Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JalviewLite	87	612	293	0.00%	Show methods
JalviewLite.LoadJmolThread	1791	16	9	0.00%	Show methods
JalviewLite.LoadingThread	1840	231	81	0.00%	Show methods

Class JalviewLite

Class JalviewLite	Line # 87	Total Statements 612	Complexity 293	TOTAL Coverage 0.00%
getStructureSelectionManager() : StructureSelectionManager   getStructureSelectionManager() : StructureSelectionManager	9595	1.01	1.01	0.0 0.00%
getSelectedSequences() : String   getSelectedSequences() : String	108108	1.01	1.01	0.0 0.00%
getSelectedSequences(String) : String   getSelectedSequences(String) : String	119119	1.01	1.01	0.0 0.00%
getSelectedSequencesFrom(AlignFrame) : String   getSelectedSequencesFrom(AlignFrame) : String	132132	1.01	1.01	0.0 0.00%
getSelectedSequencesFrom(AlignFrame,String) : String   getSelectedSequencesFrom(AlignFrame,String) : String	145145	9.09	5.05	0.0 0.00%
highlight(String,String,String) : void   highlight(String,String,String) : void	174174	1.01	1.01	0.0 0.00%
run() : void   run() : void	216216	1.01	1.01	0.0 0.00%
run() : void   run() : void	228228	1.01	1.01	0.0 0.00%
highlightIn(AlignFrame,String,String,String) : void   highlightIn(AlignFrame,String,String,String) : void	188188	13.013	6.06	0.0 0.00%
select(String,String) : void   select(String,String) : void	245245	1.01	1.01	0.0 0.00%
select(String,String,String) : void   select(String,String,String) : void	257257	1.01	1.01	0.0 0.00%
selectIn(AlignFrame,String,String) : void   selectIn(AlignFrame,String,String) : void	269269	1.01	1.01	0.0 0.00%
run() : void   run() : void	487487	1.01	1.01	0.0 0.00%
selectIn(AlignFrame,String,String,String) : void   selectIn(AlignFrame,String,String,String) : void	281281	93.093	37.037	0.0 0.00%
getSelectedSequencesAsAlignment(String,String) : String   getSelectedSequencesAsAlignment(String,String) : String	504504	1.01	1.01	0.0 0.00%
getSelectedSequencesAsAlignmentFrom(AlignFrame,String,String) : String   getSelectedSequencesAsAlignmentFrom(AlignFrame,String,String) : String	519519	9.09	3.03	0.0 0.00%
getAlignmentOrder() : String   getAlignmentOrder() : String	551551	1.01	1.01	0.0 0.00%
getAlignmentOrderFrom(AlignFrame) : String   getAlignmentOrderFrom(AlignFrame) : String	564564	1.01	1.01	0.0 0.00%
getAlignmentOrderFrom(AlignFrame,String) : String   getAlignmentOrderFrom(AlignFrame,String) : String	577577	5.05	2.02	0.0 0.00%
orderBy(String,String) : String   orderBy(String,String) : String	595595	1.01	1.01	0.0 0.00%
orderBy(String,String,String) : String   orderBy(String,String,String) : String	607607	1.01	1.01	0.0 0.00%
orderAlignmentBy(AlignFrame,String,String,String) : String   orderAlignmentBy(AlignFrame,String,String,String) : String	620620	25.025	11.011	0.0 0.00%
getAlignment(String) : String   getAlignment(String) : String	677677	1.01	1.01	0.0 0.00%
getAlignmentFrom(AlignFrame,String) : String   getAlignmentFrom(AlignFrame,String) : String	690690	1.01	1.01	0.0 0.00%
getAlignment(String,String) : String   getAlignment(String,String) : String	702702	1.01	1.01	0.0 0.00%
getAlignmentFrom(AlignFrame,String,String) : String   getAlignmentFrom(AlignFrame,String,String) : String	715715	7.07	2.02	0.0 0.00%
loadAnnotation(String) : void   loadAnnotation(String) : void	740740	1.01	1.01	0.0 0.00%
loadAnnotationFrom(AlignFrame,String) : void   loadAnnotationFrom(AlignFrame,String) : void	753753	4.04	2.02	0.0 0.00%
loadFeatures(String,boolean) : void   loadFeatures(String,boolean) : void	773773	1.01	1.01	0.0 0.00%
loadFeaturesFrom(AlignFrame,String,boolean) : boolean   loadFeaturesFrom(AlignFrame,String,boolean) : boolean	786786	1.01	1.01	0.0 0.00%
getFeatures(String) : String   getFeatures(String) : String	799799	1.01	1.01	0.0 0.00%
getFeaturesFrom(AlignFrame,String) : String   getFeaturesFrom(AlignFrame,String) : String	812812	1.01	1.01	0.0 0.00%
getAnnotation() : String   getAnnotation() : String	823823	1.01	1.01	0.0 0.00%
getAnnotationFrom(AlignFrame) : String   getAnnotationFrom(AlignFrame) : String	836836	1.01	1.01	0.0 0.00%
newView() : AlignFrame   newView() : AlignFrame	847847	1.01	1.01	0.0 0.00%
newView(String) : AlignFrame   newView(String) : AlignFrame	858858	1.01	1.01	0.0 0.00%
newViewFrom(AlignFrame) : AlignFrame   newViewFrom(AlignFrame) : AlignFrame	869869	1.01	1.01	0.0 0.00%
newViewFrom(AlignFrame,String) : AlignFrame   newViewFrom(AlignFrame,String) : AlignFrame	881881	1.01	1.01	0.0 0.00%
loadAlignment(String,String) : AlignFrame   loadAlignment(String,String) : AlignFrame	893893	8.08	3.03	0.0 0.00%
setMouseoverListener(String) : void   setMouseoverListener(String) : void	920920	1.01	1.01	0.0 0.00%
setMouseoverListener(AlignFrame,String) : void   setMouseoverListener(AlignFrame,String) : void	935935	11.011	5.05	0.0 0.00%
setSelectionListener(String) : void   setSelectionListener(String) : void	969969	1.01	1.01	0.0 0.00%
setSelectionListener(AlignFrame,String) : void   setSelectionListener(AlignFrame,String) : void	982982	11.011	5.05	0.0 0.00%
setStructureListener(String,String) : void   setStructureListener(String,String) : void	10221022	11.011	4.04	0.0 0.00%
removeJavascriptListener(AlignFrame,String) : void   removeJavascriptListener(AlignFrame,String) : void	10571057	20.020	11.011	0.0 0.00%
stop() : void   stop() : void	11071107	2.02	1.01	0.0 0.00%
destroy() : void   destroy() : void	11141114	2.02	1.01	0.0 0.00%
tidyUp() : void   tidyUp() : void	11211121	21.021	8.08	0.0 0.00%
run() : void   run() : void	11781178	5.05	3.03	0.0 0.00%
mouseOverStructure(String,String,String) : void   mouseOverStructure(String,String,String) : void	11711171	2.02	1.01	0.0 0.00%
run() : void   run() : void	12161216	4.04	2.02	0.0 0.00%
scrollViewToIn(AlignFrame,String,String) : void   scrollViewToIn(AlignFrame,String,String) : void	12101210	1.01	1.01	0.0 0.00%
run() : void   run() : void	12491249	4.04	2.02	0.0 0.00%
scrollViewToRowIn(AlignFrame,String) : void   scrollViewToRowIn(AlignFrame,String) : void	12431243	1.01	1.01	0.0 0.00%
run() : void   run() : void	12821282	4.04	2.02	0.0 0.00%
scrollViewToColumnIn(AlignFrame,String) : void   scrollViewToColumnIn(AlignFrame,String) : void	12751275	1.01	1.01	0.0 0.00%
initBuildDetails() : void   initBuildDetails() : void	13531353	17.017	8.08	0.0 0.00%
getBuildDate() : String   getBuildDate() : String	13921392	2.02	1.01	0.0 0.00%
getInstallation() : String   getInstallation() : String	13981398	2.02	1.01	0.0 0.00%
getVersion() : String   getVersion() : String	14041404	2.02	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	15541554	2.02	1.01	0.0 0.00%
init() : void   init() : void	14151415	67.067	22.022	0.0 0.00%
initLiveConnect() : void   initLiveConnect() : void	15741574	15.015	8.08	0.0 0.00%
callInitCallback() : void   callInitCallback() : void	16131613	16.016	6.06	0.0 0.00%
windowClosing(WindowEvent) : void   windowClosing(WindowEvent) : void	16801680	13.013	4.04	0.0 0.00%
windowActivated(WindowEvent) : void   windowActivated(WindowEvent) : void	17051705	5.05	3.03	0.0 0.00%
addFrame(Frame,String,int,int) : void   addFrame(Frame,String,int,int) : void	16701670	7.07	1.01	0.0 0.00%
paint(Graphics) : void   paint(Graphics) : void	17431743	12.012	3.03	0.0 0.00%
getAppletWindow(Class) : Vector   getAppletWindow(Class) : Vector	17741774	7.07	4.04	0.0 0.00%
getDefaultTargetFrame() : AlignFrame   getDefaultTargetFrame() : AlignFrame	25002500	6.06	3.03	0.0 0.00%
separatorListToArray(String) : String[]   separatorListToArray(String) : String[]	25332533	1.01	1.01	0.0 0.00%
separatorListToArray(String,String) : String[]   separatorListToArray(String,String) : String[]	25452545	25.025	12.012	0.0 0.00%
arrayToSeparatorList(String[]) : String   arrayToSeparatorList(String[]) : String	26012601	1.01	1.01	0.0 0.00%
arrayToSeparatorList(String[],String) : String   arrayToSeparatorList(String[],String) : String	26132613	14.014	8.08	0.0 0.00%
getFeatureGroups() : String   getFeatureGroups() : String	26512651	2.02	1.01	0.0 0.00%
getFeatureGroupsOn(AlignFrame) : String   getFeatureGroupsOn(AlignFrame) : String	26662666	2.02	1.01	0.0 0.00%
getFeatureGroupsOfState(boolean) : String   getFeatureGroupsOfState(boolean) : String	26782678	1.01	1.01	0.0 0.00%
getFeatureGroupsOfStateOn(AlignFrame,boolean) : String   getFeatureGroupsOfStateOn(AlignFrame,boolean) : String	26922692	1.01	1.01	0.0 0.00%
run() : void   run() : void	27122712	1.01	1.01	0.0 0.00%
setFeatureGroupStateOn(AlignFrame,String,boolean) : void   setFeatureGroupStateOn(AlignFrame,String,boolean) : void	27042704	2.02	1.01	0.0 0.00%
setFeatureGroupState(String,boolean) : void   setFeatureGroupState(String,boolean) : void	27262726	1.01	1.01	0.0 0.00%
getSeparator() : String   getSeparator() : String	27372737	1.01	1.01	0.0 0.00%
setSeparator(String) : void   setSeparator(String) : void	27482748	5.05	4.04	0.0 0.00%
getDefaultParameter(String,boolean) : boolean   getDefaultParameter(String,boolean) : boolean	27742774	6.06	3.03	0.0 0.00%
addPdbFile(AlignFrame,String,String,String) : boolean   addPdbFile(AlignFrame,String,String,String) : boolean	27942794	1.01	1.01	0.0 0.00%
setAlignPdbStructures(boolean) : void   setAlignPdbStructures(boolean) : void	28012801	1.01	1.01	0.0 0.00%
isAlignPdbStructures() : boolean   isAlignPdbStructures() : boolean	28062806	1.01	1.01	0.0 0.00%
start() : void   start() : void	28112811	0.00	1.01	-1.0 -1.0 -
setJsMessageSet(String,String,String[]) : void   setJsMessageSet(String,String,String[]) : void	28212821	9.09	3.03	0.0 0.00%
getJsMessage(String,String) : String   getJsMessage(String,String) : String	28452845	10.010	5.05	0.0 0.00%
isJsMessageSetChanged(String,String,String[]) : boolean   isJsMessageSetChanged(String,String,String[]) : boolean	28682868	7.07	5.05	0.0 0.00%
getJsExecQueue() : Vector   getJsExecQueue() : Vector	28882888	1.01	1.01	0.0 0.00%
setExecutor(JSFunctionExec) : void   setExecutor(JSFunctionExec) : void	28932893	1.01	1.01	0.0 0.00%
getDefaultColourParameter(String,Color) : Color   getDefaultColourParameter(String,Color) : Color	29062906	7.07	5.05	0.0 0.00%
openJalviewHelpUrl() : void   openJalviewHelpUrl() : void	29222922	4.04	3.03	0.0 0.00%
resolveUrlForLocalOrAbsolute(String,URL) : String   resolveUrlForLocalOrAbsolute(String,URL) : String	29432943	17.017	5.05	0.0 0.00%
showURL(String,String) : void   showURL(String,String) : void	29992999	12.012	7.07	0.0 0.00%

 

Class JalviewLite.LoadJmolThread

Class JalviewLite.LoadJmolThread	Line # 1791	Total Statements 16	Complexity 9	TOTAL Coverage 0.00%
run() : void   run() : void	17951795	15.015	8.08	0.0 0.00%
notFinished() : boolean   notFinished() : boolean	18341834	1.01	1.01	0.0 0.00%

 

Class JalviewLite.LoadingThread

Class JalviewLite.LoadingThread	Line # 1840	Total Statements 231	Complexity 81	TOTAL Coverage 0.00%
dbgMsg(String) : void   dbgMsg(String) : void	18531853	2.02	2.02	0.0 0.00%
resolveFileProtocol(String) : String   resolveFileProtocol(String) : String	18681868	23.023	9.09	0.0 0.00%
LoadingThread(String,String,JalviewLite)   LoadingThread(String,String,JalviewLite)	19331933	3.03	1.01	0.0 0.00%
run() : void   run() : void	19401940	6.06	3.03	0.0 0.00%
startLoading() : void   startLoading() : void	19631963	16.016	2.02	0.0 0.00%
addToDisplay(AlignFrame,AlignFrame) : void   addToDisplay(AlignFrame,AlignFrame) : void	20022002	13.013	6.06	0.0 0.00%
readAlignment(String) : AlignFrame   readAlignment(String) : AlignFrame	20362036	33.033	10.010	0.0 0.00%
loadPdbFiles(AlignFrame) : boolean   loadPdbFiles(AlignFrame) : boolean	21132113	60.060	20.020	0.0 0.00%
loadJnetFile(AlignFrame) : boolean   loadJnetFile(AlignFrame) : boolean	22772277	15.015	4.04	0.0 0.00%
loadAnnotations(AlignFrame) : boolean   loadAnnotations(AlignFrame) : boolean	23162316	10.010	3.03	0.0 0.00%
loadFeatures(AlignFrame) : boolean   loadFeatures(AlignFrame) : boolean	23482348	16.016	6.06	0.0 0.00%
loadScoreFile(AlignFrame) : boolean   loadScoreFile(AlignFrame) : boolean	23952395	11.011	6.06	0.0 0.00%
loadTree(AlignFrame) : boolean   loadTree(AlignFrame) : boolean	24312431	16.016	5.05	0.0 0.00%
inArchive(String) : boolean   inArchive(String) : boolean	24732473	7.07	4.04	0.0 0.00%

 

Contributing tests

Source view

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