.analysis.SequenceIdMatcher(
2142		alignFrame.getAlignViewport().getAlignment()
2143		.getSequencesArray())
2144		: null;
2145
2146	0	String param;
2147	0	do
2148		{
2149	0	if (pdbFileCount > 0)
2150		{
2151	0	param = applet.getParameter("PDBFILE" + pdbFileCount);
2152		}
2153		else
2154		{
2155	0	param = applet.getParameter("PDBFILE");
2156		}
2157
2158	0	if (param != null)
2159		{
2160	0	PDBEntry pdb = new PDBEntry();
2161
2162	0	String seqstring;
2163	0	SequenceI[] seqs = null;
2164	0	String[] chains = null;
2165
2166	0	StringTokenizer st = new StringTokenizer(param, " ");
2167
2168	0	if (st.countTokens() < 2)
2169		{
2170	0	String sequence = applet.getParameter("PDBSEQ");
2171	0	if (sequence != null)
2172		{
2173	0	seqs = new SequenceI[] { matcher == null
2174		? (Sequence) alignFrame.getAlignViewport()
2175		.getAlignment().findName(sequence)
2176		: matcher.findIdMatch(sequence) };
2177		}
2178
2179		}
2180		else
2181		{
2182	0	param = st.nextToken();
2183	0	List<SequenceI> tmp = new ArrayList<>();
2184	0	List<String> tmp2 = new ArrayList<>();
2185
2186	0	while (st.hasMoreTokens())
2187		{
2188	0	seqstring = st.nextToken();
2189	0	StringTokenizer st2 = new StringTokenizer(seqstring, "=");
2190	0	if (st2.countTokens() > 1)
2191		{
2192		// This is the chain
2193	0	tmp2.add(st2.nextToken());
2194	0	seqstring = st2.nextToken();
2195		}
2196	0	tmp.add(matcher == null
2197		? (Sequence) alignFrame.getAlignViewport()
2198		.getAlignment().findName(seqstring)
2199		: matcher.findIdMatch(seqstring));
2200		}
2201
2202	0	seqs = tmp.toArray(new SequenceI[tmp.size()]);
2203	0	if (tmp2.size() == tmp.size())
2204		{
2205	0	chains = tmp2.toArray(new String[tmp2.size()]);
2206		}
2207		}
2208	0	param = resolveFileProtocol(param);
2209		// TODO check JAL-357 for files in a jar (CLASSLOADER)
2210	0	pdb.setFile(param);
2211
2212	0	if (seqs != null)
2213		{
2214	0	for (int i = 0; i < seqs.length; i++)
2215		{
2216	0	if (seqs[i] != null)
2217		{
2218	0	((Sequence) seqs[i]).addPDBId(pdb);
2219	0	StructureSelectionManager
2220		.getStructureSelectionManager(applet)
2221		.registerPDBEntry(pdb);
2222		}
2223		else
2224		{
2225	0	if (JalviewLite.debug)
2226		{
2227		// this may not really be a problem but we give a warning
2228		// anyway
2229	0	jalview.bin.Console.errPrintln(
2230		"Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
2231		+ i + ")");
2232		}
2233		}
2234		}
2235
2236	0	if (!alignPdbStructures)
2237		{
2238	0	alignFrame.newStructureView(applet, pdb, seqs, chains,
2239		protocol);
2240		}
2241		else
2242		{
2243	0	pdbs.addElement(new Object[] { pdb, seqs, chains, protocol });
2244		}
2245		}
2246		}
2247
2248	0	pdbFileCount++;
2249	0	} while (param != null || pdbFileCount < 10);
2250	0	if (pdbs.size() > 0)
2251		{
2252	0	SequenceI[][] seqs = new SequenceI[pdbs.size()][];
2253	0	PDBEntry[] pdb = new PDBEntry[pdbs.size()];
2254	0	String[][] chains = new String[pdbs.size()][];
2255	0	String[] protocols = new String[pdbs.size()];
2256	0	for (int pdbsi = 0, pdbsiSize = pdbs
2257	0	.size(); pdbsi < pdbsiSize; pdbsi++)
2258		{
2259	0	Object[] o = (Object[]) pdbs.elementAt(pdbsi);
2260	0	pdb[pdbsi] = (PDBEntry) o[0];
2261	0	seqs[pdbsi] = (SequenceI[]) o[1];
2262	0	chains[pdbsi] = (String[]) o[2];
2263	0	protocols[pdbsi] = (String) o[3];
2264		}
2265	0	alignFrame.alignedStructureView(applet, pdb, seqs, chains,
2266		protocols);
2267	0	result = true;
2268		}
2269	0	return result;
2270		}
2271
2272		/**
2273		* Load in a Jnetfile if specified by parameter. Returns true if loaded,
2274		* else false.
2275		*
2276		* @param alignFrame
2277		* @return
2278		*/
		0% Uncovered Elements: 19 (19) Complexity: 4 Complexity Density: 0.27
2279	0	protected boolean loadJnetFile(AlignFrame alignFrame)...
2280		{
2281	0	boolean result = false;
2282	0	String param = applet.getParameter("jnetfile");
2283	0	if (param == null)
2284		{
2285		// jnet became jpred around 2016
2286	0	param = applet.getParameter("jpredfile");
2287		}
2288	0	if (param != null)
2289		{
2290	0	try
2291		{
2292	0	param = resolveFileProtocol(param);
2293	0	JPredFile predictions = new JPredFile(param, protocol);
2294	0	JnetAnnotationMaker.add_annotation(predictions,
2295		alignFrame.viewport.getAlignment(), 0, false);
2296		// false == do not add sequence profile from concise output
2297
2298	0	alignFrame.viewport.getAlignment().setupJPredAlignment();
2299
2300	0	alignFrame.alignPanel.fontChanged();
2301	0	alignFrame.alignPanel.setScrollValues(0, 0);
2302	0	result = true;
2303		} catch (Exception ex)
2304		{
2305	0	ex.printStackTrace();
2306		}
2307		}
2308	0	return result;
2309		}
2310
2311		/**
2312		* Load annotations if specified by parameter. Returns true if loaded, else
2313		* false.
2314		*
2315		* @param alignFrame
2316		* @return
2317		*/
		0% Uncovered Elements: 14 (14) Complexity: 3 Complexity Density: 0.3
2318	0	protected boolean loadAnnotations(AlignFrame alignFrame)...
2319		{
2320	0	boolean result = false;
2321	0	String param = applet.getParameter("annotations");
2322	0	if (param != null)
2323		{
2324	0	param = resolveFileProtocol(param);
2325
2326	0	if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
2327		param, protocol))
2328		{
2329	0	alignFrame.alignPanel.fontChanged();
2330	0	alignFrame.alignPanel.setScrollValues(0, 0);
2331	0	result = true;
2332		}
2333		else
2334		{
2335	0	jalview.bin.Console.errPrintln(
2336		"Annotations were not added from annotation file '"
2337		+ param + "'");
2338		}
2339		}
2340	0	return result;
2341		}
2342
2343		/**
2344		* Load features file and view settings as specified by parameters. Returns
2345		* true if features were loaded, else false.
2346		*
2347		* @param alignFrame
2348		* @return
2349		*/
		0% Uncovered Elements: 24 (24) Complexity: 6 Complexity Density: 0.38
2350	0	protected boolean loadFeatures(AlignFrame alignFrame)...
2351		{
2352	0	boolean result = false;
2353		// ///////////////////////////
2354		// modify display of features
2355		// we do this before any features have been loaded, ensuring any hidden
2356		// groups are hidden when features first displayed
2357		//
2358		// hide specific groups
2359		//
2360	0	String param = applet.getParameter("hidefeaturegroups");
2361	0	if (param != null)
2362		{
2363	0	alignFrame.setFeatureGroupState(separatorListToArray(param), false);
2364		// applet.setFeatureGroupStateOn(newAlignFrame, param, false);
2365		}
2366		// show specific groups
2367	0	param = applet.getParameter("showfeaturegroups");
2368	0	if (param != null)
2369		{
2370	0	alignFrame.setFeatureGroupState(separatorListToArray(param), true);
2371		// applet.setFeatureGroupStateOn(newAlignFrame, param, true);
2372		}
2373		// and now load features
2374	0	param = applet.getParameter("features");
2375	0	if (param != null)
2376		{
2377	0	param = resolveFileProtocol(param);
2378
2379	0	result = alignFrame.parseFeaturesFile(param, protocol);
2380		}
2381
2382	0	param = applet.getParameter("showFeatureSettings");
2383	0	if (param != null && param.equalsIgnoreCase(TRUE))
2384		{
2385	0	alignFrame.viewport.setShowSequenceFeatures(true);
2386	0	new FeatureSettings(alignFrame.alignPanel);
2387		}
2388	0	return result;
2389		}
2390
2391		/**
2392		* Load a score file if specified by parameter. Returns true if file was
2393		* loaded, else false.
2394		*
2395		* @param alignFrame
2396		*/
		0% Uncovered Elements: 17 (17) Complexity: 6 Complexity Density: 0.55
2397	0	protected boolean loadScoreFile(AlignFrame alignFrame)...
2398		{
2399	0	boolean result = false;
2400	0	String sScoreFile = applet.getParameter("scoreFile");
2401	0	if (sScoreFile != null && !"".equals(sScoreFile))
2402		{
2403	0	try
2404		{
2405	0	if (debug)
2406		{
2407	0	jalview.bin.Console.errPrintln(
2408		"Attempting to load T-COFFEE score file from the scoreFile parameter");
2409		}
2410	0	result = alignFrame.loadScoreFile(sScoreFile);
2411	0	if (!result)
2412		{
2413	0	jalview.bin.Console.errPrintln(
2414		"Failed to parse T-COFFEE parameter as a valid score file ('"
2415		+ sScoreFile + "')");
2416		}
2417		} catch (Exception e)
2418		{
2419	0	System.err.printf("Cannot read score file: '%s'. Cause: %s \n",
2420		sScoreFile, e.getMessage());
2421		}
2422		}
2423	0	return result;
2424		}
2425
2426		/**
2427		* Load a tree for the alignment if specified by parameter. Returns true if
2428		* a tree was loaded, else false.
2429		*
2430		* @param alignFrame
2431		* @return
2432		*/
		0% Uncovered Elements: 22 (22) Complexity: 5 Complexity Density: 0.31
2433	0	protected boolean loadTree(AlignFrame alignFrame)...
2434		{
2435	0	boolean result = false;
2436	0	String treeFile = applet.getParameter("tree");
2437	0	if (treeFile == null)
2438		{
2439	0	treeFile = applet.getParameter("treeFile");
2440		}
2441
2442	0	if (treeFile != null)
2443		{
2444	0	try
2445		{
2446	0	treeFile = resolveFileProtocol(treeFile);
2447	0	NewickFile fin = new NewickFile(treeFile, protocol);
2448	0	fin.parse();
2449
2450	0	if (fin.getTree() != null)
2451		{
2452	0	alignFrame.loadTree(fin, treeFile);
2453	0	result = true;
2454	0	dbgMsg("Successfully imported tree.");
2455		}
2456		else
2457		{
2458	0	dbgMsg("Tree parameter did not resolve to a valid tree.");
2459		}
2460		} catch (Exception ex)
2461		{
2462	0	ex.printStackTrace();
2463		}
2464		}
2465	0	return result;
2466		}
2467
2468		/**
2469		* Discovers whether the given file is in the Applet Archive
2470		*
2471		* @param f
2472		* String
2473		* @return boolean
2474		*/
		0% Uncovered Elements: 11 (11) Complexity: 4 Complexity Density: 0.57
2475	0	boolean inArchive(String f)...
2476		{
2477		// This might throw a security exception in certain browsers
2478		// Netscape Communicator for instance.
2479	0	try
2480		{
2481	0	boolean rtn = (getClass().getResourceAsStream("/" + f) != null);
2482	0	if (debug)
2483		{
2484	0	jalview.bin.Console.errPrintln("Resource '" + f + "' was "
2485	0	+ (rtn ? "" : "not ") + "located by classloader.");
2486		}
2487	0	return rtn;
2488		} catch (Exception ex)
2489		{
2490	0	jalview.bin.Console.outPrintln(
2491		"Exception checking resources: " + f + " " + ex);
2492	0	return false;
2493		}
2494		}
2495		}
2496
2497		/**
2498		* @return the default alignFrame acted on by the public applet methods. May
2499		* return null with an error message on System.err indicating the
2500		* fact.
2501		*/
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
2502	0	public AlignFrame getDefaultTargetFrame()...
2503		{
2504	0	if (currentAlignFrame != null)
2505		{
2506	0	return currentAlignFrame;
2507		}
2508	0	if (initialAlignFrame != null)
2509		{
2510	0	return initialAlignFrame;
2511		}
2512	0	jalview.bin.Console.errPrintln(
2513		"Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
2514	0	return null;
2515		}
2516
2517		/**
2518		* separator used for separatorList
2519		*/
2520		protected String separator = "" + ((char) 0x00AC); // the default used to be
2521		// '|' but many sequence
2522		// IDS include pipes.
2523
2524		/**
2525		* set to enable the URL based javascript execution mechanism
2526		*/
2527		public boolean jsfallbackEnabled = false;
2528
2529		/**
2530		* parse the string into a list
2531		*
2532		* @param list
2533		* @return elements separated by separator
2534		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2535	0	public String[] separatorListToArray(String list)...
2536		{
2537	0	return separatorListToArray(list, separator);
2538		}
2539
2540		/**
2541		* parse the string into a list
2542		*
2543		* @param list
2544		* @param separator
2545		* @return elements separated by separator
2546		*/
		53.5% Uncovered Elements: 20 (43) Complexity: 12 Complexity Density: 0.48
2547	7	public static String[] separatorListToArray(String list, String separator)...
2548		{
2549		// TODO use StringUtils version (slightly different...)
2550	7	int seplen = separator.length();
2551	7	if (list == null || list.equals("") || list.equals(separator))
2552		{
2553	4	return null;
2554		}
2555	3	java.util.Vector jv = new Vector();
2556	3	int cp = 0, pos;
2557	?	while ((pos = list.indexOf(separator, cp)) > cp)
2558		{
2559	5	jv.addElement(list.substring(cp, pos));
2560	5	cp = pos + seplen;
2561		}
2562	3	if (cp < list.length())
2563		{
2564	0	String c = list.substring(cp);
2565	0	if (!c.equals(separator))
2566		{
2567	0	jv.addElement(c);
2568		}
2569		}
2570	3	if (jv.size() > 0)
2571		{
2572	3	String[] v = new String[jv.size()];
2573	8	for (int i = 0; i < v.length; i++)
2574		{
2575	5	v[i] = (String) jv.elementAt(i);
2576		}
2577	3	jv.removeAllElements();
2578	3	if (debug)
2579		{
2580	0	jalview.bin.Console.errPrintln("Array from '" + separator
2581		+ "' separated List:\n" + v.length);
2582	0	for (int i = 0; i < v.length; i++)
2583		{
2584	0	jalview.bin.Console.errPrintln("item " + i + " '" + v[i] + "'");
2585		}
2586		}
2587	3	return v;
2588		}
2589	0	if (debug)
2590		{
2591	0	jalview.bin.Console.errPrintln(
2592		"Empty Array from '" + separator + "' separated List");
2593		}
2594	0	return null;
2595		}
2596
2597		/**
2598		* concatenate the list with separator
2599		*
2600		* @param list
2601		* @return concatenated string
2602		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2603	0	public String arrayToSeparatorList(String[] list)...
2604		{
2605	0	return arrayToSeparatorList(list, separator);
2606		}
2607
2608		/**
2609		* concatenate the list with separator
2610		*
2611		* @param list
2612		* @param separator
2613		* @return concatenated string
2614		*/
		0% Uncovered Elements: 26 (26) Complexity: 8 Complexity Density: 0.57
2615	0	public static String arrayToSeparatorList(String[] list, String separator)...
2616		{
2617		// TODO use StringUtils version
2618	0	StringBuffer v = new StringBuffer();
2619	0	if (list != null && list.length > 0)
2620		{
2621	0	for (int i = 0, iSize = list.length; i < iSize; i++)
2622		{
2623	0	if (list[i] != null)
2624		{
2625	0	if (i > 0)
2626		{
2627	0	v.append(separator);
2628		}
2629	0	v.append(list[i]);
2630		}
2631		}
2632	0	if (debug)
2633		{
2634	0	System.err
2635		.println("Returning '" + separator + "' separated List:\n");
2636	0	jalview.bin.Console.errPrintln(v);
2637		}
2638	0	return v.toString();
2639		}
2640	0	if (debug)
2641		{
2642	0	jalview.bin.Console.errPrintln(
2643		"Returning empty '" + separator + "' separated List\n");
2644		}
2645	0	return "" + separator;
2646		}
2647
2648		/*
2649		* (non-Javadoc)
2650		*
2651		* @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
2652		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
2653	0	@Override...
2654		public String getFeatureGroups()
2655		{
2656	0	String lst = arrayToSeparatorList(
2657		getDefaultTargetFrame().getFeatureGroups());
2658	0	return lst;
2659		}
2660
2661		/*
2662		* (non-Javadoc)
2663		*
2664		* @see
2665		* jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame
2666		* )
2667		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
2668	0	@Override...
2669		public String getFeatureGroupsOn(AlignFrame alf)
2670		{
2671	0	String lst = arrayToSeparatorList(alf.getFeatureGroups());
2672	0	return lst;
2673		}
2674
2675		/*
2676		* (non-Javadoc)
2677		*
2678		* @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
2679		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2680	0	@Override...
2681		public String getFeatureGroupsOfState(boolean visible)
2682		{
2683	0	return arrayToSeparatorList(
2684		getDefaultTargetFrame().getFeatureGroupsOfState(visible));
2685		}
2686
2687		/*
2688		* (non-Javadoc)
2689		*
2690		* @see
2691		* jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui
2692		* .AlignFrame, boolean)
2693		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2694	0	@Override...
2695		public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
2696		{
2697	0	return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
2698		}
2699
2700		/*
2701		* (non-Javadoc)
2702		*
2703		* @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui.
2704		* AlignFrame, java.lang.String, boolean)
2705		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
2706	0	@Override...
2707		public void setFeatureGroupStateOn(final AlignFrame alf,
2708		final String groups, boolean state)
2709		{
2710	0	final boolean st = state;// !(state==null || state.equals("") ||
2711		// state.toLowerCase(Locale.ROOT).equals("false"));
2712	0	java.awt.EventQueue.invokeLater(new Runnable()
2713		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2714	0	@Override...
2715		public void run()
2716		{
2717	0	alf.setFeatureGroupState(separatorListToArray(groups), st);
2718		}
2719		});
2720		}
2721
2722		/*
2723		* (non-Javadoc)
2724		*
2725		* @see jalview.bin.JalviewLiteJsApi#setFeatureGroupState(java.lang.String,
2726		* boolean)
2727		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2728	0	@Override...
2729		public void setFeatureGroupState(String groups, boolean state)
2730		{
2731	0	setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
2732		}
2733
2734		/*
2735		* (non-Javadoc)
2736		*
2737		* @see jalview.bin.JalviewLiteJsApi#getSeparator()
2738		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2739	0	@Override...
2740		public String getSeparator()
2741		{
2742	0	return separator;
2743		}
2744
2745		/*
2746		* (non-Javadoc)
2747		*
2748		* @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String)
2749		*/
		0% Uncovered Elements: 9 (9) Complexity: 4 Complexity Density: 0.8
2750	0	@Override...
2751		public void setSeparator(String separator)
2752		{
2753	0	if (separator == null || separator.length() < 1)
2754		{
2755		// reset to default
2756	0	separator = "" + ((char) 0x00AC);
2757		}
2758	0	this.separator = separator;
2759	0	if (debug)
2760		{
2761	0	jalview.bin.Console
2762		.errPrintln("Default Separator now: '" + separator + "'");
2763		}
2764		}
2765
2766		/**
2767		* get boolean value of applet parameter 'name' and return default if
2768		* parameter is not set
2769		*
2770		* @param name
2771		* name of paremeter
2772		* @param def
2773		* the value to return otherwise
2774		* @return true or false
2775		*/
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
2776	0	public boolean getDefaultParameter(String name, boolean def)...
2777		{
2778	0	String stn;
2779	0	if ((stn = getParameter(name)) == null)
2780		{
2781	0	return def;
2782		}
2783	0	if (TRUE.equalsIgnoreCase(stn))
2784		{
2785	0	return true;
2786		}
2787	0	return false;
2788		}
2789
2790		/*
2791		* (non-Javadoc)
2792		*
2793		* @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame,
2794		* java.lang.String, java.lang.String, java.lang.String)
2795		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2796	0	@Override...
2797		public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
2798		String pdbEntryString, String pdbFile)
2799		{
2800	0	return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);
2801		}
2802
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2803	0	protected void setAlignPdbStructures(boolean alignPdbStructures)...
2804		{
2805	0	this.alignPdbStructures = alignPdbStructures;
2806		}
2807
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2808	0	public boolean isAlignPdbStructures()...
2809		{
2810	0	return alignPdbStructures;
2811		}
2812
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
2813	0	@Override...
2814		public void start()
2815		{
2816		// callInitCallback();
2817		}
2818
2819		private Hashtable<String, long[]> jshashes = new Hashtable<>();
2820
2821		private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<>();
2822
		0% Uncovered Elements: 13 (13) Complexity: 3 Complexity Density: 0.33
2823	0	public void setJsMessageSet(String messageclass, String viewId,...
2824		String[] colcommands)
2825		{
2826	0	Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
2827	0	if (msgset == null)
2828		{
2829	0	msgset = new Hashtable<>();
2830	0	jsmessages.put(messageclass, msgset);
2831		}
2832	0	msgset.put(viewId, colcommands);
2833	0	long[] l = new long[colcommands.length];
2834	0	for (int i = 0; i < colcommands.length; i++)
2835		{
2836	0	l[i] = colcommands[i].hashCode();
2837		}
2838	0	jshashes.put(messageclass + "|" + viewId, l);
2839		}
2840
2841		/*
2842		* (non-Javadoc)
2843		*
2844		* @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String,
2845		* java.lang.String)
2846		*/
		0% Uncovered Elements: 18 (18) Complexity: 5 Complexity Density: 0.5
2847	0	@Override...
2848		public String getJsMessage(String messageclass, String viewId)
2849		{
2850	0	Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
2851	0	if (msgset != null)
2852		{
2853	0	String[] msgs = msgset.get(viewId);
2854	0	if (msgs != null)
2855		{
2856	0	for (int i = 0; i < msgs.length; i++)
2857		{
2858	0	if (msgs[i] != null)
2859		{
2860	0	String m = msgs[i];
2861	0	msgs[i] = null;
2862	0	return m;
2863		}
2864		}
2865		}
2866		}
2867	0	return "";
2868		}
2869
		0% Uncovered Elements: 13 (13) Complexity: 5 Complexity Density: 0.71
2870	0	public boolean isJsMessageSetChanged(String string, String string2,...
2871		String[] colcommands)
2872		{
2873	0	long[] l = jshashes.get(string + "|" + string2);
2874	0	if (l == null && colcommands != null)
2875		{
2876	0	return true;
2877		}
2878	0	for (int i = 0; i < colcommands.length; i++)
2879		{
2880	0	if (l[i] != colcommands[i].hashCode())
2881		{
2882	0	return true;
2883		}
2884		}
2885	0	return false;
2886		}
2887
2888		private Vector jsExecQueue = new Vector();
2889
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2890	0	public Vector getJsExecQueue()...
2891		{
2892	0	return jsExecQueue;
2893		}
2894
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
2895	0	public void setExecutor(JSFunctionExec jsFunctionExec2)...
2896		{
2897	0	jsFunctionExec = jsFunctionExec2;
2898		}
2899
2900		/**
2901		* return the given colour value parameter or the given default if parameter
2902		* not given
2903		*
2904		* @param colparam
2905		* @param defcolour
2906		* @return
2907		*/
		0% Uncovered Elements: 13 (13) Complexity: 5 Complexity Density: 0.71
2908	0	public Color getDefaultColourParameter(String colparam, Color defcolour)...
2909		{
2910	0	String colprop = getParameter(colparam);
2911	0	if (colprop == null || colprop.trim().length() == 0)
2912		{
2913	0	return defcolour;
2914		}
2915	0	Color col = ColorUtils.parseColourString(colprop);
2916	0	if (col == null)
2917		{
2918	0	jalview.bin.Console.errPrintln("Couldn't parse '" + colprop
2919		+ "' as a colour for " + colparam);
2920		}
2921	0	return (col == null) ? defcolour : col;
2922		}
2923
		0% Uncovered Elements: 6 (6) Complexity: 3 Complexity Density: 0.75
2924	0	public void openJalviewHelpUrl()...
2925		{
2926	0	String helpUrl = getParameter("jalviewhelpurl");
2927	0	if (helpUrl == null || helpUrl.trim().length() < 5)
2928		{
2929	0	helpUrl = "http://www.jalview.org/help.html";
2930		}
2931	0	showURL(helpUrl, "HELP");
2932		}
2933
2934		/**
2935		* form a complete URL given a path to a resource and a reference location on
2936		* the same server
2937		*
2938		* @param targetPath
2939		* - an absolute path on the same server as localref or a document
2940		* located relative to localref
2941		* @param localref
2942		* - a URL on the same server as url
2943		* @return a complete URL for the resource located by url
2944		*/
		0% Uncovered Elements: 25 (25) Complexity: 5 Complexity Density: 0.29
2945	0	private String resolveUrlForLocalOrAbsolute(String targetPath,...
2946		URL localref)
2947		{
2948	0	String resolvedPath = "";
2949	0	if (targetPath.startsWith("/"))
2950		{
2951	0	String codebase = localref.toString();
2952	0	String localfile = localref.getFile();
2953	0	resolvedPath = codebase.substring(0,
2954		codebase.length() - localfile.length()) + targetPath;
2955	0	return resolvedPath;
2956		}
2957
2958		/*
2959		* get URL path and strip off any trailing file e.g.
2960		* www.jalview.org/examples/index.html#applets?a=b is trimmed to
2961		* www.jalview.org/examples/
2962		*/
2963	0	String urlPath = localref.toString();
2964	0	String directoryPath = urlPath;
2965	0	int lastSeparator = directoryPath.lastIndexOf("/");
2966	0	if (lastSeparator > 0)
2967		{
2968	0	directoryPath = directoryPath.substring(0, lastSeparator + 1);
2969		}
2970
2971	0	if (targetPath.startsWith("/"))
2972		{
2973		/*
2974		* construct absolute URL to a file on the server - this is not allowed?
2975		*/
2976		// String localfile = localref.getFile();
2977		// resolvedPath = urlPath.substring(0,
2978		// urlPath.length() - localfile.length())
2979		// + targetPath;
2980	0	resolvedPath = directoryPath + targetPath.substring(1);
2981		}
2982		else
2983		{
2984	0	resolvedPath = directoryPath + targetPath;
2985		}
2986	0	if (debug)
2987		{
2988	0	jalview.bin.Console.errPrintln(
2989		"resolveUrlForLocalOrAbsolute returning " + resolvedPath);
2990		}
2991	0	return resolvedPath;
2992		}
2993
2994		/**
2995		* open a URL in the browser - resolving it according to relative refs and
2996		* coping with javascript: protocol if necessary.
2997		*
2998		* @param url
2999		* @param target
3000		*/
		0% Uncovered Elements: 22 (22) Complexity: 7 Complexity Density: 0.58
3001	0	public void showURL(String url, String target)...
3002		{
3003	0	try
3004		{
3005	0	if (url.indexOf(":") == -1)
3006		{
3007		// TODO: verify (Bas Vroling bug) prepend codebase or server URL to
3008		// form valid URL
3009		// Should really use docbase, not codebase.
3010	0	URL prepend;
3011	0	url = resolveUrlForLocalOrAbsolute(url,
3012	0	prepend = getDefaultParameter("resolvetocodebase", false)
3013		? getCodeBase()
3014		: getDocumentBase());
3015	0	if (debug)
3016		{
3017	0	jalview.bin.Console.errPrintln("Show url (prepended " + prepend
3018		+ " - toggle resolvetocodebase if code/docbase resolution is wrong): "
3019		+ url);
3020		}
3021		}
3022		else
3023		{
3024	0	if (debug)
3025		{
3026	0	jalview.bin.Console.errPrintln("Show url: " + url);
3027		}
3028		}
3029	0	if (url.indexOf("javascript:") == 0)
3030		{
3031		// no target for the javascript context
3032	0	getAppletContext().showDocument(new java.net.URL(url));
3033		}
3034		else
3035		{
3036	0	getAppletContext().showDocument(new java.net.URL(url), target);
3037		}
3038		} catch (Exception ex)
3039		{
3040	0	ex.printStackTrace();
3041		}
3042		}
3043
3044		/**
3045		* bind structures in a viewer to any matching sequences in an alignFrame (use
3046		* sequenceIds to limit scope of search to specific sequences)
3047		*
3048		* @param alFrame
3049		* @param viewer
3050		* @param sequenceIds
3051		* @return TODO: consider making an exception structure for indicating when
3052		* binding fails public SequenceStructureBinding
3053		* addStructureViewInstance( AlignFrame alFrame, Object viewer, String
3054		* sequenceIds) {
3055		*
3056		* if (sequenceIds != null && sequenceIds.length() > 0) { return
3057		* alFrame.addStructureViewInstance(viewer,
3058		* separatorListToArray(sequenceIds)); } else { return
3059		* alFrame.addStructureViewInstance(viewer, null); } // return null; }
3060		*/
3061		}