Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
CrossRef2xmlTests	56	211	51	0.073170737.3%	Show methods

Class CrossRef2xmlTests

Class CrossRef2xmlTests	Line # 56	Total Statements 211	Complexity 51	TOTAL Coverage 0.073170737.3%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5959	2.02	1.01	1.0 1.0100%
openCrossrefsForEnsemblTwice() : void   openCrossrefsForEnsemblTwice() : void	6767	19.019	3.03	0.8947368 0.894736889.5%
getAccessions() : Object[][]   getAccessions() : Object[][]	112112	1.01	1.01	0.0 0.00%
testRetrieveAndShowCrossref(String,String) : void   testRetrieveAndShowCrossref(String,String) : void	127127	140.0140	27.027	0.0 0.00%
filterDbRefs(List<String>,List<String>) : void   filterDbRefs(List<String>,List<String>) : void	521521	6.06	4.04	0.0 0.00%
assertDatasetIsNormalisedKnownDefect(AlignmentI,String) : void   assertDatasetIsNormalisedKnownDefect(AlignmentI,String) : void	546546	5.05	3.03	0.0 0.00%
assertProtein(AlignmentViewPanel,String) : void   assertProtein(AlignmentViewPanel,String) : void	567567	1.01	1.01	0.0 0.00%
assertNucleotide(AlignmentViewPanel,String) : void   assertNucleotide(AlignmentViewPanel,String) : void	573573	1.01	1.01	0.0 0.00%
assertType(boolean,AlignmentViewPanel,String) : void   assertType(boolean,AlignmentViewPanel,String) : void	579579	6.06	4.04	0.0 0.00%
stringify(Map<String, String>,Map<String, File>,String,AlignmentViewPanel) : void   stringify(Map<String, String>,Map<String, File>,String,AlignmentViewPanel) : void	619619	30.030	6.06	0.0 0.00%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.06271777	jalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwicejalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwice	1PASS

 

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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.io;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertNotNull;
25		import static org.testng.Assert.assertTrue;
26
27		import java.io.File;
28		import java.io.IOException;
29		import java.util.ArrayList;
30		import java.util.Arrays;
31		import java.util.HashMap;
32		import java.util.List;
33		import java.util.Map;
34
35		import org.testng.Assert;
36		import org.testng.annotations.BeforeClass;
37		import org.testng.annotations.DataProvider;
38		import org.testng.annotations.Test;
39
40		import jalview.analysis.CrossRef;
41		import jalview.api.AlignmentViewPanel;
42		import jalview.datamodel.AlignedCodonFrame;
43		import jalview.datamodel.AlignmentI;
44		import jalview.datamodel.AlignmentTest;
45		import jalview.datamodel.SequenceI;
46		import jalview.gui.AlignFrame;
47		import jalview.gui.CrossRefAction;
48		import jalview.gui.Desktop;
49		import jalview.gui.JvOptionPane;
50		import jalview.gui.SequenceFetcher;
51		import jalview.project.Jalview2XML;
52		import jalview.util.DBRefUtils;
53		import junit.extensions.PA;
54
55		@Test(singleThreaded = true)
		7.3% Uncovered Elements: 266 (287) Complexity: 51 Complexity Density: 0.24
56		public class CrossRef2xmlTests extends Jalview2xmlBase
57		{
58
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
59	1	@Override...
60		@BeforeClass(alwaysRun = true)
61		public void setUpJvOptionPane()
62		{
63	1	JvOptionPane.setInteractiveMode(false);
64	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
65		}
66
		89.5% Uncovered Elements: 2 (19) Complexity: 3 Complexity Density: 0.16 1PASS
67	1	@Test(groups = { "Functional" }, enabled = true)...
68		public void openCrossrefsForEnsemblTwice()
69		{
70	1	AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
71		"examples/testdata/CantShowEnsemblCrossrefsTwice.jvp",
72		DataSourceType.FILE);
73	1	assertNotNull(af, "Couldn't load test's project.");
74	1	AlignmentI origAlig = af.getViewport().getAlignment();
75	1	List<String> source = new CrossRef(origAlig.getSequencesArray(),
76		origAlig.getDataset()).findXrefSourcesForSequences(true);
77	1	assertEquals(source.size(), 1, "Expected just one crossref to show.");
78	1	List<AlignmentViewPanel> views;
79		{
80		// try to show once - in a code block so handler is forgotten about
81	1	CrossRefAction xref1 = CrossRefAction.getHandlerFor(
82		origAlig.getSequencesArray(), true, source.get(0), af);
83	1	try
84		{
85	1	xref1.run();
86	1	views = (List<AlignmentViewPanel>) PA.getValue(xref1, "xrefViews");
87	1	assertTrue(views.size() > 0,
88		"Couldn't get cross ref on first attempt (SERIOUS FAIL).");
89		} catch (Exception ex)
90		{
91	0	Assert.fail("Unexpected Exception for first xref action", ex);
92		}
93		}
94
95	1	views = null;
96		// now just try it again
97	1	CrossRefAction xref2 = CrossRefAction.getHandlerFor(
98		origAlig.getSequencesArray(), true, source.get(0), af);
99	1	try
100		{
101	1	xref2.run();
102	1	views = (List<AlignmentViewPanel>) PA.getValue(xref2, "xrefViews");
103	1	assertTrue(views.size() > 0,
104		"Couldn't get cross ref on second attempt (SERIOUS FAIL).");
105		} catch (Exception ex)
106		{
107	0	Assert.fail("Unexpected Exception for second xref action", ex);
108		}
109		// TODO : check that both views contain the same data
110		}
111
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
112	0	@DataProvider(name = "initialAccessions")...
113		static Object[][] getAccessions()
114		{
115	0	return new String[][] { { "UNIPROT", "P00338" },
116		{ "UNIPROT", "Q8Z9G6" },
117		{ "ENSEMBLGENOMES", "CAD01290" } };
118		}
119
120		/**
121		* test store and recovery of all reachable cross refs from all reachable
122		* crossrefs for one or more fetched db refs. Currently, this test has a known
123		* failure case.
124		*
125		* @throws Exception
126		*/
		0% Uncovered Elements: 184 (184) Complexity: 27 Complexity Density: 0.19 1PASS
127	0	@Test(...
128		groups =
129		{ "Operational" },
130		dataProvider = "initialAccessions",
131		enabled = true)
132		public void testRetrieveAndShowCrossref(String forSource,
133		String forAccession) throws Exception
134		{
135
136	0	List<String> failedDBRetr = new ArrayList<>();
137	0	List<String> failedXrefMenuItems = new ArrayList<>();
138	0	List<String> failedProjectRecoveries = new ArrayList<>();
139		// only search for ensembl or Uniprot crossrefs
140	0	List<String> limit = Arrays
141		.asList(new String[]
142		{ DBRefUtils.getCanonicalName("ENSEMBL"),
143		DBRefUtils.getCanonicalName("Uniprot") });
144		// for every set of db queries
145		// retrieve db query
146		// verify presence of expected xrefs
147		// show xrefs - verify expected type of frame is shown for each xref
148		// show xrefs again
149		// - verify original -> xref -> xref(original) recovers frame containing at
150		// least the first retrieved sequence
151		// store
152		// 1. whole project
153		// 2. individual frames
154		// 3. load each one back and verify
155		// . aligned sequences (.toString() )
156		// . xrefs (.toString() )
157		// . codonframes
158		//
159		//
160	0	Map<String, String> dbtoviewBit = new HashMap<>();
161	0	List<String> keyseq = new ArrayList<>();
162	0	Map<String, File> savedProjects = new HashMap<>();
163
164		// for (String[] did : new String[][] { { "UNIPROT", "P00338" } })
165		// {
166		// pass counters - 0 - first pass, 1 means retrieve project rather than
167		// perform action
168	0	int pass1 = 0, pass2 = 0, pass3 = 0;
169		// each do loop performs two iterations in the first outer loop pass, but
170		// only performs one iteration on the second outer loop
171		// ie. pass 1 = 0 {pass 2= 0 { pass 3 = 0,1 }, pass 2=1 { pass 3 = 0 }}, 1
172		// { pass 2 = 0 { pass 3 = 0 } }
173	0	do
174		{
175	0	String first = forSource + " " + forAccession;// did[0] + " " + did[1];
176	0	AlignFrame af = null;
177	0	boolean dna;
178	0	AlignmentI retral;
179	0	AlignmentI dataset;
180	0	SequenceI[] seqs;
181	0	List<String> ptypes = null;
182	0	if (pass1 == 0)
183		{
184		// retrieve dbref
185
186	0	SequenceFetcher sf = new SequenceFetcher(Desktop.instance,
187		forSource, forAccession);
188	0	sf.run();
189	0	AlignFrame[] afs = Desktop.getDesktopAlignFrames();
190	0	if (afs.length == 0)
191		{
192	0	failedDBRetr.add("Didn't retrieve " + first);
193	0	break;
194		}
195	0	keyseq.add(first);
196	0	af = afs[0];
197
198		// verify references for retrieved data
199	0	AlignmentTest.assertAlignmentDatasetRefs(
200		af.getViewport().getAlignment(), "Pass (" + pass1 + ","
201		+ pass2 + "," + pass3 + "): Fetch " + first + ":");
202	0	assertDatasetIsNormalisedKnownDefect(
203		af.getViewport().getAlignment(), "Pass (" + pass1 + ","
204		+ pass2 + "," + pass3 + "): Fetch " + first + ":");
205	0	dna = af.getViewport().getAlignment().isNucleotide();
206	0	retral = af.getViewport().getAlignment();
207	0	dataset = retral.getDataset();
208	0	seqs = retral.getSequencesArray();
209
210		}
211		else
212		{
213	0	if (Desktop.instance != null)
214	0	Desktop.instance.closeAll_actionPerformed(null);
215		// recover stored project
216	0	af = new FileLoader(false).LoadFileWaitTillLoaded(
217		savedProjects.get(first).toString(), DataSourceType.FILE);
218	0	System.out.println("Recovered view for '" + first + "' from '"
219		+ savedProjects.get(first).toString() + "'");
220	0	dna = af.getViewport().getAlignment().isNucleotide();
221	0	retral = af.getViewport().getAlignment();
222	0	dataset = retral.getDataset();
223	0	seqs = retral.getSequencesArray();
224
225		// verify references for recovered data
226	0	AlignmentTest.assertAlignmentDatasetRefs(
227		af.getViewport().getAlignment(),
228		"Pass (" + pass1 + "," + pass2 + "," + pass3 + "): Recover "
229		+ first + ":");
230	0	assertDatasetIsNormalisedKnownDefect(
231		af.getViewport().getAlignment(),
232		"Pass (" + pass1 + "," + pass2 + "," + pass3 + "): Recover "
233		+ first + ":");
234
235		}
236
237		// store project on first pass, compare next pass
238	0	stringify(dbtoviewBit, savedProjects, first, af.alignPanel);
239
240	0	ptypes = (seqs == null || seqs.length == 0) ? null
241		: new CrossRef(seqs, dataset)
242		.findXrefSourcesForSequences(dna);
243	0	filterDbRefs(ptypes, limit);
244
245		// start of pass2: retrieve each cross-ref for fetched or restored
246		// project.
247	0	do // first cross ref and recover crossref loop
248		{
249
250	0	for (String db : ptypes)
251		{
252		// counter for splitframe views retrieved via crossref
253	0	int firstcr_ap = 0;
254		// build next key so we an retrieve all views
255	0	String nextxref = first + " -> " + db + "{" + firstcr_ap + "}";
256		// perform crossref action, or retrieve stored project
257	0	List<AlignmentViewPanel> cra_views = new ArrayList<>();
258	0	CrossRefAction cra = null;
259
260	0	if (pass2 == 0)
261		{ // retrieve and show cross-refs in this thread
262	0	cra = CrossRefAction.getHandlerFor(seqs, dna, db, af);
263	0	cra.run();
264	0	cra_views = (List<AlignmentViewPanel>) PA.getValue(cra,
265		"xrefViews");
266	0	if (cra_views.size() == 0)
267		{
268	0	failedXrefMenuItems.add(
269		"No crossrefs retrieved for " + first + " -> " + db);
270	0	continue;
271		}
272	0	assertNucleotide(cra_views.get(0),
273		"Nucleotide panel included proteins for " + first
274		+ " -> " + db);
275	0	assertProtein(cra_views.get(1),
276		"Protein panel included nucleotides for " + first
277		+ " -> " + db);
278		}
279		else
280		{
281	0	if (Desktop.instance != null)
282	0	Desktop.instance.closeAll_actionPerformed(null);
283	0	pass3 = 0;
284		// recover stored project
285	0	File storedProject = savedProjects.get(nextxref);
286	0	if (storedProject == null)
287		{
288	0	failedProjectRecoveries
289		.add("Failed to store a view for '" + nextxref + "'");
290	0	continue;
291		}
292
293		// recover stored project
294	0	AlignFrame af2 = new FileLoader(false).LoadFileWaitTillLoaded(
295		savedProjects.get(nextxref).toString(),
296		DataSourceType.FILE);
297	0	System.out
298		.println("Recovered view for '" + nextxref + "' from '"
299		+ savedProjects.get(nextxref).toString() + "'");
300		// gymnastics to recover the alignPanel/Complementary alignPanel
301	0	if (af2.getViewport().isNucleotide())
302		{
303		// top view, then bottom
304	0	cra_views.add(af2.getViewport().getAlignPanel());
305	0	cra_views.add(((jalview.gui.AlignViewport) af2.getViewport()
306		.getCodingComplement()).getAlignPanel());
307
308		}
309		else
310		{
311		// bottom view, then top
312	0	cra_views.add(((jalview.gui.AlignViewport) af2.getViewport()
313		.getCodingComplement()).getAlignPanel());
314	0	cra_views.add(af2.getViewport().getAlignPanel());
315
316		}
317		}
318	0	HashMap<String, List<String>> xrptypes = new HashMap<>();
319		// first save/verify views.
320	0	for (AlignmentViewPanel avp : cra_views)
321		{
322	0	nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
323		// verify references for this panel
324	0	AlignmentTest.assertAlignmentDatasetRefs(avp.getAlignment(),
325		"Pass (" + pass1 + "," + pass2 + "," + pass3
326		+ "): before start of pass3: " + nextxref
327		+ ":");
328	0	assertDatasetIsNormalisedKnownDefect(avp.getAlignment(),
329		"Pass (" + pass1 + "," + pass2 + "," + pass3
330		+ "): before start of pass3: " + nextxref
331		+ ":");
332
333	0	SequenceI[] xrseqs = avp.getAlignment().getSequencesArray();
334
335	0	List<String> _xrptypes = (seqs == null || seqs.length == 0)
336		? null
337		: new CrossRef(xrseqs, dataset)
338		.findXrefSourcesForSequences(
339		avp.getAlignViewport().isNucleotide());
340
341	0	stringify(dbtoviewBit, savedProjects, nextxref, avp);
342	0	xrptypes.put(nextxref, _xrptypes);
343
344		}
345
346		// now do the second xref pass starting from either saved or just
347		// recovered split pane, in sequence
348	0	do // retrieve second set of cross refs or recover and verify
349		{
350	0	firstcr_ap = 0;
351	0	for (AlignmentViewPanel avp : cra_views)
352		{
353	0	nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
354	0	for (String xrefdb : xrptypes.get(nextxref))
355		{
356	0	List<AlignmentViewPanel> cra_views2 = new ArrayList<>();
357	0	int q = 0;
358	0	String nextnextxref = nextxref + " -> " + xrefdb + "{" + q
359		+ "}";
360
361	0	if (pass3 == 0)
362		{
363	0	SequenceI[] xrseqs = avp.getAlignment()
364		.getSequencesArray();
365	0	AlignFrame nextaf = Desktop
366		.getAlignFrameFor(avp.getAlignViewport());
367
368	0	cra = CrossRefAction.getHandlerFor(xrseqs,
369		avp.getAlignViewport().isNucleotide(), xrefdb,
370		nextaf);
371	0	cra.run();
372	0	cra_views2 = (List<AlignmentViewPanel>) PA.getValue(cra,
373		"xrefViews");
374	0	if (cra_views2.size() == 0)
375		{
376	0	failedXrefMenuItems.add("No crossrefs retrieved for '"
377		+ nextxref + "' to " + xrefdb + " via '"
378		+ nextaf.getTitle() + "'");
379	0	continue;
380		}
381	0	assertNucleotide(cra_views2.get(0),
382		"Nucleotide panel included proteins for '"
383		+ nextxref + "' to " + xrefdb + " via '"
384		+ nextaf.getTitle() + "'");
385	0	assertProtein(cra_views2.get(1),
386		"Protein panel included nucleotides for '"
387		+ nextxref + "' to " + xrefdb + " via '"
388		+ nextaf.getTitle() + "'");
389
390		}
391		else
392		{
393	0	if (Desktop.instance != null)
394	0	Desktop.instance.closeAll_actionPerformed(null);
395		// recover stored project
396	0	File storedProject = savedProjects.get(nextnextxref);
397	0	if (storedProject == null)
398		{
399	0	failedProjectRecoveries
400		.add("Failed to store a view for '"
401		+ nextnextxref + "'");
402	0	continue;
403		}
404	0	AlignFrame af2 = new FileLoader(false)
405		.LoadFileWaitTillLoaded(savedProjects
406		.get(nextnextxref).toString(),
407		DataSourceType.FILE);
408	0	System.out
409		.println("Recovered view for '" + nextnextxref
410		+ "' from '" + savedProjects
411		.get(nextnextxref).toString()
412		+ "'");
413		// gymnastics to recover the alignPanel/Complementary
414		// alignPanel
415	0	if (af2.getViewport().isNucleotide())
416		{
417		// top view, then bottom
418	0	cra_views2.add(af2.getViewport().getAlignPanel());
419	0	cra_views2.add(((jalview.gui.AlignViewport) af2
420		.getViewport().getCodingComplement())
421		.getAlignPanel());
422
423		}
424		else
425		{
426		// bottom view, then top
427	0	cra_views2.add(((jalview.gui.AlignViewport) af2
428		.getViewport().getCodingComplement())
429		.getAlignPanel());
430	0	cra_views2.add(af2.getViewport().getAlignPanel());
431		}
432	0	Assert.assertEquals(cra_views2.size(), 2);
433	0	Assert.assertNotNull(cra_views2.get(0));
434	0	Assert.assertNotNull(cra_views2.get(1));
435		}
436
437	0	for (AlignmentViewPanel nextavp : cra_views2)
438		{
439	0	nextnextxref = nextxref + " -> " + xrefdb + "{" + q++
440		+ "}";
441
442		// verify references for this panel
443	0	AlignmentTest.assertAlignmentDatasetRefs(
444		nextavp.getAlignment(),
445		"" + "Pass (" + pass1 + "," + pass2 + "): For "
446		+ nextnextxref + ":");
447	0	assertDatasetIsNormalisedKnownDefect(
448		nextavp.getAlignment(),
449		"" + "Pass (" + pass1 + "," + pass2 + "): For "
450		+ nextnextxref + ":");
451
452	0	stringify(dbtoviewBit, savedProjects, nextnextxref,
453		nextavp);
454	0	keyseq.add(nextnextxref);
455		}
456		} // end of loop around showing all xrefdb for crossrf2
457
458		} // end of loop around all viewpanels from crossrf1
459	0	} while (pass2 == 2 && pass3++ < 2);
460		// fetchdb->crossref1->crossref-2->verify for xrefs we
461		// either loop twice when pass2=0, or just once when pass2=1
462		// (recovered project from previous crossref)
463
464		} // end of loop over db-xrefs for crossref-2
465
466		// fetchdb-->crossref1
467		// for each xref we try to retrieve xref, store and verify when
468		// pass1=0, or just retrieve and verify when pass1=1
469	0	} while (pass1 == 1 && pass2++ < 2);
470		// fetchdb
471		// for each ref we
472		// loop twice: first, do the retrieve, second recover from saved project
473
474		// increment pass counters, so we repeat traversal starting from the
475		// oldest saved project first.
476	0	if (pass1 == 0)
477		{
478		// verify stored projects for first set of cross references
479	0	pass1 = 1;
480		// and verify cross-references retrieved from stored projects
481	0	pass2 = 0;
482	0	pass3 = 0;
483		}
484		else
485		{
486	0	pass1++;
487		}
488	0	} while (pass1 < 3);
489
490	0	if (failedXrefMenuItems.size() > 0)
491		{
492	0	for (String s : failedXrefMenuItems)
493		{
494	0	System.err.println(s);
495		}
496	0	Assert.fail("Faulty xref menu (" + failedXrefMenuItems.size()
497		+ " counts)");
498		}
499	0	if (failedProjectRecoveries.size() > 0)
500		{
501
502	0	for (String s : failedProjectRecoveries)
503		{
504	0	System.err.println(s);
505		}
506	0	Assert.fail(
507		"Didn't recover projects for some retrievals (did they retrieve ?) ("
508		+ failedProjectRecoveries.size() + " counts)");
509		}
510	0	if (failedDBRetr.size() > 0)
511		{
512	0	for (String s : failedProjectRecoveries)
513		{
514	0	System.err.println(s);
515		}
516	0	Assert.fail("Didn't retrieve some db refs for checking cross-refs ("
517		+ failedDBRetr.size() + " counts)");
518		}
519		}
520
		0% Uncovered Elements: 12 (12) Complexity: 4 Complexity Density: 0.67
521	0	private void filterDbRefs(List<String> ptypes, List<String> limit)...
522		{
523	0	if (limit != null)
524		{
525	0	int p = 0;
526	0	while (ptypes.size() > p)
527		{
528	0	if (!limit.contains(ptypes.get(p)))
529		{
530	0	ptypes.remove(p);
531		}
532		else
533		{
534	0	p++;
535		}
536		}
537		}
538		}
539
540		/**
541		* wrapper to trap known defect for AH002001 testcase
542		*
543		* @param alignment
544		* @param string
545		*/
		0% Uncovered Elements: 7 (7) Complexity: 3 Complexity Density: 0.6
546	0	private void assertDatasetIsNormalisedKnownDefect(AlignmentI al,...
547		String message)
548		{
549	0	try
550		{
551	0	AlignmentTest.assertDatasetIsNormalised(al, message);
552		} catch (AssertionError ae)
553		{
554	0	if (!ae.getMessage().endsWith("EMBL|AH002001"))
555		{
556	0	throw ae;
557		}
558		else
559		{
560	0	System.out.println("Ignored exception for known defect: JAL-2179 : "
561		+ message);
562		}
563
564		}
565		}
566
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
567	0	private void assertProtein(AlignmentViewPanel alignmentViewPanel,...
568		String message)
569		{
570	0	assertType(true, alignmentViewPanel, message);
571		}
572
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
573	0	private void assertNucleotide(AlignmentViewPanel alignmentViewPanel,...
574		String message)
575		{
576	0	assertType(false, alignmentViewPanel, message);
577		}
578
		0% Uncovered Elements: 12 (12) Complexity: 4 Complexity Density: 0.67
579	0	private void assertType(boolean expectProtein,...
580		AlignmentViewPanel alignmentViewPanel, String message)
581		{
582	0	List<SequenceI> nonType = new ArrayList<>();
583	0	for (SequenceI sq : alignmentViewPanel.getAlignViewport().getAlignment()
584		.getSequences())
585		{
586	0	if (sq.isProtein() != expectProtein)
587		{
588	0	nonType.add(sq);
589		}
590		}
591	0	if (nonType.size() > 0)
592		{
593	0	Assert.fail(message + " [ "
594	0	+ (expectProtein ? "nucleotides were " : "proteins were ")
595		+ nonType.toString() + " ]");
596		}
597		}
598
599		/**
600		* first time called, record strings derived from alignment and
601		* alignedcodonframes, and save view to a project file. Second time called,
602		* compare strings to existing ones. org.testng.Assert.assertTrue on
603		* stringmatch
604		*
605		* @param dbtoviewBit
606		* map between xrefpath and view string
607		* @param savedProjects
608		* - map from xrefpath to saved project filename (createTempFile)
609		* @param xrefpath
610		* - xrefpath - unique ID for this context (composed of sequence of
611		* db-fetch/cross-ref actions preceeding state)
612		* @param avp
613		* - viewpanel to store (for viewpanels in splitframe, the same
614		* project should be written for both panels, only one needs
615		* recovering for comparison on the next stringify call, but each
616		* viewpanel needs to be called with a distinct xrefpath to ensure
617		* each one's strings are compared)
618		*/
		0% Uncovered Elements: 38 (38) Complexity: 6 Complexity Density: 0.2
619	0	private void stringify(Map<String, String> dbtoviewBit,...
620		Map<String, File> savedProjects, String xrefpath,
621		AlignmentViewPanel avp)
622		{
623	0	if (savedProjects != null)
624		{
625	0	if (savedProjects.get(xrefpath) == null)
626		{
627		// write a project file for this view. On the second pass, this will be
628		// recovered and cross-references verified
629	0	try
630		{
631	0	File prfile = File.createTempFile("crossRefTest", ".jvp");
632	0	AlignFrame af = Desktop.getAlignFrameFor(avp.getAlignViewport());
633	0	new Jalview2XML(false).saveAlignment(af, prfile.toString(),
634		af.getTitle());
635	0	System.out.println("Written view from '" + xrefpath + "' as '"
636		+ prfile.getAbsolutePath() + "'");
637	0	savedProjects.put(xrefpath, prfile);
638		} catch (IOException q)
639		{
640	0	Assert.fail("Unexpected IO Exception", q);
641		}
642		}
643		else
644		{
645	0	System.out.println("Stringify check on view from '" + xrefpath
646		+ "' [ possibly retrieved from '"
647		+ savedProjects.get(xrefpath).getAbsolutePath() + "' ]");
648
649		}
650		}
651
652	0	StringBuilder sbr = new StringBuilder();
653	0	sbr.append(avp.getAlignment().toString());
654	0	sbr.append("\n");
655	0	sbr.append("<End of alignment>");
656	0	sbr.append("\n");
657	0	sbr.append(avp.getAlignment().getDataset());
658	0	sbr.append("\n");
659	0	sbr.append("<End of dataset>");
660	0	sbr.append("\n");
661	0	int p = 0;
662	0	if (avp.getAlignment().getCodonFrames() != null)
663		{
664	0	for (AlignedCodonFrame ac : avp.getAlignment().getCodonFrames())
665		{
666	0	sbr.append("<AlignedCodonFrame " + p++ + ">");
667	0	sbr.append("\n");
668	0	sbr.append(ac.toString());
669	0	sbr.append("\n");
670		}
671		}
672	0	String dbt = dbtoviewBit.get(xrefpath);
673	0	if (dbt == null)
674		{
675	0	dbtoviewBit.put(xrefpath, sbr.toString());
676		}
677		else
678		{
679	0	Assert.assertEquals(sbr.toString(), dbt,
680		"stringify mismatch for " + xrefpath);
681		}
682		}
683		}