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Coverage Report

  1. Project Clover database Mon Nov 18 2024 09:56:54 GMT
  2. Package jalview.ws.dbsources

File Pdb.java

 

Coverage histogram

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

Code metrics

28
70
12
1
328
199
34
0.49
5.83
12
2.83

Classes

Class Line # Actions
Pdb 53 70 34
0.072727277.3%
 

Contributing tests

This file is covered by 183 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.bin.Cache;
26    import jalview.datamodel.AlignmentAnnotation;
27    import jalview.datamodel.AlignmentI;
28    import jalview.datamodel.DBRefEntry;
29    import jalview.datamodel.DBRefSource;
30    import jalview.datamodel.PDBEntry;
31    import jalview.datamodel.PDBEntry.Type;
32    import jalview.datamodel.SequenceI;
33    import jalview.io.DataSourceType;
34    import jalview.io.FileFormat;
35    import jalview.io.FileFormatI;
36    import jalview.io.FormatAdapter;
37    import jalview.io.PDBFeatureSettings;
38    import jalview.structure.StructureImportSettings;
39    import jalview.util.MessageManager;
40    import jalview.ws.ebi.EBIFetchClient;
41   
42    import java.io.File;
43    import java.util.ArrayList;
44    import java.util.List;
45    import java.util.Locale;
46   
47    import com.stevesoft.pat.Regex;
48   
49    /**
50    * @author JimP
51    *
52    */
 
53    public class Pdb extends EbiFileRetrievedProxy
54    {
55    private static final String SEPARATOR = "|";
56   
57    private static final String COLON = ":";
58   
59    private static final int PDB_ID_LENGTH = 4;
60   
 
61  59 toggle public Pdb()
62    {
63  59 super();
64    }
65   
66    /*
67    * (non-Javadoc)
68    *
69    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
70    */
 
71  0 toggle @Override
72    public String getAccessionSeparator()
73    {
74  0 return null;
75    }
76   
77    /*
78    * (non-Javadoc)
79    *
80    * @see jalview.ws.DbSourceProxy#getAccessionValidator()
81    */
 
82  0 toggle @Override
83    public Regex getAccessionValidator()
84    {
85  0 return new Regex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)");
86    }
87   
88    /*
89    * (non-Javadoc)
90    *
91    * @see jalview.ws.DbSourceProxy#getDbSource()
92    */
 
93  2152 toggle @Override
94    public String getDbSource()
95    {
96  2152 return DBRefSource.PDB;
97    }
98   
99    /*
100    * (non-Javadoc)
101    *
102    * @see jalview.ws.DbSourceProxy#getDbVersion()
103    */
 
104  0 toggle @Override
105    public String getDbVersion()
106    {
107  0 return "0";
108    }
109   
110    /*
111    * (non-Javadoc)
112    *
113    * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
114    */
 
115  0 toggle @Override
116    public AlignmentI getSequenceRecords(String queries) throws Exception
117    {
118  0 updateConfiguration();
119  0 AlignmentI pdbAlignment = null;
120  0 String chain = null;
121  0 String id = null;
122  0 if (queries.indexOf(COLON) > -1)
123    {
124  0 chain = queries.substring(queries.indexOf(COLON) + 1);
125  0 id = queries.substring(0, queries.indexOf(COLON));
126    }
127    else
128    {
129  0 id = queries;
130    }
131   
132    /*
133    * extract chain code if it is appended to the id and we
134    * don't already have one
135    */
136  0 if (queries.length() > PDB_ID_LENGTH && chain == null)
137    {
138  0 chain = queries.substring(PDB_ID_LENGTH, PDB_ID_LENGTH + 1);
139  0 id = queries.substring(0, PDB_ID_LENGTH);
140    }
141   
142  0 if (!isValidReference(id))
143    {
144  0 jalview.bin.Console
145    .errPrintln("Ignoring invalid pdb query: '" + id + "'");
146  0 stopQuery();
147  0 return null;
148    }
149   
150    /*
151    * ensure that an mmCIF format structure file is saved with extension.cif,
152    * because the Chimera "open" command recognises this extension
153    */
154  0 Type pdbFileFormat = StructureImportSettings
155    .getDefaultStructureFileFormat();
156  0 String ext = pdbFileFormat.getExtension();
157  0 String fetchFormat = pdbFileFormat.getFormat();
158   
159  0 EBIFetchClient ebi = new EBIFetchClient();
160  0 File tmpFile = ebi.fetchDataAsFile("pdb:" + id, fetchFormat, ext);
161  0 file = tmpFile.getAbsolutePath();
162  0 stopQuery();
163  0 if (file == null)
164    {
165  0 return null;
166    }
167  0 try
168    {
169    // todo get rid of Type and use FileFormatI instead?
170  0 FileFormatI fileFormat = (pdbFileFormat == Type.PDB) ? FileFormat.PDB
171    : FileFormat.MMCif;
172  0 pdbAlignment = new FormatAdapter().readFile(tmpFile,
173    DataSourceType.FILE, fileFormat);
174  0 if (pdbAlignment != null)
175    {
176  0 List<SequenceI> toremove = new ArrayList<SequenceI>();
177  0 for (SequenceI pdbcs : pdbAlignment.getSequences())
178    {
179  0 String chid = null;
180    // Mapping map=null;
181  0 for (PDBEntry pid : pdbcs.getAllPDBEntries())
182    {
183  0 if (pid.getFile() == file)
184    {
185  0 chid = pid.getChainCode();
186   
187    }
188    }
189  0 if (chain == null || (chid != null && (chid.equals(chain)
190    || chid.trim().equals(chain.trim())
191    || (chain.trim().length() == 0 && chid.equals("_")))))
192    {
193    // FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
194    // TODO: suggest simplify naming to 1qip|A as default name defined
195  0 if (legacyJalviewPDBeName)
196    {
197  0 pdbcs.setName(jalview.datamodel.DBRefSource.PDB + SEPARATOR + id
198    + SEPARATOR + pdbcs.getName());
199    } else {
200  0 if (simpleChainName)
201    {
202  0 int sep_pos = pdbcs.getName().indexOf(SEPARATOR);
203  0 String cid = pdbcs.getName().substring(0,sep_pos);
204  0 cid = cid.toLowerCase(Locale.ROOT);
205  0 pdbcs.setName(cid+"_"+pdbcs.getName().substring(sep_pos+1));
206  0 };
207    }
208    // Might need to add more metadata to the PDBEntry object
209    // like below
210    /*
211    * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
212    * entry.setId(id); if (entry.getProperty() == null)
213    * entry.setProperty(new Hashtable());
214    * entry.getProperty().put("chains", pdbchain.id + "=" +
215    * sq.getStart() + "-" + sq.getEnd());
216    * sq.getDatasetSequence().addPDBId(entry);
217    */
218    // Add PDB DB Refs
219    // We make a DBRefEtntry because we have obtained the PDB file from
220    // a
221    // verifiable source
222    // JBPNote - PDB DBRefEntry should also carry the chain and mapping
223    // information
224  0 DBRefEntry dbentry = new DBRefEntry(getDbSource(),
225  0 getDbVersion(), (chid == null ? id : id + chid));
226    // dbentry.setMap()
227  0 pdbcs.addDBRef(dbentry);
228    }
229    else
230    {
231    // mark this sequence to be removed from the alignment
232    // - since it's not from the right chain
233  0 toremove.add(pdbcs);
234    }
235    }
236    // now remove marked sequences
237  0 for (SequenceI pdbcs : toremove)
238    {
239  0 pdbAlignment.deleteSequence(pdbcs);
240  0 if (pdbcs.getAnnotation() != null)
241    {
242  0 for (AlignmentAnnotation aa : pdbcs.getAnnotation())
243    {
244  0 pdbAlignment.deleteAnnotation(aa);
245    }
246    }
247    }
248    }
249   
250  0 if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
251    {
252  0 throw new Exception(MessageManager.formatMessage(
253    "exception.no_pdb_records_for_chain", new String[]
254  0 { id, ((chain == null) ? "' '" : chain) }));
255    }
256   
257    } catch (Exception ex) // Problem parsing PDB file
258    {
259  0 stopQuery();
260  0 throw (ex);
261    }
262  0 return pdbAlignment;
263    }
264   
265    boolean simpleChainName=false;
266    boolean legacyJalviewPDBeName=true;
267   
268    private static String SIMPLE="SIMPLE";
269    private static String LEGACY="LEGACY";
270   
271    /**
272    * update the chain naming conventions based on the configuration
273    */
 
274  0 toggle private void updateConfiguration()
275    {
276  0 final String nameConf = Cache.getDefault(Cache.PDB_CHAIN_NAME, "SIMPLE");
277  0 simpleChainName = SIMPLE.equals(nameConf);
278  0 legacyJalviewPDBeName = LEGACY.equals(nameConf);
279    }
280   
281    /*
282    * (non-Javadoc)
283    *
284    * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
285    */
 
286  0 toggle @Override
287    public boolean isValidReference(String accession)
288    {
289  0 Regex r = getAccessionValidator();
290  0 return r.search(accession.trim());
291    }
292   
293    /**
294    * human glyoxalase
295    */
 
296  0 toggle @Override
297    public String getTestQuery()
298    {
299  0 return "1QIP";
300    }
301   
 
302  2136 toggle @Override
303    public String getDbName()
304    {
305  2136 return "PDB"; // getDbSource();
306    }
307   
 
308  0 toggle @Override
309    public int getTier()
310    {
311  0 return 0;
312    }
313   
314    /**
315    * Returns a descriptor for suitable feature display settings with
316    * <ul>
317    * <li>ResNums or insertions features visible</li>
318    * <li>insertions features coloured red</li>
319    * <li>ResNum features coloured by label</li>
320    * <li>Insertions displayed above (on top of) ResNums</li>
321    * </ul>
322    */
 
323  43 toggle @Override
324    public FeatureSettingsModelI getFeatureColourScheme()
325    {
326  43 return new PDBFeatureSettings();
327    }
328    }
  • Report generated by OpenClover v 4.4.1 on Mon Nov 18 2024 10:04:05 GMT using coverage data from Mon Nov 18 2024 10:03:47 GMT.
  • OpenClover is free and open-source software.