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Coverage Report

  1. Project Clover database Mon Nov 11 2024 17:27:16 GMT
  2. Package jalview.gui

File CrossRefAction.java

 

Coverage histogram

../../img/srcFileCovDistChart6.png
36% of files have more coverage

Code metrics

70
141
9
1
550
336
55
0.39
15.67
9
6.11

Classes

Class Line # Actions
CrossRefAction 59 141 55
0.5136363551.4%
 

Contributing tests

This file is covered by 1 test. .

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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.gui;
22   
23    import jalview.analysis.AlignmentUtils;
24    import jalview.analysis.CrossRef;
25    import jalview.api.AlignmentViewPanel;
26    import jalview.api.FeatureSettingsModelI;
27    import jalview.bin.Cache;
28    import jalview.bin.Console;
29    import jalview.datamodel.Alignment;
30    import jalview.datamodel.AlignmentI;
31    import jalview.datamodel.DBRefEntry;
32    import jalview.datamodel.DBRefSource;
33    import jalview.datamodel.GeneLociI;
34    import jalview.datamodel.SequenceI;
35    import jalview.ext.ensembl.EnsemblInfo;
36    import jalview.ext.ensembl.EnsemblMap;
37    import jalview.io.gff.SequenceOntologyI;
38    import jalview.structure.StructureSelectionManager;
39    import jalview.util.DBRefUtils;
40    import jalview.util.MapList;
41    import jalview.util.MappingUtils;
42    import jalview.util.MessageManager;
43    import jalview.viewmodel.seqfeatures.FeatureRendererModel;
44    import jalview.ws.SequenceFetcher;
45   
46    import java.util.ArrayList;
47    import java.util.HashMap;
48    import java.util.List;
49    import java.util.Map;
50    import java.util.Set;
51   
52    /**
53    * Factory constructor and runnable for discovering and displaying
54    * cross-references for a set of aligned sequences
55    *
56    * @author jprocter
57    *
58    */
 
59    public class CrossRefAction implements Runnable
60    {
61    private AlignFrame alignFrame;
62   
63    private SequenceI[] sel;
64   
65    private final boolean _odna;
66   
67    private String source;
68   
69    List<AlignmentViewPanel> xrefViews = new ArrayList<>();
70   
 
71  0 toggle List<AlignmentViewPanel> getXrefViews()
72    {
73  0 return xrefViews;
74    }
75   
 
76  2 toggle @Override
77    public void run()
78    {
79  2 final long sttime = System.currentTimeMillis();
80  2 alignFrame.setProgressBar(MessageManager.formatMessage(
81    "status.searching_for_sequences_from", new Object[]
82    { source }), sttime);
83  2 try
84    {
85  2 AlignmentI alignment = alignFrame.getViewport().getAlignment();
86  2 AlignmentI dataset = alignment.getDataset() == null ? alignment
87    : alignment.getDataset();
88  2 boolean dna = alignment.isNucleotide();
89  2 if (_odna != dna)
90    {
91  0 System.err
92    .println("Conflict: showProducts for alignment originally "
93  0 + "thought to be " + (_odna ? "DNA" : "Protein")
94  0 + " now searching for " + (dna ? "DNA" : "Protein")
95    + " Context.");
96    }
97  2 AlignmentI xrefs = new CrossRef(sel, dataset)
98    .findXrefSequences(source, dna);
99  2 if (xrefs == null)
100    {
101  0 return;
102    }
103   
104    /*
105    * try to look up chromosomal coordinates for nucleotide
106    * sequences (if not already retrieved)
107    */
108  2 findGeneLoci(xrefs.getSequences());
109   
110    /*
111    * get display scheme (if any) to apply to features
112    */
113  2 FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
114    .getFeatureColourScheme(source);
115   
116  2 if (dna && AlignmentUtils.looksLikeEnsembl(alignment))
117    {
118    // override default featureColourScheme so products have Ensembl variant
119    // colours
120  2 featureColourScheme = new SequenceFetcher()
121    .getFeatureColourScheme(DBRefSource.ENSEMBL);
122    }
123   
124  2 AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
125    xrefs);
126  2 if (!dna)
127    {
128  0 xrefsAlignment = AlignmentUtils.makeCdsAlignment(
129    xrefsAlignment.getSequencesArray(), dataset, sel);
130  0 xrefsAlignment.alignAs(alignment);
131    }
132   
133    /*
134    * If we are opening a splitframe, make a copy of this alignment (sharing the same dataset
135    * sequences). If we are DNA, drop introns and update mappings
136    */
137  2 AlignmentI copyAlignment = null;
138   
139  2 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
140    {
141  2 copyAlignment = copyAlignmentForSplitFrame(alignment, dataset, dna,
142    xrefs, xrefsAlignment);
143  2 if (copyAlignment == null)
144    {
145  0 return; // failed
146    }
147    }
148   
149    /*
150    * build AlignFrame(s) according to available alignment data
151    */
152  2 AlignFrame newFrame = new AlignFrame(xrefsAlignment,
153    AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
154  2 if (Cache.getDefault("HIDE_INTRONS", true))
155    {
156  2 newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
157    }
158  2 String newtitle = String.format("%s %s %s",
159  2 dna ? MessageManager.getString("label.proteins")
160    : MessageManager.getString("label.nucleotides"),
161    MessageManager.getString("label.for"), alignFrame.getTitle());
162  2 newFrame.setTitle(newtitle);
163   
164  2 if (copyAlignment == null)
165    {
166    /*
167    * split frame display is turned off in preferences file
168    */
169  0 Desktop.addInternalFrame(newFrame, newtitle,
170    AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
171  0 xrefViews.add(newFrame.alignPanel);
172  0 return; // via finally clause
173    }
174   
175  2 AlignFrame copyThis = new AlignFrame(copyAlignment,
176    AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
177  2 copyThis.setTitle(alignFrame.getTitle());
178   
179  2 boolean showSequenceFeatures = alignFrame.getViewport()
180    .isShowSequenceFeatures();
181  2 newFrame.setShowSeqFeatures(showSequenceFeatures);
182  2 copyThis.setShowSeqFeatures(showSequenceFeatures);
183  2 FeatureRendererModel myFeatureStyling = alignFrame.alignPanel
184    .getSeqPanel().seqCanvas.getFeatureRenderer();
185   
186    /*
187    * copy feature rendering settings to split frame
188    */
189  2 FeatureRendererModel fr1 = newFrame.alignPanel.getSeqPanel().seqCanvas
190    .getFeatureRenderer();
191  2 fr1.transferSettings(myFeatureStyling);
192  2 fr1.findAllFeatures(true);
193  2 FeatureRendererModel fr2 = copyThis.alignPanel.getSeqPanel().seqCanvas
194    .getFeatureRenderer();
195  2 fr2.transferSettings(myFeatureStyling);
196  2 fr2.findAllFeatures(true);
197   
198    /*
199    * apply 'database source' feature configuration
200    * if any - first to the new splitframe view about to be displayed
201    */
202   
203  2 newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
204  2 copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
205   
206    /*
207    * and for JAL-3330 also to original alignFrame view(s)
208    * this currently trashes any original settings.
209    */
210  2 for (AlignmentViewPanel origpanel : alignFrame.getAlignPanels())
211    {
212  2 origpanel.getAlignViewport()
213    .mergeFeaturesStyle(featureColourScheme);
214    }
215   
216  2 SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
217  2 dna ? newFrame : copyThis);
218   
219  2 newFrame.setVisible(true);
220  2 copyThis.setVisible(true);
221  2 String linkedTitle = MessageManager
222    .getString("label.linked_view_title");
223  2 Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
224  2 sf.adjustInitialLayout();
225   
226    // finally add the top, then bottom frame to the view list
227  2 xrefViews.add(dna ? copyThis.alignPanel : newFrame.alignPanel);
228  2 xrefViews.add(!dna ? copyThis.alignPanel : newFrame.alignPanel);
229   
230    } catch (OutOfMemoryError e)
231    {
232  0 new OOMWarning("whilst fetching crossreferences", e);
233    } catch (Throwable e)
234    {
235  0 Console.error("Error when finding crossreferences", e);
236    } finally
237    {
238  2 alignFrame.setProgressBar(MessageManager.formatMessage(
239    "status.finished_searching_for_sequences_from", new Object[]
240    { source }), sttime);
241    }
242    }
243   
244    /**
245    * Tries to add chromosomal coordinates to any nucleotide sequence which does
246    * not already have them. Coordinates are retrieved from Ensembl given an
247    * Ensembl identifier, either on the sequence itself or on a peptide sequence
248    * it has a reference to.
249    *
250    * <pre>
251    * Example (human):
252    * - fetch EMBLCDS cross-references for Uniprot entry P30419
253    * - the EMBL sequences do not have xrefs to Ensembl
254    * - the Uniprot entry has xrefs to
255    * ENSP00000258960, ENSP00000468424, ENST00000258960, ENST00000592782
256    * - either of the transcript ids can be used to retrieve gene loci e.g.
257    * http://rest.ensembl.org/map/cds/ENST00000592782/1..100000
258    * Example (invertebrate):
259    * - fetch EMBLCDS cross-references for Uniprot entry Q43517 (FER1_SOLLC)
260    * - the Uniprot entry has an xref to ENSEMBLPLANTS Solyc10g044520.1.1
261    * - can retrieve gene loci with
262    * http://rest.ensemblgenomes.org/map/cds/Solyc10g044520.1.1/1..100000
263    * </pre>
264    *
265    * @param sequences
266    */
 
267  2 toggle public static void findGeneLoci(List<SequenceI> sequences)
268    {
269  2 Map<DBRefEntry, GeneLociI> retrievedLoci = new HashMap<>();
270  2 for (SequenceI seq : sequences)
271    {
272  22 findGeneLoci(seq, retrievedLoci);
273    }
274    }
275   
276    /**
277    * Tres to find chromosomal coordinates for the sequence, by searching its
278    * direct and indirect cross-references for Ensembl. If the loci have already
279    * been retrieved, just reads them out of the map of retrievedLoci; this is
280    * the case of an alternative transcript for the same protein. Otherwise calls
281    * a REST service to retrieve the loci, and if successful, adds them to the
282    * sequence and to the retrievedLoci.
283    *
284    * @param seq
285    * @param retrievedLoci
286    */
 
287  22 toggle static void findGeneLoci(SequenceI seq,
288    Map<DBRefEntry, GeneLociI> retrievedLoci)
289    {
290    /*
291    * don't replace any existing chromosomal coordinates
292    */
293  22 if (seq == null || seq.isProtein() || seq.getGeneLoci() != null
294    || seq.getDBRefs() == null)
295    {
296  22 return;
297    }
298   
299  0 Set<String> ensemblDivisions = new EnsemblInfo().getDivisions();
300   
301    /*
302    * first look for direct dbrefs from sequence to Ensembl
303    */
304  0 String[] divisionsArray = ensemblDivisions
305    .toArray(new String[ensemblDivisions.size()]);
306  0 List<DBRefEntry> seqRefs = seq.getDBRefs();
307  0 List<DBRefEntry> directEnsemblRefs = DBRefUtils.selectRefs(seqRefs,
308    divisionsArray);
309  0 if (directEnsemblRefs != null)
310    {
311  0 for (DBRefEntry ensemblRef : directEnsemblRefs)
312    {
313  0 if (fetchGeneLoci(seq, ensemblRef, retrievedLoci))
314    {
315  0 return;
316    }
317    }
318    }
319   
320    /*
321    * else look for indirect dbrefs from sequence to Ensembl
322    */
323  0 for (DBRefEntry dbref : seq.getDBRefs())
324    {
325  0 if (dbref.getMap() != null && dbref.getMap().getTo() != null)
326    {
327  0 List<DBRefEntry> dbrefs = dbref.getMap().getTo().getDBRefs();
328  0 List<DBRefEntry> indirectEnsemblRefs = DBRefUtils.selectRefs(dbrefs,
329    divisionsArray);
330  0 if (indirectEnsemblRefs != null)
331    {
332  0 for (DBRefEntry ensemblRef : indirectEnsemblRefs)
333    {
334  0 if (fetchGeneLoci(seq, ensemblRef, retrievedLoci))
335    {
336  0 return;
337    }
338    }
339    }
340    }
341    }
342    }
343   
344    /**
345    * Retrieves chromosomal coordinates for the Ensembl (or EnsemblGenomes)
346    * identifier in dbref. If successful, and the sequence length matches gene
347    * loci length, then add it to the sequence, and to the retrievedLoci map.
348    * Answers true if successful, else false.
349    *
350    * @param seq
351    * @param dbref
352    * @param retrievedLoci
353    * @return
354    */
 
355  0 toggle static boolean fetchGeneLoci(SequenceI seq, DBRefEntry dbref,
356    Map<DBRefEntry, GeneLociI> retrievedLoci)
357    {
358  0 String accession = dbref.getAccessionId();
359  0 String division = dbref.getSource();
360   
361    /*
362    * hack: ignore cross-references to Ensembl protein ids
363    * (or use map/translation perhaps?)
364    * todo: is there an equivalent in EnsemblGenomes?
365    */
366  0 if (accession.startsWith("ENSP"))
367    {
368  0 return false;
369    }
370  0 EnsemblMap mapper = new EnsemblMap();
371   
372    /*
373    * try CDS mapping first
374    */
375  0 GeneLociI geneLoci = mapper.getCdsMapping(division, accession, 1,
376    seq.getLength());
377  0 if (geneLoci != null)
378    {
379  0 MapList map = geneLoci.getMapping();
380  0 int mappedFromLength = MappingUtils.getLength(map.getFromRanges());
381  0 if (mappedFromLength == seq.getLength())
382    {
383  0 seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
384    geneLoci.getChromosomeId(), map);
385  0 retrievedLoci.put(dbref, geneLoci);
386  0 return true;
387    }
388    }
389   
390    /*
391    * else try CDNA mapping
392    */
393  0 geneLoci = mapper.getCdnaMapping(division, accession, 1,
394    seq.getLength());
395  0 if (geneLoci != null)
396    {
397  0 MapList map = geneLoci.getMapping();
398  0 int mappedFromLength = MappingUtils.getLength(map.getFromRanges());
399  0 if (mappedFromLength == seq.getLength())
400    {
401  0 seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
402    geneLoci.getChromosomeId(), map);
403  0 retrievedLoci.put(dbref, geneLoci);
404  0 return true;
405    }
406    }
407   
408  0 return false;
409    }
410   
411    /**
412    * @param alignment
413    * @param dataset
414    * @param dna
415    * @param xrefs
416    * @param xrefsAlignment
417    * @return
418    */
 
419  2 toggle protected AlignmentI copyAlignmentForSplitFrame(AlignmentI alignment,
420    AlignmentI dataset, boolean dna, AlignmentI xrefs,
421    AlignmentI xrefsAlignment)
422    {
423  2 AlignmentI copyAlignment;
424  2 boolean copyAlignmentIsAligned = false;
425  2 if (dna)
426    {
427  2 copyAlignment = AlignmentUtils.makeCdsAlignment(sel, dataset,
428    xrefsAlignment.getSequencesArray());
429  2 if (copyAlignment.getHeight() == 0)
430    {
431  0 JvOptionPane.showMessageDialog(alignFrame,
432    MessageManager.getString("label.cant_map_cds"),
433    MessageManager.getString("label.operation_failed"),
434    JvOptionPane.OK_OPTION);
435  0 jalview.bin.Console.errPrintln("Failed to make CDS alignment");
436  0 return null;
437    }
438   
439    /*
440    * pending getting Embl transcripts to 'align',
441    * we are only doing this for Ensembl
442    */
443    // TODO proper criteria for 'can align as cdna'
444  2 if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
445    || AlignmentUtils.looksLikeEnsembl(alignment))
446    {
447  2 copyAlignment.alignAs(alignment);
448  2 copyAlignmentIsAligned = true;
449    }
450    }
451    else
452    {
453  0 copyAlignment = AlignmentUtils.makeCopyAlignment(sel,
454    xrefs.getSequencesArray(), dataset);
455    }
456  2 copyAlignment.setGapCharacter(alignFrame.viewport.getGapCharacter());
457   
458  2 StructureSelectionManager ssm = StructureSelectionManager
459    .getStructureSelectionManager(Desktop.instance);
460   
461    /*
462    * register any new mappings for sequence mouseover etc
463    * (will not duplicate any previously registered mappings)
464    */
465  2 ssm.registerMappings(dataset.getCodonFrames());
466   
467  2 if (copyAlignment.getHeight() <= 0)
468    {
469  0 jalview.bin.Console
470    .errPrintln("No Sequences generated for xRef type " + source);
471  0 return null;
472    }
473   
474    /*
475    * align protein to dna
476    */
477  2 if (dna && copyAlignmentIsAligned)
478    {
479  2 xrefsAlignment.alignAs(copyAlignment);
480    }
481    else
482    {
483    /*
484    * align cdna to protein - currently only if
485    * fetching and aligning Ensembl transcripts!
486    */
487    // TODO: generalise for other sources of locus/transcript/cds data
488  0 if (dna && DBRefSource.ENSEMBL.equalsIgnoreCase(source))
489    {
490  0 copyAlignment.alignAs(xrefsAlignment);
491    }
492    }
493   
494  2 return copyAlignment;
495    }
496   
497    /**
498    * Makes an alignment containing the given sequences, and adds them to the
499    * given dataset, which is also set as the dataset for the new alignment
500    *
501    * TODO: refactor to DatasetI method
502    *
503    * @param dataset
504    * @param seqs
505    * @return
506    */
 
507  2 toggle protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
508    AlignmentI seqs)
509    {
510  2 SequenceI[] sprods = new SequenceI[seqs.getHeight()];
511  24 for (int s = 0; s < sprods.length; s++)
512    {
513  22 sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
514  22 if (dataset.getSequences() == null || !dataset.getSequences()
515    .contains(sprods[s].getDatasetSequence()))
516    {
517  0 dataset.addSequence(sprods[s].getDatasetSequence());
518    }
519  22 sprods[s].updatePDBIds();
520    }
521  2 Alignment al = new Alignment(sprods);
522  2 al.setDataset(dataset);
523  2 return al;
524    }
525   
526    /**
527    * Constructor
528    *
529    * @param af
530    * @param seqs
531    * @param fromDna
532    * @param dbSource
533    */
 
534  2 toggle CrossRefAction(AlignFrame af, SequenceI[] seqs, boolean fromDna,
535    String dbSource)
536    {
537  2 this.alignFrame = af;
538  2 this.sel = seqs;
539  2 this._odna = fromDna;
540  2 this.source = dbSource;
541    }
542   
 
543  2 toggle public static CrossRefAction getHandlerFor(final SequenceI[] sel,
544    final boolean fromDna, final String source,
545    final AlignFrame alignFrame)
546    {
547  2 return new CrossRefAction(alignFrame, sel, fromDna, source);
548    }
549   
550    }