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jalviewX

  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.gui

File StructureChooser.java

 

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../../img/srcFileCovDistChart3.png
47% of files have more coverage

Code metrics

174
488
51
3
1,387
1,111
165
0.34
9.57
17
3.24

Classes

Class Line # Actions
StructureChooser 69 458 147 493
0.2619760326.2%
StructureChooser.PDBEntryTableModel 1263 26 15 30
0.2105263221.1%
StructureChooser.CachedPDB 1339 4 3 7
0.00%
 

Contributing tests

This file is covered by 3 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   
22    package jalview.gui;
23   
24    import jalview.api.structures.JalviewStructureDisplayI;
25    import jalview.bin.Cache;
26    import jalview.bin.Jalview;
27    import jalview.datamodel.DBRefEntry;
28    import jalview.datamodel.DBRefSource;
29    import jalview.datamodel.PDBEntry;
30    import jalview.datamodel.SequenceI;
31    import jalview.fts.api.FTSData;
32    import jalview.fts.api.FTSDataColumnI;
33    import jalview.fts.api.FTSRestClientI;
34    import jalview.fts.core.FTSRestRequest;
35    import jalview.fts.core.FTSRestResponse;
36    import jalview.fts.service.pdb.PDBFTSRestClient;
37    import jalview.io.DataSourceType;
38    import jalview.jbgui.GStructureChooser;
39    import jalview.structure.StructureMapping;
40    import jalview.structure.StructureSelectionManager;
41    import jalview.util.MessageManager;
42    import jalview.ws.DBRefFetcher;
43    import jalview.ws.sifts.SiftsSettings;
44   
45    import java.awt.event.ItemEvent;
46    import java.util.ArrayList;
47    import java.util.Collection;
48    import java.util.HashSet;
49    import java.util.LinkedHashSet;
50    import java.util.List;
51    import java.util.Objects;
52    import java.util.Set;
53    import java.util.Vector;
54   
55    import javax.swing.JCheckBox;
56    import javax.swing.JComboBox;
57    import javax.swing.JLabel;
58    import javax.swing.JTable;
59    import javax.swing.SwingUtilities;
60    import javax.swing.table.AbstractTableModel;
61   
62    /**
63    * Provides the behaviors for the Structure chooser Panel
64    *
65    * @author tcnofoegbu
66    *
67    */
68    @SuppressWarnings("serial")
 
69    public class StructureChooser extends GStructureChooser
70    implements IProgressIndicator
71    {
72    private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
73   
74    private static int MAX_QLENGTH = 7820;
75   
76    private SequenceI selectedSequence;
77   
78    private SequenceI[] selectedSequences;
79   
80    private IProgressIndicator progressIndicator;
81   
82    private Collection<FTSData> discoveredStructuresSet;
83   
84    private FTSRestRequest lastPdbRequest;
85   
86    private FTSRestClientI pdbRestCleint;
87   
88    private String selectedPdbFileName;
89   
90    private boolean isValidPBDEntry;
91   
92    private boolean cachedPDBExists;
93   
94    private static StructureViewer lastTargetedView = null;
95   
 
96  1 toggle public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
97    AlignmentPanel ap)
98    {
99  1 this.ap = ap;
100  1 this.selectedSequence = selectedSeq;
101  1 this.selectedSequences = selectedSeqs;
102  1 this.progressIndicator = (ap == null) ? null : ap.alignFrame;
103  1 init();
104    }
105   
106    /**
107    * Initializes parameters used by the Structure Chooser Panel
108    */
 
109  1 toggle protected void init()
110    {
111  1 if (!Jalview.isHeadlessMode())
112    {
113  1 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
114    }
115   
116  1 chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true));
117   
118    // ensure a filter option is in force for search
119  1 populateFilterComboBox(true, cachedPDBExists);
120  1 Thread discoverPDBStructuresThread = new Thread(new Runnable()
121    {
 
122  1 toggle @Override
123    public void run()
124    {
125  1 long startTime = System.currentTimeMillis();
126  1 updateProgressIndicator(MessageManager
127    .getString("status.loading_cached_pdb_entries"), startTime);
128  1 loadLocalCachedPDBEntries();
129  1 updateProgressIndicator(null, startTime);
130  1 updateProgressIndicator(MessageManager.getString(
131    "status.searching_for_pdb_structures"), startTime);
132  1 fetchStructuresMetaData();
133    // revise filter options if no results were found
134  1 populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
135  1 discoverStructureViews();
136  0 updateProgressIndicator(null, startTime);
137  0 mainFrame.setVisible(true);
138  0 updateCurrentView();
139    }
140    });
141  1 discoverPDBStructuresThread.start();
142    }
143   
144    /**
145    * Builds a drop-down choice list of existing structure viewers to which new
146    * structures may be added. If this list is empty then it, and the 'Add'
147    * button, are hidden.
148    */
 
149  1 toggle private void discoverStructureViews()
150    {
151  1 if (Desktop.instance != null)
152    {
153  1 targetView.removeAllItems();
154  1 if (lastTargetedView != null && !lastTargetedView.isVisible())
155    {
156  0 lastTargetedView = null;
157    }
158  1 int linkedViewsAt = 0;
159  1 for (StructureViewerBase view : Desktop.instance
160    .getStructureViewers(null, null))
161    {
162  1 StructureViewer viewHandler = (lastTargetedView != null
163    && lastTargetedView.sview == view) ? lastTargetedView
164    : StructureViewer.reconfigure(view);
165   
166  0 if (view.isLinkedWith(ap))
167    {
168  0 targetView.insertItemAt(viewHandler,
169    linkedViewsAt++);
170    }
171    else
172    {
173  0 targetView.addItem(viewHandler);
174    }
175    }
176   
177    /*
178    * show option to Add to viewer if at least 1 viewer found
179    */
180  0 targetView.setVisible(false);
181  0 if (targetView.getItemCount() > 0)
182    {
183  0 targetView.setVisible(true);
184  0 if (lastTargetedView != null)
185    {
186  0 targetView.setSelectedItem(lastTargetedView);
187    }
188    else
189    {
190  0 targetView.setSelectedIndex(0);
191    }
192    }
193  0 btn_add.setVisible(targetView.isVisible());
194    }
195    }
196   
197    /**
198    * Updates the progress indicator with the specified message
199    *
200    * @param message
201    * displayed message for the operation
202    * @param id
203    * unique handle for this indicator
204    */
 
205  3 toggle protected void updateProgressIndicator(String message, long id)
206    {
207  3 if (progressIndicator != null)
208    {
209  0 progressIndicator.setProgressBar(message, id);
210    }
211    }
212   
213    /**
214    * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
215    * selection group
216    */
 
217  1 toggle void fetchStructuresMetaData()
218    {
219  1 long startTime = System.currentTimeMillis();
220  1 pdbRestCleint = PDBFTSRestClient.getInstance();
221  1 Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
222    .getStructureSummaryFields();
223   
224  1 discoveredStructuresSet = new LinkedHashSet<>();
225  1 HashSet<String> errors = new HashSet<>();
226  1 for (SequenceI seq : selectedSequences)
227    {
228  1 FTSRestRequest pdbRequest = new FTSRestRequest();
229  1 pdbRequest.setAllowEmptySeq(false);
230  1 pdbRequest.setResponseSize(500);
231  1 pdbRequest.setFieldToSearchBy("(");
232  1 FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
233    .getSelectedItem());
234  1 pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(),
235    !chk_invertFilter.isSelected());
236  1 pdbRequest.setWantedFields(wantedFields);
237  1 pdbRequest.setSearchTerm(buildQuery(seq) + ")");
238  1 pdbRequest.setAssociatedSequence(seq);
239  1 FTSRestResponse resultList;
240  1 try
241    {
242  1 resultList = pdbRestCleint.executeRequest(pdbRequest);
243    } catch (Exception e)
244    {
245  1 e.printStackTrace();
246  1 errors.add(e.getMessage());
247  1 continue;
248    }
249  0 lastPdbRequest = pdbRequest;
250  0 if (resultList.getSearchSummary() != null
251    && !resultList.getSearchSummary().isEmpty())
252    {
253  0 discoveredStructuresSet.addAll(resultList.getSearchSummary());
254    }
255    }
256   
257  1 int noOfStructuresFound = 0;
258  1 String totalTime = (System.currentTimeMillis() - startTime)
259    + " milli secs";
260  1 if (discoveredStructuresSet != null
261    && !discoveredStructuresSet.isEmpty())
262    {
263  0 getResultTable().setModel(FTSRestResponse
264    .getTableModel(lastPdbRequest, discoveredStructuresSet));
265  0 noOfStructuresFound = discoveredStructuresSet.size();
266  0 mainFrame.setTitle(MessageManager.formatMessage(
267    "label.structure_chooser_no_of_structures",
268    noOfStructuresFound, totalTime));
269    }
270    else
271    {
272  1 mainFrame.setTitle(MessageManager
273    .getString("label.structure_chooser_manual_association"));
274  1 if (errors.size() > 0)
275    {
276  1 StringBuilder errorMsg = new StringBuilder();
277  1 for (String error : errors)
278    {
279  1 errorMsg.append(error).append("\n");
280    }
281  1 JvOptionPane.showMessageDialog(this, errorMsg.toString(),
282    MessageManager.getString("label.pdb_web-service_error"),
283    JvOptionPane.ERROR_MESSAGE);
284    }
285    }
286    }
287   
 
288  1 toggle protected void loadLocalCachedPDBEntries()
289    {
290  1 ArrayList<CachedPDB> entries = new ArrayList<>();
291  1 for (SequenceI seq : selectedSequences)
292    {
293  1 if (seq.getDatasetSequence() != null
294    && seq.getDatasetSequence().getAllPDBEntries() != null)
295    {
296  1 for (PDBEntry pdbEntry : seq.getDatasetSequence()
297    .getAllPDBEntries())
298    {
299  0 if (pdbEntry.getFile() != null)
300    {
301  0 entries.add(new CachedPDB(seq, pdbEntry));
302    }
303    }
304    }
305    }
306  1 cachedPDBExists = !entries.isEmpty();
307  1 PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
308  1 tbl_local_pdb.setModel(tableModelx);
309    }
310   
311    /**
312    * Builds a query string for a given sequences using its DBRef entries
313    *
314    * @param seq
315    * the sequences to build a query for
316    * @return the built query string
317    */
318   
 
319  5 toggle static String buildQuery(SequenceI seq)
320    {
321  5 boolean isPDBRefsFound = false;
322  5 boolean isUniProtRefsFound = false;
323  5 StringBuilder queryBuilder = new StringBuilder();
324  5 Set<String> seqRefs = new LinkedHashSet<>();
325   
326  5 if (seq.getAllPDBEntries() != null
327    && queryBuilder.length() < MAX_QLENGTH)
328    {
329  5 for (PDBEntry entry : seq.getAllPDBEntries())
330    {
331  2 if (isValidSeqName(entry.getId()))
332    {
333  2 queryBuilder.append("pdb_id:").append(entry.getId().toLowerCase())
334    .append(" OR ");
335  2 isPDBRefsFound = true;
336    }
337    }
338    }
339   
340  5 if (seq.getDBRefs() != null && seq.getDBRefs().length != 0)
341    {
342  4 for (DBRefEntry dbRef : seq.getDBRefs())
343    {
344  18 if (isValidSeqName(getDBRefId(dbRef))
345    && queryBuilder.length() < MAX_QLENGTH)
346    {
347  18 if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
348    {
349  1 queryBuilder.append("uniprot_accession:")
350    .append(getDBRefId(dbRef)).append(" OR ");
351  1 queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef))
352    .append(" OR ");
353  1 isUniProtRefsFound = true;
354    }
355  17 else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
356    {
357   
358  1 queryBuilder.append("pdb_id:")
359    .append(getDBRefId(dbRef).toLowerCase()).append(" OR ");
360  1 isPDBRefsFound = true;
361    }
362    else
363    {
364  16 seqRefs.add(getDBRefId(dbRef));
365    }
366    }
367    }
368    }
369   
370  5 if (!isPDBRefsFound && !isUniProtRefsFound)
371    {
372  2 String seqName = seq.getName();
373  2 seqName = sanitizeSeqName(seqName);
374  2 String[] names = seqName.toLowerCase().split("\\|");
375  2 for (String name : names)
376    {
377    // System.out.println("Found name : " + name);
378  8 name.trim();
379  8 if (isValidSeqName(name))
380    {
381  4 seqRefs.add(name);
382    }
383    }
384   
385  2 for (String seqRef : seqRefs)
386    {
387  6 queryBuilder.append("text:").append(seqRef).append(" OR ");
388    }
389    }
390   
391  5 int endIndex = queryBuilder.lastIndexOf(" OR ");
392  5 if (queryBuilder.toString().length() < 6)
393    {
394  0 return null;
395    }
396  5 String query = queryBuilder.toString().substring(0, endIndex);
397  5 return query;
398    }
399   
400    /**
401    * Remove the following special characters from input string +, -, &, !, (, ),
402    * {, }, [, ], ^, ", ~, *, ?, :, \
403    *
404    * @param seqName
405    * @return
406    */
 
407  6 toggle static String sanitizeSeqName(String seqName)
408    {
409  6 Objects.requireNonNull(seqName);
410  6 return seqName.replaceAll("\\[\\d*\\]", "")
411    .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
412    }
413   
414    /**
415    * Ensures sequence ref names are not less than 3 characters and does not
416    * contain a database name
417    *
418    * @param seqName
419    * @return
420    */
 
421  28 toggle static boolean isValidSeqName(String seqName)
422    {
423    // System.out.println("seqName : " + seqName);
424  28 String ignoreList = "pdb,uniprot,swiss-prot";
425  28 if (seqName.length() < 3)
426    {
427  2 return false;
428    }
429  26 if (seqName.contains(":"))
430    {
431  0 return false;
432    }
433  26 seqName = seqName.toLowerCase();
434  26 for (String ignoredEntry : ignoreList.split(","))
435    {
436  74 if (seqName.contains(ignoredEntry))
437    {
438  2 return false;
439    }
440    }
441  24 return true;
442    }
443   
 
444  37 toggle static String getDBRefId(DBRefEntry dbRef)
445    {
446  37 String ref = dbRef.getAccessionId().replaceAll("GO:", "");
447  37 return ref;
448    }
449   
450    /**
451    * Filters a given list of discovered structures based on supplied argument
452    *
453    * @param fieldToFilterBy
454    * the field to filter by
455    */
 
456  0 toggle void filterResultSet(final String fieldToFilterBy)
457    {
458  0 Thread filterThread = new Thread(new Runnable()
459    {
 
460  0 toggle @Override
461    public void run()
462    {
463  0 long startTime = System.currentTimeMillis();
464  0 pdbRestCleint = PDBFTSRestClient.getInstance();
465  0 lbl_loading.setVisible(true);
466  0 Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
467    .getStructureSummaryFields();
468  0 Collection<FTSData> filteredResponse = new HashSet<>();
469  0 HashSet<String> errors = new HashSet<>();
470   
471  0 for (SequenceI seq : selectedSequences)
472    {
473  0 FTSRestRequest pdbRequest = new FTSRestRequest();
474  0 if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
475    {
476  0 pdbRequest.setAllowEmptySeq(false);
477  0 pdbRequest.setResponseSize(1);
478  0 pdbRequest.setFieldToSearchBy("(");
479  0 pdbRequest.setSearchTerm(buildQuery(seq) + ")");
480  0 pdbRequest.setWantedFields(wantedFields);
481  0 pdbRequest.setAssociatedSequence(seq);
482  0 pdbRequest.setFacet(true);
483  0 pdbRequest.setFacetPivot(fieldToFilterBy + ",entry_entity");
484  0 pdbRequest.setFacetPivotMinCount(1);
485    }
486    else
487    {
488  0 pdbRequest.setAllowEmptySeq(false);
489  0 pdbRequest.setResponseSize(1);
490  0 pdbRequest.setFieldToSearchBy("(");
491  0 pdbRequest.setFieldToSortBy(fieldToFilterBy,
492    !chk_invertFilter.isSelected());
493  0 pdbRequest.setSearchTerm(buildQuery(seq) + ")");
494  0 pdbRequest.setWantedFields(wantedFields);
495  0 pdbRequest.setAssociatedSequence(seq);
496    }
497  0 FTSRestResponse resultList;
498  0 try
499    {
500  0 resultList = pdbRestCleint.executeRequest(pdbRequest);
501    } catch (Exception e)
502    {
503  0 e.printStackTrace();
504  0 errors.add(e.getMessage());
505  0 continue;
506    }
507  0 lastPdbRequest = pdbRequest;
508  0 if (resultList.getSearchSummary() != null
509    && !resultList.getSearchSummary().isEmpty())
510    {
511  0 filteredResponse.addAll(resultList.getSearchSummary());
512    }
513    }
514   
515  0 String totalTime = (System.currentTimeMillis() - startTime)
516    + " milli secs";
517  0 if (!filteredResponse.isEmpty())
518    {
519  0 final int filterResponseCount = filteredResponse.size();
520  0 Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>();
521  0 reorderedStructuresSet.addAll(filteredResponse);
522  0 reorderedStructuresSet.addAll(discoveredStructuresSet);
523  0 getResultTable().setModel(FTSRestResponse
524    .getTableModel(lastPdbRequest, reorderedStructuresSet));
525   
526  0 FTSRestResponse.configureTableColumn(getResultTable(),
527    wantedFields, tempUserPrefs);
528  0 getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
529  0 getResultTable().getColumn("Ref Sequence").setMinWidth(100);
530  0 getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
531    // Update table selection model here
532  0 getResultTable().addRowSelectionInterval(0,
533    filterResponseCount - 1);
534  0 mainFrame.setTitle(MessageManager.formatMessage(
535    "label.structure_chooser_filter_time", totalTime));
536    }
537    else
538    {
539  0 mainFrame.setTitle(MessageManager.formatMessage(
540    "label.structure_chooser_filter_time", totalTime));
541  0 if (errors.size() > 0)
542    {
543  0 StringBuilder errorMsg = new StringBuilder();
544  0 for (String error : errors)
545    {
546  0 errorMsg.append(error).append("\n");
547    }
548  0 JvOptionPane.showMessageDialog(null, errorMsg.toString(),
549    MessageManager.getString("label.pdb_web-service_error"),
550    JvOptionPane.ERROR_MESSAGE);
551    }
552    }
553   
554  0 lbl_loading.setVisible(false);
555   
556  0 validateSelections();
557    }
558    });
559  0 filterThread.start();
560    }
561   
562    /**
563    * Handles action event for btn_pdbFromFile
564    */
 
565  0 toggle @Override
566    protected void pdbFromFile_actionPerformed()
567    {
568    // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and StructureChooser
569    // works
570  0 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
571    jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
572  0 chooser.setFileView(new jalview.io.JalviewFileView());
573  0 chooser.setDialogTitle(
574    MessageManager.formatMessage("label.select_pdb_file_for",
575    selectedSequence.getDisplayId(false)));
576  0 chooser.setToolTipText(MessageManager.formatMessage(
577    "label.load_pdb_file_associate_with_sequence",
578    selectedSequence.getDisplayId(false)));
579   
580  0 int value = chooser.showOpenDialog(null);
581  0 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
582    {
583  0 selectedPdbFileName = chooser.getSelectedFile().getPath();
584  0 jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
585  0 validateSelections();
586    }
587    }
588   
589    /**
590    * Populates the filter combo-box options dynamically depending on discovered
591    * structures
592    */
 
593  5 toggle protected void populateFilterComboBox(boolean haveData,
594    boolean cachedPDBExist)
595    {
596    /*
597    * temporarily suspend the change listener behaviour
598    */
599  5 cmb_filterOption.removeItemListener(this);
600   
601  5 cmb_filterOption.removeAllItems();
602  5 if (haveData)
603    {
604  3 cmb_filterOption.addItem(new FilterOption(
605    MessageManager.getString("label.best_quality"),
606    "overall_quality", VIEWS_FILTER, false));
607  3 cmb_filterOption.addItem(new FilterOption(
608    MessageManager.getString("label.best_resolution"),
609    "resolution", VIEWS_FILTER, false));
610  3 cmb_filterOption.addItem(new FilterOption(
611    MessageManager.getString("label.most_protein_chain"),
612    "number_of_protein_chains", VIEWS_FILTER, false));
613  3 cmb_filterOption.addItem(new FilterOption(
614    MessageManager.getString("label.most_bound_molecules"),
615    "number_of_bound_molecules", VIEWS_FILTER, false));
616  3 cmb_filterOption.addItem(new FilterOption(
617    MessageManager.getString("label.most_polymer_residues"),
618    "number_of_polymer_residues", VIEWS_FILTER, true));
619    }
620  5 cmb_filterOption.addItem(
621    new FilterOption(MessageManager.getString("label.enter_pdb_id"),
622    "-", VIEWS_ENTER_ID, false));
623  5 cmb_filterOption.addItem(
624    new FilterOption(MessageManager.getString("label.from_file"),
625    "-", VIEWS_FROM_FILE, false));
626   
627  5 if (cachedPDBExist)
628    {
629  1 FilterOption cachedOption = new FilterOption(
630    MessageManager.getString("label.cached_structures"),
631    "-", VIEWS_LOCAL_PDB, false);
632  1 cmb_filterOption.addItem(cachedOption);
633  1 cmb_filterOption.setSelectedItem(cachedOption);
634    }
635   
636  5 cmb_filterOption.addItemListener(this);
637    }
638   
639    /**
640    * Updates the displayed view based on the selected filter option
641    */
 
642  0 toggle protected void updateCurrentView()
643    {
644  0 FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
645    .getSelectedItem());
646  0 layout_switchableViews.show(pnl_switchableViews,
647    selectedFilterOpt.getView());
648  0 String filterTitle = mainFrame.getTitle();
649  0 mainFrame.setTitle(frameTitle);
650  0 chk_invertFilter.setVisible(false);
651  0 if (selectedFilterOpt.getView() == VIEWS_FILTER)
652    {
653  0 mainFrame.setTitle(filterTitle);
654  0 chk_invertFilter.setVisible(true);
655  0 filterResultSet(selectedFilterOpt.getValue());
656    }
657  0 else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
658    || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
659    {
660  0 mainFrame.setTitle(MessageManager
661    .getString("label.structure_chooser_manual_association"));
662  0 idInputAssSeqPanel.loadCmbAssSeq();
663  0 fileChooserAssSeqPanel.loadCmbAssSeq();
664    }
665  0 validateSelections();
666    }
667   
668    /**
669    * Validates user selection and enables the 'Add' and 'New View' buttons if
670    * all parameters are correct (the Add button will only be visible if there is
671    * at least one existing structure viewer open). This basically means at least
672    * one structure selected and no error messages.
673    * <p>
674    * The 'Superpose Structures' option is enabled if either more than one
675    * structure is selected, or the 'Add' to existing view option is enabled, and
676    * disabled if the only option is to open a new view of a single structure.
677    */
 
678  0 toggle @Override
679    protected void validateSelections()
680    {
681  0 FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
682    .getSelectedItem());
683  0 btn_add.setEnabled(false);
684  0 String currentView = selectedFilterOpt.getView();
685  0 int selectedCount = 0;
686  0 if (currentView == VIEWS_FILTER)
687    {
688  0 selectedCount = getResultTable().getSelectedRows().length;
689  0 if (selectedCount > 0)
690    {
691  0 btn_add.setEnabled(true);
692    }
693    }
694  0 else if (currentView == VIEWS_LOCAL_PDB)
695    {
696  0 selectedCount = tbl_local_pdb.getSelectedRows().length;
697  0 if (selectedCount > 0)
698    {
699  0 btn_add.setEnabled(true);
700    }
701    }
702  0 else if (currentView == VIEWS_ENTER_ID)
703    {
704  0 validateAssociationEnterPdb();
705    }
706  0 else if (currentView == VIEWS_FROM_FILE)
707    {
708  0 validateAssociationFromFile();
709    }
710   
711  0 btn_newView.setEnabled(btn_add.isEnabled());
712   
713    /*
714    * enable 'Superpose' option if more than one structure is selected,
715    * or there are view(s) available to add structure(s) to
716    */
717  0 chk_superpose
718    .setEnabled(selectedCount > 1 || targetView.getItemCount() > 0);
719    }
720   
721    /**
722    * Validates inputs from the Manual PDB entry panel
723    */
 
724  0 toggle protected void validateAssociationEnterPdb()
725    {
726  0 AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
727    .getCmb_assSeq().getSelectedItem();
728  0 lbl_pdbManualFetchStatus.setIcon(errorImage);
729  0 lbl_pdbManualFetchStatus.setToolTipText("");
730  0 if (txt_search.getText().length() > 0)
731    {
732  0 lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true,
733    MessageManager.formatMessage("info.no_pdb_entry_found_for",
734    txt_search.getText())));
735    }
736   
737  0 if (errorWarning.length() > 0)
738    {
739  0 lbl_pdbManualFetchStatus.setIcon(warningImage);
740  0 lbl_pdbManualFetchStatus.setToolTipText(
741    JvSwingUtils.wrapTooltip(true, errorWarning.toString()));
742    }
743   
744  0 if (selectedSequences.length == 1 || !assSeqOpt.getName()
745    .equalsIgnoreCase("-Select Associated Seq-"))
746    {
747  0 txt_search.setEnabled(true);
748  0 if (isValidPBDEntry)
749    {
750  0 btn_add.setEnabled(true);
751  0 lbl_pdbManualFetchStatus.setToolTipText("");
752  0 lbl_pdbManualFetchStatus.setIcon(goodImage);
753    }
754    }
755    else
756    {
757  0 txt_search.setEnabled(false);
758  0 lbl_pdbManualFetchStatus.setIcon(errorImage);
759    }
760    }
761   
762    /**
763    * Validates inputs for the manual PDB file selection options
764    */
 
765  0 toggle protected void validateAssociationFromFile()
766    {
767  0 AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
768    .getCmb_assSeq().getSelectedItem();
769  0 lbl_fromFileStatus.setIcon(errorImage);
770  0 if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt
771    .getName().equalsIgnoreCase("-Select Associated Seq-")))
772    {
773  0 btn_pdbFromFile.setEnabled(true);
774  0 if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
775    {
776  0 btn_add.setEnabled(true);
777  0 lbl_fromFileStatus.setIcon(goodImage);
778    }
779    }
780    else
781    {
782  0 btn_pdbFromFile.setEnabled(false);
783  0 lbl_fromFileStatus.setIcon(errorImage);
784    }
785    }
786   
 
787  0 toggle @Override
788    protected void cmbAssSeqStateChanged()
789    {
790  0 validateSelections();
791    }
792   
793    /**
794    * Handles the state change event for the 'filter' combo-box and 'invert'
795    * check-box
796    */
 
797  0 toggle @Override
798    protected void stateChanged(ItemEvent e)
799    {
800  0 if (e.getSource() instanceof JCheckBox)
801    {
802  0 updateCurrentView();
803    }
804    else
805    {
806  0 if (e.getStateChange() == ItemEvent.SELECTED)
807    {
808  0 updateCurrentView();
809    }
810    }
811   
812    }
813   
814    /**
815    * select structures for viewing by their PDB IDs
816    *
817    * @param pdbids
818    * @return true if structures were found and marked as selected
819    */
 
820  0 toggle public boolean selectStructure(String... pdbids)
821    {
822  0 boolean found = false;
823   
824  0 FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
825    .getSelectedItem());
826  0 String currentView = selectedFilterOpt.getView();
827  0 JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
828  0 : (currentView == VIEWS_LOCAL_PDB) ? tbl_local_pdb : null;
829   
830  0 if (restable == null)
831    {
832    // can't select (enter PDB ID, or load file - need to also select which
833    // sequence to associate with)
834  0 return false;
835    }
836   
837  0 int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex();
838  0 for (int r = 0; r < restable.getRowCount(); r++)
839    {
840  0 for (int p = 0; p < pdbids.length; p++)
841    {
842  0 if (String.valueOf(restable.getValueAt(r, pdbIdColIndex))
843    .equalsIgnoreCase(pdbids[p]))
844    {
845  0 restable.setRowSelectionInterval(r, r);
846  0 found = true;
847    }
848    }
849    }
850  0 return found;
851    }
852   
853    /**
854    * Handles the 'New View' action
855    */
 
856  0 toggle @Override
857    protected void newView_ActionPerformed()
858    {
859  0 targetView.setSelectedItem(null);
860  0 showStructures(false);
861    }
862   
863    /**
864    * Handles the 'Add to existing viewer' action
865    */
 
866  0 toggle @Override
867    protected void add_ActionPerformed()
868    {
869  0 showStructures(false);
870    }
871   
872    /**
873    * structure viewer opened by this dialog, or null
874    */
875    private StructureViewer sViewer = null;
876   
 
877  0 toggle public void showStructures(boolean waitUntilFinished)
878    {
879   
880  0 final StructureSelectionManager ssm = ap.getStructureSelectionManager();
881   
882  0 final int preferredHeight = pnl_filter.getHeight();
883   
884  0 Runnable viewStruc = new Runnable()
885    {
 
886  0 toggle @Override
887    public void run()
888    {
889  0 FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
890    .getSelectedItem());
891  0 String currentView = selectedFilterOpt.getView();
892  0 JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
893    : tbl_local_pdb;
894   
895  0 if (currentView == VIEWS_FILTER)
896    {
897  0 int pdbIdColIndex = restable.getColumn("PDB Id")
898    .getModelIndex();
899  0 int refSeqColIndex = restable.getColumn("Ref Sequence")
900    .getModelIndex();
901  0 int[] selectedRows = restable.getSelectedRows();
902  0 PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
903  0 int count = 0;
904  0 List<SequenceI> selectedSeqsToView = new ArrayList<>();
905  0 for (int row : selectedRows)
906    {
907  0 String pdbIdStr = restable
908    .getValueAt(row, pdbIdColIndex).toString();
909  0 SequenceI selectedSeq = (SequenceI) restable
910    .getValueAt(row, refSeqColIndex);
911  0 selectedSeqsToView.add(selectedSeq);
912  0 PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
913  0 if (pdbEntry == null)
914    {
915  0 pdbEntry = getFindEntry(pdbIdStr,
916    selectedSeq.getAllPDBEntries());
917    }
918   
919  0 if (pdbEntry == null)
920    {
921  0 pdbEntry = new PDBEntry();
922  0 pdbEntry.setId(pdbIdStr);
923  0 pdbEntry.setType(PDBEntry.Type.PDB);
924  0 selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
925    }
926  0 pdbEntriesToView[count++] = pdbEntry;
927    }
928  0 SequenceI[] selectedSeqs = selectedSeqsToView
929    .toArray(new SequenceI[selectedSeqsToView.size()]);
930  0 sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
931    selectedSeqs);
932    }
933  0 else if (currentView == VIEWS_LOCAL_PDB)
934    {
935  0 int[] selectedRows = tbl_local_pdb.getSelectedRows();
936  0 PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
937  0 int count = 0;
938  0 int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
939    .getModelIndex();
940  0 int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
941    .getModelIndex();
942  0 List<SequenceI> selectedSeqsToView = new ArrayList<>();
943  0 for (int row : selectedRows)
944    {
945  0 PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
946    pdbIdColIndex);
947  0 pdbEntriesToView[count++] = pdbEntry;
948  0 SequenceI selectedSeq = (SequenceI) tbl_local_pdb
949    .getValueAt(row, refSeqColIndex);
950  0 selectedSeqsToView.add(selectedSeq);
951    }
952  0 SequenceI[] selectedSeqs = selectedSeqsToView
953    .toArray(new SequenceI[selectedSeqsToView.size()]);
954  0 sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
955    selectedSeqs);
956    }
957  0 else if (currentView == VIEWS_ENTER_ID)
958    {
959  0 SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
960    .getCmb_assSeq().getSelectedItem()).getSequence();
961  0 if (userSelectedSeq != null)
962    {
963  0 selectedSequence = userSelectedSeq;
964    }
965  0 String pdbIdStr = txt_search.getText();
966  0 PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
967  0 if (pdbEntry == null)
968    {
969  0 pdbEntry = new PDBEntry();
970  0 if (pdbIdStr.split(":").length > 1)
971    {
972  0 pdbEntry.setId(pdbIdStr.split(":")[0]);
973  0 pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase());
974    }
975    else
976    {
977  0 pdbEntry.setId(pdbIdStr);
978    }
979  0 pdbEntry.setType(PDBEntry.Type.PDB);
980  0 selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
981    }
982   
983  0 PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
984  0 sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
985    new SequenceI[]
986    { selectedSequence });
987    }
988  0 else if (currentView == VIEWS_FROM_FILE)
989    {
990  0 SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
991    .getCmb_assSeq().getSelectedItem()).getSequence();
992  0 if (userSelectedSeq != null)
993    {
994  0 selectedSequence = userSelectedSeq;
995    }
996  0 PDBEntry fileEntry = new AssociatePdbFileWithSeq()
997    .associatePdbWithSeq(selectedPdbFileName,
998    DataSourceType.FILE, selectedSequence, true,
999    Desktop.instance);
1000   
1001  0 sViewer = launchStructureViewer(
1002    ssm, new PDBEntry[]
1003    { fileEntry }, ap,
1004    new SequenceI[]
1005    { selectedSequence });
1006    }
1007  0 SwingUtilities.invokeLater(new Runnable()
1008    {
 
1009  0 toggle @Override
1010    public void run()
1011    {
1012  0 closeAction(preferredHeight);
1013  0 mainFrame.dispose();
1014    }
1015    });
1016    }
1017    };
1018  0 Thread runner = new Thread(viewStruc);
1019  0 runner.start();
1020  0 if (waitUntilFinished)
1021    {
1022  0 while (sViewer == null ? runner.isAlive()
1023  0 : (sViewer.sview == null ? true
1024    : !sViewer.sview.hasMapping()))
1025    {
1026  0 try
1027    {
1028  0 Thread.sleep(300);
1029    } catch (InterruptedException ie)
1030    {
1031   
1032    }
1033    }
1034    }
1035    }
1036   
 
1037  0 toggle private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
1038    {
1039  0 Objects.requireNonNull(id);
1040  0 Objects.requireNonNull(pdbEntries);
1041  0 PDBEntry foundEntry = null;
1042  0 for (PDBEntry entry : pdbEntries)
1043    {
1044  0 if (entry.getId().equalsIgnoreCase(id))
1045    {
1046  0 return entry;
1047    }
1048    }
1049  0 return foundEntry;
1050    }
1051   
1052    /**
1053    * Answers a structure viewer (new or existing) configured to superimpose
1054    * added structures or not according to the user's choice
1055    *
1056    * @param ssm
1057    * @return
1058    */
 
1059  0 toggle StructureViewer getTargetedStructureViewer(
1060    StructureSelectionManager ssm)
1061    {
1062  0 Object sv = targetView.getSelectedItem();
1063   
1064  0 return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv;
1065    }
1066   
1067    /**
1068    * Adds PDB structures to a new or existing structure viewer
1069    *
1070    * @param ssm
1071    * @param pdbEntriesToView
1072    * @param alignPanel
1073    * @param sequences
1074    * @return
1075    */
 
1076  0 toggle private StructureViewer launchStructureViewer(
1077    StructureSelectionManager ssm,
1078    final PDBEntry[] pdbEntriesToView,
1079    final AlignmentPanel alignPanel, SequenceI[] sequences)
1080    {
1081  0 long progressId = sequences.hashCode();
1082  0 setProgressBar(MessageManager
1083    .getString("status.launching_3d_structure_viewer"), progressId);
1084  0 final StructureViewer theViewer = getTargetedStructureViewer(ssm);
1085  0 boolean superimpose = chk_superpose.isSelected();
1086  0 theViewer.setSuperpose(superimpose);
1087   
1088    /*
1089    * remember user's choice of superimpose or not
1090    */
1091  0 Cache.setProperty(AUTOSUPERIMPOSE,
1092    Boolean.valueOf(superimpose).toString());
1093   
1094  0 setProgressBar(null, progressId);
1095  0 if (SiftsSettings.isMapWithSifts())
1096    {
1097  0 List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
1098  0 int p = 0;
1099    // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
1100    // real PDB ID. For moment, we can also safely do this if there is already
1101    // a known mapping between the PDBEntry and the sequence.
1102  0 for (SequenceI seq : sequences)
1103    {
1104  0 PDBEntry pdbe = pdbEntriesToView[p++];
1105  0 if (pdbe != null && pdbe.getFile() != null)
1106    {
1107  0 StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
1108  0 if (smm != null && smm.length > 0)
1109    {
1110  0 for (StructureMapping sm : smm)
1111    {
1112  0 if (sm.getSequence() == seq)
1113    {
1114  0 continue;
1115    }
1116    }
1117    }
1118    }
1119  0 if (seq.getPrimaryDBRefs().isEmpty())
1120    {
1121  0 seqsWithoutSourceDBRef.add(seq);
1122  0 continue;
1123    }
1124    }
1125  0 if (!seqsWithoutSourceDBRef.isEmpty())
1126    {
1127  0 int y = seqsWithoutSourceDBRef.size();
1128  0 setProgressBar(MessageManager.formatMessage(
1129    "status.fetching_dbrefs_for_sequences_without_valid_refs",
1130    y), progressId);
1131  0 SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
1132    .toArray(new SequenceI[y]);
1133  0 DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
1134  0 dbRefFetcher.fetchDBRefs(true);
1135   
1136  0 setProgressBar("Fetch complete.", progressId); // todo i18n
1137    }
1138    }
1139  0 if (pdbEntriesToView.length > 1)
1140    {
1141  0 setProgressBar(MessageManager.getString(
1142    "status.fetching_3d_structures_for_selected_entries"),
1143    progressId);
1144  0 theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
1145    }
1146    else
1147    {
1148  0 setProgressBar(MessageManager.formatMessage(
1149    "status.fetching_3d_structures_for",
1150    pdbEntriesToView[0].getId()),progressId);
1151  0 theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
1152    }
1153  0 setProgressBar(null, progressId);
1154    // remember the last viewer we used...
1155  0 lastTargetedView = theViewer;
1156  0 return theViewer;
1157    }
1158   
1159    /**
1160    * Populates the combo-box used in associating manually fetched structures to
1161    * a unique sequence when more than one sequence selection is made.
1162    */
 
1163  0 toggle @Override
1164    protected void populateCmbAssociateSeqOptions(
1165    JComboBox<AssociateSeqOptions> cmb_assSeq,
1166    JLabel lbl_associateSeq)
1167    {
1168  0 cmb_assSeq.removeAllItems();
1169  0 cmb_assSeq.addItem(
1170    new AssociateSeqOptions("-Select Associated Seq-", null));
1171  0 lbl_associateSeq.setVisible(false);
1172  0 if (selectedSequences.length > 1)
1173    {
1174  0 for (SequenceI seq : selectedSequences)
1175    {
1176  0 cmb_assSeq.addItem(new AssociateSeqOptions(seq));
1177    }
1178    }
1179    else
1180    {
1181  0 String seqName = selectedSequence.getDisplayId(false);
1182  0 seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
1183  0 lbl_associateSeq.setText(seqName);
1184  0 lbl_associateSeq.setVisible(true);
1185  0 cmb_assSeq.setVisible(false);
1186    }
1187    }
1188   
 
1189  1 toggle protected boolean isStructuresDiscovered()
1190    {
1191  1 return discoveredStructuresSet != null
1192    && !discoveredStructuresSet.isEmpty();
1193    }
1194   
 
1195  0 toggle @Override
1196    protected void txt_search_ActionPerformed()
1197    {
1198  0 new Thread()
1199    {
 
1200  0 toggle @Override
1201    public void run()
1202    {
1203  0 errorWarning.setLength(0);
1204  0 isValidPBDEntry = false;
1205  0 if (txt_search.getText().length() > 0)
1206    {
1207  0 String searchTerm = txt_search.getText().toLowerCase();
1208  0 searchTerm = searchTerm.split(":")[0];
1209    // System.out.println(">>>>> search term : " + searchTerm);
1210  0 List<FTSDataColumnI> wantedFields = new ArrayList<>();
1211  0 FTSRestRequest pdbRequest = new FTSRestRequest();
1212  0 pdbRequest.setAllowEmptySeq(false);
1213  0 pdbRequest.setResponseSize(1);
1214  0 pdbRequest.setFieldToSearchBy("(pdb_id:");
1215  0 pdbRequest.setWantedFields(wantedFields);
1216  0 pdbRequest.setSearchTerm(searchTerm + ")");
1217  0 pdbRequest.setAssociatedSequence(selectedSequence);
1218  0 pdbRestCleint = PDBFTSRestClient.getInstance();
1219  0 wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
1220  0 FTSRestResponse resultList;
1221  0 try
1222    {
1223  0 resultList = pdbRestCleint.executeRequest(pdbRequest);
1224    } catch (Exception e)
1225    {
1226  0 errorWarning.append(e.getMessage());
1227  0 return;
1228    } finally
1229    {
1230  0 validateSelections();
1231    }
1232  0 if (resultList.getSearchSummary() != null
1233    && resultList.getSearchSummary().size() > 0)
1234    {
1235  0 isValidPBDEntry = true;
1236    }
1237    }
1238  0 validateSelections();
1239    }
1240    }.start();
1241    }
1242   
 
1243  1 toggle @Override
1244    protected void tabRefresh()
1245    {
1246  1 if (selectedSequences != null)
1247    {
1248  0 Thread refreshThread = new Thread(new Runnable()
1249    {
 
1250  0 toggle @Override
1251    public void run()
1252    {
1253  0 fetchStructuresMetaData();
1254  0 filterResultSet(
1255    ((FilterOption) cmb_filterOption.getSelectedItem())
1256    .getValue());
1257    }
1258    });
1259  0 refreshThread.start();
1260    }
1261    }
1262   
 
1263    public class PDBEntryTableModel extends AbstractTableModel
1264    {
1265    String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type",
1266    "File" };
1267   
1268    private List<CachedPDB> pdbEntries;
1269   
 
1270  1 toggle public PDBEntryTableModel(List<CachedPDB> pdbEntries)
1271    {
1272  1 this.pdbEntries = new ArrayList<>(pdbEntries);
1273    }
1274   
 
1275  5 toggle @Override
1276    public String getColumnName(int columnIndex)
1277    {
1278  5 return columns[columnIndex];
1279    }
1280   
 
1281  4 toggle @Override
1282    public int getRowCount()
1283    {
1284  4 return pdbEntries.size();
1285    }
1286   
 
1287  6 toggle @Override
1288    public int getColumnCount()
1289    {
1290  6 return columns.length;
1291    }
1292   
 
1293  0 toggle @Override
1294    public boolean isCellEditable(int row, int column)
1295    {
1296  0 return false;
1297    }
1298   
 
1299  0 toggle @Override
1300    public Object getValueAt(int rowIndex, int columnIndex)
1301    {
1302  0 Object value = "??";
1303  0 CachedPDB entry = pdbEntries.get(rowIndex);
1304  0 switch (columnIndex)
1305    {
1306  0 case 0:
1307  0 value = entry.getSequence();
1308  0 break;
1309  0 case 1:
1310  0 value = entry.getPdbEntry();
1311  0 break;
1312  0 case 2:
1313  0 value = entry.getPdbEntry().getChainCode() == null ? "_"
1314    : entry.getPdbEntry().getChainCode();
1315  0 break;
1316  0 case 3:
1317  0 value = entry.getPdbEntry().getType();
1318  0 break;
1319  0 case 4:
1320  0 value = entry.getPdbEntry().getFile();
1321  0 break;
1322    }
1323  0 return value;
1324    }
1325   
 
1326  0 toggle @Override
1327    public Class<?> getColumnClass(int columnIndex)
1328    {
1329  0 return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
1330    }
1331   
 
1332  0 toggle public CachedPDB getPDBEntryAt(int row)
1333    {
1334  0 return pdbEntries.get(row);
1335    }
1336   
1337    }
1338   
 
1339    private class CachedPDB
1340    {
1341    private SequenceI sequence;
1342   
1343    private PDBEntry pdbEntry;
1344   
 
1345  0 toggle public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
1346    {
1347  0 this.sequence = sequence;
1348  0 this.pdbEntry = pdbEntry;
1349    }
1350   
 
1351  0 toggle public SequenceI getSequence()
1352    {
1353  0 return sequence;
1354    }
1355   
 
1356  0 toggle public PDBEntry getPdbEntry()
1357    {
1358  0 return pdbEntry;
1359    }
1360   
1361    }
1362   
1363    private IProgressIndicator progressBar;
1364   
 
1365  0 toggle @Override
1366    public void setProgressBar(String message, long id)
1367    {
1368  0 progressBar.setProgressBar(message, id);
1369    }
1370   
 
1371  0 toggle @Override
1372    public void registerHandler(long id, IProgressIndicatorHandler handler)
1373    {
1374  0 progressBar.registerHandler(id, handler);
1375    }
1376   
 
1377  0 toggle @Override
1378    public boolean operationInProgress()
1379    {
1380  0 return progressBar.operationInProgress();
1381    }
1382   
 
1383  0 toggle public JalviewStructureDisplayI getOpenedStructureViewer()
1384    {
1385  0 return sViewer == null ? null : sViewer.sview;
1386    }
1387    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.