Clover icon

Coverage Report

  1. Project Clover database Thu Dec 4 2025 14:43:25 GMT
  2. Package jalview.ws.dbsources

File Pdb.java

 

Coverage histogram

../../../img/srcFileCovDistChart1.png
57% of files have more coverage

Code metrics

26
61
11
1
306
182
32
0.52
5.55
11
2.91

Classes

Class Line # Actions
Pdb 52 61 32
0.081632658.2%
 

Contributing tests

This file is covered by 193 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.util.Platform;
40    import jalview.ws.ebi.EBIFetchClient;
41   
42    import java.io.File;
43    import java.util.ArrayList;
44    import java.util.List;
45   
46    import com.stevesoft.pat.Regex;
47   
48    /**
49    * @author JimP
50    *
51    */
 
52    public class Pdb extends EbiFileRetrievedProxy
53    {
54    private static final String SEPARATOR = "|";
55   
56    private static final String COLON = ":";
57   
58    private static final int PDB_ID_LENGTH = 4;
59   
60    private static Regex ACCESSION_REGEX;
61   
 
62  70 toggle public Pdb()
63    {
64  70 super();
65    }
66   
67    /*
68    * (non-Javadoc)
69    *
70    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
71    */
 
72  0 toggle @Override
73    public String getAccessionSeparator()
74    {
75  0 return null;
76    }
77   
78    /*
79    * (non-Javadoc)
80    *
81    * @see jalview.ws.DbSourceProxy#getAccessionValidator()
82    */
 
83  0 toggle @Override
84    public Regex getAccessionValidator()
85    {
86  0 if (ACCESSION_REGEX == null)
87    {
88  0 ACCESSION_REGEX = Platform
89    .newRegex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)");
90    }
91  0 return ACCESSION_REGEX;
92    }
93   
94    /*
95    * (non-Javadoc)
96    *
97    * @see jalview.ws.DbSourceProxy#getDbSource()
98    */
 
99  8263 toggle @Override
100    public String getDbSource()
101    {
102  8263 return DBRefSource.PDB;
103    }
104   
105    /*
106    * (non-Javadoc)
107    *
108    * @see jalview.ws.DbSourceProxy#getDbVersion()
109    */
 
110  0 toggle @Override
111    public String getDbVersion()
112    {
113  0 return "0";
114    }
115   
116    /*
117    * (non-Javadoc)
118    *
119    * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
120    */
 
121  0 toggle @Override
122    public AlignmentI getSequenceRecords(String queries) throws Exception
123    {
124  0 AlignmentI pdbAlignment = null;
125  0 String chain = null;
126  0 String id = null;
127  0 if (queries.indexOf(COLON) > -1)
128    {
129  0 chain = queries.substring(queries.indexOf(COLON) + 1);
130  0 id = queries.substring(0, queries.indexOf(COLON));
131    }
132    else
133    {
134  0 id = queries;
135    }
136   
137    /*
138    * extract chain code if it is appended to the id and we
139    * don't already have one
140    */
141  0 if (queries.length() > PDB_ID_LENGTH && chain == null)
142    {
143  0 chain = queries.substring(PDB_ID_LENGTH, PDB_ID_LENGTH + 1);
144  0 id = queries.substring(0, PDB_ID_LENGTH);
145    }
146   
147  0 if (!isValidReference(id))
148    {
149  0 jalview.bin.Console
150    .errPrintln("Ignoring invalid pdb query: '" + id + "'");
151  0 stopQuery();
152  0 return null;
153    }
154   
155    /*
156    * ensure that an mmCIF format structure file is saved with extension.cif,
157    * because the Chimera "open" command recognises this extension
158    */
159  0 Type pdbFileFormat = StructureImportSettings
160    .getDefaultStructureFileFormat();
161  0 String ext = pdbFileFormat.getExtension();
162  0 String fetchFormat = pdbFileFormat.getFormat();
163   
164  0 EBIFetchClient ebi = new EBIFetchClient();
165  0 File tmpFile = ebi.fetchDataAsFile("pdb:" + id, fetchFormat, ext);
166  0 file = tmpFile.getAbsolutePath();
167  0 stopQuery();
168  0 if (file == null)
169    {
170  0 return null;
171    }
172  0 try
173    {
174    // todo get rid of Type and use FileFormatI instead?
175  0 FileFormatI fileFormat = (pdbFileFormat == Type.PDB) ? FileFormat.PDB
176    : FileFormat.MMCif;
177  0 pdbAlignment = new FormatAdapter().readFile(tmpFile,
178    DataSourceType.FILE, fileFormat);
179  0 if (pdbAlignment != null)
180    {
181  0 List<SequenceI> toremove = new ArrayList<SequenceI>();
182  0 for (SequenceI pdbcs : pdbAlignment.getSequences())
183    {
184  0 String chid = null;
185    // Mapping map=null;
186  0 for (PDBEntry pid : pdbcs.getAllPDBEntries())
187    {
188  0 if (pid.getFile() == file)
189    {
190  0 chid = pid.getChainCode();
191   
192    }
193    }
194  0 if (chain == null || (chid != null && (chid.equals(chain)
195    || chid.trim().equals(chain.trim())
196    || (chain.trim().length() == 0 && chid.equals("_")))))
197    {
198    // FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
199    // TODO: suggest simplify naming to 1qip|A as default name defined
200  0 pdbcs.setName(jalview.datamodel.DBRefSource.PDB + SEPARATOR + id
201    + SEPARATOR + pdbcs.getName());
202    // Might need to add more metadata to the PDBEntry object
203    // like below
204    /*
205    * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
206    * entry.setId(id); if (entry.getProperty() == null)
207    * entry.setProperty(new Hashtable());
208    * entry.getProperty().put("chains", pdbchain.id + "=" +
209    * sq.getStart() + "-" + sq.getEnd());
210    * sq.getDatasetSequence().addPDBId(entry);
211    */
212    // Add PDB DB Refs
213    // We make a DBRefEtntry because we have obtained the PDB file from
214    // a
215    // verifiable source
216    // JBPNote - PDB DBRefEntry should also carry the chain and mapping
217    // information
218  0 DBRefEntry dbentry = new DBRefEntry(getDbSource(),
219  0 getDbVersion(), (chid == null ? id : id + chid));
220    // dbentry.setMap()
221  0 pdbcs.addDBRef(dbentry);
222    }
223    else
224    {
225    // mark this sequence to be removed from the alignment
226    // - since it's not from the right chain
227  0 toremove.add(pdbcs);
228    }
229    }
230    // now remove marked sequences
231  0 for (SequenceI pdbcs : toremove)
232    {
233  0 pdbAlignment.deleteSequence(pdbcs);
234  0 if (pdbcs.getAnnotation() != null)
235    {
236  0 for (AlignmentAnnotation aa : pdbcs.getAnnotation())
237    {
238  0 pdbAlignment.deleteAnnotation(aa);
239    }
240    }
241    }
242    }
243   
244  0 if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
245    {
246  0 throw new Exception(MessageManager.formatMessage(
247    "exception.no_pdb_records_for_chain", new String[]
248  0 { id, ((chain == null) ? "' '" : chain) }));
249    }
250   
251    } catch (Exception ex) // Problem parsing PDB file
252    {
253  0 stopQuery();
254  0 throw (ex);
255    }
256  0 return pdbAlignment;
257    }
258   
259    /*
260    * (non-Javadoc)
261    *
262    * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
263    */
 
264  0 toggle @Override
265    public boolean isValidReference(String accession)
266    {
267  0 Regex r = getAccessionValidator();
268  0 return r.search(accession.trim());
269    }
270   
271    /**
272    * human glyoxalase
273    */
 
274  0 toggle @Override
275    public String getTestQuery()
276    {
277  0 return "1QIP";
278    }
279   
 
280  8246 toggle @Override
281    public String getDbName()
282    {
283  8246 return "PDB"; // getDbSource();
284    }
285   
 
286  0 toggle @Override
287    public int getTier()
288    {
289  0 return 0;
290    }
291   
292    /**
293    * Returns a descriptor for suitable feature display settings with
294    * <ul>
295    * <li>ResNums or insertions features visible</li>
296    * <li>insertions features coloured red</li>
297    * <li>ResNum features coloured by label</li>
298    * <li>Insertions displayed above (on top of) ResNums</li>
299    * </ul>
300    */
 
301  53 toggle @Override
302    public FeatureSettingsModelI getFeatureColourScheme()
303    {
304  53 return new PDBFeatureSettings();
305    }
306    }
  • Report generated by OpenClover v 4.4.1 on Thu Dec 4 2025 14:53:28 GMT using coverage data from Thu Dec 4 2025 14:53:14 GMT.
  • OpenClover is free and open-source software.