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Coverage Report

  1. Project Clover database Mon Sep 2 2024 17:57:51 BST
  2. Package jalview.ws.dbsources

File Pdb.java

 

Coverage histogram

../../../img/srcFileCovDistChart1.png
56% of files have more coverage

Code metrics

24
59
11
1
298
175
31
0.53
5.36
11
2.82

Classes

Class Line # Actions
Pdb 51 59 31
0.085106388.5%
 

Contributing tests

This file is covered by 203 tests. .

Source view

1   
2    /*
3    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4    * Copyright (C) $$Year-Rel$$ The Jalview Authors
5    *
6    * This file is part of Jalview.
7    *
8    * Jalview is free software: you can redistribute it and/or
9    * modify it under the terms of the GNU General Public License
10    * as published by the Free Software Foundation, either version 3
11    * of the License, or (at your option) any later version.
12    *
13    * Jalview is distributed in the hope that it will be useful, but
14    * WITHOUT ANY WARRANTY; without even the implied warranty
15    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16    * PURPOSE. See the GNU General Public License for more details.
17    *
18    * You should have received a copy of the GNU General Public License
19    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20    * The Jalview Authors are detailed in the 'AUTHORS' file.
21    */
22    package jalview.ws.dbsources;
23   
24    import jalview.api.FeatureSettingsModelI;
25    import jalview.datamodel.AlignmentAnnotation;
26    import jalview.datamodel.AlignmentI;
27    import jalview.datamodel.DBRefEntry;
28    import jalview.datamodel.DBRefSource;
29    import jalview.datamodel.PDBEntry;
30    import jalview.datamodel.PDBEntry.Type;
31    import jalview.datamodel.SequenceI;
32    import jalview.io.DataSourceType;
33    import jalview.io.FileFormat;
34    import jalview.io.FileFormatI;
35    import jalview.io.FormatAdapter;
36    import jalview.io.PDBFeatureSettings;
37    import jalview.structure.StructureImportSettings;
38    import jalview.util.MessageManager;
39    import jalview.ws.ebi.EBIFetchClient;
40   
41    import java.io.File;
42    import java.util.ArrayList;
43    import java.util.List;
44   
45    import com.stevesoft.pat.Regex;
46   
47    /**
48    * @author JimP
49    *
50    */
 
51    public class Pdb extends EbiFileRetrievedProxy
52    {
53    private static final String SEPARATOR = "|";
54   
55    private static final String COLON = ":";
56   
57    private static final int PDB_ID_LENGTH = 4;
58   
 
59  58 toggle public Pdb()
60    {
61  58 super();
62    }
63   
64    /*
65    * (non-Javadoc)
66    *
67    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
68    */
 
69  0 toggle @Override
70    public String getAccessionSeparator()
71    {
72  0 return null;
73    }
74   
75    /*
76    * (non-Javadoc)
77    *
78    * @see jalview.ws.DbSourceProxy#getAccessionValidator()
79    */
 
80  0 toggle @Override
81    public Regex getAccessionValidator()
82    {
83  0 return new Regex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)");
84    }
85   
86    /*
87    * (non-Javadoc)
88    *
89    * @see jalview.ws.DbSourceProxy#getDbSource()
90    */
 
91  3496 toggle @Override
92    public String getDbSource()
93    {
94  3496 return DBRefSource.PDB;
95    }
96   
97    /*
98    * (non-Javadoc)
99    *
100    * @see jalview.ws.DbSourceProxy#getDbVersion()
101    */
 
102  0 toggle @Override
103    public String getDbVersion()
104    {
105  0 return "0";
106    }
107   
108    /*
109    * (non-Javadoc)
110    *
111    * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
112    */
 
113  0 toggle @Override
114    public AlignmentI getSequenceRecords(String queries) throws Exception
115    {
116  0 AlignmentI pdbAlignment = null;
117  0 String chain = null;
118  0 String id = null;
119  0 if (queries.indexOf(COLON) > -1)
120    {
121  0 chain = queries.substring(queries.indexOf(COLON) + 1);
122  0 id = queries.substring(0, queries.indexOf(COLON));
123    }
124    else
125    {
126  0 id = queries;
127    }
128   
129    /*
130    * extract chain code if it is appended to the id and we
131    * don't already have one
132    */
133  0 if (queries.length() > PDB_ID_LENGTH && chain == null)
134    {
135  0 chain = queries.substring(PDB_ID_LENGTH, PDB_ID_LENGTH + 1);
136  0 id = queries.substring(0, PDB_ID_LENGTH);
137    }
138   
139  0 if (!isValidReference(id))
140    {
141  0 jalview.bin.Console
142    .errPrintln("Ignoring invalid pdb query: '" + id + "'");
143  0 stopQuery();
144  0 return null;
145    }
146   
147    /*
148    * ensure that an mmCIF format structure file is saved with extension.cif,
149    * because the Chimera "open" command recognises this extension
150    */
151  0 Type pdbFileFormat = StructureImportSettings
152    .getDefaultStructureFileFormat();
153  0 String ext = pdbFileFormat.getExtension();
154  0 String fetchFormat = pdbFileFormat.getFormat();
155   
156  0 EBIFetchClient ebi = new EBIFetchClient();
157  0 File tmpFile = ebi.fetchDataAsFile("pdb:" + id, fetchFormat, ext);
158  0 file = tmpFile.getAbsolutePath();
159  0 stopQuery();
160  0 if (file == null)
161    {
162  0 return null;
163    }
164  0 try
165    {
166    // todo get rid of Type and use FileFormatI instead?
167  0 FileFormatI fileFormat = (pdbFileFormat == Type.PDB) ? FileFormat.PDB
168    : FileFormat.MMCif;
169  0 pdbAlignment = new FormatAdapter().readFile(tmpFile,
170    DataSourceType.FILE, fileFormat);
171  0 if (pdbAlignment != null)
172    {
173  0 List<SequenceI> toremove = new ArrayList<SequenceI>();
174  0 for (SequenceI pdbcs : pdbAlignment.getSequences())
175    {
176  0 String chid = null;
177    // Mapping map=null;
178  0 for (PDBEntry pid : pdbcs.getAllPDBEntries())
179    {
180  0 if (pid.getFile() == file)
181    {
182  0 chid = pid.getChainCode();
183   
184    }
185    }
186  0 if (chain == null || (chid != null && (chid.equals(chain)
187    || chid.trim().equals(chain.trim())
188    || (chain.trim().length() == 0 && chid.equals("_")))))
189    {
190    // FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
191    // TODO: suggest simplify naming to 1qip|A as default name defined
192  0 pdbcs.setName(jalview.datamodel.DBRefSource.PDB + SEPARATOR + id
193    + SEPARATOR + pdbcs.getName());
194    // Might need to add more metadata to the PDBEntry object
195    // like below
196    /*
197    * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
198    * entry.setId(id); if (entry.getProperty() == null)
199    * entry.setProperty(new Hashtable());
200    * entry.getProperty().put("chains", pdbchain.id + "=" +
201    * sq.getStart() + "-" + sq.getEnd());
202    * sq.getDatasetSequence().addPDBId(entry);
203    */
204    // Add PDB DB Refs
205    // We make a DBRefEtntry because we have obtained the PDB file from
206    // a
207    // verifiable source
208    // JBPNote - PDB DBRefEntry should also carry the chain and mapping
209    // information
210  0 DBRefEntry dbentry = new DBRefEntry(getDbSource(),
211  0 getDbVersion(), (chid == null ? id : id + chid));
212    // dbentry.setMap()
213  0 pdbcs.addDBRef(dbentry);
214    }
215    else
216    {
217    // mark this sequence to be removed from the alignment
218    // - since it's not from the right chain
219  0 toremove.add(pdbcs);
220    }
221    }
222    // now remove marked sequences
223  0 for (SequenceI pdbcs : toremove)
224    {
225  0 pdbAlignment.deleteSequence(pdbcs);
226  0 if (pdbcs.getAnnotation() != null)
227    {
228  0 for (AlignmentAnnotation aa : pdbcs.getAnnotation())
229    {
230  0 pdbAlignment.deleteAnnotation(aa);
231    }
232    }
233    }
234    }
235   
236  0 if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
237    {
238  0 throw new Exception(MessageManager.formatMessage(
239    "exception.no_pdb_records_for_chain", new String[]
240  0 { id, ((chain == null) ? "' '" : chain) }));
241    }
242   
243    } catch (Exception ex) // Problem parsing PDB file
244    {
245  0 stopQuery();
246  0 throw (ex);
247    }
248  0 return pdbAlignment;
249    }
250   
251    /*
252    * (non-Javadoc)
253    *
254    * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
255    */
 
256  0 toggle @Override
257    public boolean isValidReference(String accession)
258    {
259  0 Regex r = getAccessionValidator();
260  0 return r.search(accession.trim());
261    }
262   
263    /**
264    * human glyoxalase
265    */
 
266  0 toggle @Override
267    public String getTestQuery()
268    {
269  0 return "1QIP";
270    }
271   
 
272  3480 toggle @Override
273    public String getDbName()
274    {
275  3480 return "PDB"; // getDbSource();
276    }
277   
 
278  0 toggle @Override
279    public int getTier()
280    {
281  0 return 0;
282    }
283   
284    /**
285    * Returns a descriptor for suitable feature display settings with
286    * <ul>
287    * <li>ResNums or insertions features visible</li>
288    * <li>insertions features coloured red</li>
289    * <li>ResNum features coloured by label</li>
290    * <li>Insertions displayed above (on top of) ResNums</li>
291    * </ul>
292    */
 
293  42 toggle @Override
294    public FeatureSettingsModelI getFeatureColourScheme()
295    {
296  42 return new PDBFeatureSettings();
297    }
298    }
  • Report generated by OpenClover v 4.4.1 on Mon Sep 2 2024 18:05:00 BST using coverage data from Mon Sep 2 2024 18:04:45 BST.
  • OpenClover is free and open-source software.