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
55 List<String> failedXrefMenuItems = new ArrayList<String>();
56 List<String> failedProjectRecoveries = new ArrayList<String>();
58 // for every set of db queries
60 // verify presence of expected xrefs
61 // show xrefs - verify expected type of frame is shown for each xref
63 // - verify original -> xref -> xref(original) recovers frame containing at
64 // least the first retrieved sequence
67 // 2. individual frames
68 // 3. load each one back and verify
69 // . aligned sequences (.toString() )
70 // . xrefs (.toString() )
74 HashMap<String, String> dbtoviewBit = new HashMap<String, String>();
75 List<String> keyseq = new ArrayList<String>();
76 HashMap<String, File> savedProjects = new HashMap<String, File>();
78 for (String[] did : new String[][] { { "UNIPROT", "P01731" } })
80 // pass counters - 0 - first pass, 1 means retrieve project rather than
82 int pass1 = 0, pass2 = 0, pass3 = 0;
83 // each do loop performs two iterations in the first outer loop pass, but
84 // only performs one iteration on the second outer loop
85 // ie. pass 1 = 0 {pass 2= 0 { pass 3 = 0,1 }, pass 2=1 { pass 3 = 0 }}, 1
86 // { pass 2 = 0 { pass 3 = 0 } }
89 String first = did[0] + " " + did[1];
95 List<String> ptypes = null;
102 af = jalview.gui.SequenceFetcher.fetchAndShow(did[0], did[1])
104 Assert.assertTrue(af != null, "Didn't retrieve " + first);
106 // verify references for retrieved data
107 AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
108 .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
109 + pass3 + "): Fetch " + first + ":");
110 dna = af.getViewport().getAlignment().isNucleotide();
111 retral = af.getViewport().getAlignment();
112 dataset = retral.getDataset();
113 seqs = retral.getSequencesArray();
118 Desktop.instance.closeAll_actionPerformed(null);
119 // recover stored project
120 af = new FileLoader(false).LoadFileWaitTillLoaded(savedProjects
121 .get(first).toString(), FormatAdapter.FILE);
122 System.out.println("Recovered view for '" + first + "' from '"
123 + savedProjects.get(first).toString() + "'");
124 dna = af.getViewport().getAlignment().isNucleotide();
125 retral = af.getViewport().getAlignment();
126 dataset = retral.getDataset();
127 seqs = retral.getSequencesArray();
129 // verify references for recovered data
130 AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
131 .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
132 + pass3 + "): Recover " + first + ":");
136 // store project on first pass, compare next pass
137 stringify(dbtoviewBit, savedProjects, first, af.alignPanel);
139 ptypes = (seqs == null || seqs.length == 0) ? null : new CrossRef(
140 seqs, dataset).findXrefSourcesForSequences(dna);
142 // start of pass2: retrieve each cross-ref for fetched or restored
144 do // first cross ref and recover crossref loop
147 for (String db : ptypes)
149 // counter for splitframe views retrieved via crossref
151 // build next key so we an retrieve all views
152 String nextxref = first + " -> " + db + "{" + firstcr_ap + "}";
153 // perform crossref action, or retrieve stored project
154 List<AlignmentViewPanel> cra_views = new ArrayList<AlignmentViewPanel>();
155 CrossRefAction cra = null;
158 { // retrieve and show cross-refs in this thread
159 cra = new CrossRefAction(af, seqs, dna, db);
161 if (cra.getXrefViews().size() == 0)
163 failedXrefMenuItems.add("No crossrefs retrieved for "
164 + first + " -> " + db);
167 cra_views = cra.getXrefViews();
168 assertNucleotide(cra_views.get(0),
169 "Nucleotide panel included proteins for " + first
171 assertProtein(cra_views.get(1),
172 "Protein panel included nucleotides for " + first
177 Desktop.instance.closeAll_actionPerformed(null);
179 // recover stored project
180 File storedProject = savedProjects.get(nextxref);
181 if (storedProject == null)
183 failedProjectRecoveries.add("Failed to store a view for '"
188 // recover stored project
189 AlignFrame af2 = new FileLoader(false)
190 .LoadFileWaitTillLoaded(savedProjects.get(nextxref)
191 .toString(), FormatAdapter.FILE);
192 System.out.println("Recovered view for '" + nextxref
193 + "' from '" + savedProjects.get(nextxref).toString()
195 // gymnastics to recover the alignPanel/Complementary alignPanel
196 if (af2.getViewport().isNucleotide())
198 // top view, then bottom
199 cra_views.add(af2.getViewport().getAlignPanel());
200 cra_views.add(((jalview.gui.AlignViewport) af2
201 .getViewport().getCodingComplement())
207 // bottom view, then top
208 cra_views.add(((jalview.gui.AlignViewport) af2
209 .getViewport().getCodingComplement())
211 cra_views.add(af2.getViewport().getAlignPanel());
215 HashMap<String, List<String>> xrptypes = new HashMap<String, List<String>>();
216 // first save/verify views.
217 for (AlignmentViewPanel avp : cra_views)
219 nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
220 // verify references for this panel
221 AlignmentTest.assertAlignmentDatasetRefs(avp.getAlignment(),
222 "Pass (" + pass1 + "," + pass2 + "," + pass3
223 + "): before start of pass3: " + nextxref
226 SequenceI[] xrseqs = avp.getAlignment().getSequencesArray();
228 List<String> _xrptypes = (seqs == null || seqs.length == 0) ? null
229 : new CrossRef(xrseqs, dataset)
230 .findXrefSourcesForSequences(avp
231 .getAlignViewport().isNucleotide());
233 stringify(dbtoviewBit, savedProjects, nextxref, avp);
234 xrptypes.put(nextxref, _xrptypes);
238 // now do the second xref pass starting from either saved or just
239 // recovered split pane, in sequence
240 do // retrieve second set of cross refs or recover and verify
243 for (AlignmentViewPanel avp : cra_views)
245 nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
246 for (String xrefdb : xrptypes.get(nextxref))
248 List<AlignmentViewPanel> cra_views2 = new ArrayList<AlignmentViewPanel>();
250 String nextnextxref = nextxref
251 + " -> " + xrefdb + "{" + q + "}";
256 SequenceI[] xrseqs = avp.getAlignment()
257 .getSequencesArray();
258 AlignFrame nextaf = Desktop.getAlignFrameFor(avp
259 .getAlignViewport());
261 cra = new CrossRefAction(nextaf, xrseqs, avp
262 .getAlignViewport().isNucleotide(), xrefdb);
264 if (cra.getXrefViews().size() == 0)
267 .add("No crossrefs retrieved for '"
268 + nextxref + "' to " + xrefdb + " via '"
269 + nextaf.getTitle() + "'");
272 cra_views2 = cra.getXrefViews();
273 assertNucleotide(cra_views2.get(0),
274 "Nucleotide panel included proteins for '"
275 + nextxref + "' to " + xrefdb
276 + " via '" + nextaf.getTitle() + "'");
277 assertProtein(cra_views2.get(1),
278 "Protein panel included nucleotides for '"
279 + nextxref + "' to " + xrefdb
280 + " via '" + nextaf.getTitle() + "'");
285 Desktop.instance.closeAll_actionPerformed(null);
286 // recover stored project
287 File storedProject = savedProjects.get(nextnextxref);
288 if (storedProject == null)
290 failedProjectRecoveries
291 .add("Failed to store a view for '"
292 + nextnextxref + "'");
295 AlignFrame af2 = new FileLoader(false)
296 .LoadFileWaitTillLoaded(
297 savedProjects.get(nextnextxref)
298 .toString(), FormatAdapter.FILE);
299 System.out.println("Recovered view for '"
300 + nextnextxref + "' from '"
301 + savedProjects.get(nextnextxref).toString()
303 // gymnastics to recover the alignPanel/Complementary
305 if (af2.getViewport().isNucleotide())
307 // top view, then bottom
308 cra_views2.add(af2.getViewport().getAlignPanel());
309 cra_views2.add(((jalview.gui.AlignViewport) af2
310 .getViewport().getCodingComplement())
316 // bottom view, then top
317 cra_views2.add(((jalview.gui.AlignViewport) af2
318 .getViewport().getCodingComplement())
320 cra_views2.add(af2.getViewport().getAlignPanel());
322 Assert.assertEquals(cra_views2.size(), 2);
323 Assert.assertNotNull(cra_views2.get(0));
324 Assert.assertNotNull(cra_views2.get(1));
327 for (AlignmentViewPanel nextavp : cra_views2)
329 nextnextxref = nextxref
330 + " -> " + xrefdb + "{" + q++ + "}";
332 // verify references for this panel
333 AlignmentTest.assertAlignmentDatasetRefs(
334 nextavp.getAlignment(), "" + "Pass (" + pass1
335 + "," + pass2 + "): For "
336 + nextnextxref + ":");
338 stringify(dbtoviewBit, savedProjects, nextnextxref,
340 keyseq.add(nextnextxref);
342 } // end of loop around showing all xrefdb for crossrf2
344 } // end of loop around all viewpanels from crossrf1
345 } while (pass2 == 2 && pass3++ < 2);
346 // fetchdb->crossref1->crossref-2->verify for xrefs we
347 // either loop twice when pass2=0, or just once when pass2=1
348 // (recovered project from previous crossref)
350 } // end of loop over db-xrefs for crossref-2
352 // fetchdb-->crossref1
353 // for each xref we try to retrieve xref, store and verify when
354 // pass1=0, or just retrieve and verify when pass1=1
355 } while (pass1 == 1 && pass2++ < 2);
358 // loop twice: first, do the retrieve, second recover from saved project
360 // increment pass counters, so we repeat traversal starting from the
361 // oldest saved project first.
364 // verify stored projects for first set of cross references
366 // and verify cross-references retrieved from stored projects
375 // verify stored projects for second set of cross references
377 // and verify cross-references retrievable from those stored projects.
383 if (failedXrefMenuItems.size() > 0)
385 for (String s : failedXrefMenuItems)
387 System.err.println(s);
389 Assert.fail("Faulty xref menu (" + failedXrefMenuItems.size()
392 if (failedProjectRecoveries.size() > 0)
395 for (String s : failedProjectRecoveries)
397 System.err.println(s);
399 Assert.fail("Didn't recover projects for some retrievals (did they retrieve ?) ("
400 + failedProjectRecoveries.size() + " counts)");
404 private void assertProtein(AlignmentViewPanel alignmentViewPanel,
407 assertType(true, alignmentViewPanel, message);
410 private void assertNucleotide(AlignmentViewPanel alignmentViewPanel,
413 assertType(false, alignmentViewPanel, message);
416 private void assertType(boolean expectProtein,
417 AlignmentViewPanel alignmentViewPanel, String message)
419 List<SequenceI> nonType = new ArrayList<SequenceI>();
420 for (SequenceI sq : alignmentViewPanel.getAlignViewport()
424 if (sq.isProtein() != expectProtein)
429 if (nonType.size() > 0)
431 Assert.fail(message + " [ "
432 + (expectProtein ? "nucleotides were " : "proteins were ")
439 * first time called, record strings derived from alignment and
440 * alignedcodonframes, and save view to a project file. Second time called,
441 * compare strings to existing ones. org.testng.Assert.assertTrue on
445 * map between xrefpath and view string
446 * @param savedProjects
447 * - map from xrefpath to saved project filename (createTempFile)
449 * - xrefpath - unique ID for this context (composed of sequence of
450 * db-fetch/cross-ref actions preceeding state)
452 * - viewpanel to store (for viewpanels in splitframe, the same
453 * project should be written for both panels, only one needs
454 * recovering for comparison on the next stringify call, but each
455 * viewpanel needs to be called with a distinct xrefpath to ensure
456 * each one's strings are compared)
458 private void stringify(HashMap<String, String> dbtoviewBit,
459 HashMap<String, File> savedProjects, String xrefpath,
460 AlignmentViewPanel avp)
462 if (savedProjects != null)
464 if (savedProjects.get(xrefpath) == null)
466 // write a project file for this view. On the second pass, this will be
467 // recovered and cross-references verified
470 File prfile = File.createTempFile("crossRefTest", ".jvp");
471 AlignFrame af = Desktop.getAlignFrameFor(avp.getAlignViewport());
472 new Jalview2XML(false).saveAlignment(af, prfile.toString(),
474 System.out.println("Written view from '" + xrefpath + "' as '"
475 + prfile.getAbsolutePath() + "'");
476 savedProjects.put(xrefpath, prfile);
477 } catch (IOException q)
479 Assert.fail("Unexpected IO Exception", q);
484 System.out.println("Stringify check on view from '" + xrefpath
485 + "' [ possibly retrieved from '"
486 + savedProjects.get(xrefpath).getAbsolutePath() + "' ]");
491 StringBuilder sbr = new StringBuilder();
492 sbr.append(avp.getAlignment().toString());
494 sbr.append("<End of alignment>");
496 sbr.append(avp.getAlignment().getDataset());
498 sbr.append("<End of dataset>");
501 if (avp.getAlignment().getCodonFrames() != null)
503 for (AlignedCodonFrame ac : avp.getAlignment().getCodonFrames())
505 sbr.append("<AlignedCodonFrame " + p++ + ">");
507 sbr.append(ac.toString());
511 String dbt = dbtoviewBit.get(xrefpath);
514 dbtoviewBit.put(xrefpath, sbr.toString());
518 Assert.assertEquals(sbr.toString(), dbt, "stringify mismatch for "