2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
23 import jalview.analysis.CrossRef;
24 import jalview.api.AlignmentViewPanel;
25 import jalview.datamodel.AlignedCodonFrame;
26 import jalview.datamodel.AlignmentI;
27 import jalview.datamodel.AlignmentTest;
28 import jalview.datamodel.SequenceI;
29 import jalview.gui.AlignFrame;
30 import jalview.gui.CrossRefAction;
31 import jalview.gui.Desktop;
32 import jalview.gui.Jalview2XML;
35 import java.io.IOException;
36 import java.util.ArrayList;
37 import java.util.HashMap;
38 import java.util.List;
40 import org.testng.Assert;
41 import org.testng.annotations.Test;
43 @Test(singleThreaded = true)
44 public class CrossRef2xmlTests extends Jalview2xmlBase
48 * test store and recovery of expanded views
52 @Test(groups = { "Operational" }, enabled = true)
53 public void testRetrieveAndShowCrossref() throws Exception
56 List<String> failedDBRetr = new ArrayList<String>();
57 List<String> failedXrefMenuItems = new ArrayList<String>();
58 List<String> failedProjectRecoveries = new ArrayList<String>();
60 // for every set of db queries
62 // verify presence of expected xrefs
63 // show xrefs - verify expected type of frame is shown for each xref
65 // - verify original -> xref -> xref(original) recovers frame containing at
66 // least the first retrieved sequence
69 // 2. individual frames
70 // 3. load each one back and verify
71 // . aligned sequences (.toString() )
72 // . xrefs (.toString() )
76 HashMap<String, String> dbtoviewBit = new HashMap<String, String>();
77 List<String> keyseq = new ArrayList<String>();
78 HashMap<String, File> savedProjects = new HashMap<String, File>();
80 for (String[] did : new String[][] { { "ENSEMBL", "ENSG00000157764" },
81 { "UNIPROT", "P01731" } })
83 // pass counters - 0 - first pass, 1 means retrieve project rather than
85 int pass1 = 0, pass2 = 0, pass3 = 0;
86 // each do loop performs two iterations in the first outer loop pass, but
87 // only performs one iteration on the second outer loop
88 // ie. pass 1 = 0 {pass 2= 0 { pass 3 = 0,1 }, pass 2=1 { pass 3 = 0 }}, 1
89 // { pass 2 = 0 { pass 3 = 0 } }
92 String first = did[0] + " " + did[1];
98 List<String> ptypes = null;
103 List<AlignFrame> afs = jalview.gui.SequenceFetcher.fetchAndShow(
107 failedDBRetr.add("Didn't retrieve " + first);
113 // verify references for retrieved data
114 AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
115 .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
116 + pass3 + "): Fetch " + first + ":");
117 AlignmentTest.assertDatasetIsNormalised(af.getViewport()
118 .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
119 + pass3 + "): Fetch " + first + ":");
120 dna = af.getViewport().getAlignment().isNucleotide();
121 retral = af.getViewport().getAlignment();
122 dataset = retral.getDataset();
123 seqs = retral.getSequencesArray();
128 Desktop.instance.closeAll_actionPerformed(null);
129 // recover stored project
130 af = new FileLoader(false).LoadFileWaitTillLoaded(savedProjects
131 .get(first).toString(), FormatAdapter.FILE);
132 System.out.println("Recovered view for '" + first + "' from '"
133 + savedProjects.get(first).toString() + "'");
134 dna = af.getViewport().getAlignment().isNucleotide();
135 retral = af.getViewport().getAlignment();
136 dataset = retral.getDataset();
137 seqs = retral.getSequencesArray();
139 // verify references for recovered data
140 AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
141 .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
142 + pass3 + "): Recover " + first + ":");
143 AlignmentTest.assertDatasetIsNormalised(af.getViewport()
144 .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
145 + pass3 + "): Recover " + first + ":");
149 // store project on first pass, compare next pass
150 stringify(dbtoviewBit, savedProjects, first, af.alignPanel);
152 ptypes = (seqs == null || seqs.length == 0) ? null : new CrossRef(
153 seqs, dataset).findXrefSourcesForSequences(dna);
155 // start of pass2: retrieve each cross-ref for fetched or restored
157 do // first cross ref and recover crossref loop
160 for (String db : ptypes)
162 // counter for splitframe views retrieved via crossref
164 // build next key so we an retrieve all views
165 String nextxref = first + " -> " + db + "{" + firstcr_ap + "}";
166 // perform crossref action, or retrieve stored project
167 List<AlignmentViewPanel> cra_views = new ArrayList<AlignmentViewPanel>();
168 CrossRefAction cra = null;
171 { // retrieve and show cross-refs in this thread
172 cra = new CrossRefAction(af, seqs, dna, db);
174 if (cra.getXrefViews().size() == 0)
176 failedXrefMenuItems.add("No crossrefs retrieved for "
177 + first + " -> " + db);
180 cra_views = cra.getXrefViews();
181 assertNucleotide(cra_views.get(0),
182 "Nucleotide panel included proteins for " + first
184 assertProtein(cra_views.get(1),
185 "Protein panel included nucleotides for " + first
190 Desktop.instance.closeAll_actionPerformed(null);
192 // recover stored project
193 File storedProject = savedProjects.get(nextxref);
194 if (storedProject == null)
196 failedProjectRecoveries.add("Failed to store a view for '"
201 // recover stored project
202 AlignFrame af2 = new FileLoader(false)
203 .LoadFileWaitTillLoaded(savedProjects.get(nextxref)
204 .toString(), FormatAdapter.FILE);
205 System.out.println("Recovered view for '" + nextxref
206 + "' from '" + savedProjects.get(nextxref).toString()
208 // gymnastics to recover the alignPanel/Complementary alignPanel
209 if (af2.getViewport().isNucleotide())
211 // top view, then bottom
212 cra_views.add(af2.getViewport().getAlignPanel());
213 cra_views.add(((jalview.gui.AlignViewport) af2
214 .getViewport().getCodingComplement())
220 // bottom view, then top
221 cra_views.add(((jalview.gui.AlignViewport) af2
222 .getViewport().getCodingComplement())
224 cra_views.add(af2.getViewport().getAlignPanel());
228 HashMap<String, List<String>> xrptypes = new HashMap<String, List<String>>();
229 // first save/verify views.
230 for (AlignmentViewPanel avp : cra_views)
232 nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
233 // verify references for this panel
234 AlignmentTest.assertAlignmentDatasetRefs(avp.getAlignment(),
235 "Pass (" + pass1 + "," + pass2 + "," + pass3
236 + "): before start of pass3: " + nextxref
238 AlignmentTest.assertDatasetIsNormalised(avp.getAlignment(),
239 "Pass (" + pass1 + "," + pass2 + "," + pass3
240 + "): before start of pass3: " + nextxref
243 SequenceI[] xrseqs = avp.getAlignment().getSequencesArray();
245 List<String> _xrptypes = (seqs == null || seqs.length == 0) ? null
246 : new CrossRef(xrseqs, dataset)
247 .findXrefSourcesForSequences(avp
248 .getAlignViewport().isNucleotide());
250 stringify(dbtoviewBit, savedProjects, nextxref, avp);
251 xrptypes.put(nextxref, _xrptypes);
255 // now do the second xref pass starting from either saved or just
256 // recovered split pane, in sequence
257 do // retrieve second set of cross refs or recover and verify
260 for (AlignmentViewPanel avp : cra_views)
262 nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
263 for (String xrefdb : xrptypes.get(nextxref))
265 List<AlignmentViewPanel> cra_views2 = new ArrayList<AlignmentViewPanel>();
267 String nextnextxref = nextxref
268 + " -> " + xrefdb + "{" + q + "}";
273 SequenceI[] xrseqs = avp.getAlignment()
274 .getSequencesArray();
275 AlignFrame nextaf = Desktop.getAlignFrameFor(avp
276 .getAlignViewport());
278 cra = new CrossRefAction(nextaf, xrseqs, avp
279 .getAlignViewport().isNucleotide(), xrefdb);
281 if (cra.getXrefViews().size() == 0)
284 .add("No crossrefs retrieved for '"
285 + nextxref + "' to " + xrefdb + " via '"
286 + nextaf.getTitle() + "'");
289 cra_views2 = cra.getXrefViews();
290 assertNucleotide(cra_views2.get(0),
291 "Nucleotide panel included proteins for '"
292 + nextxref + "' to " + xrefdb
293 + " via '" + nextaf.getTitle() + "'");
294 assertProtein(cra_views2.get(1),
295 "Protein panel included nucleotides for '"
296 + nextxref + "' to " + xrefdb
297 + " via '" + nextaf.getTitle() + "'");
302 Desktop.instance.closeAll_actionPerformed(null);
303 // recover stored project
304 File storedProject = savedProjects.get(nextnextxref);
305 if (storedProject == null)
307 failedProjectRecoveries
308 .add("Failed to store a view for '"
309 + nextnextxref + "'");
312 AlignFrame af2 = new FileLoader(false)
313 .LoadFileWaitTillLoaded(
314 savedProjects.get(nextnextxref)
315 .toString(), FormatAdapter.FILE);
316 System.out.println("Recovered view for '"
317 + nextnextxref + "' from '"
318 + savedProjects.get(nextnextxref).toString()
320 // gymnastics to recover the alignPanel/Complementary
322 if (af2.getViewport().isNucleotide())
324 // top view, then bottom
325 cra_views2.add(af2.getViewport().getAlignPanel());
326 cra_views2.add(((jalview.gui.AlignViewport) af2
327 .getViewport().getCodingComplement())
333 // bottom view, then top
334 cra_views2.add(((jalview.gui.AlignViewport) af2
335 .getViewport().getCodingComplement())
337 cra_views2.add(af2.getViewport().getAlignPanel());
339 Assert.assertEquals(cra_views2.size(), 2);
340 Assert.assertNotNull(cra_views2.get(0));
341 Assert.assertNotNull(cra_views2.get(1));
344 for (AlignmentViewPanel nextavp : cra_views2)
346 nextnextxref = nextxref
347 + " -> " + xrefdb + "{" + q++ + "}";
349 // verify references for this panel
350 AlignmentTest.assertAlignmentDatasetRefs(
351 nextavp.getAlignment(), "" + "Pass (" + pass1
352 + "," + pass2 + "): For "
353 + nextnextxref + ":");
354 AlignmentTest.assertDatasetIsNormalised(
355 nextavp.getAlignment(), "" + "Pass (" + pass1
356 + "," + pass2 + "): For "
357 + nextnextxref + ":");
359 stringify(dbtoviewBit, savedProjects, nextnextxref,
361 keyseq.add(nextnextxref);
363 } // end of loop around showing all xrefdb for crossrf2
365 } // end of loop around all viewpanels from crossrf1
366 } while (pass2 == 2 && pass3++ < 2);
367 // fetchdb->crossref1->crossref-2->verify for xrefs we
368 // either loop twice when pass2=0, or just once when pass2=1
369 // (recovered project from previous crossref)
371 } // end of loop over db-xrefs for crossref-2
373 // fetchdb-->crossref1
374 // for each xref we try to retrieve xref, store and verify when
375 // pass1=0, or just retrieve and verify when pass1=1
376 } while (pass1 == 1 && pass2++ < 2);
379 // loop twice: first, do the retrieve, second recover from saved project
381 // increment pass counters, so we repeat traversal starting from the
382 // oldest saved project first.
385 // verify stored projects for first set of cross references
387 // and verify cross-references retrieved from stored projects
396 // verify stored projects for second set of cross references
398 // and verify cross-references retrievable from those stored projects.
404 if (failedXrefMenuItems.size() > 0)
406 for (String s : failedXrefMenuItems)
408 System.err.println(s);
410 Assert.fail("Faulty xref menu (" + failedXrefMenuItems.size()
413 if (failedProjectRecoveries.size() > 0)
416 for (String s : failedProjectRecoveries)
418 System.err.println(s);
420 Assert.fail("Didn't recover projects for some retrievals (did they retrieve ?) ("
421 + failedProjectRecoveries.size() + " counts)");
423 if (failedDBRetr.size() > 0)
425 for (String s : failedProjectRecoveries)
427 System.err.println(s);
429 Assert.fail("Didn't retrieve some db refs for checking cross-refs ("
430 + failedDBRetr.size() + " counts)");
434 private void assertProtein(AlignmentViewPanel alignmentViewPanel,
437 assertType(true, alignmentViewPanel, message);
440 private void assertNucleotide(AlignmentViewPanel alignmentViewPanel,
443 assertType(false, alignmentViewPanel, message);
446 private void assertType(boolean expectProtein,
447 AlignmentViewPanel alignmentViewPanel, String message)
449 List<SequenceI> nonType = new ArrayList<SequenceI>();
450 for (SequenceI sq : alignmentViewPanel.getAlignViewport()
454 if (sq.isProtein() != expectProtein)
459 if (nonType.size() > 0)
461 Assert.fail(message + " [ "
462 + (expectProtein ? "nucleotides were " : "proteins were ")
469 * first time called, record strings derived from alignment and
470 * alignedcodonframes, and save view to a project file. Second time called,
471 * compare strings to existing ones. org.testng.Assert.assertTrue on
475 * map between xrefpath and view string
476 * @param savedProjects
477 * - map from xrefpath to saved project filename (createTempFile)
479 * - xrefpath - unique ID for this context (composed of sequence of
480 * db-fetch/cross-ref actions preceeding state)
482 * - viewpanel to store (for viewpanels in splitframe, the same
483 * project should be written for both panels, only one needs
484 * recovering for comparison on the next stringify call, but each
485 * viewpanel needs to be called with a distinct xrefpath to ensure
486 * each one's strings are compared)
488 private void stringify(HashMap<String, String> dbtoviewBit,
489 HashMap<String, File> savedProjects, String xrefpath,
490 AlignmentViewPanel avp)
492 if (savedProjects != null)
494 if (savedProjects.get(xrefpath) == null)
496 // write a project file for this view. On the second pass, this will be
497 // recovered and cross-references verified
500 File prfile = File.createTempFile("crossRefTest", ".jvp");
501 AlignFrame af = Desktop.getAlignFrameFor(avp.getAlignViewport());
502 new Jalview2XML(false).saveAlignment(af, prfile.toString(),
504 System.out.println("Written view from '" + xrefpath + "' as '"
505 + prfile.getAbsolutePath() + "'");
506 savedProjects.put(xrefpath, prfile);
507 } catch (IOException q)
509 Assert.fail("Unexpected IO Exception", q);
514 System.out.println("Stringify check on view from '" + xrefpath
515 + "' [ possibly retrieved from '"
516 + savedProjects.get(xrefpath).getAbsolutePath() + "' ]");
521 StringBuilder sbr = new StringBuilder();
522 sbr.append(avp.getAlignment().toString());
524 sbr.append("<End of alignment>");
526 sbr.append(avp.getAlignment().getDataset());
528 sbr.append("<End of dataset>");
531 if (avp.getAlignment().getCodonFrames() != null)
533 for (AlignedCodonFrame ac : avp.getAlignment().getCodonFrames())
535 sbr.append("<AlignedCodonFrame " + p++ + ">");
537 sbr.append(ac.toString());
541 String dbt = dbtoviewBit.get(xrefpath);
544 dbtoviewBit.put(xrefpath, sbr.toString());
548 Assert.assertEquals(sbr.toString(), dbt, "stringify mismatch for "