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.structure;
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertTrue;
26 import jalview.datamodel.AlignmentAnnotation;
27 import jalview.datamodel.Annotation;
28 import jalview.datamodel.Sequence;
29 import jalview.datamodel.SequenceI;
30 import jalview.gui.AlignFrame;
31 import jalview.io.DataSourceType;
32 import jalview.io.FileFormat;
33 import jalview.io.FileLoader;
34 import jalview.io.StructureFile;
36 import org.testng.Assert;
37 import org.testng.AssertJUnit;
38 import org.testng.annotations.Test;
46 * 1QCF|A/101-121 SFQKGDQMVVLEESGEWWKAR Ser 114 jumps to Gly 116 at position
47 * 115 in PDB Res Numbering secondary structure numbers in jmol seem to be in
48 * msd numbering, not pdb res numbering.
50 @Test(groups = { "Functional" }, enabled = false)
51 public void pdbEntryPositionMap() throws Exception
53 Assert.fail("This test intentionally left to fail");
54 for (int offset = 0; offset < 20; offset += 6)
56 // check we put the secondary structure in the right position
57 Sequence uprot = new Sequence("TheProtSeq",
58 "DAWEIPRESLKLEKKLGAGQFGEVWMATYNKHTKVAVKTMKPGSMSVEAFLAEANVMKTL");
59 uprot.setStart(offset + 258); // make it harder - create a fake
60 // relocation problem for jalview to
62 uprot.setEnd(uprot.getStart() + uprot.getLength() - 1);
63 // original numbers taken from
64 // http://www.ebi.ac.uk/pdbe-srv/view/entry/1qcf/secondary.html
65 // these are in numbering relative to the subsequence above
66 int coils[] = { 266, 275, 278, 287, 289, 298, 302, 316 }, helices[] = new int[]
67 { 303, 315 }, sheets[] = new int[] { 267, 268, 269, 270 };
69 StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
70 StructureFile pmap = ssm.setMapping(true, new SequenceI[] { uprot },
71 new String[] { "A" }, "test/jalview/ext/jmol/1QCF.pdb",
73 assertTrue(pmap != null);
74 SequenceI protseq = pmap.getSeqsAsArray()[0];
75 AlignmentAnnotation pstra = protseq
76 .getAnnotation("Secondary Structure")[0];
78 pstra.restrict((pinds = protseq.findIndex(258) - 1),
79 pinde = (protseq.findIndex(317) - 1));
81 System.out.println("PDB Annot");
82 for (char c : protseq.getSubSequence(pinds, pinde).getSequence())
84 System.out.print(c + ", ");
86 System.out.println("\n" + pstra + "\n\nsubsequence\n");
87 for (char c : uprot.getSequence())
89 System.out.print(c + ", ");
91 System.out.println("");
92 for (AlignmentAnnotation ss : uprot
93 .getAnnotation("Secondary Structure"))
95 ss.adjustForAlignment();
96 System.out.println("Uniprot Annot\n" + ss);
97 assertTrue(ss.hasIcons);
101 Annotation a = ss.annotations[op = (uprot.findIndex(offset + p) - 1)];
103 "Expected a helix at position " + p + uprot.getCharAt(op)
104 + " but got coil", a != null);
105 assertEquals("Expected a helix at position " + p,
106 a.secondaryStructure, expected);
111 Annotation a = ss.annotations[uprot.findIndex(offset + p) - 1];
113 "Expected a strand at position " + p + " but got coil",
115 assertEquals("Expected a strand at position " + p,
116 a.secondaryStructure, expected);
121 Annotation a = ss.annotations[uprot.findIndex(offset + p) - 1];
122 assertTrue("Expected coil at position " + p + " but got "
123 + a.secondaryStructure, a == null);
129 @Test(groups = { "Functional" }, enabled = false)
130 public void testPDBentryMapping() throws Exception
132 Assert.fail("This test intentionally left to fail");
133 Sequence sq = new Sequence(
134 "1GAQ A subseq 126 to 219",
135 "EIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKM");
136 Sequence sq1 = new Sequence(sq);
138 StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
139 // Associate the 1GAQ pdb file with the subsequence 'imported' from another
141 StructureFile pde = ssm.setMapping(true, new SequenceI[] { sq },
143 { "A" }, inFile = "examples/1gaq.txt", DataSourceType.FILE);
144 assertTrue("PDB File couldn't be found", pde != null);
145 StructureMapping[] mp = ssm.getMapping(inFile);
146 assertTrue("No mappings made.", mp != null && mp.length > 0);
147 int nsecStr = 0, nsTemp = 0;
148 // test for presence of transferred annotation on sequence
149 for (AlignmentAnnotation alan : sq.getAnnotation())
155 if (alan.graph == alan.LINE_GRAPH)
161 "Only one secondary structure should be transferred to associated sequence.",
164 "Only two line graphs should be transferred to associated sequence.",
166 // Now test the transfer function and compare annotated positions
167 for (StructureMapping origMap : mp)
169 if (origMap.getSequence() == sq)
171 assertEquals("Mapping was incomplete.", sq.getLength() - 1,
172 (origMap.getPDBResNum(sq.getEnd()) - origMap
173 .getPDBResNum(sq.getStart())));
174 // sanity check - if this fails, mapping from first position in sequence
175 // we want to transfer to is not where we expect
176 assertEquals(1, origMap.getSeqPos(126));
177 SequenceI firstChain = pde.getSeqs().get(0);
178 // Compare the annotated positions on the PDB chain sequence with the
179 // annotation on the associated sequence
180 for (AlignmentAnnotation alan : firstChain.getAnnotation())
182 AlignmentAnnotation transfer = origMap.transfer(alan);
183 System.out.println("pdb:" + firstChain.getSequenceAsString());
184 System.out.println("ann:" + alan.toString());
185 System.out.println("pdb:" + sq.getSequenceAsString());
186 System.out.println("ann:" + transfer.toString());
188 for (int p = 0, pSize = firstChain.getLength(); p < pSize; p++)
190 // walk along the pdb chain's jalview sequence
192 int fpos = origMap.getSeqPos(rseqpos = firstChain
194 // only look at positions where there is a corresponding position in
200 // p is index into PDB residue entries
201 // rseqpos is pdb sequence position for position p
202 // fpos is sequence position for associated position for rseqpos
203 // tanpos is the column for the mapped sequence position
204 int tanpos = sq.findIndex(fpos) - 1;
205 if (tanpos < 0 || transfer.annotations.length <= tanpos)
207 // gone beyond mapping to the sequence
211 Annotation a = transfer.annotations[tanpos], b = alan.annotations[p];
212 assertEquals("Non-equivalent annotation element at " + p + "("
213 + rseqpos + ")" + " expected at " + fpos + " (alIndex "
214 + tanpos + ")", a == null ? a : a.toString(),
215 b == null ? b : b.toString());
216 System.out.print("(" + a + "|" + b + ")");
225 * corner case for pdb mapping - revealed a problem with the AlignSeq->Mapping
229 @Test(groups = { "Functional" })
230 public void mapFer1From3W5V() throws Exception
232 AlignFrame seqf = new FileLoader(false)
233 .LoadFileWaitTillLoaded(
234 ">FER1_MAIZE/1-150 Ferredoxin-1, chloroplast precursor\nMATVLGSPRAPAFFFSSSSLRAAPAPTAVALPAAKVGIMGRSASSRRRLRAQATYNVKLITPEGEVELQVPD\nDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKE\nEELTGA",
235 DataSourceType.PASTE, FileFormat.Fasta);
236 SequenceI newseq = seqf.getViewport().getAlignment().getSequenceAt(0);
237 StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
238 StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
239 new String[] { null }, "examples/3W5V.pdb",
240 DataSourceType.FILE);
243 AssertJUnit.fail("Couldn't make a mapping for 3W5V to FER1_MAIZE");
248 * compare reference annotation for imported pdb sequence to identical
249 * seuqence with transferred annotation from mapped pdb file
251 @Test(groups = { "Functional" })
252 public void compareTransferredToRefPDBAnnot() throws Exception
254 StructureImportSettings.setShowSeqFeatures(true);
255 AlignFrame ref = new FileLoader(false)
256 .LoadFileWaitTillLoaded("test/jalview/ext/jmol/1QCF.pdb",
257 DataSourceType.FILE);
258 SequenceI refseq = ref.getViewport().getAlignment().getSequenceAt(0);
259 SequenceI newseq = new Sequence(refseq.getName() + "Copy",
260 refseq.getSequenceAsString());
261 // make it harder by shifting the copy vs the reference
262 newseq.setStart(refseq.getStart() + 25);
263 newseq.setEnd(refseq.getLength() + 25 + refseq.getStart());
264 StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
265 ssm.setProcessSecondaryStructure(true);
266 ssm.setAddTempFacAnnot(true);
267 StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
268 new String[] { null }, "test/jalview/ext/jmol/1QCF.pdb",
269 DataSourceType.FILE);
270 assertTrue(pmap != null);
271 assertEquals("Original and copied sequence of different lengths.",
272 refseq.getLength(), newseq.getLength());
273 assertTrue(refseq.getAnnotation() != null
274 && refseq.getAnnotation().length > 0);
275 assertTrue(newseq.getAnnotation() != null
276 && newseq.getAnnotation().length > 0);
277 for (AlignmentAnnotation oannot : refseq.getAnnotation())
279 for (AlignmentAnnotation tannot : newseq.getAnnotation(oannot.label))
281 for (int p = 0, pSize = refseq.getLength(); p < pSize; p++)
283 Annotation orig = oannot.annotations[p], tran = tannot.annotations[p];
284 assertTrue("Mismatch: coil and non coil site " + p, orig == tran
285 || orig != null && tran != null);
288 assertEquals("Mismatch in secondary structure at site " + p,
289 tran.secondaryStructure, orig.secondaryStructure);