Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
JalviewLite	87	612	293	987	0.0237388722.4%	Show methods
JalviewLite.LoadJmolThread	1777	16	9	28	0.00%	Show methods
JalviewLite.LoadingThread	1826	231	81	355	0.00%	Show methods

Class JalviewLite

Class JalviewLite	Line # 87	Total Statements 612	Complexity 293	Uncovered Elements 987	TOTAL Coverage 0.0237388722.4%
getStructureSelectionManager() : StructureSelectionManager   getStructureSelectionManager() : StructureSelectionManager	9595	1.01	1.01	1.01	0.0 0.00%
getSelectedSequences() : String   getSelectedSequences() : String	108108	1.01	1.01	1.01	0.0 0.00%
getSelectedSequences(String) : String   getSelectedSequences(String) : String	119119	1.01	1.01	1.01	0.0 0.00%
getSelectedSequencesFrom(AlignFrame) : String   getSelectedSequencesFrom(AlignFrame) : String	132132	1.01	1.01	1.01	0.0 0.00%
getSelectedSequencesFrom(AlignFrame,String) : String   getSelectedSequencesFrom(AlignFrame,String) : String	145145	9.09	5.05	15.015	0.0 0.00%
highlight(String,String,String) : void   highlight(String,String,String) : void	174174	1.01	1.01	1.01	0.0 0.00%
run() : void   run() : void	215215	1.01	1.01	1.01	0.0 0.00%
run() : void   run() : void	227227	1.01	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	17.017	0.0 0.00%
select(String,String) : void   select(String,String) : void	244244	1.01	1.01	1.01	0.0 0.00%
select(String,String,String) : void   select(String,String,String) : void	256256	1.01	1.01	1.01	0.0 0.00%
selectIn(AlignFrame,String,String) : void   selectIn(AlignFrame,String,String) : void	268268	1.01	1.01	1.01	0.0 0.00%
run() : void   run() : void	484484	1.01	1.01	1.01	0.0 0.00%
selectIn(AlignFrame,String,String,String) : void   selectIn(AlignFrame,String,String,String) : void	280280	93.093	37.037	145.0145	0.0 0.00%
getSelectedSequencesAsAlignment(String,String) : String   getSelectedSequencesAsAlignment(String,String) : String	501501	1.01	1.01	1.01	0.0 0.00%
getSelectedSequencesAsAlignmentFrom(AlignFrame,String,String) : String   getSelectedSequencesAsAlignmentFrom(AlignFrame,String,String) : String	516516	9.09	3.03	11.011	0.0 0.00%
getAlignmentOrder() : String   getAlignmentOrder() : String	548548	1.01	1.01	1.01	0.0 0.00%
getAlignmentOrderFrom(AlignFrame) : String   getAlignmentOrderFrom(AlignFrame) : String	561561	1.01	1.01	1.01	0.0 0.00%
getAlignmentOrderFrom(AlignFrame,String) : String   getAlignmentOrderFrom(AlignFrame,String) : String	574574	5.05	2.02	7.07	0.0 0.00%
orderBy(String,String) : String   orderBy(String,String) : String	592592	1.01	1.01	1.01	0.0 0.00%
orderBy(String,String,String) : String   orderBy(String,String,String) : String	604604	1.01	1.01	1.01	0.0 0.00%
orderAlignmentBy(AlignFrame,String,String,String) : String   orderAlignmentBy(AlignFrame,String,String,String) : String	617617	25.025	11.011	41.041	0.0 0.00%
getAlignment(String) : String   getAlignment(String) : String	674674	1.01	1.01	1.01	0.0 0.00%
getAlignmentFrom(AlignFrame,String) : String   getAlignmentFrom(AlignFrame,String) : String	687687	1.01	1.01	1.01	0.0 0.00%
getAlignment(String,String) : String   getAlignment(String,String) : String	699699	1.01	1.01	1.01	0.0 0.00%
getAlignmentFrom(AlignFrame,String,String) : String   getAlignmentFrom(AlignFrame,String,String) : String	712712	7.07	2.02	7.07	0.0 0.00%
loadAnnotation(String) : void   loadAnnotation(String) : void	737737	1.01	1.01	1.01	0.0 0.00%
loadAnnotationFrom(AlignFrame,String) : void   loadAnnotationFrom(AlignFrame,String) : void	750750	4.04	2.02	6.06	0.0 0.00%
loadFeatures(String,boolean) : void   loadFeatures(String,boolean) : void	770770	1.01	1.01	1.01	0.0 0.00%
loadFeaturesFrom(AlignFrame,String,boolean) : boolean   loadFeaturesFrom(AlignFrame,String,boolean) : boolean	783783	1.01	1.01	1.01	0.0 0.00%
getFeatures(String) : String   getFeatures(String) : String	796796	1.01	1.01	1.01	0.0 0.00%
getFeaturesFrom(AlignFrame,String) : String   getFeaturesFrom(AlignFrame,String) : String	809809	1.01	1.01	1.01	0.0 0.00%
getAnnotation() : String   getAnnotation() : String	820820	1.01	1.01	1.01	0.0 0.00%
getAnnotationFrom(AlignFrame) : String   getAnnotationFrom(AlignFrame) : String	833833	1.01	1.01	1.01	0.0 0.00%
newView() : AlignFrame   newView() : AlignFrame	844844	1.01	1.01	1.01	0.0 0.00%
newView(String) : AlignFrame   newView(String) : AlignFrame	855855	1.01	1.01	1.01	0.0 0.00%
newViewFrom(AlignFrame) : AlignFrame   newViewFrom(AlignFrame) : AlignFrame	866866	1.01	1.01	1.01	0.0 0.00%
newViewFrom(AlignFrame,String) : AlignFrame   newViewFrom(AlignFrame,String) : AlignFrame	878878	1.01	1.01	1.01	0.0 0.00%
loadAlignment(String,String) : AlignFrame   loadAlignment(String,String) : AlignFrame	890890	8.08	3.03	10.010	0.0 0.00%
setMouseoverListener(String) : void   setMouseoverListener(String) : void	917917	1.01	1.01	1.01	0.0 0.00%
setMouseoverListener(AlignFrame,String) : void   setMouseoverListener(AlignFrame,String) : void	932932	11.011	5.05	19.019	0.0 0.00%
setSelectionListener(String) : void   setSelectionListener(String) : void	966966	1.01	1.01	1.01	0.0 0.00%
setSelectionListener(AlignFrame,String) : void   setSelectionListener(AlignFrame,String) : void	979979	11.011	5.05	19.019	0.0 0.00%
setStructureListener(String,String) : void   setStructureListener(String,String) : void	10191019	11.011	4.04	17.017	0.0 0.00%
removeJavascriptListener(AlignFrame,String) : void   removeJavascriptListener(AlignFrame,String) : void	10531053	20.020	11.011	34.034	0.0 0.00%
stop() : void   stop() : void	11021102	2.02	1.01	2.02	0.0 0.00%
destroy() : void   destroy() : void	11091109	2.02	1.01	2.02	0.0 0.00%
tidyUp() : void   tidyUp() : void	11161116	21.021	8.08	31.031	0.0 0.00%
run() : void   run() : void	11731173	5.05	3.03	7.07	0.0 0.00%
mouseOverStructure(String,String,String) : void   mouseOverStructure(String,String,String) : void	11661166	2.02	1.01	2.02	0.0 0.00%
run() : void   run() : void	12101210	4.04	2.02	4.04	0.0 0.00%
scrollViewToIn(AlignFrame,String,String) : void   scrollViewToIn(AlignFrame,String,String) : void	12041204	1.01	1.01	1.01	0.0 0.00%
run() : void   run() : void	12421242	4.04	2.02	4.04	0.0 0.00%
scrollViewToRowIn(AlignFrame,String) : void   scrollViewToRowIn(AlignFrame,String) : void	12361236	1.01	1.01	1.01	0.0 0.00%
run() : void   run() : void	12741274	4.04	2.02	4.04	0.0 0.00%
scrollViewToColumnIn(AlignFrame,String) : void   scrollViewToColumnIn(AlignFrame,String) : void	12671267	1.01	1.01	1.01	0.0 0.00%
initBuildDetails() : void   initBuildDetails() : void	13451345	17.017	8.08	29.029	0.0 0.00%
getBuildDate() : String   getBuildDate() : String	13841384	2.02	1.01	2.02	0.0 0.00%
getInstallation() : String   getInstallation() : String	13901390	2.02	1.01	2.02	0.0 0.00%
getVersion() : String   getVersion() : String	13961396	2.02	1.01	2.02	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	15431543	2.02	1.01	2.02	0.0 0.00%
init() : void   init() : void	14071407	67.067	22.022	103.0103	0.0 0.00%
initLiveConnect() : void   initLiveConnect() : void	15631563	15.015	8.08	23.023	0.0 0.00%
callInitCallback() : void   callInitCallback() : void	16001600	16.016	6.06	22.022	0.0 0.00%
windowClosing(WindowEvent) : void   windowClosing(WindowEvent) : void	16661666	13.013	4.04	19.019	0.0 0.00%
windowActivated(WindowEvent) : void   windowActivated(WindowEvent) : void	16911691	5.05	3.03	9.09	0.0 0.00%
addFrame(Frame,String,int,int) : void   addFrame(Frame,String,int,int) : void	16561656	7.07	1.01	7.07	0.0 0.00%
paint(Graphics) : void   paint(Graphics) : void	17291729	12.012	3.03	16.016	0.0 0.00%
getAppletWindow(Class) : Vector   getAppletWindow(Class) : Vector	17601760	7.07	4.04	13.013	0.0 0.00%
getDefaultTargetFrame() : AlignFrame   getDefaultTargetFrame() : AlignFrame	24852485	6.06	3.03	10.010	0.0 0.00%
separatorListToArray(String) : String[]   separatorListToArray(String) : String[]	25182518	1.01	1.01	1.01	0.0 0.00%
separatorListToArray(String,String) : String[]   separatorListToArray(String,String) : String[]	25302530	25.025	12.012	20.020	0.53488374 0.5348837453.5%
arrayToSeparatorList(String[]) : String   arrayToSeparatorList(String[]) : String	25862586	1.01	1.01	1.01	0.0 0.00%
arrayToSeparatorList(String[],String) : String   arrayToSeparatorList(String[],String) : String	25982598	14.014	8.08	26.026	0.0 0.00%
getFeatureGroups() : String   getFeatureGroups() : String	26362636	2.02	1.01	2.02	0.0 0.00%
getFeatureGroupsOn(AlignFrame) : String   getFeatureGroupsOn(AlignFrame) : String	26512651	2.02	1.01	2.02	0.0 0.00%
getFeatureGroupsOfState(boolean) : String   getFeatureGroupsOfState(boolean) : String	26632663	1.01	1.01	1.01	0.0 0.00%
getFeatureGroupsOfStateOn(AlignFrame,boolean) : String   getFeatureGroupsOfStateOn(AlignFrame,boolean) : String	26772677	1.01	1.01	1.01	0.0 0.00%
run() : void   run() : void	26972697	1.01	1.01	1.01	0.0 0.00%
setFeatureGroupStateOn(AlignFrame,String,boolean) : void   setFeatureGroupStateOn(AlignFrame,String,boolean) : void	26892689	2.02	1.01	2.02	0.0 0.00%
setFeatureGroupState(String,boolean) : void   setFeatureGroupState(String,boolean) : void	27112711	1.01	1.01	1.01	0.0 0.00%
getSeparator() : String   getSeparator() : String	27222722	1.01	1.01	1.01	0.0 0.00%
setSeparator(String) : void   setSeparator(String) : void	27332733	5.05	4.04	9.09	0.0 0.00%
getDefaultParameter(String,boolean) : boolean   getDefaultParameter(String,boolean) : boolean	27582758	6.06	3.03	10.010	0.0 0.00%
addPdbFile(AlignFrame,String,String,String) : boolean   addPdbFile(AlignFrame,String,String,String) : boolean	27782778	1.01	1.01	1.01	0.0 0.00%
setAlignPdbStructures(boolean) : void   setAlignPdbStructures(boolean) : void	27852785	1.01	1.01	1.01	0.0 0.00%
isAlignPdbStructures() : boolean   isAlignPdbStructures() : boolean	27902790	1.01	1.01	1.01	0.0 0.00%
start() : void   start() : void	27952795	0.00	1.01	0.00	-1.0 -1.0 -
setJsMessageSet(String,String,String[]) : void   setJsMessageSet(String,String,String[]) : void	28052805	9.09	3.03	13.013	0.0 0.00%
getJsMessage(String,String) : String   getJsMessage(String,String) : String	28292829	10.010	5.05	18.018	0.0 0.00%
isJsMessageSetChanged(String,String,String[]) : boolean   isJsMessageSetChanged(String,String,String[]) : boolean	28522852	7.07	5.05	13.013	0.0 0.00%
getJsExecQueue() : Vector   getJsExecQueue() : Vector	28722872	1.01	1.01	1.01	0.0 0.00%
setExecutor(JSFunctionExec) : void   setExecutor(JSFunctionExec) : void	28772877	1.01	1.01	1.01	0.0 0.00%
getDefaultColourParameter(String,Color) : Color   getDefaultColourParameter(String,Color) : Color	28902890	7.07	5.05	13.013	0.0 0.00%
openJalviewHelpUrl() : void   openJalviewHelpUrl() : void	29062906	4.04	3.03	6.06	0.0 0.00%
resolveUrlForLocalOrAbsolute(String,URL) : String   resolveUrlForLocalOrAbsolute(String,URL) : String	29272927	17.017	5.05	25.025	0.0 0.00%
showURL(String,String) : void   showURL(String,String) : void	29832983	12.012	7.07	22.022	0.0 0.00%

 

Class JalviewLite.LoadJmolThread

Class JalviewLite.LoadJmolThread	Line # 1777	Total Statements 16	Complexity 9	Uncovered Elements 28	TOTAL Coverage 0.00%
run() : void   run() : void	17811781	15.015	8.08	25.025	0.0 0.00%
notFinished() : boolean   notFinished() : boolean	18201820	1.01	1.01	1.01	0.0 0.00%

 

Class JalviewLite.LoadingThread

Class JalviewLite.LoadingThread	Line # 1826	Total Statements 231	Complexity 81	Uncovered Elements 355	TOTAL Coverage 0.00%
dbgMsg(String) : void   dbgMsg(String) : void	18391839	2.02	2.02	4.04	0.0 0.00%
resolveFileProtocol(String) : String   resolveFileProtocol(String) : String	18541854	23.023	9.09	37.037	0.0 0.00%
LoadingThread(String,String,JalviewLite)   LoadingThread(String,String,JalviewLite)	19191919	3.03	1.01	3.03	0.0 0.00%
run() : void   run() : void	19261926	6.06	3.03	8.08	0.0 0.00%
startLoading() : void   startLoading() : void	19491949	16.016	2.02	18.018	0.0 0.00%
addToDisplay(AlignFrame,AlignFrame) : void   addToDisplay(AlignFrame,AlignFrame) : void	19881988	13.013	6.06	23.023	0.0 0.00%
readAlignment(String) : AlignFrame   readAlignment(String) : AlignFrame	20222022	33.033	10.010	45.045	0.0 0.00%
loadPdbFiles(AlignFrame) : boolean   loadPdbFiles(AlignFrame) : boolean	20992099	60.060	20.020	96.096	0.0 0.00%
loadJnetFile(AlignFrame) : boolean   loadJnetFile(AlignFrame) : boolean	22632263	15.015	4.04	19.019	0.0 0.00%
loadAnnotations(AlignFrame) : boolean   loadAnnotations(AlignFrame) : boolean	23022302	10.010	3.03	14.014	0.0 0.00%
loadFeatures(AlignFrame) : boolean   loadFeatures(AlignFrame) : boolean	23342334	16.016	6.06	24.024	0.0 0.00%
loadScoreFile(AlignFrame) : boolean   loadScoreFile(AlignFrame) : boolean	23812381	11.011	6.06	17.017	0.0 0.00%
loadTree(AlignFrame) : boolean   loadTree(AlignFrame) : boolean	24172417	16.016	5.05	22.022	0.0 0.00%
inArchive(String) : boolean   inArchive(String) : boolean	24592459	7.07	4.04	11.011	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

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

 

Source view

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