Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
MouseOverStructureListener	73	68	27	106	0.00%	Show methods

Class MouseOverStructureListener

Class MouseOverStructureListener	Line # 73	Total Statements 68	Complexity 27	Uncovered Elements 106	TOTAL Coverage 0.00%
MouseOverStructureListener(JalviewLite,String,String[])   MouseOverStructureListener(JalviewLite,String,String[])	8181	6.06	3.03	10.010	0.0 0.00%
resolveModelFile(String) : String   resolveModelFile(String) : String	103103	11.011	4.04	17.017	0.0 0.00%
getStructureFiles() : String[]   getStructureFiles() : String[]	128128	1.01	1.01	1.01	0.0 0.00%
mouseOverStructure(int,String) : void   mouseOverStructure(int,String) : void	134134	0.00	1.01	0.00	-1.0 -1.0 -
highlightAtoms(List<AtomSpec>) : void   highlightAtoms(List<AtomSpec>) : void	143143	5.05	2.02	5.05	0.0 0.00%
updateColours(Object) : void   updateColours(Object) : void	167167	42.042	12.012	60.060	0.0 0.00%
getAlignFrame() : AlignFrame   getAlignFrame() : AlignFrame	288288	1.01	1.01	1.01	0.0 0.00%
getListenerFunction() : String   getListenerFunction() : String	295295	1.01	1.01	1.01	0.0 0.00%
releaseReferences(Object) : void   releaseReferences(Object) : void	301301	0.00	1.01	0.00	-1.0 -1.0 -
isListeningFor(SequenceI) : boolean   isListeningFor(SequenceI) : boolean	309309	1.01	1.01	1.01	0.0 0.00%

 

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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.javascript;
22
23		import jalview.api.AlignmentViewPanel;
24		import jalview.api.FeatureRenderer;
25		import jalview.api.SequenceRenderer;
26		import jalview.appletgui.AlignFrame;
27		import jalview.bin.JalviewLite;
28		import jalview.datamodel.SequenceI;
29		import jalview.ext.jmol.JmolCommands;
30		import jalview.structure.AtomSpec;
31		import jalview.structure.StructureListener;
32		import jalview.structure.StructureMapping;
33		import jalview.structure.StructureMappingcommandSet;
34		import jalview.structure.StructureSelectionManager;
35		import jalview.util.HttpUtils;
36
37		import java.util.ArrayList;
38		import java.util.List;
39
40		/**
41		* Propagate events involving PDB structures associated with sequences to a
42		* javascript function. Generally, the javascript handler is called with a
43		* series of arguments like (eventname, ... ). As of Jalview 2.7, the following
44		* different types of events are supported:
45		* <ul>
46		* <li>mouseover: javascript function called with arguments
47		*
48		* <pre>
49		* ['mouseover',String(pdb file URI), String(pdb file chain ID), String(residue
50		* number moused over), String(atom index corresponding to residue)]
51		* </pre>
52		*
53		* </li>
54		* <li>colourstruct: javascript function called with arguments
55		*
56		* <pre>
57		* ['colourstruct',String(alignment view id),String(number of javascript message
58		* chunks to collect),String(length of first chunk in set of messages - or zero
59		* for null message)]
60		* </pre>
61		*
62		* <br>
63		* The message contains a series of Jmol script commands that will colour
64		* structures according to their associated sequences in the current view. Use
65		* jalview
66		* .javascript.JalviewLiteJsApi.getJsMessage('colourstruct',String(alignment
67		* view id)) to retrieve successive chunks of the message.</li>
68		* </ul>
69		*
70		* @author Jim Procter (jprocter)
71		*
72		*/
		0% Uncovered Elements: 106 (106) Complexity: 27 Complexity Density: 0.4
73		public class MouseOverStructureListener extends JSFunctionExec
74		implements JsCallBack, StructureListener
75		{
76
77		String _listenerfn;
78
79		String[] modelSet;
80
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
81	0	public MouseOverStructureListener(JalviewLite jalviewLite,...
82		String listener, String[] modelList)
83		{
84	0	super(jalviewLite);
85	0	_listenerfn = listener;
86	0	modelSet = modelList;
87	0	if (modelSet != null)
88		{
89	0	for (int i = 0; i < modelSet.length; i++)
90		{
91	0	modelSet[i] = resolveModelFile(modelSet[i]);
92		}
93		}
94		}
95
96		/**
97		* Returns the first out of: file, file prefixed by document base, or file
98		* prefixed by codebase which can be resolved to a valid URL. If none can,
99		* returns the input parameter value.
100		*
101		* @param file
102		*/
		0% Uncovered Elements: 17 (17) Complexity: 4 Complexity Density: 0.36
103	0	public String resolveModelFile(String file)...
104		{
105		// TODO reuse JalviewLite.LoadingThread.addProtocol instead
106	0	if (HttpUtils.isValidUrl(file))
107		{
108	0	return file;
109		}
110
111	0	String db = jvlite.getDocumentBase().toString();
112	0	db = db.substring(0, db.lastIndexOf("/"));
113	0	String docBaseFile = db + "/" + file;
114	0	if (HttpUtils.isValidUrl(docBaseFile))
115		{
116	0	return docBaseFile;
117		}
118
119	0	String cb = jvlite.getCodeBase() + file;
120	0	if (HttpUtils.isValidUrl(cb))
121		{
122	0	return cb;
123		}
124
125	0	return file;
126		}
127
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
128	0	@Override...
129		public String[] getStructureFiles()
130		{
131	0	return modelSet;
132		}
133
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
134	0	public void mouseOverStructure(int atomIndex, String strInfo)...
135		{
136
137		// StructureSelectionManager.getStructureSelectionManager().mouseOverStructure(atomIndex,
138		// chain, pdbfile)
139		// TODO Auto-generated method stub
140
141		}
142
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.4
143	0	@Override...
144		public void highlightAtoms(List<AtomSpec> atoms)
145		{
146	0	for (AtomSpec atom : atoms)
147		{
148	0	try
149		{
150		// TODO is this right? StructureSelectionManager passes pdbFile as the
151		// field that is interpreted (in 2.8.2) as pdbId?
152		// JBPComment: yep - this is right! the Javascript harness uses the
153		// absolute pdbFile URI to locate the PDB file in the external viewer
154	0	executeJavascriptFunction(_listenerfn,
155		new String[]
156		{ "mouseover", "" + atom.getPdbFile(), "" + atom.getChain(),
157		"" + (atom.getPdbResNum()), "" + atom.getAtomIndex() });
158		} catch (Exception ex)
159		{
160	0	System.err.println("Couldn't execute callback with " + _listenerfn
161		+ " for atomSpec: " + atom);
162	0	ex.printStackTrace();
163		}
164		}
165		}
166
		0% Uncovered Elements: 60 (60) Complexity: 12 Complexity Density: 0.29
167	0	@Override...
168		public synchronized void updateColours(Object srce)
169		{
170	0	final Object source = srce;
171	0	StructureSelectionManager ssm = StructureSelectionManager
172		.getStructureSelectionManager(jvlite);
173
174	0	if (JalviewLite.debug)
175		{
176	0	System.err.println(
177		this.getClass().getName() + " modelSet[0]: " + modelSet[0]);
178	0	ssm.reportMapping();
179		}
180
181	0	if (source instanceof jalview.api.AlignmentViewPanel)
182		{
183	0	SequenceI[][] sequence = new SequenceI[modelSet.length][];
184	0	for (int m = 0; m < modelSet.length; m++)
185		{
186	0	StructureMapping[] sm = ssm.getMapping(modelSet[m]);
187	0	if (sm != null && sm.length > 0)
188		{
189	0	sequence[m] = new SequenceI[sm.length];
190	0	for (int i = 0; i < sm.length; i++)
191		{
192	0	sequence[m][i] = sm[i].getSequence();
193		}
194		}
195		else
196		{
197	0	sequence[m] = new SequenceI[0];
198		}
199		// if (jvlite.debug)
200		// {
201		// System.err.println("Mapped '" + modelSet[m] + "' to "
202		// + sequence[m].length + " sequences.");
203		// }
204		}
205
206	0	SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source)
207		.getSequenceRenderer();
208	0	FeatureRenderer fr = ((jalview.appletgui.AlignmentPanel) source).av
209		.isShowSequenceFeatures()
210		? new jalview.appletgui.FeatureRenderer(
211		((jalview.appletgui.AlignmentPanel) source).av)
212		: null;
213	0	if (fr != null)
214		{
215	0	((jalview.appletgui.FeatureRenderer) fr).transferSettings(
216		((jalview.appletgui.AlignmentPanel) source)
217		.getFeatureRenderer());
218		}
219	0	;
220
221		// Form a colour command from the given alignment panel for each distinct
222		// structure
223	0	ArrayList<String[]> ccomands = new ArrayList<String[]>();
224	0	ArrayList<String> pdbfn = new ArrayList<String>();
225	0	StructureMappingcommandSet[] colcommands = JmolCommands
226		.getColourBySequenceCommand(ssm, modelSet, sequence, sr,
227		(AlignmentViewPanel) source);
228	0	if (colcommands == null)
229		{
230	0	return;
231		}
232	0	int sz = 0;
233	0	for (jalview.structure.StructureMappingcommandSet ccset : colcommands)
234		{
235	0	sz += ccset.commands.length;
236	0	ccomands.add(ccset.commands);
237	0	pdbfn.add(ccset.mapping);
238		}
239
240	0	String mclass, mhandle;
241	0	String ccomandset[] = new String[sz];
242	0	sz = 0;
243	0	for (String[] ccset : ccomands)
244		{
245	0	System.arraycopy(ccset, 0, ccomandset, sz, ccset.length);
246	0	sz += ccset.length;
247		}
248	0	if (jvlite.isJsMessageSetChanged(mclass = "colourstruct",
249		mhandle = ((jalview.appletgui.AlignmentPanel) source).av
250		.getViewId(),
251		ccomandset))
252		{
253	0	jvlite.setJsMessageSet(mclass, mhandle, ccomandset);
254		// and notify javascript handler
255	0	String st[] = new String[] { "colourstruct",
256		"" + ((jalview.appletgui.AlignmentPanel) source).av.getViewId(),
257		"" + ccomandset.length, jvlite.arrayToSeparatorList(
258		pdbfn.toArray(new String[pdbfn.size()])) };
259	0	try
260		{
261	0	executeJavascriptFunction(true, _listenerfn, st);
262		} catch (Exception ex)
263		{
264	0	System.err.println("Couldn't execute callback with " + _listenerfn
265		+ " using args { " + st[0] + ", " + st[1] + ", " + st[2]
266		+ "," + st[3] + "}"); // + ","+st[4]+"\n");
267	0	ex.printStackTrace();
268
269		}
270		}
271		/*
272		* new Thread(new Runnable() { public void run() { // and send to
273		* javascript handler String st[] = new String[0]; int i = 0; for (String
274		* colcommand : colcommands) { // do sync execution for each chunk try {
275		* executeJavascriptFunction( false, _listenerfn, st = new String[] {
276		* "colourstruct", "" + ((jalview.appletgui.AlignmentPanel) source).av
277		* .getViewId(), handle, "" }); } catch (Exception ex) {
278		* System.err.println("Couldn't execute callback with " + _listenerfn +
279		* " using args { " + st[0] + ", " + st[1] + ", " + st[2] + "," + st[3] +
280		* "\n"); ex.printStackTrace();
281		*
282		* } } } }).start();
283		*/
284		}
285
286		}
287
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
288	0	@Override...
289		public AlignFrame getAlignFrame()
290		{
291		// associated with all alignframes, always.
292	0	return null;
293		}
294
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
295	0	@Override...
296		public String getListenerFunction()
297		{
298	0	return _listenerfn;
299		}
300
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
301	0	@Override...
302		public void releaseReferences(Object svl)
303		{
304
305		// TODO Auto-generated method stub
306
307		}
308
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
309	0	@Override...
310		public boolean isListeningFor(SequenceI seq)
311		{
312	0	return true;
313		}
314
315		}