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  1. Project Clover database Wed Nov 13 2024 16:12:26 GMT
  2. Package jalview.structure

File Mapping.java

 

Coverage histogram

../../img/srcFileCovDistChart3.png
52% of files have more coverage

Code metrics

24
109
5
1
310
238
18
0.17
21.8
5
3.6

Classes

Class Line # Actions
Mapping 42 109 18
0.275362327.5%
 

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.structure;
22   
23    import static org.testng.AssertJUnit.assertEquals;
24    import static org.testng.AssertJUnit.assertTrue;
25   
26    import org.testng.Assert;
27    import org.testng.AssertJUnit;
28    import org.testng.annotations.BeforeClass;
29    import org.testng.annotations.Test;
30   
31    import jalview.datamodel.AlignmentAnnotation;
32    import jalview.datamodel.Annotation;
33    import jalview.datamodel.Sequence;
34    import jalview.datamodel.SequenceI;
35    import jalview.gui.AlignFrame;
36    import jalview.gui.JvOptionPane;
37    import jalview.io.DataSourceType;
38    import jalview.io.FileFormat;
39    import jalview.io.FileLoader;
40    import jalview.io.StructureFile;
41   
 
42    public class Mapping
43    {
44   
 
45  1 toggle @BeforeClass(alwaysRun = true)
46    public void setUpJvOptionPane()
47    {
48  1 JvOptionPane.setInteractiveMode(false);
49  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
50    }
51   
52    /*
53    * more test data
54    *
55    * 1QCF|A/101-121 SFQKGDQMVVLEESGEWWKAR Ser 114 jumps to Gly 116 at position
56    * 115 in PDB Res Numbering secondary structure numbers in jmol seem to be in
57    * msd numbering, not pdb res numbering.
58    */
 
59  0 toggle @Test(groups = { "Functional" }, enabled = false)
60    public void pdbEntryPositionMap() throws Exception
61    {
62  0 Assert.fail("This test intentionally left to fail");
63  0 for (int offset = 0; offset < 20; offset += 6)
64    {
65    // check we put the secondary structure in the right position
66  0 Sequence uprot = new Sequence("TheProtSeq",
67    "DAWEIPRESLKLEKKLGAGQFGEVWMATYNKHTKVAVKTMKPGSMSVEAFLAEANVMKTL");
68  0 uprot.setStart(offset + 258); // make it harder - create a fake
69    // relocation problem for jalview to
70    // deal with
71  0 uprot.setEnd(uprot.getStart() + uprot.getLength() - 1);
72    // original numbers taken from
73    // http://www.ebi.ac.uk/pdbe-srv/view/entry/1qcf/secondary.html
74    // these are in numbering relative to the subsequence above
75  0 int coils[] = { 266, 275, 278, 287, 289, 298, 302, 316 },
76    helices[] = new int[]
77    { 303, 315 }, sheets[] = new int[] { 267, 268, 269, 270 };
78   
79  0 StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
80  0 StructureFile pmap = ssm.setMapping(true, new SequenceI[] { uprot },
81    new String[]
82    { "A" }, "test/jalview/ext/jmol/1QCF.pdb",
83    DataSourceType.FILE, null, null);
84  0 assertTrue(pmap != null);
85  0 SequenceI protseq = pmap.getSeqsAsArray()[0];
86  0 AlignmentAnnotation pstra = protseq
87    .getAnnotation("Secondary Structure")[0];
88  0 int pinds, pinde;
89  0 pstra.restrict((pinds = protseq.findIndex(258) - 1),
90    pinde = (protseq.findIndex(317) - 1));
91  0 int op;
92  0 System.out.println("PDB Annot");
93  0 for (char c : protseq.getSubSequence(pinds, pinde).getSequence())
94    {
95  0 System.out.print(c + ", ");
96    }
97  0 System.out.println("\n" + pstra + "\n\nsubsequence\n");
98  0 for (char c : uprot.getSequence())
99    {
100  0 System.out.print(c + ", ");
101    }
102  0 System.out.println("");
103  0 for (AlignmentAnnotation ss : uprot
104    .getAnnotation("Secondary Structure"))
105    {
106  0 ss.adjustForAlignment();
107  0 System.out.println("Uniprot Annot\n" + ss);
108  0 assertTrue(ss.hasIcons);
109  0 char expected = 'H';
110  0 for (int p : helices)
111    {
112  0 Annotation a = ss.annotations[op = (uprot.findIndex(offset + p)
113    - 1)];
114  0 assertTrue("Expected a helix at position " + p
115    + uprot.getCharAt(op) + " but got coil", a != null);
116  0 assertEquals("Expected a helix at position " + p,
117    a.secondaryStructure, expected);
118    }
119  0 expected = 'E';
120  0 for (int p : sheets)
121    {
122  0 Annotation a = ss.annotations[uprot.findIndex(offset + p) - 1];
123  0 assertTrue("Expected a strand at position " + p + " but got coil",
124    a != null);
125  0 assertEquals("Expected a strand at position " + p,
126    a.secondaryStructure, expected);
127    }
128  0 expected = ' ';
129  0 for (int p : coils)
130    {
131  0 Annotation a = ss.annotations[uprot.findIndex(offset + p) - 1];
132  0 assertTrue("Expected coil at position " + p + " but got "
133    + a.secondaryStructure, a == null);
134    }
135    }
136    }
137    }
138   
 
139  0 toggle @Test(groups = { "Functional" }, enabled = false)
140    public void testPDBentryMapping() throws Exception
141    {
142  0 Assert.fail("This test intentionally left to fail");
143  0 Sequence sq = new Sequence("1GAQ A subseq 126 to 219",
144    "EIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKM");
145  0 Sequence sq1 = new Sequence(sq);
146  0 String inFile;
147  0 StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
148    // Associate the 1GAQ pdb file with the subsequence 'imported' from another
149    // source
150  0 StructureFile pde = ssm.setMapping(true, new SequenceI[] { sq },
151    new String[]
152    { "A" }, inFile = "examples/1gaq.txt", DataSourceType.FILE,
153    null, null);
154  0 assertTrue("PDB File couldn't be found", pde != null);
155  0 StructureMapping[] mp = ssm.getMapping(inFile);
156  0 assertTrue("No mappings made.", mp != null && mp.length > 0);
157  0 int nsecStr = 0, nsTemp = 0;
158    // test for presence of transferred annotation on sequence
159  0 for (AlignmentAnnotation alan : sq.getAnnotation())
160    {
161  0 if (alan.hasIcons)
162    {
163  0 nsecStr++;
164    }
165  0 if (alan.graph == alan.LINE_GRAPH)
166    {
167  0 nsTemp++;
168    }
169    }
170  0 assertEquals(
171    "Only one secondary structure should be transferred to associated sequence.",
172    1, nsecStr);
173  0 assertEquals(
174    "Only two line graphs should be transferred to associated sequence.",
175    2, nsTemp);
176    // Now test the transfer function and compare annotated positions
177  0 for (StructureMapping origMap : mp)
178    {
179  0 if (origMap.getSequence() == sq)
180    {
181  0 assertEquals("Mapping was incomplete.", sq.getLength() - 1,
182    (origMap.getPDBResNum(sq.getEnd())
183    - origMap.getPDBResNum(sq.getStart())));
184    // sanity check - if this fails, mapping from first position in sequence
185    // we want to transfer to is not where we expect
186  0 assertEquals(1, origMap.getSeqPos(126));
187  0 SequenceI firstChain = pde.getSeqs().get(0);
188    // Compare the annotated positions on the PDB chain sequence with the
189    // annotation on the associated sequence
190  0 for (AlignmentAnnotation alan : firstChain.getAnnotation())
191    {
192  0 AlignmentAnnotation transfer = origMap.transfer(alan);
193  0 System.out.println("pdb:" + firstChain.getSequenceAsString());
194  0 System.out.println("ann:" + alan.toString());
195  0 System.out.println("pdb:" + sq.getSequenceAsString());
196  0 System.out.println("ann:" + transfer.toString());
197   
198  0 for (int p = 0, pSize = firstChain.getLength(); p < pSize; p++)
199    {
200    // walk along the pdb chain's jalview sequence
201  0 int rseqpos;
202  0 int fpos = origMap
203    .getSeqPos(rseqpos = firstChain.findPosition(p));
204    // only look at positions where there is a corresponding position in
205    // mapping
206  0 if (fpos < 1)
207    {
208  0 continue;
209    }
210    // p is index into PDB residue entries
211    // rseqpos is pdb sequence position for position p
212    // fpos is sequence position for associated position for rseqpos
213    // tanpos is the column for the mapped sequence position
214  0 int tanpos = sq.findIndex(fpos) - 1;
215  0 if (tanpos < 0 || transfer.annotations.length <= tanpos)
216    {
217    // gone beyond mapping to the sequence
218  0 break;
219    }
220   
221  0 Annotation a = transfer.annotations[tanpos],
222    b = alan.annotations[p];
223  0 assertEquals(
224    "Non-equivalent annotation element at " + p + "("
225    + rseqpos + ")" + " expected at " + fpos
226    + " (alIndex " + tanpos + ")",
227  0 a == null ? a : a.toString(),
228  0 b == null ? b : b.toString());
229  0 System.out.print("(" + a + "|" + b + ")");
230    }
231   
232    }
233    }
234    }
235    }
236   
237    /**
238    * corner case for pdb mapping - revealed a problem with the AlignSeq->Mapping
239    * transform
240    *
241    */
 
242  1 toggle @Test(groups = { "Functional" })
243    public void mapFer1From3W5V() throws Exception
244    {
245  1 AlignFrame seqf = new FileLoader(false).LoadFileWaitTillLoaded(
246    ">FER1_MAIZE/1-150 Ferredoxin-1, chloroplast precursor\nMATVLGSPRAPAFFFSSSSLRAAPAPTAVALPAAKVGIMGRSASSRRRLRAQATYNVKLITPEGEVELQVPD\nDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKE\nEELTGA",
247    DataSourceType.PASTE, FileFormat.Fasta);
248  1 SequenceI newseq = seqf.getViewport().getAlignment().getSequenceAt(0);
249  1 StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
250  1 StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
251    new String[]
252    { null }, "examples/3W5V.pdb", DataSourceType.FILE, null, null);
253  1 if (pmap == null)
254    {
255  0 AssertJUnit.fail("Couldn't make a mapping for 3W5V to FER1_MAIZE");
256    }
257    }
258   
259    /**
260    * compare reference annotation for imported pdb sequence to identical
261    * seuqence with transferred annotation from mapped pdb file
262    */
 
263  1 toggle @Test(groups = { "Functional" })
264    public void compareTransferredToRefPDBAnnot() throws Exception
265    {
266  1 StructureImportSettings.setProcessSecondaryStructure(true);
267  1 StructureImportSettings.setVisibleChainAnnotation(true);
268  1 StructureImportSettings.setShowSeqFeatures(true);
269  1 AlignFrame ref = new FileLoader(false).LoadFileWaitTillLoaded(
270    "test/jalview/ext/jmol/1QCF.pdb", DataSourceType.FILE);
271  1 SequenceI refseq = ref.getViewport().getAlignment().getSequenceAt(0);
272  1 SequenceI newseq = new Sequence(refseq.getName() + "Copy",
273    refseq.getSequenceAsString());
274    // make it harder by shifting the copy vs the reference
275  1 newseq.setStart(refseq.getStart() + 25);
276  1 newseq.setEnd(refseq.getLength() + 25 + refseq.getStart());
277  1 StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
278  1 ssm.setProcessSecondaryStructure(true);
279  1 ssm.setAddTempFacAnnot(true);
280  1 StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
281    new String[]
282    { null }, "test/jalview/ext/jmol/1QCF.pdb", DataSourceType.FILE,
283    null, null);
284  1 assertTrue(pmap != null);
285  1 assertEquals("Original and copied sequence of different lengths.",
286    refseq.getLength(), newseq.getLength());
287  1 assertTrue(refseq.getAnnotation() != null
288    && refseq.getAnnotation().length > 0);
289  1 assertTrue(newseq.getAnnotation() != null
290    && newseq.getAnnotation().length > 0);
291  1 for (AlignmentAnnotation oannot : refseq.getAnnotation())
292    {
293  2 for (AlignmentAnnotation tannot : newseq.getAnnotation(oannot.label))
294    {
295  902 for (int p = 0, pSize = refseq.getLength(); p < pSize; p++)
296    {
297  900 Annotation orig = oannot.annotations[p],
298    tran = tannot.annotations[p];
299  900 assertTrue("Mismatch: coil and non coil site " + p,
300    orig == tran || orig != null && tran != null);
301  900 if (tran != null)
302    {
303  678 assertEquals("Mismatch in secondary structure at site " + p,
304    tran.secondaryStructure, orig.secondaryStructure);
305    }
306    }
307    }
308    }
309    }
310    }