Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
CrossRef2xmlTests	57	208	48	0.075539577.6%	Show methods

Class CrossRef2xmlTests

Class CrossRef2xmlTests	Line # 57	Total Statements 208	Complexity 48	TOTAL Coverage 0.075539577.6%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	6060	2.02	1.01	1.0 1.0100%
openCrossrefsForEnsemblTwice() : void   openCrossrefsForEnsemblTwice() : void	6868	19.019	3.03	0.8947368 0.894736889.5%
getAccessions() : Object[][]   getAccessions() : Object[][]	113113	1.01	1.01	0.0 0.00%
testRetrieveAndShowCrossref(String,String) : void   testRetrieveAndShowCrossref(String,String) : void	128128	137.0137	24.024	0.0 0.00%
filterDbRefs(List<String>,List<String>) : void   filterDbRefs(List<String>,List<String>) : void	519519	6.06	4.04	0.0 0.00%
assertDatasetIsNormalisedKnownDefect(AlignmentI,String) : void   assertDatasetIsNormalisedKnownDefect(AlignmentI,String) : void	544544	5.05	3.03	0.0 0.00%
assertProtein(AlignmentViewPanel,String) : void   assertProtein(AlignmentViewPanel,String) : void	565565	1.01	1.01	0.0 0.00%
assertNucleotide(AlignmentViewPanel,String) : void   assertNucleotide(AlignmentViewPanel,String) : void	571571	1.01	1.01	0.0 0.00%
assertType(boolean,AlignmentViewPanel,String) : void   assertType(boolean,AlignmentViewPanel,String) : void	577577	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	617617	30.030	6.06	0.0 0.00%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.0647482	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 jalview.analysis.CrossRef;
28		import jalview.api.AlignmentViewPanel;
29		import jalview.datamodel.AlignedCodonFrame;
30		import jalview.datamodel.AlignmentI;
31		import jalview.datamodel.AlignmentTest;
32		import jalview.datamodel.SequenceI;
33		import jalview.gui.AlignFrame;
34		import jalview.gui.CrossRefAction;
35		import jalview.gui.Desktop;
36		import jalview.gui.JvOptionPane;
37		import jalview.gui.SequenceFetcher;
38		import jalview.project.Jalview2XML;
39		import jalview.util.DBRefUtils;
40
41		import java.io.File;
42		import java.io.IOException;
43		import java.util.ArrayList;
44		import java.util.Arrays;
45		import java.util.HashMap;
46		import java.util.List;
47		import java.util.Map;
48
49		import org.testng.Assert;
50		import org.testng.annotations.BeforeClass;
51		import org.testng.annotations.DataProvider;
52		import org.testng.annotations.Test;
53
54		import junit.extensions.PA;
55
56		@Test(singleThreaded = true)
		7.6% Uncovered Elements: 257 (278) Complexity: 48 Complexity Density: 0.23
57		public class CrossRef2xmlTests extends Jalview2xmlBase
58		{
59
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
60	1	@Override...
61		@BeforeClass(alwaysRun = true)
62		public void setUpJvOptionPane()
63		{
64	1	JvOptionPane.setInteractiveMode(false);
65	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
66		}
67
		89.5% Uncovered Elements: 2 (19) Complexity: 3 Complexity Density: 0.16 1PASS
68	1	@Test(groups = { "Functional" }, enabled = true)...
69		public void openCrossrefsForEnsemblTwice()
70		{
71	1	AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
72		"examples/testdata/CantShowEnsemblCrossrefsTwice.jvp",
73		DataSourceType.FILE);
74	1	assertNotNull(af, "Couldn't load test's project.");
75	1	AlignmentI origAlig = af.getViewport().getAlignment();
76	1	List<String> source = new CrossRef(origAlig.getSequencesArray(),
77		origAlig.getDataset()).findXrefSourcesForSequences(true);
78	1	assertEquals(source.size(), 1, "Expected just one crossref to show.");
79	1	List<AlignmentViewPanel> views;
80		{
81		// try to show once - in a code block so handler is forgotten about
82	1	CrossRefAction xref1 = CrossRefAction.getHandlerFor(
83		origAlig.getSequencesArray(), true, source.get(0), af);
84	1	try
85		{
86	1	xref1.run();
87	1	views = (List<AlignmentViewPanel>) PA.getValue(xref1, "xrefViews");
88	1	assertTrue(views.size() > 0,
89		"Couldn't get cross ref on first attempt (SERIOUS FAIL).");
90		} catch (Exception ex)
91		{
92	0	Assert.fail("Unexpected Exception for first xref action", ex);
93		}
94		}
95
96	1	views = null;
97		// now just try it again
98	1	CrossRefAction xref2 = CrossRefAction.getHandlerFor(
99		origAlig.getSequencesArray(), true, source.get(0), af);
100	1	try
101		{
102	1	xref2.run();
103	1	views = (List<AlignmentViewPanel>) PA.getValue(xref2, "xrefViews");
104	1	assertTrue(views.size() > 0,
105		"Couldn't get cross ref on second attempt (SERIOUS FAIL).");
106		} catch (Exception ex)
107		{
108	0	Assert.fail("Unexpected Exception for second xref action", ex);
109		}
110		// TODO : check that both views contain the same data
111		}
112
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
113	0	@DataProvider(name = "initialAccessions")...
114		static Object[][] getAccessions()
115		{
116	0	return new String[][] { { "UNIPROT", "P00338" },
117		{ "UNIPROT", "Q8Z9G6" },
118		{ "ENSEMBLGENOMES", "CAD01290" } };
119		}
120
121		/**
122		* test store and recovery of all reachable cross refs from all reachable
123		* crossrefs for one or more fetched db refs. Currently, this test has a known
124		* failure case.
125		*
126		* @throws Exception
127		*/
		0% Uncovered Elements: 175 (175) Complexity: 24 Complexity Density: 0.18 1PASS
128	0	@Test(...
129		groups =
130		{ "Operational" },
131		dataProvider = "initialAccessions",
132		enabled = true)
133		public void testRetrieveAndShowCrossref(String forSource,
134		String forAccession) throws Exception
135		{
136
137	0	List<String> failedDBRetr = new ArrayList<>();
138	0	List<String> failedXrefMenuItems = new ArrayList<>();
139	0	List<String> failedProjectRecoveries = new ArrayList<>();
140		// only search for ensembl or Uniprot crossrefs
141	0	List<String> limit = Arrays
142		.asList(new String[]
143		{ DBRefUtils.getCanonicalName("ENSEMBL"),
144		DBRefUtils.getCanonicalName("Uniprot") });
145		// for every set of db queries
146		// retrieve db query
147		// verify presence of expected xrefs
148		// show xrefs - verify expected type of frame is shown for each xref
149		// show xrefs again
150		// - verify original -> xref -> xref(original) recovers frame containing at
151		// least the first retrieved sequence
152		// store
153		// 1. whole project
154		// 2. individual frames
155		// 3. load each one back and verify
156		// . aligned sequences (.toString() )
157		// . xrefs (.toString() )
158		// . codonframes
159		//
160		//
161	0	Map<String, String> dbtoviewBit = new HashMap<>();
162	0	List<String> keyseq = new ArrayList<>();
163	0	Map<String, File> savedProjects = new HashMap<>();
164
165		// for (String[] did : new String[][] { { "UNIPROT", "P00338" } })
166		// {
167		// pass counters - 0 - first pass, 1 means retrieve project rather than
168		// perform action
169	0	int pass1 = 0, pass2 = 0, pass3 = 0;
170		// each do loop performs two iterations in the first outer loop pass, but
171		// only performs one iteration on the second outer loop
172		// ie. pass 1 = 0 {pass 2= 0 { pass 3 = 0,1 }, pass 2=1 { pass 3 = 0 }}, 1
173		// { pass 2 = 0 { pass 3 = 0 } }
174	0	do
175		{
176	0	String first = forSource + " " + forAccession;// did[0] + " " + did[1];
177	0	AlignFrame af = null;
178	0	boolean dna;
179	0	AlignmentI retral;
180	0	AlignmentI dataset;
181	0	SequenceI[] seqs;
182	0	List<String> ptypes = null;
183	0	if (pass1 == 0)
184		{
185		// retrieve dbref
186
187	0	SequenceFetcher sf = new SequenceFetcher(Desktop.instance,
188		forSource, forAccession);
189	0	sf.run();
190	0	AlignFrame[] afs = Desktop.getAlignFrames();
191	0	if (afs.length == 0)
192		{
193	0	failedDBRetr.add("Didn't retrieve " + first);
194	0	break;
195		}
196	0	keyseq.add(first);
197	0	af = afs[0];
198
199		// verify references for retrieved data
200	0	AlignmentTest.assertAlignmentDatasetRefs(
201		af.getViewport().getAlignment(), "Pass (" + pass1 + ","
202		+ pass2 + "," + pass3 + "): Fetch " + first + ":");
203	0	assertDatasetIsNormalisedKnownDefect(
204		af.getViewport().getAlignment(), "Pass (" + pass1 + ","
205		+ pass2 + "," + pass3 + "): Fetch " + first + ":");
206	0	dna = af.getViewport().getAlignment().isNucleotide();
207	0	retral = af.getViewport().getAlignment();
208	0	dataset = retral.getDataset();
209	0	seqs = retral.getSequencesArray();
210
211		}
212		else
213		{
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	Desktop.instance.closeAll_actionPerformed(null);
282	0	pass3 = 0;
283		// recover stored project
284	0	File storedProject = savedProjects.get(nextxref);
285	0	if (storedProject == null)
286		{
287	0	failedProjectRecoveries
288		.add("Failed to store a view for '" + nextxref + "'");
289	0	continue;
290		}
291
292		// recover stored project
293	0	AlignFrame af2 = new FileLoader(false).LoadFileWaitTillLoaded(
294		savedProjects.get(nextxref).toString(),
295		DataSourceType.FILE);
296	0	System.out
297		.println("Recovered view for '" + nextxref + "' from '"
298		+ savedProjects.get(nextxref).toString() + "'");
299		// gymnastics to recover the alignPanel/Complementary alignPanel
300	0	if (af2.getViewport().isNucleotide())
301		{
302		// top view, then bottom
303	0	cra_views.add(af2.getViewport().getAlignPanel());
304	0	cra_views.add(((jalview.gui.AlignViewport) af2.getViewport()
305		.getCodingComplement()).getAlignPanel());
306
307		}
308		else
309		{
310		// bottom view, then top
311	0	cra_views.add(((jalview.gui.AlignViewport) af2.getViewport()
312		.getCodingComplement()).getAlignPanel());
313	0	cra_views.add(af2.getViewport().getAlignPanel());
314
315		}
316		}
317	0	HashMap<String, List<String>> xrptypes = new HashMap<>();
318		// first save/verify views.
319	0	for (AlignmentViewPanel avp : cra_views)
320		{
321	0	nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
322		// verify references for this panel
323	0	AlignmentTest.assertAlignmentDatasetRefs(avp.getAlignment(),
324		"Pass (" + pass1 + "," + pass2 + "," + pass3
325		+ "): before start of pass3: " + nextxref
326		+ ":");
327	0	assertDatasetIsNormalisedKnownDefect(avp.getAlignment(),
328		"Pass (" + pass1 + "," + pass2 + "," + pass3
329		+ "): before start of pass3: " + nextxref
330		+ ":");
331
332	0	SequenceI[] xrseqs = avp.getAlignment().getSequencesArray();
333
334	0	List<String> _xrptypes = (seqs == null || seqs.length == 0)
335		? null
336		: new CrossRef(xrseqs, dataset)
337		.findXrefSourcesForSequences(
338		avp.getAlignViewport().isNucleotide());
339
340	0	stringify(dbtoviewBit, savedProjects, nextxref, avp);
341	0	xrptypes.put(nextxref, _xrptypes);
342
343		}
344
345		// now do the second xref pass starting from either saved or just
346		// recovered split pane, in sequence
347	0	do // retrieve second set of cross refs or recover and verify
348		{
349	0	firstcr_ap = 0;
350	0	for (AlignmentViewPanel avp : cra_views)
351		{
352	0	nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
353	0	for (String xrefdb : xrptypes.get(nextxref))
354		{
355	0	List<AlignmentViewPanel> cra_views2 = new ArrayList<>();
356	0	int q = 0;
357	0	String nextnextxref = nextxref + " -> " + xrefdb + "{" + q
358		+ "}";
359
360	0	if (pass3 == 0)
361		{
362	0	SequenceI[] xrseqs = avp.getAlignment()
363		.getSequencesArray();
364	0	AlignFrame nextaf = Desktop
365		.getAlignFrameFor(avp.getAlignViewport());
366
367	0	cra = CrossRefAction.getHandlerFor(xrseqs,
368		avp.getAlignViewport().isNucleotide(), xrefdb,
369		nextaf);
370	0	cra.run();
371	0	cra_views2 = (List<AlignmentViewPanel>) PA.getValue(cra,
372		"xrefViews");
373	0	if (cra_views2.size() == 0)
374		{
375	0	failedXrefMenuItems.add("No crossrefs retrieved for '"
376		+ nextxref + "' to " + xrefdb + " via '"
377		+ nextaf.getTitle() + "'");
378	0	continue;
379		}
380	0	assertNucleotide(cra_views2.get(0),
381		"Nucleotide panel included proteins for '"
382		+ nextxref + "' to " + xrefdb + " via '"
383		+ nextaf.getTitle() + "'");
384	0	assertProtein(cra_views2.get(1),
385		"Protein panel included nucleotides for '"
386		+ nextxref + "' to " + xrefdb + " via '"
387		+ nextaf.getTitle() + "'");
388
389		}
390		else
391		{
392	0	Desktop.instance.closeAll_actionPerformed(null);
393		// recover stored project
394	0	File storedProject = savedProjects.get(nextnextxref);
395	0	if (storedProject == null)
396		{
397	0	failedProjectRecoveries
398		.add("Failed to store a view for '"
399		+ nextnextxref + "'");
400	0	continue;
401		}
402	0	AlignFrame af2 = new FileLoader(false)
403		.LoadFileWaitTillLoaded(savedProjects
404		.get(nextnextxref).toString(),
405		DataSourceType.FILE);
406	0	System.out
407		.println("Recovered view for '" + nextnextxref
408		+ "' from '" + savedProjects
409		.get(nextnextxref).toString()
410		+ "'");
411		// gymnastics to recover the alignPanel/Complementary
412		// alignPanel
413	0	if (af2.getViewport().isNucleotide())
414		{
415		// top view, then bottom
416	0	cra_views2.add(af2.getViewport().getAlignPanel());
417	0	cra_views2.add(((jalview.gui.AlignViewport) af2
418		.getViewport().getCodingComplement())
419		.getAlignPanel());
420
421		}
422		else
423		{
424		// bottom view, then top
425	0	cra_views2.add(((jalview.gui.AlignViewport) af2
426		.getViewport().getCodingComplement())
427		.getAlignPanel());
428	0	cra_views2.add(af2.getViewport().getAlignPanel());
429		}
430	0	Assert.assertEquals(cra_views2.size(), 2);
431	0	Assert.assertNotNull(cra_views2.get(0));
432	0	Assert.assertNotNull(cra_views2.get(1));
433		}
434
435	0	for (AlignmentViewPanel nextavp : cra_views2)
436		{
437	0	nextnextxref = nextxref + " -> " + xrefdb + "{" + q++
438		+ "}";
439
440		// verify references for this panel
441	0	AlignmentTest.assertAlignmentDatasetRefs(
442		nextavp.getAlignment(),
443		"" + "Pass (" + pass1 + "," + pass2 + "): For "
444		+ nextnextxref + ":");
445	0	assertDatasetIsNormalisedKnownDefect(
446		nextavp.getAlignment(),
447		"" + "Pass (" + pass1 + "," + pass2 + "): For "
448		+ nextnextxref + ":");
449
450	0	stringify(dbtoviewBit, savedProjects, nextnextxref,
451		nextavp);
452	0	keyseq.add(nextnextxref);
453		}
454		} // end of loop around showing all xrefdb for crossrf2
455
456		} // end of loop around all viewpanels from crossrf1
457	0	} while (pass2 == 2 && pass3++ < 2);
458		// fetchdb->crossref1->crossref-2->verify for xrefs we
459		// either loop twice when pass2=0, or just once when pass2=1
460		// (recovered project from previous crossref)
461
462		} // end of loop over db-xrefs for crossref-2
463
464		// fetchdb-->crossref1
465		// for each xref we try to retrieve xref, store and verify when
466		// pass1=0, or just retrieve and verify when pass1=1
467	0	} while (pass1 == 1 && pass2++ < 2);
468		// fetchdb
469		// for each ref we
470		// loop twice: first, do the retrieve, second recover from saved project
471
472		// increment pass counters, so we repeat traversal starting from the
473		// oldest saved project first.
474	0	if (pass1 == 0)
475		{
476		// verify stored projects for first set of cross references
477	0	pass1 = 1;
478		// and verify cross-references retrieved from stored projects
479	0	pass2 = 0;
480	0	pass3 = 0;
481		}
482		else
483		{
484	0	pass1++;
485		}
486	0	} while (pass1 < 3);
487
488	0	if (failedXrefMenuItems.size() > 0)
489		{
490	0	for (String s : failedXrefMenuItems)
491		{
492	0	System.err.println(s);
493		}
494	0	Assert.fail("Faulty xref menu (" + failedXrefMenuItems.size()
495		+ " counts)");
496		}
497	0	if (failedProjectRecoveries.size() > 0)
498		{
499
500	0	for (String s : failedProjectRecoveries)
501		{
502	0	System.err.println(s);
503		}
504	0	Assert.fail(
505		"Didn't recover projects for some retrievals (did they retrieve ?) ("
506		+ failedProjectRecoveries.size() + " counts)");
507		}
508	0	if (failedDBRetr.size() > 0)
509		{
510	0	for (String s : failedProjectRecoveries)
511		{
512	0	System.err.println(s);
513		}
514	0	Assert.fail("Didn't retrieve some db refs for checking cross-refs ("
515		+ failedDBRetr.size() + " counts)");
516		}
517		}
518
		0% Uncovered Elements: 12 (12) Complexity: 4 Complexity Density: 0.67
519	0	private void filterDbRefs(List<String> ptypes, List<String> limit)...
520		{
521	0	if (limit != null)
522		{
523	0	int p = 0;
524	0	while (ptypes.size() > p)
525		{
526	0	if (!limit.contains(ptypes.get(p)))
527		{
528	0	ptypes.remove(p);
529		}
530		else
531		{
532	0	p++;
533		}
534		}
535		}
536		}
537
538		/**
539		* wrapper to trap known defect for AH002001 testcase
540		*
541		* @param alignment
542		* @param string
543		*/
		0% Uncovered Elements: 7 (7) Complexity: 3 Complexity Density: 0.6
544	0	private void assertDatasetIsNormalisedKnownDefect(AlignmentI al,...
545		String message)
546		{
547	0	try
548		{
549	0	AlignmentTest.assertDatasetIsNormalised(al, message);
550		} catch (AssertionError ae)
551		{
552	0	if (!ae.getMessage().endsWith("EMBL|AH002001"))
553		{
554	0	throw ae;
555		}
556		else
557		{
558	0	System.out.println("Ignored exception for known defect: JAL-2179 : "
559		+ message);
560		}
561
562		}
563		}
564
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
565	0	private void assertProtein(AlignmentViewPanel alignmentViewPanel,...
566		String message)
567		{
568	0	assertType(true, alignmentViewPanel, message);
569		}
570
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
571	0	private void assertNucleotide(AlignmentViewPanel alignmentViewPanel,...
572		String message)
573		{
574	0	assertType(false, alignmentViewPanel, message);
575		}
576
		0% Uncovered Elements: 12 (12) Complexity: 4 Complexity Density: 0.67
577	0	private void assertType(boolean expectProtein,...
578		AlignmentViewPanel alignmentViewPanel, String message)
579		{
580	0	List<SequenceI> nonType = new ArrayList<>();
581	0	for (SequenceI sq : alignmentViewPanel.getAlignViewport().getAlignment()
582		.getSequences())
583		{
584	0	if (sq.isProtein() != expectProtein)
585		{
586	0	nonType.add(sq);
587		}
588		}
589	0	if (nonType.size() > 0)
590		{
591	0	Assert.fail(message + " [ "
592	0	+ (expectProtein ? "nucleotides were " : "proteins were ")
593		+ nonType.toString() + " ]");
594		}
595		}
596
597		/**
598		* first time called, record strings derived from alignment and
599		* alignedcodonframes, and save view to a project file. Second time called,
600		* compare strings to existing ones. org.testng.Assert.assertTrue on
601		* stringmatch
602		*
603		* @param dbtoviewBit
604		* map between xrefpath and view string
605		* @param savedProjects
606		* - map from xrefpath to saved project filename (createTempFile)
607		* @param xrefpath
608		* - xrefpath - unique ID for this context (composed of sequence of
609		* db-fetch/cross-ref actions preceeding state)
610		* @param avp
611		* - viewpanel to store (for viewpanels in splitframe, the same
612		* project should be written for both panels, only one needs
613		* recovering for comparison on the next stringify call, but each
614		* viewpanel needs to be called with a distinct xrefpath to ensure
615		* each one's strings are compared)
616		*/
		0% Uncovered Elements: 38 (38) Complexity: 6 Complexity Density: 0.2
617	0	private void stringify(Map<String, String> dbtoviewBit,...
618		Map<String, File> savedProjects, String xrefpath,
619		AlignmentViewPanel avp)
620		{
621	0	if (savedProjects != null)
622		{
623	0	if (savedProjects.get(xrefpath) == null)
624		{
625		// write a project file for this view. On the second pass, this will be
626		// recovered and cross-references verified
627	0	try
628		{
629	0	File prfile = File.createTempFile("crossRefTest", ".jvp");
630	0	AlignFrame af = Desktop.getAlignFrameFor(avp.getAlignViewport());
631	0	new Jalview2XML(false).saveAlignment(af, prfile.toString(),
632		af.getTitle());
633	0	System.out.println("Written view from '" + xrefpath + "' as '"
634		+ prfile.getAbsolutePath() + "'");
635	0	savedProjects.put(xrefpath, prfile);
636		} catch (IOException q)
637		{
638	0	Assert.fail("Unexpected IO Exception", q);
639		}
640		}
641		else
642		{
643	0	System.out.println("Stringify check on view from '" + xrefpath
644		+ "' [ possibly retrieved from '"
645		+ savedProjects.get(xrefpath).getAbsolutePath() + "' ]");
646
647		}
648		}
649
650	0	StringBuilder sbr = new StringBuilder();
651	0	sbr.append(avp.getAlignment().toString());
652	0	sbr.append("\n");
653	0	sbr.append("<End of alignment>");
654	0	sbr.append("\n");
655	0	sbr.append(avp.getAlignment().getDataset());
656	0	sbr.append("\n");
657	0	sbr.append("<End of dataset>");
658	0	sbr.append("\n");
659	0	int p = 0;
660	0	if (avp.getAlignment().getCodonFrames() != null)
661		{
662	0	for (AlignedCodonFrame ac : avp.getAlignment().getCodonFrames())
663		{
664	0	sbr.append("<AlignedCodonFrame " + p++ + ">");
665	0	sbr.append("\n");
666	0	sbr.append(ac.toString());
667	0	sbr.append("\n");
668		}
669		}
670	0	String dbt = dbtoviewBit.get(xrefpath);
671	0	if (dbt == null)
672		{
673	0	dbtoviewBit.put(xrefpath, sbr.toString());
674		}
675		else
676		{
677	0	Assert.assertEquals(sbr.toString(), dbt,
678		"stringify mismatch for " + xrefpath);
679		}
680		}
681		}