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.io.AppletFormatAdapter;
29 import org.testng.annotations.Test;
31 public class AlignmentAnnotationTests
33 @Test(groups = { "Functional" })
34 public void testCopyConstructor()
36 SequenceI sq = new Sequence("Foo", "ARAARARARAWEAWEAWRAWEAWE");
38 AlignmentAnnotation alc, alo = sq.getAnnotation()[0];
39 alc = new AlignmentAnnotation(alo);
40 for (String key : alo.getProperties())
42 assertEquals("Property mismatch", alo.getProperty(key),
43 alc.getProperty(key));
48 * create some dummy annotation derived from the sequence
52 public static void createAnnotation(SequenceI sq)
54 Annotation[] al = new Annotation[sq.getLength()];
55 for (int i = 0; i < al.length; i++)
57 al[i] = new Annotation(new Annotation("" + sq.getCharAt(i), "",
58 (char) 0, sq.findPosition(i)));
60 AlignmentAnnotation alan = new AlignmentAnnotation("For "
61 + sq.getName(), "Fake alignment annot", al);
62 // create a sequence mapping for the annotation vector in its current state
63 alan.createSequenceMapping(sq, sq.getStart(), false);
64 alan.setProperty("CreatedBy", "createAnnotation");
65 sq.addAlignmentAnnotation(alan);
69 * use this to test annotation derived from method above as it is transferred
70 * across different sequences derived from same dataset coordinate frame
74 public static void testAnnotTransfer(AlignmentAnnotation ala)
77 "Failed - need annotation created by createAnnotation method",
78 ala.description, "Fake alignment annot");
79 ala.adjustForAlignment();
80 for (int p = 0; p < ala.annotations.length; p++)
82 if (ala.annotations[p] != null)
84 assertEquals("Mismatch at position " + p
85 + " between annotation position value and sequence"
86 + ala.annotations[p], (int) ala.annotations[p].value,
87 ala.sequenceRef.findPosition(p));
93 * Tests the liftOver method and also exercises the functions for remapping
94 * annotation across different reference sequences. Here, the test is between
95 * different dataset frames (annotation transferred by mapping between
98 @Test(groups = { "Functional" })
99 public void testLiftOver()
101 SequenceI sqFrom = new Sequence("fromLong", "QQQCDEWGH");
103 sqFrom.setEnd(sqFrom.findPosition(sqFrom.getLength() - 1));
104 SequenceI sqTo = new Sequence("toShort", "RCDEW");
106 sqTo.setEnd(sqTo.findPosition(sqTo.getLength() - 1));
107 createAnnotation(sqTo);
108 AlignmentAnnotation origTo = sqTo.getAnnotation()[0];
109 createAnnotation(sqFrom);
110 AlignmentAnnotation origFrom = sqFrom.getAnnotation()[0];
111 AlignSeq align = AlignSeq.doGlobalNWAlignment(sqFrom, sqTo,
113 SequenceI alSeq1 = new Sequence(sqFrom.getName(), align.getAStr1());
114 alSeq1.setStart(sqFrom.getStart() + align.getSeq1Start() - 1);
115 alSeq1.setEnd(sqFrom.getStart() + align.getSeq1End() - 1);
116 alSeq1.setDatasetSequence(sqFrom);
117 SequenceI alSeq2 = new Sequence(sqTo.getName(), align.getAStr2());
118 alSeq2.setStart(sqTo.getStart() + align.getSeq2Start() - 1);
119 alSeq2.setEnd(sqTo.getStart() + align.getSeq2End() - 1);
120 alSeq2.setDatasetSequence(sqTo);
121 System.out.println(new AppletFormatAdapter()
122 .formatSequences("STH", new Alignment(new SequenceI[] { sqFrom,
123 alSeq1, sqTo, alSeq2 }), true));
125 Mapping mp = align.getMappingFromS1(false);
127 AlignmentAnnotation almap1 = new AlignmentAnnotation(
128 sqTo.getAnnotation()[0]);
129 almap1.liftOver(sqFrom, mp);
130 assertEquals(almap1.sequenceRef, sqFrom);
131 alSeq1.addAlignmentAnnotation(almap1);
132 almap1.setSequenceRef(alSeq1);
133 almap1.adjustForAlignment();
134 AlignmentAnnotation almap2 = new AlignmentAnnotation(
135 sqFrom.getAnnotation()[0]);
136 almap2.liftOver(sqTo, mp);
137 assertEquals(almap2.sequenceRef, sqTo);
139 alSeq2.addAlignmentAnnotation(almap2);
140 almap2.setSequenceRef(alSeq2);
141 almap2.adjustForAlignment();
143 AlignmentI all = new Alignment(new SequenceI[] { alSeq1, alSeq2 });
144 all.addAnnotation(almap1);
145 all.addAnnotation(almap2);
146 System.out.println(new AppletFormatAdapter().formatSequences("STH",
149 for (int p = 0; p < alSeq1.getLength(); p++)
151 Annotation orig1, trans1, orig2, trans2;
152 trans2 = almap2.annotations[p];
153 orig2 = origFrom.annotations[alSeq1.findPosition(p)
154 - sqFrom.getStart()];
155 orig1 = origTo.annotations[alSeq2.findPosition(p) - sqTo.getStart()];
156 trans1 = almap1.annotations[p];
157 if (trans1 == trans2)
159 System.out.println("Pos " + p + " mismatch");
163 "Mismatch on Original From and transferred annotation on 2",
164 (orig2 != null) ? orig2.toString() : null,
165 (trans2 != null) ? trans2.toString() : null);
167 "Mismatch on Original To and transferred annotation on 1",
168 (orig1 != null) ? orig1.toString() : null,
169 (trans1 != null) ? trans1.toString() : null);
171 + (almap1.annotations.length > p ? almap1.annotations[p].displayCharacter
174 + (almap2.annotations.length > p ? almap2.annotations[p].displayCharacter
176 assertEquals("Position " + p + " " + alm1 + " " + alm2, alm1, alm2);
180 @Test(groups = { "Functional" })
181 public void testAdjustForAlignment()
183 SequenceI seq = new Sequence("TestSeq", "ABCDEFG");
184 seq.createDatasetSequence();
187 * Annotate positions 3/4/5 (CDE) with values 1/2/3
189 Annotation[] anns = new Annotation[] { null, null, new Annotation(1),
190 new Annotation(2), new Annotation(3) };
191 AlignmentAnnotation ann = new AlignmentAnnotation("SS",
192 "secondary structure", anns);
193 seq.addAlignmentAnnotation(ann);
196 * Check annotation map before modifying aligned sequence
198 assertNull(ann.getAnnotationForPosition(1));
199 assertNull(ann.getAnnotationForPosition(2));
200 assertNull(ann.getAnnotationForPosition(6));
201 assertNull(ann.getAnnotationForPosition(7));
202 assertEquals(1, ann.getAnnotationForPosition(3).value, 0.001d);
203 assertEquals(2, ann.getAnnotationForPosition(4).value, 0.001d);
204 assertEquals(3, ann.getAnnotationForPosition(5).value, 0.001d);
207 * Trim the displayed sequence to BCD and adjust annotations
209 seq.setSequence("BCD");
212 ann.adjustForAlignment();
215 * Should now have annotations for aligned positions 2, 3Q (CD) only
217 assertEquals(3, ann.annotations.length);
218 assertNull(ann.annotations[0]);
219 assertEquals(1, ann.annotations[1].value, 0.001);
220 assertEquals(2, ann.annotations[2].value, 0.001);
224 * Test the method that defaults rna symbol to the one matching the preceding
225 * unmatched opening bracket (if any)
227 @Test(groups = { "Functional" })
228 public void testGetDefaultRnaHelixSymbol()
230 AlignmentAnnotation ann = new AlignmentAnnotation("SS",
231 "secondary structure", null);
232 assertEquals("(", ann.getDefaultRnaHelixSymbol(4));
234 Annotation[] anns = new Annotation[20];
235 ann.annotations = anns;
236 assertEquals("(", ann.getDefaultRnaHelixSymbol(4));
238 anns[1] = new Annotation("(", "S", '(', 0f);
239 assertEquals("(", ann.getDefaultRnaHelixSymbol(0));
240 assertEquals("(", ann.getDefaultRnaHelixSymbol(1));
241 assertEquals(")", ann.getDefaultRnaHelixSymbol(2));
242 assertEquals(")", ann.getDefaultRnaHelixSymbol(3));
247 anns[1] = new Annotation("(", "S", '(', 0f);
248 anns[3] = new Annotation("[", "S", '[', 0f);
249 anns[5] = new Annotation("{", "S", '{', 0f);
250 anns[7] = new Annotation("<", "S", '<', 0f);
251 anns[9] = new Annotation("}", "S", '}', 0f);
252 anns[11] = new Annotation(">", "S", '>', 0f);
253 anns[13] = new Annotation(")", "S", ')', 0f);
254 anns[15] = new Annotation("]", "S", ']', 0f);
256 String expected = "(())]]}}>>>>]]]](";
257 for (int i = 0; i < expected.length(); i++)
259 assertEquals("column " + i, String.valueOf(expected.charAt(i)),
260 ann.getDefaultRnaHelixSymbol(i));
264 * .(.[.(.).{.}.<.].D.
266 anns[1] = new Annotation("(", "S", '(', 0f);
267 anns[3] = new Annotation("[", "S", '[', 0f);
268 anns[5] = new Annotation("(", "S", '(', 0f);
269 anns[7] = new Annotation(")", "S", ')', 0f);
270 anns[9] = new Annotation("{", "S", '{', 0f);
271 anns[11] = new Annotation("}", "S", '}', 0f);
272 anns[13] = new Annotation("<", "S", '>', 0f);
273 anns[15] = new Annotation("]", "S", ']', 0f);
274 anns[17] = new Annotation("D", "S", 'D', 0f);
276 expected = "(())]]))]]}}]]>>>>dd";
277 for (int i = 0; i < expected.length(); i++)
279 assertEquals("column " + i, String.valueOf(expected.charAt(i)),
280 ann.getDefaultRnaHelixSymbol(i));