Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
JalviewChimeraView	61	159	20	183	0.00%	Show methods

Class JalviewChimeraView

Class JalviewChimeraView	Line # 61	Total Statements 159	Complexity 20	Uncovered Elements 183	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	6464	2.02	1.01	2.02	0.0 0.00%
setUpBeforeClass() : void   setUpBeforeClass() : void	7676	7.07	1.01	7.07	0.0 0.00%
tearDownAfterClass() : void   tearDownAfterClass() : void	9595	1.01	1.01	1.01	0.0 0.00%
tearDownAfterTest() : void   tearDownAfterTest() : void	101101	3.03	2.02	5.05	0.0 0.00%
testSingleSeqViewChimera() : void   testSingleSeqViewChimera() : void	117117	21.021	3.03	23.023	0.0 0.00%
testTransferFeatures() : void   testTransferFeatures() : void	168168	76.076	4.04	78.078	0.0 0.00%
testGetAttributes() : void   testGetAttributes() : void	355355	40.040	7.07	50.050	0.0 0.00%
checkFeaturesAtRes(SequenceI,FeatureRenderer,int,String) : void   checkFeaturesAtRes(SequenceI,FeatureRenderer,int,String) : void	472472	9.09	1.01	9.09	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.ext.rbvi.chimera;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertFalse;
25		import static org.testng.Assert.assertNotNull;
26		import static org.testng.Assert.assertTrue;
27
28		import jalview.api.FeatureRenderer;
29		import jalview.api.structures.JalviewStructureDisplayI;
30		import jalview.bin.Cache;
31		import jalview.bin.Jalview;
32		import jalview.datamodel.DBRefEntry;
33		import jalview.datamodel.PDBEntry;
34		import jalview.datamodel.SequenceFeature;
35		import jalview.datamodel.SequenceI;
36		import jalview.gui.AlignFrame;
37		import jalview.gui.Desktop;
38		import jalview.gui.JvOptionPane;
39		import jalview.gui.Preferences;
40		import jalview.gui.StructureViewer;
41		import jalview.gui.StructureViewer.ViewerType;
42		import jalview.io.DataSourceType;
43		import jalview.io.FileLoader;
44		import jalview.structure.StructureMapping;
45		import jalview.structure.StructureSelectionManager;
46		import jalview.ws.sifts.SiftsClient;
47		import jalview.ws.sifts.SiftsException;
48		import jalview.ws.sifts.SiftsSettings;
49
50		import java.io.File;
51		import java.io.IOException;
52		import java.util.List;
53		import java.util.Vector;
54
55		import org.testng.annotations.AfterClass;
56		import org.testng.annotations.AfterMethod;
57		import org.testng.annotations.BeforeClass;
58		import org.testng.annotations.Test;
59
60		@Test(singleThreaded = true)
		0% Uncovered Elements: 183 (183) Complexity: 20 Complexity Density: 0.13
61		public class JalviewChimeraView
62		{
63
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
64	0	@BeforeClass(alwaysRun = true)...
65		public void setUpJvOptionPane()
66		{
67	0	JvOptionPane.setInteractiveMode(false);
68	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
69		}
70
71		private JalviewStructureDisplayI chimeraViewer;
72
73		/**
74		* @throws java.lang.Exception
75		*/
		0% Uncovered Elements: 7 (7) Complexity: 1 Complexity Density: 0.14
76	0	@BeforeClass(alwaysRun = true)...
77		public static void setUpBeforeClass() throws Exception
78		{
79	0	Jalview.main(new String[] { "-noquestionnaire", "-nonews", "-props",
80		"test/jalview/ext/rbvi/chimera/testProps.jvprops" });
81	0	Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
82		ViewerType.CHIMERA.name());
83	0	Cache.setProperty("SHOW_ANNOTATIONS", "false");
84	0	Cache.setProperty(Preferences.STRUCT_FROM_PDB, "false");
85	0	Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
86		ViewerType.CHIMERA.name());
87	0	Cache.setProperty("MAP_WITH_SIFTS", "true");
88		// TODO this should not be necessary!
89	0	SiftsSettings.setMapWithSifts(true);
90		}
91
92		/**
93		* @throws java.lang.Exception
94		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
95	0	@AfterClass(alwaysRun = true)...
96		public static void tearDownAfterClass() throws Exception
97		{
98	0	Desktop.instance.closeAll_actionPerformed(null);
99		}
100
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
101	0	@AfterMethod(alwaysRun = true)...
102		public void tearDownAfterTest() throws Exception
103		{
104	0	SiftsClient.setMockSiftsFile(null);
105	0	if (chimeraViewer != null)
106		{
107	0	chimeraViewer.closeViewer(true);
108		}
109		}
110
111		/**
112		* Load 1GAQ and view the first structure for which a PDB id is found. Note no
113		* network connection is needed - PDB file is read locally, SIFTS fetch fails
114		* so mapping falls back to Needleman-Wunsch - ok for this test.
115		*/
116		// External as local install of Chimera required
		0% Uncovered Elements: 23 (23) Complexity: 3 Complexity Density: 0.14 4-
117	0	@Test(groups = { "External" })...
118		public void testSingleSeqViewChimera()
119		{
120	0	String inFile = "examples/1gaq.txt";
121	0	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
122		DataSourceType.FILE);
123	0	assertNotNull(af, "Failed to create AlignFrame");
124	0	SequenceI sq = af.getViewport().getAlignment().getSequenceAt(0);
125	0	assertEquals(sq.getName(), "1GAQ|A");
126	0	SequenceI dsq = sq.getDatasetSequence();
127	0	Vector<PDBEntry> pdbIds = dsq.getAllPDBEntries();
128	0	assertEquals(pdbIds.size(), 1);
129	0	PDBEntry pdbEntry = pdbIds.get(0);
130	0	assertEquals(pdbEntry.getId(), "1GAQ");
131	0	StructureViewer structureViewer = new StructureViewer(af.getViewport()
132		.getStructureSelectionManager());
133	0	chimeraViewer = structureViewer.viewStructures(pdbEntry,
134		new SequenceI[] { sq }, af.getCurrentView().getAlignPanel());
135	0	JalviewChimeraBinding binding = (JalviewChimeraBinding) chimeraViewer
136		.getBinding();
137
138		/*
139		* Wait for viewer load thread to complete
140		*/
141	0	while (!binding.isFinishedInit())
142		{
143	0	try
144		{
145	0	Thread.sleep(500);
146		} catch (InterruptedException e)
147		{
148		}
149		}
150
151	0	assertTrue(binding.isChimeraRunning(), "Failed to start Chimera");
152
153	0	assertEquals(chimeraViewer.getBinding().getPdbCount(), 1);
154	0	chimeraViewer.closeViewer(true);
155	0	chimeraViewer = null;
156	0	return;
157		}
158
159		/**
160		* Test for writing Jalview features as attributes on mapped residues in
161		* Chimera. Note this uses local copies of PDB and SIFTS file, no network
162		* connection required.
163		*
164		* @throws IOException
165		* @throws SiftsException
166		*/
167		// External as this requires a local install of Chimera
		0% Uncovered Elements: 78 (78) Complexity: 4 Complexity Density: 0.05 4-
168	0	@Test(groups = { "External" })...
169		public void testTransferFeatures() throws IOException, SiftsException
170		{
171	0	String inFile = "examples/uniref50.fa";
172	0	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
173		DataSourceType.FILE);
174	0	assertNotNull(af, "Failed to create AlignFrame");
175	0	SequenceI sq = af.getViewport().getAlignment().findName("FER2_ARATH");
176	0	assertNotNull(sq, "Didn't find FER2_ARATH");
177
178		/*
179		* need a Uniprot dbref for SIFTS mapping to work!!
180		*/
181	0	sq.addDBRef(new DBRefEntry("UNIPROT", "0", "P16972", null));
182
183		/*
184		* use local test PDB and SIFTS files
185		*/
186	0	String pdbFilePath = new File(
187		"test/jalview/ext/rbvi/chimera/4zho.pdb").getPath();
188	0	PDBEntry pdbEntry = new PDBEntry("4ZHO", null, null, pdbFilePath);
189	0	String siftsFilePath = new File(
190		"test/jalview/ext/rbvi/chimera/4zho.xml.gz")
191		.getPath();
192	0	SiftsClient.setMockSiftsFile(new File(siftsFilePath));
193
194	0	StructureViewer structureViewer = new StructureViewer(af.getViewport()
195		.getStructureSelectionManager());
196	0	chimeraViewer = structureViewer.viewStructures(pdbEntry,
197		new SequenceI[] { sq }, af.getCurrentView().getAlignPanel());
198
199	0	JalviewChimeraBinding binding = (JalviewChimeraBinding) chimeraViewer
200		.getBinding();
201	0	do
202		{
203	0	try
204		{
205	0	Thread.sleep(500);
206		} catch (InterruptedException e)
207		{
208		}
209	0	} while (!binding.isFinishedInit());
210
211	0	assertTrue(binding.isChimeraRunning(), "Failed to launch Chimera");
212
213	0	assertEquals(binding.getPdbCount(), 1);
214
215		/*
216		* check mapping is (sequence) 53-145 to (structure) 2-94 A/B
217		* (or possibly 52-145 to 1-94 - see JAL-2319)
218		*/
219	0	StructureSelectionManager ssm = binding.getSsm();
220	0	String pdbFile = binding.getStructureFiles()[0];
221	0	StructureMapping[] mappings = ssm.getMapping(pdbFile);
222	0	assertTrue(mappings[0].getMappingDetailsOutput().contains("SIFTS"),
223		"Failed to perform SIFTS mapping");
224	0	assertEquals(mappings.length, 2);
225	0	assertEquals(mappings[0].getChain(), "A");
226	0	assertEquals(mappings[0].getPDBResNum(53), 2);
227	0	assertEquals(mappings[0].getPDBResNum(145), 94);
228	0	assertEquals(mappings[1].getChain(), "B");
229	0	assertEquals(mappings[1].getPDBResNum(53), 2);
230	0	assertEquals(mappings[1].getPDBResNum(145), 94);
231
232		/*
233		* now add some features to FER2_ARATH
234		*/
235		// feature on a sequence region not mapped to structure:
236	0	sq.addSequenceFeature(new SequenceFeature("transit peptide",
237		"chloroplast", 1, 51, Float.NaN, null));
238		// feature on a region mapped to structure:
239	0	sq.addSequenceFeature(new SequenceFeature("domain",
240		"2Fe-2S ferredoxin-type", 55, 145, Float.NaN, null));
241		// on sparse positions of the sequence
242	0	sq.addSequenceFeature(new SequenceFeature("metal ion-binding site",
243		"Iron-Sulfur (2Fe-2S)", 91, 91, Float.NaN, null));
244	0	sq.addSequenceFeature(new SequenceFeature("metal ion-binding site",
245		"Iron-Sulfur (2Fe-2S)", 96, 96, Float.NaN, null));
246		// on a sequence region that is partially mapped to structure:
247	0	sq.addSequenceFeature(new SequenceFeature("helix", null, 50, 60,
248		Float.NaN, null));
249		// and again:
250	0	sq.addSequenceFeature(new SequenceFeature("chain", null, 50, 70,
251		Float.NaN, null));
252		// add numeric valued features - score is set as attribute value
253	0	sq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 62,
254		62, -2.1f, null));
255	0	sq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 65,
256		65, 3.6f, null));
257	0	sq.addSequenceFeature(new SequenceFeature("RESNUM", "ALA: 2 4zhoA",
258		53, 53, Float.NaN, null));
259
260		/*
261		* set all features visible except for chain
262		*/
263	0	af.setShowSeqFeatures(true);
264	0	FeatureRenderer fr = af.getFeatureRenderer();
265	0	fr.setVisible("transit peptide");
266	0	fr.setVisible("domain");
267	0	fr.setVisible("metal ion-binding site");
268	0	fr.setVisible("helix");
269	0	fr.setVisible("kd");
270	0	fr.setVisible("RESNUM");
271
272		/*
273		* 'perform' menu action to copy visible features to
274		* attributes in Chimera
275		*/
276		// TODO rename and pull up method to binding interface
277		// once functionality is added for Jmol as well
278	0	binding.sendFeaturesToViewer(af.getViewport().getAlignPanel());
279
280		/*
281		* give Chimera time to open the commands file and execute it
282		*/
283	0	try
284		{
285	0	Thread.sleep(1000);
286		} catch (InterruptedException e)
287		{
288		}
289
290		/*
291		* ask Chimera for its residue attribute names
292		*/
293	0	List<String> reply = binding.sendChimeraCommand("list resattr", true);
294		// prefixed and sanitised attribute names for Jalview features:
295	0	assertTrue(reply.contains("resattr jv_domain"));
296	0	assertTrue(reply.contains("resattr jv_metal_ion_binding_site"));
297	0	assertTrue(reply.contains("resattr jv_helix"));
298	0	assertTrue(reply.contains("resattr jv_kd"));
299	0	assertTrue(reply.contains("resattr jv_RESNUM"));
300		// feature is not on a mapped region - no attribute created
301	0	assertFalse(reply.contains("resattr jv_transit_peptide"));
302		// feature is not visible - no attribute created
303	0	assertFalse(reply.contains("resattr jv_chain"));
304
305		/*
306		* ask Chimera for residues with an attribute
307		* 91 and 96 on sequence --> residues 40 and 45 on chains A and B
308		*/
309	0	reply = binding.sendChimeraCommand(
310		"list resi att jv_metal_ion_binding_site", true);
311	0	assertEquals(reply.size(), 4);
312	0	assertTrue(reply
313		.contains("residue id #0:40.A jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 40"));
314	0	assertTrue(reply
315		.contains("residue id #0:45.A jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 45"));
316	0	assertTrue(reply
317		.contains("residue id #0:40.B jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 40"));
318	0	assertTrue(reply
319		.contains("residue id #0:45.B jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 45"));
320
321		/*
322		* check attributes with score values
323		* sequence positions 62 and 65 --> residues 11 and 14 on chains A and B
324		*/
325	0	reply = binding.sendChimeraCommand("list resi att jv_kd", true);
326	0	assertEquals(reply.size(), 4);
327	0	assertTrue(reply.contains("residue id #0:11.A jv_kd -2.1 index 11"));
328	0	assertTrue(reply.contains("residue id #0:14.A jv_kd 3.6 index 14"));
329	0	assertTrue(reply.contains("residue id #0:11.B jv_kd -2.1 index 11"));
330	0	assertTrue(reply.contains("residue id #0:14.B jv_kd 3.6 index 14"));
331
332		/*
333		* list residues with positive kd score
334		*/
335	0	reply = binding.sendChimeraCommand(
336		"list resi spec :*/jv_kd>0 attr jv_kd", true);
337	0	assertEquals(reply.size(), 2);
338	0	assertTrue(reply.contains("residue id #0:14.A jv_kd 3.6 index 14"));
339	0	assertTrue(reply.contains("residue id #0:14.B jv_kd 3.6 index 14"));
340
341	0	SiftsClient.setMockSiftsFile(null);
342	0	chimeraViewer.closeViewer(true);
343	0	chimeraViewer = null;
344		}
345
346		/**
347		* Test for creating Jalview features from attributes on mapped residues in
348		* Chimera. Note this uses local copies of PDB and SIFTS file, no network
349		* connection required.
350		*
351		* @throws IOException
352		* @throws SiftsException
353		*/
354		// External as this requires a local install of Chimera
		0% Uncovered Elements: 50 (50) Complexity: 7 Complexity Density: 0.17 4-
355	0	@Test(groups = { "External" })...
356		public void testGetAttributes() throws IOException, SiftsException
357		{
358	0	String inFile = "examples/uniref50.fa";
359	0	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
360		DataSourceType.FILE);
361	0	assertNotNull(af, "Failed to create AlignFrame");
362	0	SequenceI fer2Arath = af.getViewport().getAlignment()
363		.findName("FER2_ARATH");
364	0	assertNotNull(fer2Arath, "Didn't find FER2_ARATH");
365
366		/*
367		* need a Uniprot dbref for SIFTS mapping to work!!
368		*/
369	0	fer2Arath.addDBRef(new DBRefEntry("UNIPROT", "0", "P16972", null));
370
371		/*
372		* use local test PDB and SIFTS files
373		*/
374	0	String pdbFilePath = new File(
375		"test/jalview/ext/rbvi/chimera/4zho.pdb").getPath();
376	0	PDBEntry pdbEntry = new PDBEntry("4ZHO", null, null, pdbFilePath);
377	0	String siftsFilePath = new File(
378		"test/jalview/ext/rbvi/chimera/4zho.xml.gz")
379		.getPath();
380	0	SiftsClient.setMockSiftsFile(new File(siftsFilePath));
381
382	0	StructureViewer structureViewer = new StructureViewer(af.getViewport()
383		.getStructureSelectionManager());
384	0	chimeraViewer = structureViewer.viewStructures(pdbEntry,
385		new SequenceI[] { fer2Arath }, af.getCurrentView()
386		.getAlignPanel());
387
388	0	JalviewChimeraBinding binding = (JalviewChimeraBinding) chimeraViewer
389		.getBinding();
390	0	do
391		{
392	0	try
393		{
394	0	Thread.sleep(500);
395		} catch (InterruptedException e)
396		{
397		}
398	0	} while (!binding.isFinishedInit());
399
400	0	assertTrue(binding.isChimeraRunning(), "Failed to launch Chimera");
401
402	0	assertEquals(binding.getPdbCount(), 1);
403
404		/*
405		* 'perform' menu action to copy visible features to
406		* attributes in Chimera
407		*/
408		// TODO rename and pull up method to binding interface
409		// once functionality is added for Jmol as well
410	0	binding.copyStructureAttributesToFeatures("isHelix", af.getViewport()
411		.getAlignPanel());
412
413		/*
414		* verify 22 residues have isHelix feature
415		* (may merge into ranges in future)
416		*/
417	0	af.setShowSeqFeatures(true);
418	0	FeatureRenderer fr = af.getFeatureRenderer();
419	0	fr.setVisible("isHelix");
420	0	for (int res = 75; res <= 83; res++)
421		{
422	0	checkFeaturesAtRes(fer2Arath, fr, res, "isHelix");
423		}
424	0	for (int res = 117; res <= 123; res++)
425		{
426	0	checkFeaturesAtRes(fer2Arath, fr, res, "isHelix");
427		}
428	0	for (int res = 129; res <= 131; res++)
429		{
430	0	checkFeaturesAtRes(fer2Arath, fr, res, "isHelix");
431		}
432	0	for (int res = 143; res <= 145; res++)
433		{
434	0	checkFeaturesAtRes(fer2Arath, fr, res, "isHelix");
435		}
436
437		/*
438		* fetch a numeric valued attribute
439		*/
440	0	binding.copyStructureAttributesToFeatures("phi", af.getViewport()
441		.getAlignPanel());
442	0	fr.setVisible("phi");
443	0	List<SequenceFeature> fs = fer2Arath.getFeatures().findFeatures(54, 54);
444	0	assertEquals(fs.size(), 3);
445		/*
446		* order of returned features is not guaranteed
447		*/
448	0	assertTrue("RESNUM".equals(fs.get(0).getType())
449		|| "RESNUM".equals(fs.get(1).getType())
450		|| "RESNUM".equals(fs.get(2).getType()));
451	0	assertTrue(fs.contains(new SequenceFeature("phi", "A", 54, 54,
452		-131.0713f, "Chimera")));
453	0	assertTrue(fs.contains(new SequenceFeature("phi", "B", 54, 54,
454		-127.39512f, "Chimera")));
455
456		/*
457		* tear down - also in AfterMethod
458		*/
459	0	SiftsClient.setMockSiftsFile(null);
460	0	chimeraViewer.closeViewer(true);
461	0	chimeraViewer = null;
462		}
463
464		/**
465		* Helper method to verify new feature at a sequence position
466		*
467		* @param seq
468		* @param fr
469		* @param res
470		* @param featureType
471		*/
		0% Uncovered Elements: 9 (9) Complexity: 1 Complexity Density: 0.11
472	0	protected void checkFeaturesAtRes(SequenceI seq, FeatureRenderer fr,...
473		int res, String featureType)
474		{
475	0	String where = "at position " + res;
476	0	List<SequenceFeature> fs = seq.getFeatures().findFeatures(res, res);
477
478	0	assertEquals(fs.size(), 2, where);
479	0	assertEquals(fs.get(0).getType(), "RESNUM", where);
480	0	SequenceFeature sf = fs.get(1);
481	0	assertEquals(sf.getType(), featureType, where);
482	0	assertEquals(sf.getFeatureGroup(), "Chimera", where);
483	0	assertEquals(sf.getDescription(), "True", where);
484	0	assertEquals(sf.getScore(), Float.NaN, where);
485		}
486		}