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Coverage Report

  1. Project Clover database Thu Nov 28 2024 18:06:40 GMT
  2. Package jalview.gui.structurechooser

File PDBStructureChooserQuerySource.java

 

Coverage histogram

../../../img/srcFileCovDistChart7.png
31% of files have more coverage

Code metrics

34
123
12
1
391
270
33
0.27
10.25
12
2.75

Classes

Class Line # Actions
PDBStructureChooserQuerySource 56 123 33
0.621301862.1%
 

Contributing tests

This file is covered by 43 tests. .

Source view

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.gui.structurechooser;
22   
23    import java.util.Locale;
24   
25    import java.util.ArrayList;
26    import java.util.Collection;
27    import java.util.HashSet;
28    import java.util.LinkedHashSet;
29    import java.util.List;
30    import java.util.Objects;
31    import java.util.Set;
32   
33    import javax.swing.JTable;
34    import javax.swing.table.TableModel;
35   
36    import jalview.datamodel.DBRefEntry;
37    import jalview.datamodel.DBRefSource;
38    import jalview.datamodel.PDBEntry;
39    import jalview.datamodel.SequenceI;
40    import jalview.fts.api.FTSData;
41    import jalview.fts.api.FTSDataColumnI;
42    import jalview.fts.api.FTSRestClientI;
43    import jalview.fts.core.FTSDataColumnPreferences;
44    import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
45    import jalview.fts.core.FTSRestRequest;
46    import jalview.fts.core.FTSRestResponse;
47    import jalview.fts.service.pdb.PDBFTSRestClient;
48    import jalview.jbgui.FilterOption;
49    import jalview.util.MessageManager;
50   
51    /**
52    * logic for querying the PDBe API for structures of sequences
53    *
54    * @author jprocter
55    */
 
56    public class PDBStructureChooserQuerySource
57    extends StructureChooserQuerySource
58    {
59   
60    private static int MAX_QLENGTH = 7820;
61   
62    protected FTSRestRequest lastPdbRequest;
63   
64    protected FTSRestClientI pdbRestClient;
65   
 
66  68 toggle public PDBStructureChooserQuerySource()
67    {
68  68 pdbRestClient = PDBFTSRestClient.getInstance();
69  68 docFieldPrefs = new FTSDataColumnPreferences(
70    PreferenceSource.STRUCTURE_CHOOSER,
71    PDBFTSRestClient.getInstance());
72   
73    }
74   
75    /**
76    * Builds a query string for a given sequences using its DBRef entries
77    *
78    * @param seq
79    * the sequences to build a query for
80    * @return the built query string
81    */
82   
 
83  6 toggle public String buildQuery(SequenceI seq)
84    {
85  6 boolean isPDBRefsFound = false;
86  6 boolean isUniProtRefsFound = false;
87  6 StringBuilder queryBuilder = new StringBuilder();
88  6 Set<String> seqRefs = new LinkedHashSet<>();
89   
90    /*
91    * note PDBs as DBRefEntry so they are not duplicated in query
92    */
93  6 Set<String> pdbids = new HashSet<>();
94   
95  6 if (seq.getAllPDBEntries() != null
96    && queryBuilder.length() < MAX_QLENGTH)
97    {
98  6 for (PDBEntry entry : seq.getAllPDBEntries())
99    {
100  2 if (isValidSeqName(entry.getId()))
101    {
102  2 String id = entry.getId().toLowerCase(Locale.ROOT);
103  2 queryBuilder.append("pdb_id:").append(id).append(" OR ");
104  2 isPDBRefsFound = true;
105  2 pdbids.add(id);
106    }
107    }
108    }
109   
110  6 List<DBRefEntry> refs = seq.getDBRefs();
111  6 if (refs != null && refs.size() != 0)
112    {
113  24 for (int ib = 0, nb = refs.size(); ib < nb; ib++)
114    {
115  19 DBRefEntry dbRef = refs.get(ib);
116  19 if (isValidSeqName(getDBRefId(dbRef))
117    && queryBuilder.length() < MAX_QLENGTH)
118    {
119  19 if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
120    {
121  2 queryBuilder.append("uniprot_accession:")
122    .append(getDBRefId(dbRef)).append(" OR ");
123  2 queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef))
124    .append(" OR ");
125  2 isUniProtRefsFound = true;
126    }
127  17 else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
128    {
129   
130  1 String id = getDBRefId(dbRef).toLowerCase(Locale.ROOT);
131  1 if (!pdbids.contains(id))
132    {
133  1 queryBuilder.append("pdb_id:").append(id).append(" OR ");
134  1 isPDBRefsFound = true;
135  1 pdbids.add(id);
136    }
137    }
138    else
139    {
140  16 seqRefs.add(getDBRefId(dbRef));
141    }
142    }
143    }
144    }
145   
146  6 if (!isPDBRefsFound && !isUniProtRefsFound)
147    {
148  2 String seqName = seq.getName();
149  2 seqName = sanitizeSeqName(seqName);
150  2 String[] names = seqName.toLowerCase(Locale.ROOT).split("\\|");
151  2 for (String name : names)
152    {
153    // jalview.bin.Console.outPrintln("Found name : " + name);
154  8 name.trim();
155  8 if (isValidSeqName(name))
156    {
157  4 seqRefs.add(name);
158    }
159    }
160   
161  2 for (String seqRef : seqRefs)
162    {
163  6 queryBuilder.append("text:").append(seqRef).append(" OR ");
164    }
165    }
166   
167  6 int endIndex = queryBuilder.lastIndexOf(" OR ");
168  6 if (queryBuilder.toString().length() < 6)
169    {
170  0 return null;
171    }
172  6 String query = queryBuilder.toString().substring(0, endIndex);
173  6 return query;
174    }
175   
176    /**
177    * Remove the following special characters from input string +, -, &, !, (, ),
178    * {, }, [, ], ^, ", ~, *, ?, :, \
179    *
180    * @param seqName
181    * @return
182    */
 
183  10 toggle public static String sanitizeSeqName(String seqName)
184    {
185  10 Objects.requireNonNull(seqName);
186  10 return seqName.replaceAll("\\[\\d*\\]", "")
187    .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
188    }
189   
190    /**
191    * Ensures sequence ref names are not less than 3 characters and does not
192    * contain a database name
193    *
194    * @param seqName
195    * @return
196    */
 
197  29 toggle static boolean isValidSeqName(String seqName)
198    {
199    // jalview.bin.Console.outPrintln("seqName : " + seqName);
200  29 String ignoreList = "pdb,uniprot,swiss-prot";
201  29 if (seqName.length() < 3)
202    {
203  2 return false;
204    }
205  27 if (seqName.contains(":"))
206    {
207  0 return false;
208    }
209  27 seqName = seqName.toLowerCase(Locale.ROOT);
210  27 for (String ignoredEntry : ignoreList.split(","))
211    {
212  77 if (seqName.contains(ignoredEntry))
213    {
214  2 return false;
215    }
216    }
217  25 return true;
218    }
219   
 
220  40 toggle static String getDBRefId(DBRefEntry dbRef)
221    {
222  40 String ref = dbRef.getAccessionId().replaceAll("GO:", "");
223  40 return ref;
224    }
225   
226    /**
227    * FTSRestClient specific query builder to recover associated structure data
228    * records for a sequence
229    *
230    * @param seq
231    * - seq to generate a query for
232    * @param wantedFields
233    * - fields to retrieve
234    * @param selectedFilterOpt
235    * - criterion for ranking results (e.g. resolution)
236    * @param b
237    * - sort ascending or descending
238    * @return
239    * @throws Exception
240    */
 
241  2 toggle public FTSRestResponse fetchStructuresMetaData(SequenceI seq,
242    Collection<FTSDataColumnI> wantedFields,
243    FilterOption selectedFilterOpt, boolean b) throws Exception
244    {
245  2 FTSRestResponse resultList;
246  2 FTSRestRequest pdbRequest = new FTSRestRequest();
247  2 pdbRequest.setAllowEmptySeq(false);
248  2 pdbRequest.setResponseSize(500);
249  2 pdbRequest.setFieldToSearchBy("(");
250  2 pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(), b);
251  2 pdbRequest.setWantedFields(wantedFields);
252  2 pdbRequest.setSearchTerm(buildQuery(seq) + ")");
253  2 pdbRequest.setAssociatedSequence(seq);
254  2 resultList = pdbRestClient.executeRequest(pdbRequest);
255   
256  0 lastPdbRequest = pdbRequest;
257  0 return resultList;
258    }
259   
 
260  11 toggle public List<FilterOption> getAvailableFilterOptions(String VIEWS_FILTER)
261    {
262  11 List<FilterOption> filters = new ArrayList<FilterOption>();
263  11 filters.add(new FilterOption(
264    "PDBe " + MessageManager.getString("label.best_quality"),
265    "overall_quality", VIEWS_FILTER, false, this));
266  11 filters.add(new FilterOption(
267    "PDBe " + MessageManager.getString("label.best_resolution"),
268    "resolution", VIEWS_FILTER, false, this));
269  11 filters.add(new FilterOption(
270    "PDBe " + MessageManager.getString("label.most_protein_chain"),
271    "number_of_protein_chains", VIEWS_FILTER, false, this));
272  11 filters.add(new FilterOption(
273    "PDBe " + MessageManager
274    .getString("label.most_bound_molecules"),
275    "number_of_bound_molecules", VIEWS_FILTER, false, this));
276  11 filters.add(new FilterOption(
277    "PDBe " + MessageManager
278    .getString("label.most_polymer_residues"),
279    "number_of_polymer_residues", VIEWS_FILTER, true, this));
280   
281  11 return filters;
282    }
283   
 
284  0 toggle @Override
285    public boolean needsRefetch(FilterOption selectedFilterOpt)
286    {
287    // PDBe queries never need a refetch first
288  0 return false;
289    }
290   
291    /**
292    * FTSRestClient specific query builder to pick top ranked entry from a
293    * fetchStructuresMetaData query
294    *
295    * @param seq
296    * - seq to generate a query for
297    * @param wantedFields
298    * - fields to retrieve
299    * @param selectedFilterOpt
300    * - criterion for ranking results (e.g. resolution)
301    * @param b
302    * - sort ascending or descending
303    * @return
304    * @throws Exception
305    */
 
306  0 toggle public FTSRestResponse selectFirstRankedQuery(SequenceI seq,
307    Collection<FTSData> collectedResults,
308    Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
309    boolean b) throws Exception
310    {
311   
312  0 FTSRestResponse resultList;
313  0 FTSRestRequest pdbRequest = new FTSRestRequest();
314  0 if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
315    {
316  0 pdbRequest.setAllowEmptySeq(false);
317  0 pdbRequest.setResponseSize(1);
318  0 pdbRequest.setFieldToSearchBy("(");
319  0 pdbRequest.setSearchTerm(buildQuery(seq) + ")");
320  0 pdbRequest.setWantedFields(wantedFields);
321  0 pdbRequest.setAssociatedSequence(seq);
322  0 pdbRequest.setFacet(true);
323  0 pdbRequest.setFacetPivot(fieldToFilterBy + ",entry_entity");
324  0 pdbRequest.setFacetPivotMinCount(1);
325    }
326    else
327    {
328  0 pdbRequest.setAllowEmptySeq(false);
329  0 pdbRequest.setResponseSize(1);
330  0 pdbRequest.setFieldToSearchBy("(");
331  0 pdbRequest.setFieldToSortBy(fieldToFilterBy, b);
332  0 pdbRequest.setSearchTerm(buildQuery(seq) + ")");
333  0 pdbRequest.setWantedFields(wantedFields);
334  0 pdbRequest.setAssociatedSequence(seq);
335    }
336  0 resultList = pdbRestClient.executeRequest(pdbRequest);
337   
338  0 lastPdbRequest = pdbRequest;
339  0 return resultList;
340    }
341   
 
342  0 toggle @Override
343    public PDBEntry[] collectSelectedRows(JTable restable, int[] selectedRows,
344    List<SequenceI> selectedSeqsToView)
345    {
346  0 int refSeqColIndex = restable.getColumn("Ref Sequence").getModelIndex();
347   
348  0 PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
349  0 int count = 0;
350  0 int idColumnIndex = -1;
351  0 boolean fromTDB = true;
352  0 idColumnIndex = restable.getColumn("PDB Id").getModelIndex();
353   
354  0 for (int row : selectedRows)
355    {
356   
357  0 String pdbIdStr = restable.getValueAt(row, idColumnIndex).toString();
358  0 SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
359    refSeqColIndex);
360  0 selectedSeqsToView.add(selectedSeq);
361  0 PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
362  0 if (pdbEntry == null)
363    {
364  0 pdbEntry = getFindEntry(pdbIdStr, selectedSeq.getAllPDBEntries());
365    }
366   
367  0 if (pdbEntry == null)
368    {
369  0 pdbEntry = new PDBEntry();
370  0 pdbEntry.setId(pdbIdStr);
371  0 pdbEntry.setType(PDBEntry.Type.MMCIF);
372  0 selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
373    }
374  0 pdbEntriesToView[count++] = pdbEntry;
375    }
376  0 return pdbEntriesToView;
377    }
378   
 
379  0 toggle @Override
380    protected FTSRestRequest getLastFTSRequest()
381    {
382  0 return lastPdbRequest;
383    }
384   
 
385  32 toggle public FTSRestResponse executePDBFTSRestRequest(FTSRestRequest pdbRequest)
386    throws Exception
387    {
388  32 return pdbRestClient.executeRequest(pdbRequest);
389    }
390   
391    }
  • Report generated by OpenClover v 4.4.1 on Thu Nov 28 2024 18:14:23 GMT using coverage data from Thu Nov 28 2024 18:14:06 GMT.
  • OpenClover is free and open-source software.