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.FileLoader;
32 import jalview.io.FormatAdapter;
33 import jalview.io.StructureFile;
35 import org.testng.Assert;
36 import org.testng.AssertJUnit;
37 import org.testng.annotations.Test;
45 * 1QCF|A/101-121 SFQKGDQMVVLEESGEWWKAR Ser 114 jumps to Gly 116 at position
46 * 115 in PDB Res Numbering secondary structure numbers in jmol seem to be in
47 * msd numbering, not pdb res numbering.
49 @Test(groups = { "Functional" }, enabled = false)
50 public void pdbEntryPositionMap() throws Exception
52 Assert.fail("This test intentionally left to fail");
53 for (int offset = 0; offset < 20; offset += 6)
55 // check we put the secondary structure in the right position
56 Sequence uprot = new Sequence("TheProtSeq",
57 "DAWEIPRESLKLEKKLGAGQFGEVWMATYNKHTKVAVKTMKPGSMSVEAFLAEANVMKTL");
58 uprot.setStart(offset + 258); // make it harder - create a fake
59 // relocation problem for jalview to
61 uprot.setEnd(uprot.getStart() + uprot.getLength() - 1);
62 // original numbers taken from
63 // http://www.ebi.ac.uk/pdbe-srv/view/entry/1qcf/secondary.html
64 // these are in numbering relative to the subsequence above
65 int coils[] = { 266, 275, 278, 287, 289, 298, 302, 316 }, helices[] = new int[]
66 { 303, 315 }, sheets[] = new int[] { 267, 268, 269, 270 };
68 StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
69 StructureFile pmap = ssm.setMapping(true, new SequenceI[] { uprot },
70 new String[] { "A" }, "test/jalview/ext/jmol/1QCF.pdb",
71 jalview.io.FormatAdapter.FILE);
72 assertTrue(pmap != null);
73 SequenceI protseq = pmap.getSeqsAsArray()[0];
74 AlignmentAnnotation pstra = protseq
75 .getAnnotation("Secondary Structure")[0];
77 pstra.restrict((pinds = protseq.findIndex(258) - 1),
78 pinde = (protseq.findIndex(317) - 1));
80 System.out.println("PDB Annot");
81 for (char c : protseq.getSubSequence(pinds, pinde).getSequence())
83 System.out.print(c + ", ");
85 System.out.println("\n" + pstra + "\n\nsubsequence\n");
86 for (char c : uprot.getSequence())
88 System.out.print(c + ", ");
90 System.out.println("");
91 for (AlignmentAnnotation ss : uprot
92 .getAnnotation("Secondary Structure"))
94 ss.adjustForAlignment();
95 System.out.println("Uniprot Annot\n" + ss);
96 assertTrue(ss.hasIcons);
100 Annotation a = ss.annotations[op = (uprot.findIndex(offset + p) - 1)];
102 "Expected a helix at position " + p + uprot.getCharAt(op)
103 + " but got coil", a != null);
104 assertEquals("Expected a helix at position " + p,
105 a.secondaryStructure, expected);
110 Annotation a = ss.annotations[uprot.findIndex(offset + p) - 1];
112 "Expected a strand at position " + p + " but got coil",
114 assertEquals("Expected a strand at position " + p,
115 a.secondaryStructure, expected);
120 Annotation a = ss.annotations[uprot.findIndex(offset + p) - 1];
121 assertTrue("Expected coil at position " + p + " but got "
122 + a.secondaryStructure, a == null);
128 @Test(groups = { "Functional" }, enabled = false)
129 public void testPDBentryMapping() throws Exception
131 Assert.fail("This test intentionally left to fail");
132 Sequence sq = new Sequence(
133 "1GAQ A subseq 126 to 219",
134 "EIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKM");
135 Sequence sq1 = new Sequence(sq);
137 StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
138 // Associate the 1GAQ pdb file with the subsequence 'imported' from another
140 StructureFile pde = ssm.setMapping(true, new SequenceI[] { sq },
142 { "A" }, inFile = "examples/1gaq.txt", jalview.io.FormatAdapter.FILE);
143 assertTrue("PDB File couldn't be found", pde != null);
144 StructureMapping[] mp = ssm.getMapping(inFile);
145 assertTrue("No mappings made.", mp != null && mp.length > 0);
146 int nsecStr = 0, nsTemp = 0;
147 // test for presence of transferred annotation on sequence
148 for (AlignmentAnnotation alan : sq.getAnnotation())
154 if (alan.graph == alan.LINE_GRAPH)
160 "Only one secondary structure should be transferred to associated sequence.",
163 "Only two line graphs should be transferred to associated sequence.",
165 // Now test the transfer function and compare annotated positions
166 for (StructureMapping origMap : mp)
168 if (origMap.getSequence() == sq)
170 assertEquals("Mapping was incomplete.", sq.getLength() - 1,
171 (origMap.getPDBResNum(sq.getEnd()) - origMap
172 .getPDBResNum(sq.getStart())));
173 // sanity check - if this fails, mapping from first position in sequence
174 // we want to transfer to is not where we expect
175 assertEquals(1, origMap.getSeqPos(126));
176 SequenceI firstChain = pde.getSeqs().get(0);
177 // Compare the annotated positions on the PDB chain sequence with the
178 // annotation on the associated sequence
179 for (AlignmentAnnotation alan : firstChain.getAnnotation())
181 AlignmentAnnotation transfer = origMap.transfer(alan);
182 System.out.println("pdb:" + firstChain.getSequenceAsString());
183 System.out.println("ann:" + alan.toString());
184 System.out.println("pdb:" + sq.getSequenceAsString());
185 System.out.println("ann:" + transfer.toString());
187 for (int p = 0, pSize = firstChain.getLength(); p < pSize; p++)
189 // walk along the pdb chain's jalview sequence
191 int fpos = origMap.getSeqPos(rseqpos = firstChain
193 // only look at positions where there is a corresponding position in
199 // p is index into PDB residue entries
200 // rseqpos is pdb sequence position for position p
201 // fpos is sequence position for associated position for rseqpos
202 // tanpos is the column for the mapped sequence position
203 int tanpos = sq.findIndex(fpos) - 1;
204 if (tanpos < 0 || transfer.annotations.length <= tanpos)
206 // gone beyond mapping to the sequence
210 Annotation a = transfer.annotations[tanpos], b = alan.annotations[p];
211 assertEquals("Non-equivalent annotation element at " + p + "("
212 + rseqpos + ")" + " expected at " + fpos + " (alIndex "
213 + tanpos + ")", a == null ? a : a.toString(),
214 b == null ? b : b.toString());
215 System.out.print("(" + a + "|" + b + ")");
224 * corner case for pdb mapping - revealed a problem with the AlignSeq->Mapping
228 @Test(groups = { "Functional" })
229 public void mapFer1From3W5V() throws Exception
231 AlignFrame seqf = new FileLoader(false)
232 .LoadFileWaitTillLoaded(
233 ">FER1_MAIZE/1-150 Ferredoxin-1, chloroplast precursor\nMATVLGSPRAPAFFFSSSSLRAAPAPTAVALPAAKVGIMGRSASSRRRLRAQATYNVKLITPEGEVELQVPD\nDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKE\nEELTGA",
234 FormatAdapter.PASTE, "FASTA");
235 SequenceI newseq = seqf.getViewport().getAlignment().getSequenceAt(0);
236 StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
237 StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
238 new String[] { null }, "examples/3W5V.pdb",
239 jalview.io.FormatAdapter.FILE);
242 AssertJUnit.fail("Couldn't make a mapping for 3W5V to FER1_MAIZE");
247 * compare reference annotation for imported pdb sequence to identical
248 * seuqence with transferred annotation from mapped pdb file
250 @Test(groups = { "Functional" })
251 public void compareTransferredToRefPDBAnnot() throws Exception
253 AlignFrame ref = new FileLoader(false)
254 .LoadFileWaitTillLoaded("test/jalview/ext/jmol/1QCF.pdb",
255 jalview.io.FormatAdapter.FILE);
256 SequenceI refseq = ref.getViewport().getAlignment().getSequenceAt(0);
257 SequenceI newseq = new Sequence(refseq.getName() + "Copy",
258 refseq.getSequenceAsString());
259 // make it harder by shifting the copy vs the reference
260 newseq.setStart(refseq.getStart() + 25);
261 newseq.setEnd(refseq.getLength() + 25 + refseq.getStart());
262 StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
263 ssm.setProcessSecondaryStructure(true);
264 ssm.setAddTempFacAnnot(true);
265 StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
266 new String[] { null }, "test/jalview/ext/jmol/1QCF.pdb",
267 jalview.io.FormatAdapter.FILE);
268 assertTrue(pmap != null);
269 assertEquals("Original and copied sequence of different lengths.",
270 refseq.getLength(), newseq.getLength());
271 assertTrue(refseq.getAnnotation() != null
272 && refseq.getAnnotation().length > 0);
273 assertTrue(newseq.getAnnotation() != null
274 && newseq.getAnnotation().length > 0);
275 for (AlignmentAnnotation oannot : refseq.getAnnotation())
277 for (AlignmentAnnotation tannot : newseq.getAnnotation(oannot.label))
279 for (int p = 0, pSize = refseq.getLength(); p < pSize; p++)
281 Annotation orig = oannot.annotations[p], tran = tannot.annotations[p];
282 assertTrue("Mismatch: coil and non coil site " + p, orig == tran
283 || orig != null && tran != null);
286 assertEquals("Mismatch in secondary structure at site " + p,
287 tran.secondaryStructure, orig.secondaryStructure);