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 = {
26 {1.0f,2.0f,3.0f,4.0f,5.0f},
27 {2.0f,1.0f,2.0f,3.0f,4.0f},
28 {3.0f,2.0f,1.0f,2.0f,3.0f},
29 {4.0f,3.0f,2.0f,1.0f,2.0f},
30 {5.0f,4.0f,3.0f,2.0f,1.0f}};
33 * test associations for a PAE matrix
35 @Test(groups = { "Functional" })
36 public void testSeqAssociatedPAEMatrix()
38 Sequence seq = new Sequence("Seq","ASDQE");
39 AlignmentAnnotation aa = seq.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);
62 cm = seq.getContactListFor(aa, 0);
63 assertEquals(cm.getContactAt(0),1d);
64 verifyPAEmatrix(seq, aa, 0, 0, 4);
66 // remap - test the MappableContactMatrix.liftOver method
67 SequenceI newseq = new Sequence("Seq","ASDQEASDQEASDQE");
68 Mapping sqmap = new Mapping(seq, new MapList(new int[] {5,8,10,10},new int[] { 5,9}, 1, 1));
69 assertTrue(paematrix instanceof MappableContactMatrixI);
71 MappableContactMatrixI remapped = ((MappableContactMatrixI)paematrix).liftOver(newseq, sqmap);
72 assertTrue(remapped instanceof PAEContactMatrix);
74 AlignmentAnnotation newaa = newseq.addContactList(remapped);
75 assertNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(1)));
76 assertNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(4)));
77 assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(5)));
78 assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(6)));
79 assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(7)));
80 assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(8)));
81 // no mapping for position 9
82 assertNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(9)));
84 assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(10)));
86 // verify MappedPositions includes discontinuity
87 int[] mappedCl = newseq.getContactListFor(newaa, 5).getMappedPositionsFor(0, 4);
88 assertEquals(4,mappedCl.length,"getMappedPositionsFor doesn't support discontinuous mappings to contactList");
92 SequenceI alseq = newseq.getSubSequence(6, 10);
93 alseq.insertCharAt(2, 2, '-');
94 AlignmentI alForSeq=new Alignment(new SequenceI[] { alseq });
95 newaa = AlignmentUtils.addReferenceAnnotationTo(alForSeq, alseq, newaa, null);
96 ContactListI alcl = alForSeq.getContactListFor(newaa, 1);
98 mappedCl = alcl.getMappedPositionsFor(0, 4);
99 assertNotNull(mappedCl);
100 assertEquals(4,mappedCl.length,"getMappedPositionsFor doesn't support discontinuous mappings to contactList");
102 // remap2 - test with original matrix map from 1-5 remapped to 5-9
104 seq = new Sequence("Seq/1-5","ASDQE");
105 paematrix = new PAEContactMatrix(seq, PAEdata);
106 assertTrue(paematrix instanceof MappableContactMatrixI);
107 aa = seq.addContactList(paematrix);
109 newseq = new Sequence("Seq","ASDQEASDQEASDQE");
110 sqmap = new Mapping(seq, new MapList(new int[] {5,9},new int[] { 1,5}, 1, 1));
112 remapped = ((MappableContactMatrixI)paematrix).liftOver(newseq, sqmap);
113 assertTrue(remapped instanceof PAEContactMatrix);
116 newaa = newseq.addContactList(remapped);
117 verify_mapping(newseq, newaa);
119 // remap3 - remap2 but mapping sense in liftover is reversed
121 seq = new Sequence("Seq/1-5","ASDQE");
122 paematrix = new PAEContactMatrix(seq, PAEdata);
123 assertTrue(paematrix instanceof MappableContactMatrixI);
124 aa = seq.addContactList(paematrix);
126 newseq = new Sequence("Seq","ASDQEASDQEASDQE");
127 sqmap = new Mapping(newseq, new MapList(new int[] { 1,5},new int[] {5,9},1, 1));
129 remapped = ((MappableContactMatrixI)paematrix).liftOver(newseq, sqmap);
130 assertTrue(remapped instanceof PAEContactMatrix);
133 newaa = newseq.addContactList(remapped);
134 verify_mapping(newseq, newaa);
137 * checks that the PAE matrix is located at positions 1-9 in newseq, and columns are not truncated.
141 private void verify_mapping(SequenceI newseq, AlignmentAnnotation newaa)
143 assertNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(1)));
144 assertNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(4)));
145 assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(5)));
146 assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(6)));
147 assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(7)));
148 assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(8)));
149 assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(9)));
150 // last column should be null this time
151 assertNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(10)));
153 verifyPAEmatrix(newseq, newaa, 4, 4, 8);
156 private void verifyPAEmatrix(SequenceI seq, AlignmentAnnotation aa, int topl, int rowl, int rowr)
159 for (int f=rowl;f<=rowr;f++) {
160 ContactListI clist = seq.getContactListFor(aa, f);
161 assertNotNull(clist,"No ContactListI for position "+(f));
162 assertEquals(clist.getContactAt(0), (double) f-topl+1,"for column "+f+" relative to "+topl);
163 mappedCl = clist.getMappedPositionsFor(0, 0);
164 assertNotNull(mappedCl);
165 assertEquals(mappedCl[0],mappedCl[1]);
166 assertEquals(mappedCl[0],seq.findIndex(seq.getStart()+topl));
167 assertEquals(clist.getContactAt(f-topl),1d, "for column and row "+f+" relative to "+topl);