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.
21 package jalview.analysis;
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
25 import static org.testng.AssertJUnit.assertTrue;
27 import jalview.datamodel.AlignmentAnnotation;
28 import jalview.datamodel.AlignmentI;
29 import jalview.datamodel.Annotation;
30 import jalview.datamodel.SequenceI;
31 import jalview.io.AppletFormatAdapter;
33 import java.io.IOException;
34 import java.util.ArrayList;
35 import java.util.BitSet;
36 import java.util.Collection;
37 import java.util.HashMap;
38 import java.util.List;
41 import org.testng.annotations.BeforeMethod;
42 import org.testng.annotations.Test;
44 public class AlignmentAnnotationUtilsTest
46 // 4 sequences x 13 positions
47 final static String EOL = "\n";
50 final static String TEST_DATA =
51 ">FER_CAPAA Ferredoxin" + EOL +
52 "TIETHKEAELVG-" + EOL +
53 ">FER_CAPAN Ferredoxin, chloroplast precursor" + EOL +
54 "TIETHKEAELVG-" + EOL +
55 ">FER1_SOLLC Ferredoxin-1, chloroplast precursor" + EOL +
56 "TIETHKEEELTA-" + EOL +
57 ">Q93XJ9_SOLTU Ferredoxin I precursor" + EOL +
58 "TIETHKEEELTA-" + EOL;
61 private static final int SEQ_ANN_COUNT = 12;
63 private AlignmentI alignment;
66 * Test method that converts a (possibly null) array to a list.
68 @Test(groups = { "Functional" })
69 public void testAsList()
72 Collection<AlignmentAnnotation> c1 = AlignmentAnnotationUtils
74 assertTrue(c1.isEmpty());
77 AlignmentAnnotation[] anns = new AlignmentAnnotation[0];
78 c1 = AlignmentAnnotationUtils.asList(anns);
79 assertTrue(c1.isEmpty());
82 anns = new AlignmentAnnotation[2];
83 anns[0] = new AlignmentAnnotation("label0", "desc0", 0.0f);
84 anns[1] = new AlignmentAnnotation("label1", "desc1", 1.0f);
85 c1 = AlignmentAnnotationUtils.asList(anns);
86 assertEquals(2, c1.size());
87 assertTrue(c1.contains(anns[0]));
88 assertTrue(c1.contains(anns[1]));
92 * This output is not part of the test but may help make sense of it...
97 protected void consoleDebug(Map<String, List<List<String>>> shownTypes,
98 Map<String, List<List<String>>> hiddenTypes)
100 for (String calcId : shownTypes.keySet())
102 System.out.println("Visible annotation types for calcId=" + calcId);
103 for (List<String> type : shownTypes.get(calcId))
105 System.out.println(" " + type);
108 for (String calcId : hiddenTypes.keySet())
110 System.out.println("Hidden annotation types for calcId=" + calcId);
111 for (List<String> type : hiddenTypes.get(calcId))
113 System.out.println(" " + type);
119 * Add a sequence group to the alignment with the specified sequences (base 0)
125 private List<SequenceI> selectSequences(int... selected)
127 List<SequenceI> result = new ArrayList<SequenceI>();
128 SequenceI[] seqs = alignment.getSequencesArray();
129 for (int i : selected)
137 * Load the test alignment and generate annotations on it
139 * @throws IOException
141 @BeforeMethod(alwaysRun = true)
142 public void setUp() throws IOException
144 alignment = new jalview.io.FormatAdapter().readFile(TEST_DATA,
145 AppletFormatAdapter.PASTE, "FASTA");
147 AlignmentAnnotation[] anns = new AlignmentAnnotation[SEQ_ANN_COUNT];
148 for (int i = 0; i < anns.length; i++)
151 * Use the constructor for a positional annotation (with an Annotation
154 anns[i] = new AlignmentAnnotation("Label" + i, "Desc " + i,
155 new Annotation[] {});
156 anns[i].setCalcId("CalcId" + i);
157 anns[i].visible = true;
158 alignment.addAnnotation(anns[i]);
163 * Test a mixture of show/hidden annotations in/outside selection group.
165 @Test(groups = { "Functional" })
166 public void testGetShownHiddenTypes_forSelectionGroup()
168 Map<String, List<List<String>>> shownTypes = new HashMap<String, List<List<String>>>();
169 Map<String, List<List<String>>> hiddenTypes = new HashMap<String, List<List<String>>>();
170 AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
171 SequenceI[] seqs = alignment.getSequencesArray();
174 * Configure annotation properties for test
176 // not in selection group (should be ignored):
177 // hidden annotation Label4 not in selection group
178 anns[4].sequenceRef = seqs[2];
179 anns[4].visible = false;
180 anns[7].sequenceRef = seqs[1];
181 anns[7].visible = true;
184 * in selection group, hidden:
186 anns[2].sequenceRef = seqs[3]; // CalcId2/Label2
187 anns[2].visible = false;
188 anns[3].sequenceRef = seqs[3]; // CalcId3/Label2
189 anns[3].visible = false;
190 anns[3].label = "Label2";
191 anns[4].sequenceRef = seqs[3]; // CalcId2/Label3
192 anns[4].visible = false;
193 anns[4].label = "Label3";
194 anns[4].setCalcId("CalcId2");
195 anns[8].sequenceRef = seqs[0]; // CalcId9/Label9
196 anns[8].visible = false;
197 anns[8].label = "Label9";
198 anns[8].setCalcId("CalcId9");
200 * in selection group, visible
202 anns[6].sequenceRef = seqs[0]; // CalcId6/Label6
203 anns[6].visible = true;
204 anns[9].sequenceRef = seqs[3]; // CalcId9/Label9
205 anns[9].visible = true;
207 List<SequenceI> selected = selectSequences(0, 3);
208 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
209 AlignmentAnnotationUtils.asList(anns), selected);
211 // check results; note CalcId9/Label9 is both hidden and shown (for
212 // different sequences) so should be in both
213 // shown: CalcId6/Label6 and CalcId9/Label9
214 assertEquals(2, shownTypes.size());
215 assertEquals(1, shownTypes.get("CalcId6").size());
216 assertEquals(1, shownTypes.get("CalcId6").get(0).size());
217 assertEquals("Label6", shownTypes.get("CalcId6").get(0).get(0));
218 assertEquals(1, shownTypes.get("CalcId9").size());
219 assertEquals(1, shownTypes.get("CalcId9").get(0).size());
220 assertEquals("Label9", shownTypes.get("CalcId9").get(0).get(0));
222 // hidden: CalcId2/Label2, CalcId2/Label3, CalcId3/Label2, CalcId9/Label9
223 assertEquals(3, hiddenTypes.size());
224 assertEquals(2, hiddenTypes.get("CalcId2").size());
225 assertEquals(1, hiddenTypes.get("CalcId2").get(0).size());
226 assertEquals("Label2", hiddenTypes.get("CalcId2").get(0).get(0));
227 assertEquals(1, hiddenTypes.get("CalcId2").get(1).size());
228 assertEquals("Label3", hiddenTypes.get("CalcId2").get(1).get(0));
229 assertEquals(1, hiddenTypes.get("CalcId3").size());
230 assertEquals(1, hiddenTypes.get("CalcId3").get(0).size());
231 assertEquals("Label2", hiddenTypes.get("CalcId3").get(0).get(0));
232 assertEquals(1, hiddenTypes.get("CalcId9").size());
233 assertEquals(1, hiddenTypes.get("CalcId9").get(0).size());
234 assertEquals("Label9", hiddenTypes.get("CalcId9").get(0).get(0));
236 consoleDebug(shownTypes, hiddenTypes);
240 * Test case where there are 'grouped' annotations, visible and hidden, within
241 * and without the selection group.
243 @Test(groups = { "Functional" })
244 public void testGetShownHiddenTypes_withGraphGroups()
246 final int GROUP_3 = 3;
247 final int GROUP_4 = 4;
248 final int GROUP_5 = 5;
249 final int GROUP_6 = 6;
251 Map<String, List<List<String>>> shownTypes = new HashMap<String, List<List<String>>>();
252 Map<String, List<List<String>>> hiddenTypes = new HashMap<String, List<List<String>>>();
253 AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
254 SequenceI[] seqs = alignment.getSequencesArray();
257 * Annotations for selection group and graph group
259 * Hidden annotations Label2, Label3, in (hidden) group 5
261 anns[2].sequenceRef = seqs[3];
262 anns[2].visible = false;
263 anns[2].graph = AlignmentAnnotation.LINE_GRAPH;
264 anns[2].graphGroup = GROUP_5; // not a visible group
265 anns[3].sequenceRef = seqs[0];
266 anns[3].visible = false;
267 anns[3].graph = AlignmentAnnotation.LINE_GRAPH;
268 anns[3].graphGroup = GROUP_5;
269 // need to ensure annotations have the same calcId as well
270 anns[3].setCalcId("CalcId2");
271 // annotations for a different hidden group generating the same group label
272 anns[10].sequenceRef = seqs[0];
273 anns[10].visible = false;
274 anns[10].graph = AlignmentAnnotation.LINE_GRAPH;
275 anns[10].graphGroup = GROUP_3;
276 anns[10].label = "Label3";
277 anns[10].setCalcId("CalcId2");
278 anns[11].sequenceRef = seqs[3];
279 anns[11].visible = false;
280 anns[11].graph = AlignmentAnnotation.LINE_GRAPH;
281 anns[11].graphGroup = GROUP_3;
282 anns[11].label = "Label2";
283 anns[11].setCalcId("CalcId2");
285 // annotations Label1 (hidden), Label5 (visible) in group 6 (visible)
286 anns[1].sequenceRef = seqs[3];
287 // being in a visible group should take precedence over this visibility
288 anns[1].visible = false;
289 anns[1].graph = AlignmentAnnotation.LINE_GRAPH;
290 anns[1].graphGroup = GROUP_6;
291 anns[5].sequenceRef = seqs[0];
292 anns[5].visible = true;
293 anns[5].graph = AlignmentAnnotation.LINE_GRAPH;
294 anns[5].graphGroup = GROUP_6;
295 anns[5].setCalcId("CalcId1");
297 * Annotations 0 and 4 are visible, for a different CalcId and graph group.
298 * They produce the same label as annotations 1 and 5, which should not be
299 * duplicated in the results. This case corresponds to (e.g.) many
300 * occurrences of an IUPred Short/Long annotation group, one per sequence.
302 anns[4].sequenceRef = seqs[0];
303 anns[4].visible = false;
304 anns[4].graph = AlignmentAnnotation.LINE_GRAPH;
305 anns[4].graphGroup = GROUP_4;
306 anns[4].label = "Label1";
307 anns[4].setCalcId("CalcId1");
308 anns[0].sequenceRef = seqs[0];
309 anns[0].visible = true;
310 anns[0].graph = AlignmentAnnotation.LINE_GRAPH;
311 anns[0].graphGroup = GROUP_4;
312 anns[0].label = "Label5";
313 anns[0].setCalcId("CalcId1");
316 * Annotations outwith selection group - should be ignored.
318 // Hidden grouped annotations
319 anns[6].sequenceRef = seqs[2];
320 anns[6].visible = false;
321 anns[6].graph = AlignmentAnnotation.LINE_GRAPH;
322 anns[6].graphGroup = GROUP_4;
323 anns[8].sequenceRef = seqs[1];
324 anns[8].visible = false;
325 anns[8].graph = AlignmentAnnotation.LINE_GRAPH;
326 anns[8].graphGroup = GROUP_4;
328 // visible grouped annotations Label7, Label9
329 anns[7].sequenceRef = seqs[2];
330 anns[7].visible = true;
331 anns[7].graph = AlignmentAnnotation.LINE_GRAPH;
332 anns[7].graphGroup = GROUP_4;
333 anns[9].sequenceRef = seqs[1];
334 anns[9].visible = true;
335 anns[9].graph = AlignmentAnnotation.LINE_GRAPH;
336 anns[9].graphGroup = GROUP_4;
339 * Generate annotations[] arrays to match aligned columns
341 // adjustForAlignment(anns);
343 List<SequenceI> selected = selectSequences(0, 3);
344 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
345 AlignmentAnnotationUtils.asList(anns), selected);
347 consoleDebug(shownTypes, hiddenTypes);
349 // CalcId1 / Label1, Label5 (only) should be 'shown', once, as a compound
351 assertEquals(1, shownTypes.size());
352 assertEquals(1, shownTypes.get("CalcId1").size());
353 assertEquals(2, shownTypes.get("CalcId1").get(0).size());
354 assertEquals("Label1", shownTypes.get("CalcId1").get(0).get(0));
355 assertEquals("Label5", shownTypes.get("CalcId1").get(0).get(1));
357 // CalcId2 / Label2, Label3 (only) should be 'hidden'
358 assertEquals(1, hiddenTypes.size());
359 assertEquals(1, hiddenTypes.get("CalcId2").size());
360 assertEquals(2, hiddenTypes.get("CalcId2").get(0).size());
361 assertEquals("Label2", hiddenTypes.get("CalcId2").get(0).get(0));
362 assertEquals("Label3", hiddenTypes.get("CalcId2").get(0).get(1));
366 * Test method that determines visible graph groups.
368 @Test(groups = { "Functional" })
369 public void testGetVisibleGraphGroups()
371 AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
373 * a bar graph group is not included
375 anns[0].graph = AlignmentAnnotation.BAR_GRAPH;
376 anns[0].graphGroup = 1;
377 anns[0].visible = true;
380 * a line graph group is included as long as one of its members is visible
382 anns[1].graph = AlignmentAnnotation.LINE_GRAPH;
383 anns[1].graphGroup = 5;
384 anns[1].visible = false;
385 anns[2].graph = AlignmentAnnotation.LINE_GRAPH;
386 anns[2].graphGroup = 5;
387 anns[2].visible = true;
390 * a line graph group with no visible rows is not included
392 anns[3].graph = AlignmentAnnotation.LINE_GRAPH;
393 anns[3].graphGroup = 3;
394 anns[3].visible = false;
396 // a visible line graph with no graph group is not included
397 anns[4].graph = AlignmentAnnotation.LINE_GRAPH;
398 anns[4].graphGroup = -1;
399 anns[4].visible = true;
401 BitSet result = AlignmentAnnotationUtils
402 .getVisibleLineGraphGroups(AlignmentAnnotationUtils
404 assertTrue(result.get(5));
405 assertFalse(result.get(0));
406 assertFalse(result.get(1));
407 assertFalse(result.get(2));
408 assertFalse(result.get(3));
412 * Test for case where no sequence is selected. Shouldn't normally arise but
413 * check it handles it gracefully.
415 @Test(groups = { "Functional" })
416 public void testGetShownHiddenTypes_noSequenceSelected()
418 Map<String, List<List<String>>> shownTypes = new HashMap<String, List<List<String>>>();
419 Map<String, List<List<String>>> hiddenTypes = new HashMap<String, List<List<String>>>();
420 AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
421 // selected sequences null
422 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
423 AlignmentAnnotationUtils.asList(anns), null);
424 assertTrue(shownTypes.isEmpty());
425 assertTrue(hiddenTypes.isEmpty());
427 List<SequenceI> sequences = new ArrayList<SequenceI>();
428 // selected sequences empty list
429 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
430 AlignmentAnnotationUtils.asList(anns), sequences);
431 assertTrue(shownTypes.isEmpty());
432 assertTrue(hiddenTypes.isEmpty());