1 package jalview.structure;
3 import static org.junit.Assert.assertEquals;
4 import static org.junit.Assert.assertTrue;
5 import jalview.datamodel.AlignmentAnnotation;
6 import jalview.datamodel.Annotation;
7 import jalview.datamodel.Sequence;
8 import jalview.datamodel.SequenceI;
10 import org.junit.Test;
12 import MCview.PDBfile;
18 public void testPDBentryMapping() throws Exception
20 Sequence sq = new Sequence(
21 "1GAQ A subseq 126 to 219",
22 "EIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKM");
23 Sequence sq1 = new Sequence(sq);
25 StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
26 // Associate the 1GAQ pdb file with the subsequence 'imported' from another
28 PDBfile pde = ssm.setMapping(new SequenceI[]
30 { "A" }, inFile = "examples/1gaq.txt", jalview.io.FormatAdapter.FILE);
31 assertTrue("PDB File couldn't be found", pde != null);
32 StructureMapping[] mp = ssm.getMapping(inFile);
33 assertTrue("No mappings made.", mp != null && mp.length > 0);
34 boolean hasSecStr=false,hasTemp=false;
35 for (StructureMapping origMap:mp)
37 if (origMap.getSequence()==sq)
39 assertEquals("Mapping was incomplete.", sq.getLength() - 1,
40 (origMap.getPDBResNum(sq.getEnd()) - origMap
41 .getPDBResNum(sq.getStart())));
42 // sanity check - if this fails, mapping from first position in sequence
43 // we want to transfer to is not where we expect
44 assertEquals(1, origMap.getSeqPos(126));
45 SequenceI firstChain = pde.getSeqs().get(0);
46 // Compare the annotated positions on the PDB chain sequence with the
47 // annotation on the associated sequence
48 for (AlignmentAnnotation alan : firstChain.getAnnotation())
54 if (alan.graph == alan.LINE_GRAPH)
59 AlignmentAnnotation transfer = origMap.transfer(alan);
60 System.out.println("pdb:" + firstChain.getSequenceAsString());
61 System.out.println("ann:" + alan.toString());
62 System.out.println("pdb:" + sq.getSequenceAsString());
63 System.out.println("ann:" + transfer.toString());
65 for (int p = 0, pSize = firstChain.getLength() - 1; p < pSize; p++)
67 // walk along the pdb chain's jalview sequence
69 int fpos = origMap.getSeqPos(rseqpos = firstChain
71 // only look at positions where there is a corresponding position in
77 // p is index into PDB residue entries
78 // rseqpos is pdb sequence position for position p
79 // fpos is sequence position for associated position for rseqpos
80 int tanpos = sq.findIndex(fpos);
81 if (transfer.annotations.length <= tanpos)
83 // gone beyond mapping to the sequence
86 Annotation a = transfer.annotations[sq.findIndex(fpos)], b = alan.annotations[p];
87 assertEquals("Non-equivalent annotation element at " + p + "("
89 + " expected at " + fpos + " (alIndex "
90 + sq.findIndex(fpos) + ")",
91 a == null ? a : a.toString(),
92 b == null ? b : b.toString());
93 System.out.print("(" + a + "|" + b + ")");
99 assertTrue("No secondary structure transferred to associated sequence.",hasSecStr);
100 assertTrue("No temperature factor transferred to associated sequence.",hasTemp);