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())
50 AlignmentAnnotation transfer = origMap.transfer(alan);
51 System.out.println("pdb:" + firstChain.getSequenceAsString());
52 System.out.println("ann:" + alan.toString());
53 System.out.println("pdb:" + sq.getSequenceAsString());
54 System.out.println("ann:" + transfer.toString());
56 for (int p = 0, pSize = firstChain.getLength() - 1; p < pSize; p++)
58 // walk along the pdb chain's jalview sequence
60 int fpos = origMap.getSeqPos(rseqpos = firstChain
62 // only look at positions where there is a corresponding position in
68 // p is index into PDB residue entries
69 // rseqpos is pdb sequence position for position p
70 // fpos is sequence position for associated position for rseqpos
71 int tanpos = sq.findIndex(fpos);
72 if (transfer.annotations.length <= tanpos)
74 // gone beyond mapping to the sequence
77 Annotation a = transfer.annotations[sq.findIndex(fpos)], b = alan.annotations[p];
78 assertEquals("Non-equivalent annotation element at " + p + "("
80 + " expected at " + fpos + " (alIndex "
81 + sq.findIndex(fpos) + ")",
82 a == null ? a : a.toString(),
83 b == null ? b : b.toString());
84 System.out.print("(" + a + "|" + b + ")");
92 // test for presence of transferred annotation on sequence
93 for (AlignmentAnnotation alan : sq.getAnnotation())
99 if (alan.graph == alan.LINE_GRAPH)
104 assertTrue("No secondary structure transferred to associated sequence.",hasSecStr);
105 assertTrue("No temperature factor transferred to associated sequence.",hasTemp);