1 package jalview.datamodel;
3 import static org.testng.Assert.*;
5 import org.testng.Assert;
6 import org.testng.annotations.BeforeClass;
7 import org.testng.annotations.Test;
9 import jalview.analysis.AlignmentUtils;
10 import jalview.analysis.SeqsetUtils;
11 import jalview.gui.JvOptionPane;
12 import jalview.util.MapList;
13 import jalview.ws.datamodel.MappableContactMatrixI;
14 import jalview.ws.datamodel.alphafold.PAEContactMatrix;
16 public class PAEContactMatrixTest
18 @BeforeClass(alwaysRun = true)
19 public void setUpJvOptionPane()
21 JvOptionPane.setInteractiveMode(false);
22 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
25 static float[][] PAEdata = { { 1.0f, 2.0f, 3.0f, 4.0f, 5.0f },
26 { 2.0f, 1.0f, 2.0f, 3.0f, 4.0f },
27 { 3.0f, 2.0f, 1.0f, 2.0f, 3.0f },
28 { 4.0f, 3.0f, 2.0f, 1.0f, 2.0f },
29 { 5.0f, 4.0f, 3.0f, 2.0f, 1.0f } };
32 * test associations for a PAE matrix
34 @Test(groups = { "Functional" })
35 public void testSeqAssociatedPAEMatrix()
37 Sequence seq = new Sequence("Seq", "ASDQE");
38 AlignmentAnnotation aa = seq
39 .addContactList(new PAEContactMatrix(seq, PAEdata));
40 assertNotNull(seq.getContactListFor(aa, 0));
41 assertEquals(seq.getContactListFor(aa, 0).getContactAt(0), 1.0);
42 assertNotNull(seq.getContactListFor(aa, 1));
43 assertEquals(seq.getContactListFor(aa, 1).getContactAt(1), 1.0);
44 assertNotNull(seq.getContactListFor(aa, 2));
45 assertEquals(seq.getContactListFor(aa, 2).getContactAt(2), 1.0);
46 assertNotNull(seq.getContactListFor(aa, 3));
47 assertEquals(seq.getContactListFor(aa, 3).getContactAt(3), 1.0);
48 assertNotNull(seq.getContactListFor(aa, 4));
49 assertEquals(seq.getContactListFor(aa, 4).getContactAt(4), 1.0);
51 assertNotNull(seq.getContactListFor(aa, seq.getEnd() - 1));
52 assertNull(seq.getContactListFor(aa, seq.getEnd()));
54 ContactListI cm = seq.getContactListFor(aa, seq.getStart());
55 assertEquals(cm.getContactAt(seq.getStart()), 1d);
56 verifyPAEmatrix(seq, aa, 0, 0, 4);
58 // Now associated with sequence not starting at 1
59 seq = new Sequence("Seq/5-9", "ASDQE");
60 ContactMatrixI paematrix = new PAEContactMatrix(seq, PAEdata);
61 aa = seq.addContactList(paematrix);
63 // individual annotation elements need to be distinct for Matrix associated
65 Annotation ae5 = aa.getAnnotationForPosition(5);
66 Annotation ae6 = aa.getAnnotationForPosition(6);
69 assertTrue(ae5 != ae6);
71 cm = seq.getContactListFor(aa, 0);
72 assertEquals(cm.getContactAt(0), 1d);
73 verifyPAEmatrix(seq, aa, 0, 0, 4);
76 paematrix.setGroupSet(GroupSet.makeGroups(paematrix, false,0.1f, false));
78 // remap - test the MappableContactMatrix.liftOver method
79 SequenceI newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
80 Mapping sqmap = new Mapping(seq,
82 { 5, 8, 10, 10 }, new int[] { 5, 9 }, 1, 1));
83 assertTrue(paematrix instanceof MappableContactMatrixI);
85 MappableContactMatrixI remapped = ((MappableContactMatrixI) paematrix)
86 .liftOver(newseq, sqmap);
87 assertTrue(remapped instanceof PAEContactMatrix);
89 AlignmentAnnotation newaa = newseq.addContactList(remapped);
90 assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(1)));
91 assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(4)));
93 newseq.getContactListFor(newaa, -1 + newseq.findIndex(5)));
95 newseq.getContactListFor(newaa, -1 + newseq.findIndex(6)));
97 newseq.getContactListFor(newaa, -1 + newseq.findIndex(7)));
99 newseq.getContactListFor(newaa, -1 + newseq.findIndex(8)));
100 // no mapping for position 9
101 assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(9)));
104 newseq.getContactListFor(newaa, -1 + newseq.findIndex(10)));
106 // verify MappedPositions includes discontinuity
107 int[] mappedCl = newseq.getContactListFor(newaa, 5)
108 .getMappedPositionsFor(0, 4);
109 assertEquals(4, mappedCl.length,
110 "getMappedPositionsFor doesn't support discontinuous mappings to contactList");
114 SequenceI alseq = newseq.getSubSequence(6, 10);
115 alseq.insertCharAt(2, 2, '-');
116 AlignmentI alForSeq = new Alignment(new SequenceI[] { alseq });
117 newaa = AlignmentUtils.addReferenceAnnotationTo(alForSeq, alseq, newaa,
119 ContactListI alcl = alForSeq.getContactListFor(newaa, 1);
121 mappedCl = alcl.getMappedPositionsFor(0, 4);
122 assertNotNull(mappedCl);
123 assertEquals(4, mappedCl.length,
124 "getMappedPositionsFor doesn't support discontinuous mappings to contactList");
126 // remap2 - test with original matrix map from 1-5 remapped to 5-9
128 seq = new Sequence("Seq/1-5", "ASDQE");
129 paematrix = new PAEContactMatrix(seq, PAEdata);
130 assertTrue(paematrix instanceof MappableContactMatrixI);
131 aa = seq.addContactList(paematrix);
133 newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
134 sqmap = new Mapping(seq,
135 new MapList(new int[]
136 { 5, 9 }, new int[] { 1, 5 }, 1, 1));
138 remapped = ((MappableContactMatrixI) paematrix).liftOver(newseq, sqmap);
139 assertTrue(remapped instanceof PAEContactMatrix);
141 newaa = newseq.addContactList(remapped);
142 verify_mapping(newseq, newaa);
144 // remap3 - remap2 but mapping sense in liftover is reversed
146 seq = new Sequence("Seq/1-5", "ASDQE");
147 paematrix = new PAEContactMatrix(seq, PAEdata);
148 assertTrue(paematrix instanceof MappableContactMatrixI);
149 aa = seq.addContactList(paematrix);
151 newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
152 sqmap = new Mapping(newseq,
153 new MapList(new int[]
154 { 1, 5 }, new int[] { 5, 9 }, 1, 1));
156 remapped = ((MappableContactMatrixI) paematrix).liftOver(newseq, sqmap);
157 assertTrue(remapped instanceof PAEContactMatrix);
159 newaa = newseq.addContactList(remapped);
160 verify_mapping(newseq, newaa);
164 * checks that the PAE matrix is located at positions 1-9 in newseq, and
165 * columns are not truncated.
170 private void verify_mapping(SequenceI newseq, AlignmentAnnotation newaa)
172 assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(1)));
173 assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(4)));
175 newseq.getContactListFor(newaa, -1 + newseq.findIndex(5)));
177 newseq.getContactListFor(newaa, -1 + newseq.findIndex(6)));
179 newseq.getContactListFor(newaa, -1 + newseq.findIndex(7)));
181 newseq.getContactListFor(newaa, -1 + newseq.findIndex(8)));
183 newseq.getContactListFor(newaa, -1 + newseq.findIndex(9)));
184 // last column should be null this time
185 assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(10)));
187 verifyPAEmatrix(newseq, newaa, 4, 4, 8);
190 private void verifyPAEmatrix(SequenceI seq, AlignmentAnnotation aa,
191 int topl, int rowl, int rowr)
194 for (int f = rowl; f <= rowr; f++)
196 ContactListI clist = seq.getContactListFor(aa, f);
197 assertNotNull(clist, "No ContactListI for position " + (f));
198 assertEquals(clist.getContactAt(0), (double) f - topl + 1,
199 "for column " + f + " relative to " + topl);
200 mappedCl = clist.getMappedPositionsFor(0, 0);
201 assertNotNull(mappedCl);
202 assertEquals(mappedCl[0], mappedCl[1]);
203 assertEquals(mappedCl[0], seq.findIndex(seq.getStart() + topl));
204 assertEquals(clist.getContactAt(f - topl), 1d,
205 "for column and row " + f + " relative to " + topl);
210 * check mapping and resolution methods work
212 @Test(groups= {"Functional"})
213 public void testMappableContactMatrix() {
214 SequenceI newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
215 MapList map = new MapList(new int[]
216 { 5, 9 }, new int[] { 1, 5 }, 1, 1);
217 AlignmentAnnotation aa = newseq
218 .addContactList(new PAEContactMatrix(newseq,map, PAEdata,null));
219 ContactListI clist = newseq.getContactListFor(aa, 4);
220 assertNotNull(clist);
221 clist = newseq.getContactListFor(aa, 3);
224 ContactMatrixI cm = newseq.getContactMatrixFor(aa);
225 MappableContactMatrixI mcm = (MappableContactMatrixI) cm;
226 int[] pos = mcm.getMappedPositionsFor(newseq, 0);
229 pos = mcm.getMappedPositionsFor(newseq, 1);
231 assertEquals(pos[0],4+newseq.getStart());
233 pos = mcm.getMappedPositionsFor(newseq, 6); // after end of matrix
235 pos = mcm.getMappedPositionsFor(newseq, 5); // at end of matrix
237 assertEquals(pos[0],8+newseq.getStart());
238 SequenceI alseq = newseq.deriveSequence();
239 alseq.insertCharAt(5,'-');
240 pos = mcm.getMappedPositionsFor(alseq, 5); // at end of matrix
242 assertEquals(pos[0],8+newseq.getStart());