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.datamodel;
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertNull;
26 import jalview.analysis.AlignSeq;
27 import jalview.gui.JvOptionPane;
28 import jalview.io.AppletFormatAdapter;
29 import jalview.io.FileFormat;
31 import org.testng.annotations.BeforeClass;
32 import org.testng.annotations.Test;
34 public class AlignmentAnnotationTests
37 @BeforeClass(alwaysRun = true)
38 public void setUpJvOptionPane()
40 JvOptionPane.setInteractiveMode(false);
41 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
44 @Test(groups = { "Functional" })
45 public void testCopyConstructor()
47 SequenceI sq = new Sequence("Foo", "ARAARARARAWEAWEAWRAWEAWE");
49 AlignmentAnnotation alc, alo = sq.getAnnotation()[0];
50 alc = new AlignmentAnnotation(alo);
51 for (String key : alo.getProperties())
53 assertEquals("Property mismatch", alo.getProperty(key),
54 alc.getProperty(key));
59 * create some dummy annotation derived from the sequence
63 public static void createAnnotation(SequenceI sq)
65 Annotation[] al = new Annotation[sq.getLength()];
66 for (int i = 0; i < al.length; i++)
68 al[i] = new Annotation(new Annotation("" + sq.getCharAt(i), "",
69 (char) 0, sq.findPosition(i)));
71 AlignmentAnnotation alan = new AlignmentAnnotation("For "
72 + sq.getName(), "Fake alignment annot", al);
73 // create a sequence mapping for the annotation vector in its current state
74 alan.createSequenceMapping(sq, sq.getStart(), false);
75 alan.setProperty("CreatedBy", "createAnnotation");
76 sq.addAlignmentAnnotation(alan);
80 * use this to test annotation derived from method above as it is transferred
81 * across different sequences derived from same dataset coordinate frame
85 public static void testAnnotTransfer(AlignmentAnnotation ala)
88 "Failed - need annotation created by createAnnotation method",
89 ala.description, "Fake alignment annot");
90 ala.adjustForAlignment();
91 for (int p = 0; p < ala.annotations.length; p++)
93 if (ala.annotations[p] != null)
95 assertEquals("Mismatch at position " + p
96 + " between annotation position value and sequence"
97 + ala.annotations[p], (int) ala.annotations[p].value,
98 ala.sequenceRef.findPosition(p));
104 * Tests the liftOver method and also exercises the functions for remapping
105 * annotation across different reference sequences. Here, the test is between
106 * different dataset frames (annotation transferred by mapping between
109 @Test(groups = { "Functional" })
110 public void testLiftOver()
112 SequenceI sqFrom = new Sequence("fromLong", "QQQCDEWGH");
114 sqFrom.setEnd(sqFrom.findPosition(sqFrom.getLength() - 1));
115 SequenceI sqTo = new Sequence("toShort", "RCDEW");
117 sqTo.setEnd(sqTo.findPosition(sqTo.getLength() - 1));
118 createAnnotation(sqTo);
119 AlignmentAnnotation origTo = sqTo.getAnnotation()[0];
120 createAnnotation(sqFrom);
121 AlignmentAnnotation origFrom = sqFrom.getAnnotation()[0];
122 AlignSeq align = AlignSeq.doGlobalNWAlignment(sqFrom, sqTo,
124 SequenceI alSeq1 = new Sequence(sqFrom.getName(), align.getAStr1());
125 alSeq1.setStart(sqFrom.getStart() + align.getSeq1Start() - 1);
126 alSeq1.setEnd(sqFrom.getStart() + align.getSeq1End() - 1);
127 alSeq1.setDatasetSequence(sqFrom);
128 SequenceI alSeq2 = new Sequence(sqTo.getName(), align.getAStr2());
129 alSeq2.setStart(sqTo.getStart() + align.getSeq2Start() - 1);
130 alSeq2.setEnd(sqTo.getStart() + align.getSeq2End() - 1);
131 alSeq2.setDatasetSequence(sqTo);
132 System.out.println(new AppletFormatAdapter()
134 FileFormat.Stockholm, new Alignment(new SequenceI[] { sqFrom,
135 alSeq1, sqTo, alSeq2 }), true));
137 Mapping mp = align.getMappingFromS1(false);
139 AlignmentAnnotation almap1 = new AlignmentAnnotation(
140 sqTo.getAnnotation()[0]);
141 almap1.liftOver(sqFrom, mp);
142 assertEquals(almap1.sequenceRef, sqFrom);
143 alSeq1.addAlignmentAnnotation(almap1);
144 almap1.setSequenceRef(alSeq1);
145 almap1.adjustForAlignment();
146 AlignmentAnnotation almap2 = new AlignmentAnnotation(
147 sqFrom.getAnnotation()[0]);
148 almap2.liftOver(sqTo, mp);
149 assertEquals(almap2.sequenceRef, sqTo);
151 alSeq2.addAlignmentAnnotation(almap2);
152 almap2.setSequenceRef(alSeq2);
153 almap2.adjustForAlignment();
155 AlignmentI all = new Alignment(new SequenceI[] { alSeq1, alSeq2 });
156 all.addAnnotation(almap1);
157 all.addAnnotation(almap2);
158 System.out.println(new AppletFormatAdapter().formatSequences(
159 FileFormat.Stockholm,
162 for (int p = 0; p < alSeq1.getLength(); p++)
164 Annotation orig1, trans1, orig2, trans2;
165 trans2 = almap2.annotations[p];
166 orig2 = origFrom.annotations[alSeq1.findPosition(p)
167 - sqFrom.getStart()];
168 orig1 = origTo.annotations[alSeq2.findPosition(p) - sqTo.getStart()];
169 trans1 = almap1.annotations[p];
170 if (trans1 == trans2)
172 System.out.println("Pos " + p + " mismatch");
176 "Mismatch on Original From and transferred annotation on 2",
177 (orig2 != null) ? orig2.toString() : null,
178 (trans2 != null) ? trans2.toString() : null);
180 "Mismatch on Original To and transferred annotation on 1",
181 (orig1 != null) ? orig1.toString() : null,
182 (trans1 != null) ? trans1.toString() : null);
184 + (almap1.annotations.length > p ? almap1.annotations[p].displayCharacter
187 + (almap2.annotations.length > p ? almap2.annotations[p].displayCharacter
189 assertEquals("Position " + p + " " + alm1 + " " + alm2, alm1, alm2);
193 @Test(groups = { "Functional" })
194 public void testAdjustForAlignment()
196 SequenceI seq = new Sequence("TestSeq", "ABCDEFG");
197 seq.createDatasetSequence();
200 * Annotate positions 3/4/5 (CDE) with values 1/2/3
202 Annotation[] anns = new Annotation[] { null, null, new Annotation(1),
203 new Annotation(2), new Annotation(3) };
204 AlignmentAnnotation ann = new AlignmentAnnotation("SS",
205 "secondary structure", anns);
206 seq.addAlignmentAnnotation(ann);
209 * Check annotation map before modifying aligned sequence
211 assertNull(ann.getAnnotationForPosition(1));
212 assertNull(ann.getAnnotationForPosition(2));
213 assertNull(ann.getAnnotationForPosition(6));
214 assertNull(ann.getAnnotationForPosition(7));
215 assertEquals(1, ann.getAnnotationForPosition(3).value, 0.001d);
216 assertEquals(2, ann.getAnnotationForPosition(4).value, 0.001d);
217 assertEquals(3, ann.getAnnotationForPosition(5).value, 0.001d);
220 * Trim the displayed sequence to BCD and adjust annotations
222 seq.setSequence("BCD");
225 ann.adjustForAlignment();
228 * Should now have annotations for aligned positions 2, 3Q (CD) only
230 assertEquals(3, ann.annotations.length);
231 assertNull(ann.annotations[0]);
232 assertEquals(1, ann.annotations[1].value, 0.001);
233 assertEquals(2, ann.annotations[2].value, 0.001);
237 * Test the method that defaults rna symbol to the one matching the preceding
238 * unmatched opening bracket (if any)
240 @Test(groups = { "Functional" })
241 public void testGetDefaultRnaHelixSymbol()
243 AlignmentAnnotation ann = new AlignmentAnnotation("SS",
244 "secondary structure", null);
245 assertEquals("(", ann.getDefaultRnaHelixSymbol(4));
247 Annotation[] anns = new Annotation[20];
248 ann.annotations = anns;
249 assertEquals("(", ann.getDefaultRnaHelixSymbol(4));
251 anns[1] = new Annotation("(", "S", '(', 0f);
252 assertEquals("(", ann.getDefaultRnaHelixSymbol(0));
253 assertEquals("(", ann.getDefaultRnaHelixSymbol(1));
254 assertEquals(")", ann.getDefaultRnaHelixSymbol(2));
255 assertEquals(")", ann.getDefaultRnaHelixSymbol(3));
260 anns[1] = new Annotation("(", "S", '(', 0f);
261 anns[3] = new Annotation("[", "S", '[', 0f);
262 anns[5] = new Annotation("{", "S", '{', 0f);
263 anns[7] = new Annotation("<", "S", '<', 0f);
264 anns[9] = new Annotation("}", "S", '}', 0f);
265 anns[11] = new Annotation(">", "S", '>', 0f);
266 anns[13] = new Annotation(")", "S", ')', 0f);
267 anns[15] = new Annotation("]", "S", ']', 0f);
269 String expected = "(())]]}}>>>>]]]](";
270 for (int i = 0; i < expected.length(); i++)
272 assertEquals("column " + i, String.valueOf(expected.charAt(i)),
273 ann.getDefaultRnaHelixSymbol(i));
277 * .(.[.(.).{.}.<.].D.
279 anns[1] = new Annotation("(", "S", '(', 0f);
280 anns[3] = new Annotation("[", "S", '[', 0f);
281 anns[5] = new Annotation("(", "S", '(', 0f);
282 anns[7] = new Annotation(")", "S", ')', 0f);
283 anns[9] = new Annotation("{", "S", '{', 0f);
284 anns[11] = new Annotation("}", "S", '}', 0f);
285 anns[13] = new Annotation("<", "S", '>', 0f);
286 anns[15] = new Annotation("]", "S", ']', 0f);
287 anns[17] = new Annotation("D", "S", 'D', 0f);
289 expected = "(())]]))]]}}]]>>>>dd";
290 for (int i = 0; i < expected.length(); i++)
292 assertEquals("column " + i, String.valueOf(expected.charAt(i)),
293 ann.getDefaultRnaHelixSymbol(i));