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 static org.testng.AssertJUnit.assertTrue;
25 import jalview.analysis.CrossRef;
26 import jalview.api.AlignmentViewPanel;
27 import jalview.datamodel.AlignedCodonFrame;
28 import jalview.datamodel.AlignmentI;
29 import jalview.datamodel.SequenceI;
30 import jalview.gui.AlignFrame;
31 import jalview.gui.CrossRefAction;
32 import jalview.gui.Desktop;
33 import jalview.gui.Jalview2XML;
36 import java.io.IOException;
37 import java.util.ArrayList;
38 import java.util.HashMap;
39 import java.util.IdentityHashMap;
40 import java.util.List;
42 import org.testng.Assert;
43 import org.testng.annotations.Test;
45 @Test(singleThreaded = true)
46 public class CrossRef2xmlTests extends Jalview2xmlBase
50 * test store and recovery of expanded views
54 @Test(groups = { "Operational" }, enabled = true)
55 public void testRetrieveAndShowCrossref() throws Exception
57 // for every set of db queries
59 // verify presence of expected xrefs
60 // show xrefs - verify expected type of frame is shown for each xref
62 // - verify original -> xref -> xref(original) recovers frame containing at
63 // least the first retrieved sequence
66 // 2. individual frames
67 // 3. load each one back and verify
68 // . aligned sequences (.toString() )
69 // . xrefs (.toString() )
73 HashMap<String, String> dbtoviewBit = new HashMap<String, String>();
74 List<String> keyseq = new ArrayList<String>();
75 HashMap<String, File> savedProjects = new HashMap<String, File>();
77 for (String[] did : new String[][] { { "UNIPROT", "P01731" } })
79 // pass counters - 0 - first pass, 1 means retrieve project rather than
81 int pass1 = 0, pass2 = 0, pass3 = 0;
82 // each do loop performs two iterations in the first outer loop pass, but
83 // only performs one iteration on the second outer loop
84 // ie. pass 1 = 0 {pass 2= 0 { pass 3 = 0,1 }, pass 2=1 { pass 3 = 0 }}, 1
85 // { pass 2 = 0 { pass 3 = 0 } }
88 String first = did[0] + " " + did[1];
96 af = jalview.gui.SequenceFetcher.fetchAndShow(did[0], did[1])
98 assertTrue("Didn't retrieve " + first, af != null);
99 // store project to recover on next pass
100 stringify(dbtoviewBit, savedProjects, first, af.alignPanel);
104 Desktop.instance.closeAll_actionPerformed(null);
105 // recover stored project
106 af = new FileLoader(false).LoadFileWaitTillLoaded(savedProjects
107 .get(first).toString(), FormatAdapter.FILE);
110 boolean dna = af.getViewport().getAlignment().isNucleotide();
111 AlignmentI retral = af.getViewport().getAlignment();
112 AlignmentI dataset = retral.getDataset();
113 SequenceI[] seqs = retral.getSequencesArray();
114 List<String> ptypes = (seqs == null || seqs.length == 0) ? null
115 : new CrossRef(seqs, dataset)
116 .findXrefSourcesForSequences(dna);
119 * map between a view, and views generated after retrieving xrefs
121 IdentityHashMap<AlignmentViewPanel, List<AlignmentViewPanel>> viewxrefview = new IdentityHashMap<AlignmentViewPanel, List<AlignmentViewPanel>>();
123 * map between a particular view and it's originating dbref path
125 IdentityHashMap<AlignmentViewPanel, String> viewsourcedb = new IdentityHashMap<AlignmentViewPanel, String>();
127 viewsourcedb.put(af.alignPanel, first);
128 for (String db : ptypes)
131 do // second cross ref and recover crossref loop
133 // counter for splitframe views retrieved via crossref
135 // build next key so we an retrieve all views
136 String nextxref = first + " -> " + db + "{" + p + "}";
137 // perform crossref action, or retrieve stored project
138 List<AlignmentViewPanel> cra_views = new ArrayList<AlignmentViewPanel>();
139 CrossRefAction cra = null;
141 { // retrieve and show cross-refs in this thread
142 cra = new CrossRefAction(af, seqs, dna, db);
144 Assert.assertTrue(cra.getXrefViews().size() > 0,
145 "No crossrefs retrieved for " + db);
146 cra_views = cra.getXrefViews();
147 viewxrefview.put(af.alignPanel, cra.getXrefViews());
151 Desktop.instance.closeAll_actionPerformed(null);
152 // recover stored project
153 AlignFrame af2 = new FileLoader(false)
154 .LoadFileWaitTillLoaded(savedProjects.get(first)
155 .toString(), FormatAdapter.FILE);
156 // gymnastics to recover the alignPanel/Complementary alignPanel
157 if (af2.getViewport().isNucleotide())
159 // top view, then bottom
160 cra_views.add(af2.getViewport().getAlignPanel());
161 cra_views.add(((jalview.gui.AlignViewport) af2
162 .getViewport().getCodingComplement())
168 // bottom view, then top
169 cra_views.add(((jalview.gui.AlignViewport) af2
170 .getViewport().getCodingComplement())
172 cra_views.add(af2.getViewport().getAlignPanel());
176 for (AlignmentViewPanel avp : cra_views)
179 SequenceI[] xrseqs = avp.getAlignment().getSequencesArray();
180 nextxref = first + " -> " + db + "{" + p++ + "}";
182 viewsourcedb.put(avp, nextxref);
183 stringify(dbtoviewBit, savedProjects, nextxref, avp);
184 keyseq.add(nextxref);
186 List<String> xrptypes = (seqs == null || seqs.length == 0) ? null
187 : new CrossRef(xrseqs, dataset)
188 .findXrefSourcesForSequences(avp
189 .getAlignViewport().isNucleotide());
190 for (String xrefdb : xrptypes)
193 do // 3rd cross ref and recover crossref loop
195 List<AlignmentViewPanel> cra_views2 = new ArrayList<AlignmentViewPanel>();
197 String nextnextxref = "{" + p + "}" + nextxref + " -> "
198 + xrefdb + "{" + q + "}";
200 AlignFrame nextaf = Desktop.getAlignFrameFor(avp
201 .getAlignViewport());
205 cra = new CrossRefAction(nextaf, xrseqs, avp
206 .getAlignViewport().isNucleotide(), xrefdb);
208 Assert.assertTrue(cra.getXrefViews().size() > 0,
209 "No crossrefs found for '" + nextxref + "' to "
210 + xrefdb + " via '" + nextaf.getTitle()
212 cra_views2 = cra.getXrefViews();
216 Desktop.instance.closeAll_actionPerformed(null);
217 // recover stored project
218 AlignFrame af2 = new FileLoader(false)
219 .LoadFileWaitTillLoaded(
220 savedProjects.get(nextnextxref)
221 .toString(), FormatAdapter.FILE);
222 // gymnastics to recover the alignPanel/Complementary
224 if (af2.getViewport().isNucleotide())
226 // top view, then bottom
227 cra_views2.add(af2.getViewport().getAlignPanel());
228 cra_views2.add(((jalview.gui.AlignViewport) af2
229 .getViewport().getCodingComplement())
235 // bottom view, then top
236 cra_views2.add(((jalview.gui.AlignViewport) af2
237 .getViewport().getCodingComplement())
239 cra_views2.add(af2.getViewport().getAlignPanel());
241 Assert.assertEquals(cra_views2.size(), 2);
242 Assert.assertNotNull(cra_views2.get(0));
243 Assert.assertNotNull(cra_views2.get(1));
246 for (AlignmentViewPanel nextavp : cra_views2)
248 nextnextxref = "{" + p + "}" + nextxref + " -> "
249 + xrefdb + "{" + q++ + "}";
250 viewsourcedb.put(nextavp, nextnextxref);
251 stringify(dbtoviewBit, savedProjects, nextnextxref,
253 keyseq.add(nextnextxref);
255 } while (pass3++ < 2 && pass2 < 1);
258 } while (pass2++ < 2 && pass1 < 1);
260 } while (++pass1 < 2);
265 * first time called, record strings derived from alignment and
266 * alignedcodonframes, and save view to a project file. Second time called,
267 * compare strings to existing ones. org.testng.Assert.assertTrue on
271 * map between xrefpath and view string
272 * @param savedProjects
273 * - map from xrefpath to saved project filename (createTempFile)
275 * - xrefpath - unique ID for this context (composed of sequence of
276 * db-fetch/cross-ref actions preceeding state)
278 * - viewpanel to store (for viewpanels in splitframe, the same
279 * project should be written for both panels, only one needs
280 * recovering for comparison on the next stringify call, but each
281 * viewpanel needs to be called with a distinct xrefpath to ensure
282 * each one's strings are compared)
284 private void stringify(HashMap<String, String> dbtoviewBit,
285 HashMap<String, File> savedProjects, String xrefpath,
286 AlignmentViewPanel avp)
288 if (savedProjects != null)
290 if (savedProjects.get(xrefpath) == null)
292 // write a project file for this view. On the second pass, this will be
293 // recovered and cross-references verified
296 File prfile = File.createTempFile("crossRefTest", ".jvp");
297 AlignFrame af = Desktop.getAlignFrameFor(avp.getAlignViewport());
298 new Jalview2XML(false).saveAlignment(af, prfile.toString(),
300 System.out.println("Written view from '" + xrefpath + "' as '"
301 + prfile.getAbsolutePath() + "'");
302 savedProjects.put(xrefpath, prfile);
303 } catch (IOException q)
305 Assert.fail("Unexpected IO Exception", q);
310 System.out.println("Stringify check on view from '" + xrefpath
311 + "' [ possibly retrieved from '"
312 + savedProjects.get(xrefpath).getAbsolutePath() + "' ]");
317 StringBuilder sbr = new StringBuilder();
318 sbr.append(avp.getAlignment().toString());
320 sbr.append("<End of alignment>");
322 sbr.append(avp.getAlignment().getDataset());
324 sbr.append("<End of dataset>");
327 if (avp.getAlignment().getCodonFrames() != null)
329 for (AlignedCodonFrame ac : avp.getAlignment().getCodonFrames())
331 sbr.append("<AlignedCodonFrame " + p++ + ">");
333 sbr.append(ac.toString());
337 String dbt = dbtoviewBit.get(xrefpath);
340 dbtoviewBit.put(xrefpath, sbr.toString());
344 Assert.assertEquals(sbr.toString(), dbt, "stringify mismatch for "