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Coverage Report

  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.gui

File SequenceFetcher.java

 

Coverage histogram

../../img/srcFileCovDistChart1.png
52% of files have more coverage

Code metrics

100
296
33
1
916
682
101
0.34
8.97
33
3.06

Classes

Class Line # Actions
SequenceFetcher 67 296 101
0.0139860141.4%
 

Contributing tests

This file is covered by 105 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;
22   
23    import jalview.api.FeatureSettingsModelI;
24    import jalview.bin.Cache;
25    import jalview.datamodel.AlignmentI;
26    import jalview.datamodel.DBRefEntry;
27    import jalview.datamodel.SequenceI;
28    import jalview.fts.core.GFTSPanel;
29    import jalview.fts.service.pdb.PDBFTSPanel;
30    import jalview.fts.service.uniprot.UniprotFTSPanel;
31    import jalview.io.FileFormatI;
32    import jalview.io.gff.SequenceOntologyI;
33    import jalview.util.DBRefUtils;
34    import jalview.util.MessageManager;
35    import jalview.util.Platform;
36    import jalview.ws.seqfetcher.DbSourceProxy;
37   
38    import java.awt.BorderLayout;
39    import java.awt.Font;
40    import java.awt.event.ActionEvent;
41    import java.awt.event.ActionListener;
42    import java.awt.event.KeyAdapter;
43    import java.awt.event.KeyEvent;
44    import java.util.ArrayList;
45    import java.util.Arrays;
46    import java.util.HashSet;
47    import java.util.Iterator;
48    import java.util.List;
49   
50    import javax.swing.JButton;
51    import javax.swing.JCheckBox;
52    import javax.swing.JComboBox;
53    import javax.swing.JInternalFrame;
54    import javax.swing.JLabel;
55    import javax.swing.JPanel;
56    import javax.swing.JScrollPane;
57    import javax.swing.JTextArea;
58    import javax.swing.SwingConstants;
59   
60    /**
61    * A panel where the use may choose a database source, and enter one or more
62    * accessions, to retrieve entries from the database.
63    * <p>
64    * If the selected source is Uniprot or PDB, a free text search panel is opened
65    * instead to perform the search and selection.
66    */
 
67    public class SequenceFetcher extends JPanel implements Runnable
68    {
69    private static jalview.ws.SequenceFetcher sfetch = null;
70   
71    JLabel exampleAccession;
72   
73    JComboBox<String> database;
74   
75    JCheckBox replacePunctuation;
76   
77    JButton okBtn;
78   
79    JButton exampleBtn;
80   
81    JButton closeBtn;
82   
83    JButton backBtn;
84   
85    JTextArea textArea;
86   
87    JInternalFrame frame;
88   
89    IProgressIndicator guiWindow;
90   
91    AlignFrame alignFrame;
92   
93    GFTSPanel parentSearchPanel;
94   
95    IProgressIndicator progressIndicator;
96   
97    volatile boolean _isConstructing = false;
98   
99    /**
100    * Returns the shared instance of the SequenceFetcher client
101    *
102    * @return
103    */
 
104  1746 toggle public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton()
105    {
106  1746 if (sfetch == null)
107    {
108  1 sfetch = new jalview.ws.SequenceFetcher();
109    }
110  1746 return sfetch;
111    }
112   
113    /**
114    * Constructor given a client to receive any status or progress messages
115    * (currently either the Desktop, or an AlignFrame panel)
116    *
117    * @param guiIndic
118    */
 
119  0 toggle public SequenceFetcher(IProgressIndicator guiIndic)
120    {
121  0 this(guiIndic, null, null);
122    }
123   
124    /**
125    * Constructor with specified database and accession(s) to retrieve
126    *
127    * @param guiIndic
128    * @param selectedDb
129    * @param queryString
130    */
 
131  0 toggle public SequenceFetcher(IProgressIndicator guiIndic,
132    final String selectedDb, final String queryString)
133    {
134  0 this.progressIndicator = guiIndic;
135  0 getSequenceFetcherSingleton();
136  0 this.guiWindow = progressIndicator;
137   
138  0 if (progressIndicator instanceof AlignFrame)
139    {
140  0 alignFrame = (AlignFrame) progressIndicator;
141    }
142   
143  0 jbInit(selectedDb);
144  0 textArea.setText(queryString);
145   
146  0 frame = new JInternalFrame();
147  0 frame.setContentPane(this);
148  0 Desktop.addInternalFrame(frame, getFrameTitle(), true, 400,
149  0 Platform.isAMacAndNotJS() ? 240 : 180);
150    }
151   
 
152  0 toggle private String getFrameTitle()
153    {
154  0 return ((alignFrame == null)
155    ? MessageManager.getString("label.new_sequence_fetcher")
156    : MessageManager
157    .getString("label.additional_sequence_fetcher"));
158    }
159   
 
160  0 toggle private void jbInit(String selectedDb)
161    {
162  0 this.setLayout(new BorderLayout());
163   
164  0 database = new JComboBox<>();
165  0 database.setFont(JvSwingUtils.getLabelFont());
166  0 database.setPrototypeDisplayValue("ENSEMBLGENOMES ");
167  0 String[] sources = new jalview.ws.SequenceFetcher().getSupportedDb();
168  0 Arrays.sort(sources, String.CASE_INSENSITIVE_ORDER);
169  0 database.addItem(MessageManager.getString("action.select_ddbb"));
170  0 for (String source : sources)
171    {
172  0 database.addItem(source);
173    }
174  0 database.setSelectedItem(selectedDb);
175  0 if (database.getSelectedIndex() == -1)
176    {
177  0 database.setSelectedIndex(0);
178    }
179  0 database.setMaximumRowCount(database.getItemCount());
180  0 database.addActionListener(new ActionListener()
181    {
 
182  0 toggle @Override
183    public void actionPerformed(ActionEvent e)
184    {
185  0 String currentSelection = (String) database.getSelectedItem();
186  0 updateExampleQuery(currentSelection);
187   
188  0 if ("pdb".equalsIgnoreCase(currentSelection))
189    {
190  0 frame.dispose();
191  0 new PDBFTSPanel(SequenceFetcher.this);
192    }
193  0 else if ("uniprot".equalsIgnoreCase(currentSelection))
194    {
195  0 frame.dispose();
196  0 new UniprotFTSPanel(SequenceFetcher.this);
197    }
198    else
199    {
200  0 otherSourceAction();
201    }
202    }
203    });
204   
205  0 exampleAccession = new JLabel("");
206  0 exampleAccession.setFont(new Font("Verdana", Font.BOLD, 11));
207  0 JLabel jLabel1 = new JLabel(MessageManager
208    .getString("label.separate_multiple_accession_ids"));
209  0 jLabel1.setFont(new Font("Verdana", Font.ITALIC, 11));
210  0 jLabel1.setHorizontalAlignment(SwingConstants.LEFT);
211   
212  0 replacePunctuation = new JCheckBox(
213    MessageManager.getString("label.replace_commas_semicolons"));
214  0 replacePunctuation.setHorizontalAlignment(SwingConstants.LEFT);
215  0 replacePunctuation.setFont(new Font("Verdana", Font.ITALIC, 11));
216  0 okBtn = new JButton(MessageManager.getString("action.ok"));
217  0 okBtn.addActionListener(new ActionListener()
218    {
 
219  0 toggle @Override
220    public void actionPerformed(ActionEvent e)
221    {
222  0 ok_actionPerformed();
223    }
224    });
225  0 JButton clear = new JButton(MessageManager.getString("action.clear"));
226  0 clear.addActionListener(new ActionListener()
227    {
 
228  0 toggle @Override
229    public void actionPerformed(ActionEvent e)
230    {
231  0 clear_actionPerformed();
232    }
233    });
234   
235  0 exampleBtn = new JButton(MessageManager.getString("label.example"));
236  0 exampleBtn.addActionListener(new ActionListener()
237    {
 
238  0 toggle @Override
239    public void actionPerformed(ActionEvent e)
240    {
241  0 example_actionPerformed();
242    }
243    });
244  0 closeBtn = new JButton(MessageManager.getString("action.cancel"));
245  0 closeBtn.addActionListener(new ActionListener()
246    {
 
247  0 toggle @Override
248    public void actionPerformed(ActionEvent e)
249    {
250  0 close_actionPerformed(e);
251    }
252    });
253  0 backBtn = new JButton(MessageManager.getString("action.back"));
254  0 backBtn.addActionListener(new ActionListener()
255    {
 
256  0 toggle @Override
257    public void actionPerformed(ActionEvent e)
258    {
259  0 parentSearchPanel.btn_back_ActionPerformed();
260    }
261    });
262    // back not visible unless embedded
263  0 backBtn.setVisible(false);
264   
265  0 textArea = new JTextArea();
266  0 textArea.setFont(JvSwingUtils.getLabelFont());
267  0 textArea.setLineWrap(true);
268  0 textArea.addKeyListener(new KeyAdapter()
269    {
 
270  0 toggle @Override
271    public void keyPressed(KeyEvent e)
272    {
273  0 if (e.getKeyCode() == KeyEvent.VK_ENTER)
274    {
275  0 ok_actionPerformed();
276    }
277    }
278    });
279   
280  0 JPanel actionPanel = new JPanel();
281  0 actionPanel.add(backBtn);
282  0 actionPanel.add(exampleBtn);
283  0 actionPanel.add(clear);
284  0 actionPanel.add(okBtn);
285  0 actionPanel.add(closeBtn);
286   
287  0 JPanel databasePanel = new JPanel();
288  0 databasePanel.setLayout(new BorderLayout());
289  0 databasePanel.add(database, BorderLayout.NORTH);
290  0 databasePanel.add(exampleAccession, BorderLayout.CENTER);
291  0 JPanel jPanel2a = new JPanel(new BorderLayout());
292  0 jPanel2a.add(jLabel1, BorderLayout.NORTH);
293  0 jPanel2a.add(replacePunctuation, BorderLayout.SOUTH);
294  0 databasePanel.add(jPanel2a, BorderLayout.SOUTH);
295   
296  0 JPanel idsPanel = new JPanel();
297  0 idsPanel.setLayout(new BorderLayout(0, 5));
298  0 JScrollPane jScrollPane1 = new JScrollPane();
299  0 jScrollPane1.getViewport().add(textArea);
300  0 idsPanel.add(jScrollPane1, BorderLayout.CENTER);
301   
302  0 this.add(actionPanel, BorderLayout.SOUTH);
303  0 this.add(idsPanel, BorderLayout.CENTER);
304  0 this.add(databasePanel, BorderLayout.NORTH);
305    }
306   
307    /**
308    * Answers a semi-colon-delimited string with the example query or queries for
309    * the selected database
310    *
311    * @param db
312    * @return
313    */
 
314  0 toggle protected String getExampleQueries(String db)
315    {
316  0 StringBuilder sb = new StringBuilder();
317  0 HashSet<String> hs = new HashSet<>();
318  0 for (DbSourceProxy dbs : sfetch.getSourceProxy(db))
319    {
320  0 String tq = dbs.getTestQuery();
321  0 if (hs.add(tq)) // not a duplicate source
322    {
323  0 if (sb.length() > 0)
324    {
325  0 sb.append(";");
326    }
327  0 sb.append(tq);
328    }
329    }
330  0 return sb.toString();
331    }
332   
333    /**
334    * Action on selecting a database other than Uniprot or PDB is to enable or
335    * disable 'Replace commas', and await input in the query field
336    */
 
337  0 toggle protected void otherSourceAction()
338    {
339  0 try
340    {
341  0 String eq = exampleAccession.getText();
342    // TODO this should be a property of the SequenceFetcher whether commas
343    // are allowed in the IDs...
344   
345  0 boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
346  0 replacePunctuation.setEnabled(enablePunct);
347   
348    } catch (Exception ex)
349    {
350  0 exampleAccession.setText("");
351  0 replacePunctuation.setEnabled(true);
352    }
353  0 repaint();
354    }
355   
356    /**
357    * Sets the text of the example query to incorporate the example accession
358    * provided by the selected database source
359    *
360    * @param selectedDatabase
361    * @return
362    */
 
363  0 toggle protected String updateExampleQuery(String selectedDatabase)
364    {
365  0 String eq = getExampleQueries(selectedDatabase);
366  0 exampleAccession.setText(MessageManager
367    .formatMessage("label.example_query_param", new String[]
368    { eq }));
369  0 return eq;
370    }
371   
372    /**
373    * Action on clicking the 'Example' button is to write the example accession
374    * as the query text field value
375    */
 
376  0 toggle protected void example_actionPerformed()
377    {
378  0 String eq = getExampleQueries((String) database.getSelectedItem());
379  0 textArea.setText(eq);
380  0 repaint();
381    }
382   
383    /**
384    * Clears the query input field
385    */
 
386  0 toggle protected void clear_actionPerformed()
387    {
388  0 textArea.setText("");
389  0 repaint();
390    }
391   
392    /**
393    * Action on Close button is to close this frame, and also (if it is embedded
394    * in a search panel) to close the search panel
395    *
396    * @param e
397    */
 
398  0 toggle protected void close_actionPerformed(ActionEvent e)
399    {
400  0 try
401    {
402  0 frame.setClosed(true);
403  0 if (parentSearchPanel != null)
404    {
405  0 parentSearchPanel.btn_cancel_ActionPerformed();
406    }
407    } catch (Exception ex)
408    {
409    }
410    }
411   
412    /**
413    * Action on OK is to start the fetch for entered accession(s)
414    */
 
415  0 toggle public void ok_actionPerformed()
416    {
417    /*
418    * tidy inputs and check there is something to search for
419    */
420  0 String t0 = textArea.getText();
421  0 String text = t0.trim();
422  0 if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
423    {
424  0 text = text.replace(",", ";");
425    }
426  0 text = text.replaceAll("(\\s|[; ])+", ";");
427  0 if (!t0.equals(text))
428    {
429  0 textArea.setText(text);
430    }
431  0 if (text.isEmpty())
432    {
433    // todo i18n
434  0 showErrorMessage(
435    "Please enter a (semi-colon separated list of) database id(s)");
436  0 resetDialog();
437  0 return;
438    }
439  0 if (database.getSelectedIndex() == 0)
440    {
441    // todo i18n
442  0 showErrorMessage("Please choose a database");
443  0 resetDialog();
444  0 return;
445    }
446   
447  0 exampleBtn.setEnabled(false);
448  0 textArea.setEnabled(false);
449  0 okBtn.setEnabled(false);
450  0 closeBtn.setEnabled(false);
451  0 backBtn.setEnabled(false);
452   
453  0 Thread worker = new Thread(this);
454  0 worker.start();
455    }
456   
 
457  0 toggle private void resetDialog()
458    {
459  0 exampleBtn.setEnabled(true);
460  0 textArea.setEnabled(true);
461  0 okBtn.setEnabled(true);
462  0 closeBtn.setEnabled(true);
463  0 backBtn.setEnabled(parentSearchPanel != null);
464    }
465   
 
466  0 toggle @Override
467    public void run()
468    {
469  0 boolean addToLast = false;
470  0 List<String> aresultq = new ArrayList<>();
471  0 List<String> presultTitle = new ArrayList<>();
472  0 List<AlignmentI> presult = new ArrayList<>();
473  0 List<AlignmentI> aresult = new ArrayList<>();
474  0 List<DbSourceProxy> sources = sfetch
475    .getSourceProxy((String) database.getSelectedItem());
476  0 Iterator<DbSourceProxy> proxies = sources.iterator();
477  0 String[] qries = textArea.getText().trim().split(";");
478  0 List<String> nextFetch = Arrays.asList(qries);
479  0 Iterator<String> en = Arrays.asList(new String[0]).iterator();
480  0 int nqueries = qries.length;
481   
482  0 FeatureSettingsModelI preferredFeatureColours = null;
483  0 while (proxies.hasNext() && (en.hasNext() || nextFetch.size() > 0))
484    {
485  0 if (!en.hasNext() && nextFetch.size() > 0)
486    {
487  0 en = nextFetch.iterator();
488  0 nqueries = nextFetch.size();
489    // save the remaining queries in the original array
490  0 qries = nextFetch.toArray(new String[nqueries]);
491  0 nextFetch = new ArrayList<>();
492    }
493   
494  0 DbSourceProxy proxy = proxies.next();
495  0 try
496    {
497    // update status
498  0 guiWindow.setProgressBar(MessageManager.formatMessage(
499    "status.fetching_sequence_queries_from", new String[]
500    { Integer.valueOf(nqueries).toString(),
501    proxy.getDbName() }),
502    Thread.currentThread().hashCode());
503  0 if (proxy.getMaximumQueryCount() == 1)
504    {
505    /*
506    * proxy only handles one accession id at a time
507    */
508  0 while (en.hasNext())
509    {
510  0 String acc = en.next();
511  0 if (!fetchSingleAccession(proxy, acc, aresultq, aresult))
512    {
513  0 nextFetch.add(acc);
514    }
515    }
516    }
517    else
518    {
519    /*
520    * proxy can fetch multiple accessions at one time
521    */
522  0 fetchMultipleAccessions(proxy, en, aresultq, aresult, nextFetch);
523    }
524    } catch (Exception e)
525    {
526  0 showErrorMessage("Error retrieving " + textArea.getText() + " from "
527    + database.getSelectedItem());
528    // error
529    // +="Couldn't retrieve sequences from "+database.getSelectedItem();
530  0 System.err.println("Retrieval failed for source ='"
531    + database.getSelectedItem() + "' and query\n'"
532    + textArea.getText() + "'\n");
533  0 e.printStackTrace();
534    } catch (OutOfMemoryError e)
535    {
536  0 showErrorMessage("Out of Memory when retrieving "
537    + textArea.getText() + " from " + database.getSelectedItem()
538    + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
539  0 e.printStackTrace();
540    } catch (Error e)
541    {
542  0 showErrorMessage("Serious Error retrieving " + textArea.getText()
543    + " from " + database.getSelectedItem());
544  0 e.printStackTrace();
545    }
546   
547    // Stack results ready for opening in alignment windows
548  0 if (aresult != null && aresult.size() > 0)
549    {
550  0 FeatureSettingsModelI proxyColourScheme = proxy
551    .getFeatureColourScheme();
552  0 if (proxyColourScheme != null)
553    {
554  0 preferredFeatureColours = proxyColourScheme;
555    }
556   
557  0 AlignmentI ar = null;
558  0 if (proxy.isAlignmentSource())
559    {
560  0 addToLast = false;
561    // new window for each result
562  0 while (aresult.size() > 0)
563    {
564  0 presult.add(aresult.remove(0));
565  0 presultTitle.add(
566    aresultq.remove(0) + " " + getDefaultRetrievalTitle());
567    }
568    }
569    else
570    {
571  0 String titl = null;
572  0 if (addToLast && presult.size() > 0)
573    {
574  0 ar = presult.remove(presult.size() - 1);
575  0 titl = presultTitle.remove(presultTitle.size() - 1);
576    }
577    // concatenate all results in one window
578  0 while (aresult.size() > 0)
579    {
580  0 if (ar == null)
581    {
582  0 ar = aresult.remove(0);
583    }
584    else
585    {
586  0 ar.append(aresult.remove(0));
587    }
588    }
589  0 addToLast = true;
590  0 presult.add(ar);
591  0 presultTitle.add(titl);
592    }
593    }
594  0 guiWindow.setProgressBar(
595    MessageManager.getString("status.finshed_querying"),
596    Thread.currentThread().hashCode());
597    }
598  0 guiWindow
599    .setProgressBar(
600  0 (presult.size() > 0)
601    ? MessageManager
602    .getString("status.parsing_results")
603    : MessageManager.getString("status.processing"),
604    Thread.currentThread().hashCode());
605    // process results
606  0 while (presult.size() > 0)
607    {
608  0 parseResult(presult.remove(0), presultTitle.remove(0), null,
609    preferredFeatureColours);
610    }
611    // only remove visual delay after we finished parsing.
612  0 guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
613  0 if (nextFetch.size() > 0)
614    {
615  0 StringBuffer sb = new StringBuffer();
616  0 sb.append("Didn't retrieve the following "
617  0 + (nextFetch.size() == 1 ? "query"
618    : nextFetch.size() + " queries")
619    + ": \n");
620  0 int l = sb.length(), lr = 0;
621  0 for (String s : nextFetch)
622    {
623  0 if (l != sb.length())
624    {
625  0 sb.append("; ");
626    }
627  0 if (lr - sb.length() > 40)
628    {
629  0 sb.append("\n");
630    }
631  0 sb.append(s);
632    }
633  0 showErrorMessage(sb.toString());
634    }
635  0 resetDialog();
636    }
637   
638    /**
639    * Tries to fetch one or more accession ids from the database proxy
640    *
641    * @param proxy
642    * @param accessions
643    * the queries to fetch
644    * @param aresultq
645    * a successful queries list to add to
646    * @param aresult
647    * a list of retrieved alignments to add to
648    * @param nextFetch
649    * failed queries are added to this list
650    * @throws Exception
651    */
 
652  0 toggle void fetchMultipleAccessions(DbSourceProxy proxy,
653    Iterator<String> accessions, List<String> aresultq,
654    List<AlignmentI> aresult, List<String> nextFetch) throws Exception
655    {
656  0 StringBuilder multiacc = new StringBuilder();
657  0 List<String> tosend = new ArrayList<>();
658  0 while (accessions.hasNext())
659    {
660  0 String nel = accessions.next();
661  0 tosend.add(nel);
662  0 multiacc.append(nel);
663  0 if (accessions.hasNext())
664    {
665  0 multiacc.append(proxy.getAccessionSeparator());
666    }
667    }
668   
669  0 try
670    {
671  0 String query = multiacc.toString();
672  0 AlignmentI rslt = proxy.getSequenceRecords(query);
673  0 if (rslt == null || rslt.getHeight() == 0)
674    {
675    // no results - pass on all queries to next source
676  0 nextFetch.addAll(tosend);
677    }
678    else
679    {
680  0 aresultq.add(query);
681  0 aresult.add(rslt);
682  0 if (tosend.size() > 1)
683    {
684  0 checkResultForQueries(rslt, tosend, nextFetch, proxy);
685    }
686    }
687    } catch (OutOfMemoryError oome)
688    {
689  0 new OOMWarning("fetching " + multiacc + " from "
690    + database.getSelectedItem(), oome, this);
691    }
692    }
693   
694    /**
695    * Query for a single accession id via the database proxy
696    *
697    * @param proxy
698    * @param accession
699    * @param aresultq
700    * a list of successful queries to add to
701    * @param aresult
702    * a list of retrieved alignments to add to
703    * @return true if the fetch was successful, else false
704    */
 
705  0 toggle boolean fetchSingleAccession(DbSourceProxy proxy, String accession,
706    List<String> aresultq, List<AlignmentI> aresult)
707    {
708  0 boolean success = false;
709  0 try
710    {
711  0 if (aresult != null)
712    {
713  0 try
714    {
715    // give the server a chance to breathe
716  0 Thread.sleep(5);
717    } catch (Exception e)
718    {
719    //
720    }
721    }
722   
723  0 AlignmentI indres = null;
724  0 try
725    {
726  0 indres = proxy.getSequenceRecords(accession);
727    } catch (OutOfMemoryError oome)
728    {
729  0 new OOMWarning(
730    "fetching " + accession + " from " + proxy.getDbName(),
731    oome, this);
732    }
733  0 if (indres != null)
734    {
735  0 aresultq.add(accession);
736  0 aresult.add(indres);
737  0 success = true;
738    }
739    } catch (Exception e)
740    {
741  0 Cache.log.info("Error retrieving " + accession + " from "
742    + proxy.getDbName(), e);
743    }
744  0 return success;
745    }
746   
747    /**
748    * Checks which of the queries were successfully retrieved by searching the
749    * DBRefs of the retrieved sequences for a match. Any not found are added to
750    * the 'nextFetch' list.
751    *
752    * @param rslt
753    * @param queries
754    * @param nextFetch
755    * @param proxy
756    */
 
757  0 toggle void checkResultForQueries(AlignmentI rslt, List<String> queries,
758    List<String> nextFetch, DbSourceProxy proxy)
759    {
760  0 SequenceI[] rs = rslt.getSequencesArray();
761   
762  0 for (String q : queries)
763    {
764    // BH 2019.01.25 dbr is never used.
765    // DBRefEntry dbr = new DBRefEntry();
766    // dbr.setSource(proxy.getDbSource());
767    // dbr.setVersion(null);
768  0 String accId = proxy.getAccessionIdFromQuery(q);
769    // dbr.setAccessionId(accId);
770  0 boolean rfound = false;
771  0 for (int r = 0, nr = rs.length; r < nr; r++)
772    {
773  0 if (rs[r] != null)
774    {
775  0 List<DBRefEntry> found = DBRefUtils.searchRefs(rs[r].getDBRefs(),
776    accId);
777  0 if (!found.isEmpty())
778    {
779  0 rfound = true;
780  0 break;
781    }
782    }
783    }
784  0 if (!rfound)
785    {
786  0 nextFetch.add(q);
787    }
788    }
789    }
790   
791    /**
792    *
793    * @return a standard title for any results retrieved using the currently
794    * selected source and settings
795    */
 
796  0 toggle public String getDefaultRetrievalTitle()
797    {
798  0 return "Retrieved from " + database.getSelectedItem();
799    }
800   
 
801  0 toggle AlignmentI parseResult(AlignmentI al, String title,
802    FileFormatI currentFileFormat,
803    FeatureSettingsModelI preferredFeatureColours)
804    {
805   
806  0 if (al != null && al.getHeight() > 0)
807    {
808  0 if (title == null)
809    {
810  0 title = getDefaultRetrievalTitle();
811    }
812  0 if (alignFrame == null)
813    {
814  0 AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
815    AlignFrame.DEFAULT_HEIGHT);
816  0 if (currentFileFormat != null)
817    {
818  0 af.currentFileFormat = currentFileFormat;
819    }
820   
821  0 List<SequenceI> alsqs = al.getSequences();
822  0 synchronized (alsqs)
823    {
824  0 for (SequenceI sq : alsqs)
825    {
826  0 if (sq.getFeatures().hasFeatures())
827    {
828  0 af.setShowSeqFeatures(true);
829  0 break;
830    }
831    }
832    }
833   
834  0 if (preferredFeatureColours != null)
835    {
836  0 af.getViewport().applyFeaturesStyle(preferredFeatureColours);
837    }
838  0 if (Cache.getDefault("HIDE_INTRONS", true))
839    {
840  0 af.hideFeatureColumns(SequenceOntologyI.EXON, false);
841    }
842  0 Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
843    AlignFrame.DEFAULT_HEIGHT);
844   
845  0 af.setStatus(MessageManager
846    .getString("label.successfully_pasted_alignment_file"));
847   
848  0 try
849    {
850  0 af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false));
851    } catch (Exception ex)
852    {
853    }
854    }
855    else
856    {
857  0 alignFrame.viewport.addAlignment(al, title);
858    }
859    }
860  0 return al;
861    }
862   
 
863  0 toggle void showErrorMessage(final String error)
864    {
865  0 resetDialog();
866  0 javax.swing.SwingUtilities.invokeLater(new Runnable()
867    {
 
868  0 toggle @Override
869    public void run()
870    {
871  0 JvOptionPane.showInternalMessageDialog(Desktop.desktop, error,
872    MessageManager.getString("label.error_retrieving_data"),
873    JvOptionPane.WARNING_MESSAGE);
874    }
875    });
876    }
877   
 
878  0 toggle public IProgressIndicator getProgressIndicator()
879    {
880  0 return progressIndicator;
881    }
882   
 
883  0 toggle public void setProgressIndicator(IProgressIndicator progressIndicator)
884    {
885  0 this.progressIndicator = progressIndicator;
886    }
887   
888    /**
889    * Hide this panel (on clicking the database button to open the database
890    * chooser)
891    */
 
892  0 toggle void hidePanel()
893    {
894  0 frame.setVisible(false);
895    }
896   
 
897  0 toggle public void setQuery(String ids)
898    {
899  0 textArea.setText(ids);
900    }
901   
902    /**
903    * Called to modify the search panel for embedding as an alternative tab of a
904    * free text search panel. The database choice list is hidden (since the
905    * choice has been made), and a Back button is made visible (which reopens the
906    * Sequence Fetcher panel).
907    *
908    * @param parentPanel
909    */
 
910  0 toggle public void embedIn(GFTSPanel parentPanel)
911    {
912  0 database.setVisible(false);
913  0 backBtn.setVisible(true);
914  0 parentSearchPanel = parentPanel;
915    }
916    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.