JAL-2668 fix broken factory method for colour scheme
[jalview.git] / src / jalview / gui / StructureChooser.java
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.bin.Jalview;
25 import jalview.datamodel.DBRefEntry;
26 import jalview.datamodel.DBRefSource;
27 import jalview.datamodel.PDBEntry;
28 import jalview.datamodel.SequenceI;
29 import jalview.fts.api.FTSData;
30 import jalview.fts.api.FTSDataColumnI;
31 import jalview.fts.api.FTSRestClientI;
32 import jalview.fts.core.FTSRestRequest;
33 import jalview.fts.core.FTSRestResponse;
34 import jalview.fts.service.pdb.PDBFTSRestClient;
35 import jalview.io.DataSourceType;
36 import jalview.jbgui.GStructureChooser;
37 import jalview.structure.StructureMapping;
38 import jalview.structure.StructureSelectionManager;
39 import jalview.util.MessageManager;
40 import jalview.ws.DBRefFetcher;
41 import jalview.ws.sifts.SiftsSettings;
42
43 import java.awt.event.ItemEvent;
44 import java.util.ArrayList;
45 import java.util.Collection;
46 import java.util.HashSet;
47 import java.util.LinkedHashSet;
48 import java.util.List;
49 import java.util.Objects;
50 import java.util.Set;
51 import java.util.Vector;
52
53 import javax.swing.JCheckBox;
54 import javax.swing.JComboBox;
55 import javax.swing.JLabel;
56 import javax.swing.table.AbstractTableModel;
57
58 /**
59  * Provides the behaviors for the Structure chooser Panel
60  * 
61  * @author tcnofoegbu
62  *
63  */
64 @SuppressWarnings("serial")
65 public class StructureChooser extends GStructureChooser
66         implements IProgressIndicator
67 {
68   private static int MAX_QLENGTH = 7820;
69
70   private SequenceI selectedSequence;
71
72   private SequenceI[] selectedSequences;
73
74   private IProgressIndicator progressIndicator;
75
76   private Collection<FTSData> discoveredStructuresSet;
77
78   private FTSRestRequest lastPdbRequest;
79
80   private FTSRestClientI pdbRestCleint;
81
82   private String selectedPdbFileName;
83
84   private boolean isValidPBDEntry;
85
86   private boolean cachedPDBExists;
87
88   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
89           AlignmentPanel ap)
90   {
91     this.ap = ap;
92     this.selectedSequence = selectedSeq;
93     this.selectedSequences = selectedSeqs;
94     this.progressIndicator = (ap == null) ? null : ap.alignFrame;
95     init();
96   }
97
98   /**
99    * Initializes parameters used by the Structure Chooser Panel
100    */
101   public void init()
102   {
103     if (!Jalview.isHeadlessMode())
104     {
105       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
106     }
107
108     // ensure a filter option is in force for search
109     populateFilterComboBox(true, cachedPDBExists);
110     Thread discoverPDBStructuresThread = new Thread(new Runnable()
111     {
112       @Override
113       public void run()
114       {
115         long startTime = System.currentTimeMillis();
116         updateProgressIndicator(MessageManager
117                 .getString("status.loading_cached_pdb_entries"), startTime);
118         loadLocalCachedPDBEntries();
119         updateProgressIndicator(null, startTime);
120         updateProgressIndicator(MessageManager.getString(
121                 "status.searching_for_pdb_structures"), startTime);
122         fetchStructuresMetaData();
123         // revise filter options if no results were found
124         populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
125         updateProgressIndicator(null, startTime);
126         mainFrame.setVisible(true);
127         updateCurrentView();
128       }
129     });
130     discoverPDBStructuresThread.start();
131   }
132
133   /**
134    * Updates the progress indicator with the specified message
135    * 
136    * @param message
137    *          displayed message for the operation
138    * @param id
139    *          unique handle for this indicator
140    */
141   public void updateProgressIndicator(String message, long id)
142   {
143     if (progressIndicator != null)
144     {
145       progressIndicator.setProgressBar(message, id);
146     }
147   }
148
149   /**
150    * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
151    * selection group
152    */
153   public void fetchStructuresMetaData()
154   {
155     long startTime = System.currentTimeMillis();
156     pdbRestCleint = PDBFTSRestClient.getInstance();
157     Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
158             .getStructureSummaryFields();
159
160     discoveredStructuresSet = new LinkedHashSet<>();
161     HashSet<String> errors = new HashSet<>();
162     for (SequenceI seq : selectedSequences)
163     {
164       FTSRestRequest pdbRequest = new FTSRestRequest();
165       pdbRequest.setAllowEmptySeq(false);
166       pdbRequest.setResponseSize(500);
167       pdbRequest.setFieldToSearchBy("(");
168       FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
169               .getSelectedItem());
170       pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(),
171               !chk_invertFilter.isSelected());
172       pdbRequest.setWantedFields(wantedFields);
173       pdbRequest.setSearchTerm(buildQuery(seq) + ")");
174       pdbRequest.setAssociatedSequence(seq);
175       FTSRestResponse resultList;
176       try
177       {
178         resultList = pdbRestCleint.executeRequest(pdbRequest);
179       } catch (Exception e)
180       {
181         e.printStackTrace();
182         errors.add(e.getMessage());
183         continue;
184       }
185       lastPdbRequest = pdbRequest;
186       if (resultList.getSearchSummary() != null
187               && !resultList.getSearchSummary().isEmpty())
188       {
189         discoveredStructuresSet.addAll(resultList.getSearchSummary());
190       }
191     }
192
193     int noOfStructuresFound = 0;
194     String totalTime = (System.currentTimeMillis() - startTime)
195             + " milli secs";
196     if (discoveredStructuresSet != null
197             && !discoveredStructuresSet.isEmpty())
198     {
199       getResultTable().setModel(FTSRestResponse
200               .getTableModel(lastPdbRequest, discoveredStructuresSet));
201       noOfStructuresFound = discoveredStructuresSet.size();
202       mainFrame.setTitle(MessageManager.formatMessage(
203               "label.structure_chooser_no_of_structures",
204               noOfStructuresFound, totalTime));
205     }
206     else
207     {
208       mainFrame.setTitle(MessageManager
209               .getString("label.structure_chooser_manual_association"));
210       if (errors.size() > 0)
211       {
212         StringBuilder errorMsg = new StringBuilder();
213         for (String error : errors)
214         {
215           errorMsg.append(error).append("\n");
216         }
217         JvOptionPane.showMessageDialog(this, errorMsg.toString(),
218                 MessageManager.getString("label.pdb_web-service_error"),
219                 JvOptionPane.ERROR_MESSAGE);
220       }
221     }
222   }
223
224   public void loadLocalCachedPDBEntries()
225   {
226     ArrayList<CachedPDB> entries = new ArrayList<>();
227     for (SequenceI seq : selectedSequences)
228     {
229       if (seq.getDatasetSequence() != null
230               && seq.getDatasetSequence().getAllPDBEntries() != null)
231       {
232         for (PDBEntry pdbEntry : seq.getDatasetSequence()
233                 .getAllPDBEntries())
234         {
235           if (pdbEntry.getFile() != null)
236           {
237             entries.add(new CachedPDB(seq, pdbEntry));
238           }
239         }
240       }
241     }
242     cachedPDBExists = !entries.isEmpty();
243     PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
244     tbl_local_pdb.setModel(tableModelx);
245   }
246
247   /**
248    * Builds a query string for a given sequences using its DBRef entries
249    * 
250    * @param seq
251    *          the sequences to build a query for
252    * @return the built query string
253    */
254
255   public static String buildQuery(SequenceI seq)
256   {
257     boolean isPDBRefsFound = false;
258     boolean isUniProtRefsFound = false;
259     StringBuilder queryBuilder = new StringBuilder();
260     Set<String> seqRefs = new LinkedHashSet<>();
261
262     if (seq.getAllPDBEntries() != null
263             && queryBuilder.length() < MAX_QLENGTH)
264     {
265       for (PDBEntry entry : seq.getAllPDBEntries())
266       {
267         if (isValidSeqName(entry.getId()))
268         {
269           queryBuilder.append("pdb_id:").append(entry.getId().toLowerCase())
270                   .append(" OR ");
271           isPDBRefsFound = true;
272         }
273       }
274     }
275
276     if (seq.getDBRefs() != null && seq.getDBRefs().length != 0)
277     {
278       for (DBRefEntry dbRef : seq.getDBRefs())
279       {
280         if (isValidSeqName(getDBRefId(dbRef))
281                 && queryBuilder.length() < MAX_QLENGTH)
282         {
283           if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
284           {
285             queryBuilder.append("uniprot_accession:")
286                     .append(getDBRefId(dbRef)).append(" OR ");
287             queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef))
288                     .append(" OR ");
289             isUniProtRefsFound = true;
290           }
291           else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
292           {
293
294             queryBuilder.append("pdb_id:")
295                     .append(getDBRefId(dbRef).toLowerCase()).append(" OR ");
296             isPDBRefsFound = true;
297           }
298           else
299           {
300             seqRefs.add(getDBRefId(dbRef));
301           }
302         }
303       }
304     }
305
306     if (!isPDBRefsFound && !isUniProtRefsFound)
307     {
308       String seqName = seq.getName();
309       seqName = sanitizeSeqName(seqName);
310       String[] names = seqName.toLowerCase().split("\\|");
311       for (String name : names)
312       {
313         // System.out.println("Found name : " + name);
314         name.trim();
315         if (isValidSeqName(name))
316         {
317           seqRefs.add(name);
318         }
319       }
320
321       for (String seqRef : seqRefs)
322       {
323         queryBuilder.append("text:").append(seqRef).append(" OR ");
324       }
325     }
326
327     int endIndex = queryBuilder.lastIndexOf(" OR ");
328     if (queryBuilder.toString().length() < 6)
329     {
330       return null;
331     }
332     String query = queryBuilder.toString().substring(0, endIndex);
333     return query;
334   }
335
336   /**
337    * Remove the following special characters from input string +, -, &, !, (, ),
338    * {, }, [, ], ^, ", ~, *, ?, :, \
339    * 
340    * @param seqName
341    * @return
342    */
343   static String sanitizeSeqName(String seqName)
344   {
345     Objects.requireNonNull(seqName);
346     return seqName.replaceAll("\\[\\d*\\]", "")
347             .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
348   }
349
350   /**
351    * Ensures sequence ref names are not less than 3 characters and does not
352    * contain a database name
353    * 
354    * @param seqName
355    * @return
356    */
357   public static boolean isValidSeqName(String seqName)
358   {
359     // System.out.println("seqName : " + seqName);
360     String ignoreList = "pdb,uniprot,swiss-prot";
361     if (seqName.length() < 3)
362     {
363       return false;
364     }
365     if (seqName.contains(":"))
366     {
367       return false;
368     }
369     seqName = seqName.toLowerCase();
370     for (String ignoredEntry : ignoreList.split(","))
371     {
372       if (seqName.contains(ignoredEntry))
373       {
374         return false;
375       }
376     }
377     return true;
378   }
379
380   public static String getDBRefId(DBRefEntry dbRef)
381   {
382     String ref = dbRef.getAccessionId().replaceAll("GO:", "");
383     return ref;
384   }
385
386   /**
387    * Filters a given list of discovered structures based on supplied argument
388    * 
389    * @param fieldToFilterBy
390    *          the field to filter by
391    */
392   public void filterResultSet(final String fieldToFilterBy)
393   {
394     Thread filterThread = new Thread(new Runnable()
395     {
396       @Override
397       public void run()
398       {
399         long startTime = System.currentTimeMillis();
400         pdbRestCleint = PDBFTSRestClient.getInstance();
401         lbl_loading.setVisible(true);
402         Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
403                 .getStructureSummaryFields();
404         Collection<FTSData> filteredResponse = new HashSet<>();
405         HashSet<String> errors = new HashSet<>();
406
407         for (SequenceI seq : selectedSequences)
408         {
409           FTSRestRequest pdbRequest = new FTSRestRequest();
410           if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
411           {
412             pdbRequest.setAllowEmptySeq(false);
413             pdbRequest.setResponseSize(1);
414             pdbRequest.setFieldToSearchBy("(");
415             pdbRequest.setSearchTerm(buildQuery(seq) + ")");
416             pdbRequest.setWantedFields(wantedFields);
417             pdbRequest.setAssociatedSequence(seq);
418             pdbRequest.setFacet(true);
419             pdbRequest.setFacetPivot(fieldToFilterBy + ",entry_entity");
420             pdbRequest.setFacetPivotMinCount(1);
421           }
422           else
423           {
424             pdbRequest.setAllowEmptySeq(false);
425             pdbRequest.setResponseSize(1);
426             pdbRequest.setFieldToSearchBy("(");
427             pdbRequest.setFieldToSortBy(fieldToFilterBy,
428                     !chk_invertFilter.isSelected());
429             pdbRequest.setSearchTerm(buildQuery(seq) + ")");
430             pdbRequest.setWantedFields(wantedFields);
431             pdbRequest.setAssociatedSequence(seq);
432           }
433           FTSRestResponse resultList;
434           try
435           {
436             resultList = pdbRestCleint.executeRequest(pdbRequest);
437           } catch (Exception e)
438           {
439             e.printStackTrace();
440             errors.add(e.getMessage());
441             continue;
442           }
443           lastPdbRequest = pdbRequest;
444           if (resultList.getSearchSummary() != null
445                   && !resultList.getSearchSummary().isEmpty())
446           {
447             filteredResponse.addAll(resultList.getSearchSummary());
448           }
449         }
450
451         String totalTime = (System.currentTimeMillis() - startTime)
452                 + " milli secs";
453         if (!filteredResponse.isEmpty())
454         {
455           final int filterResponseCount = filteredResponse.size();
456           Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>();
457           reorderedStructuresSet.addAll(filteredResponse);
458           reorderedStructuresSet.addAll(discoveredStructuresSet);
459           getResultTable().setModel(FTSRestResponse
460                   .getTableModel(lastPdbRequest, reorderedStructuresSet));
461
462           FTSRestResponse.configureTableColumn(getResultTable(),
463                   wantedFields, tempUserPrefs);
464           getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
465           getResultTable().getColumn("Ref Sequence").setMinWidth(100);
466           getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
467           // Update table selection model here
468           getResultTable().addRowSelectionInterval(0,
469                   filterResponseCount - 1);
470           mainFrame.setTitle(MessageManager.formatMessage(
471                   "label.structure_chooser_filter_time", totalTime));
472         }
473         else
474         {
475           mainFrame.setTitle(MessageManager.formatMessage(
476                   "label.structure_chooser_filter_time", totalTime));
477           if (errors.size() > 0)
478           {
479             StringBuilder errorMsg = new StringBuilder();
480             for (String error : errors)
481             {
482               errorMsg.append(error).append("\n");
483             }
484             JvOptionPane.showMessageDialog(null, errorMsg.toString(),
485                     MessageManager.getString("label.pdb_web-service_error"),
486                     JvOptionPane.ERROR_MESSAGE);
487           }
488         }
489
490         lbl_loading.setVisible(false);
491
492         validateSelections();
493       }
494     });
495     filterThread.start();
496   }
497
498   /**
499    * Handles action event for btn_pdbFromFile
500    */
501   @Override
502   public void pdbFromFile_actionPerformed()
503   {
504     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
505             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
506     chooser.setFileView(new jalview.io.JalviewFileView());
507     chooser.setDialogTitle(
508             MessageManager.formatMessage("label.select_pdb_file_for",
509                     selectedSequence.getDisplayId(false)));
510     chooser.setToolTipText(MessageManager.formatMessage(
511             "label.load_pdb_file_associate_with_sequence",
512             selectedSequence.getDisplayId(false)));
513
514     int value = chooser.showOpenDialog(null);
515     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
516     {
517       selectedPdbFileName = chooser.getSelectedFile().getPath();
518       jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
519       validateSelections();
520     }
521   }
522
523   /**
524    * Populates the filter combo-box options dynamically depending on discovered
525    * structures
526    */
527   protected void populateFilterComboBox(boolean haveData,
528           boolean cachedPDBExist)
529   {
530     /*
531      * temporarily suspend the change listener behaviour
532      */
533     cmb_filterOption.removeItemListener(this);
534
535     cmb_filterOption.removeAllItems();
536     if (haveData)
537     {
538       cmb_filterOption.addItem(new FilterOption(
539               MessageManager.getString("label.best_quality"),
540               "overall_quality", VIEWS_FILTER, false));
541       cmb_filterOption.addItem(new FilterOption(
542               MessageManager.getString("label.best_resolution"),
543               "resolution", VIEWS_FILTER, false));
544       cmb_filterOption.addItem(new FilterOption(
545               MessageManager.getString("label.most_protein_chain"),
546               "number_of_protein_chains", VIEWS_FILTER, false));
547       cmb_filterOption.addItem(new FilterOption(
548               MessageManager.getString("label.most_bound_molecules"),
549               "number_of_bound_molecules", VIEWS_FILTER, false));
550       cmb_filterOption.addItem(new FilterOption(
551               MessageManager.getString("label.most_polymer_residues"),
552               "number_of_polymer_residues", VIEWS_FILTER, true));
553     }
554     cmb_filterOption.addItem(
555             new FilterOption(MessageManager.getString("label.enter_pdb_id"),
556                     "-", VIEWS_ENTER_ID, false));
557     cmb_filterOption.addItem(
558             new FilterOption(MessageManager.getString("label.from_file"),
559                     "-", VIEWS_FROM_FILE, false));
560
561     if (cachedPDBExist)
562     {
563       FilterOption cachedOption = new FilterOption(
564               MessageManager.getString("label.cached_structures"),
565               "-", VIEWS_LOCAL_PDB, false);
566       cmb_filterOption.addItem(cachedOption);
567       cmb_filterOption.setSelectedItem(cachedOption);
568     }
569
570     cmb_filterOption.addItemListener(this);
571   }
572
573   /**
574    * Updates the displayed view based on the selected filter option
575    */
576   protected void updateCurrentView()
577   {
578     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
579             .getSelectedItem());
580     layout_switchableViews.show(pnl_switchableViews,
581             selectedFilterOpt.getView());
582     String filterTitle = mainFrame.getTitle();
583     mainFrame.setTitle(frameTitle);
584     chk_invertFilter.setVisible(false);
585     if (selectedFilterOpt.getView() == VIEWS_FILTER)
586     {
587       mainFrame.setTitle(filterTitle);
588       chk_invertFilter.setVisible(true);
589       filterResultSet(selectedFilterOpt.getValue());
590     }
591     else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
592             || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
593     {
594       mainFrame.setTitle(MessageManager
595               .getString("label.structure_chooser_manual_association"));
596       idInputAssSeqPanel.loadCmbAssSeq();
597       fileChooserAssSeqPanel.loadCmbAssSeq();
598     }
599     validateSelections();
600   }
601
602   /**
603    * Validates user selection and activates the view button if all parameters
604    * are correct
605    */
606   @Override
607   public void validateSelections()
608   {
609     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
610             .getSelectedItem());
611     btn_view.setEnabled(false);
612     String currentView = selectedFilterOpt.getView();
613     if (currentView == VIEWS_FILTER)
614     {
615       if (getResultTable().getSelectedRows().length > 0)
616       {
617         btn_view.setEnabled(true);
618       }
619     }
620     else if (currentView == VIEWS_LOCAL_PDB)
621     {
622       if (tbl_local_pdb.getSelectedRows().length > 0)
623       {
624         btn_view.setEnabled(true);
625       }
626     }
627     else if (currentView == VIEWS_ENTER_ID)
628     {
629       validateAssociationEnterPdb();
630     }
631     else if (currentView == VIEWS_FROM_FILE)
632     {
633       validateAssociationFromFile();
634     }
635   }
636
637   /**
638    * Validates inputs from the Manual PDB entry panel
639    */
640   public void validateAssociationEnterPdb()
641   {
642     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
643             .getCmb_assSeq().getSelectedItem();
644     lbl_pdbManualFetchStatus.setIcon(errorImage);
645     lbl_pdbManualFetchStatus.setToolTipText("");
646     if (txt_search.getText().length() > 0)
647     {
648       lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true,
649               MessageManager.formatMessage("info.no_pdb_entry_found_for",
650                       txt_search.getText())));
651     }
652
653     if (errorWarning.length() > 0)
654     {
655       lbl_pdbManualFetchStatus.setIcon(warningImage);
656       lbl_pdbManualFetchStatus.setToolTipText(
657               JvSwingUtils.wrapTooltip(true, errorWarning.toString()));
658     }
659
660     if (selectedSequences.length == 1 || !assSeqOpt.getName()
661             .equalsIgnoreCase("-Select Associated Seq-"))
662     {
663       txt_search.setEnabled(true);
664       if (isValidPBDEntry)
665       {
666         btn_view.setEnabled(true);
667         lbl_pdbManualFetchStatus.setToolTipText("");
668         lbl_pdbManualFetchStatus.setIcon(goodImage);
669       }
670     }
671     else
672     {
673       txt_search.setEnabled(false);
674       lbl_pdbManualFetchStatus.setIcon(errorImage);
675     }
676   }
677
678   /**
679    * Validates inputs for the manual PDB file selection options
680    */
681   public void validateAssociationFromFile()
682   {
683     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
684             .getCmb_assSeq().getSelectedItem();
685     lbl_fromFileStatus.setIcon(errorImage);
686     if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt
687             .getName().equalsIgnoreCase("-Select Associated Seq-")))
688     {
689       btn_pdbFromFile.setEnabled(true);
690       if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
691       {
692         btn_view.setEnabled(true);
693         lbl_fromFileStatus.setIcon(goodImage);
694       }
695     }
696     else
697     {
698       btn_pdbFromFile.setEnabled(false);
699       lbl_fromFileStatus.setIcon(errorImage);
700     }
701   }
702
703   @Override
704   public void cmbAssSeqStateChanged()
705   {
706     validateSelections();
707   }
708
709   /**
710    * Handles the state change event for the 'filter' combo-box and 'invert'
711    * check-box
712    */
713   @Override
714   protected void stateChanged(ItemEvent e)
715   {
716     if (e.getSource() instanceof JCheckBox)
717     {
718       updateCurrentView();
719     }
720     else
721     {
722       if (e.getStateChange() == ItemEvent.SELECTED)
723       {
724         updateCurrentView();
725       }
726     }
727
728   }
729
730   /**
731    * Handles action event for btn_ok
732    */
733   @Override
734   public void ok_ActionPerformed()
735   {
736     final StructureSelectionManager ssm = ap.getStructureSelectionManager();
737
738     final int preferredHeight = pnl_filter.getHeight();
739
740     new Thread(new Runnable()
741     {
742       @Override
743       public void run()
744       {
745         FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
746                 .getSelectedItem());
747         String currentView = selectedFilterOpt.getView();
748         if (currentView == VIEWS_FILTER)
749         {
750           int pdbIdColIndex = getResultTable().getColumn("PDB Id")
751                   .getModelIndex();
752           int refSeqColIndex = getResultTable().getColumn("Ref Sequence")
753                   .getModelIndex();
754           int[] selectedRows = getResultTable().getSelectedRows();
755           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
756           int count = 0;
757           List<SequenceI> selectedSeqsToView = new ArrayList<>();
758           for (int row : selectedRows)
759           {
760             String pdbIdStr = getResultTable()
761                     .getValueAt(row, pdbIdColIndex).toString();
762             SequenceI selectedSeq = (SequenceI) getResultTable()
763                     .getValueAt(row, refSeqColIndex);
764             selectedSeqsToView.add(selectedSeq);
765             PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
766             if (pdbEntry == null)
767             {
768               pdbEntry = getFindEntry(pdbIdStr,
769                       selectedSeq.getAllPDBEntries());
770             }
771
772             if (pdbEntry == null)
773             {
774               pdbEntry = new PDBEntry();
775               pdbEntry.setId(pdbIdStr);
776               pdbEntry.setType(PDBEntry.Type.PDB);
777               selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
778             }
779             pdbEntriesToView[count++] = pdbEntry;
780           }
781           SequenceI[] selectedSeqs = selectedSeqsToView
782                   .toArray(new SequenceI[selectedSeqsToView.size()]);
783           launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
784         }
785         else if (currentView == VIEWS_LOCAL_PDB)
786         {
787           int[] selectedRows = tbl_local_pdb.getSelectedRows();
788           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
789           int count = 0;
790           int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
791                   .getModelIndex();
792           int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
793                   .getModelIndex();
794           List<SequenceI> selectedSeqsToView = new ArrayList<>();
795           for (int row : selectedRows)
796           {
797             PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
798                     pdbIdColIndex);
799             pdbEntriesToView[count++] = pdbEntry;
800             SequenceI selectedSeq = (SequenceI) tbl_local_pdb
801                     .getValueAt(row, refSeqColIndex);
802             selectedSeqsToView.add(selectedSeq);
803           }
804           SequenceI[] selectedSeqs = selectedSeqsToView
805                   .toArray(new SequenceI[selectedSeqsToView.size()]);
806           launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
807         }
808         else if (currentView == VIEWS_ENTER_ID)
809         {
810           SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
811                   .getCmb_assSeq().getSelectedItem()).getSequence();
812           if (userSelectedSeq != null)
813           {
814             selectedSequence = userSelectedSeq;
815           }
816           String pdbIdStr = txt_search.getText();
817           PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
818           if (pdbEntry == null)
819           {
820             pdbEntry = new PDBEntry();
821             if (pdbIdStr.split(":").length > 1)
822             {
823               pdbEntry.setId(pdbIdStr.split(":")[0]);
824               pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase());
825             }
826             else
827             {
828               pdbEntry.setId(pdbIdStr);
829             }
830             pdbEntry.setType(PDBEntry.Type.PDB);
831             selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
832           }
833
834           PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
835           launchStructureViewer(ssm, pdbEntriesToView, ap,
836                   new SequenceI[]
837                   { selectedSequence });
838         }
839         else if (currentView == VIEWS_FROM_FILE)
840         {
841           SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
842                   .getCmb_assSeq().getSelectedItem()).getSequence();
843           if (userSelectedSeq != null)
844           {
845             selectedSequence = userSelectedSeq;
846           }
847           PDBEntry fileEntry = new AssociatePdbFileWithSeq()
848                   .associatePdbWithSeq(selectedPdbFileName,
849                           DataSourceType.FILE, selectedSequence, true,
850                           Desktop.instance);
851
852           launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
853                   new SequenceI[]
854                   { selectedSequence });
855         }
856         closeAction(preferredHeight);
857         mainFrame.dispose();
858       }
859     }).start();
860   }
861
862   private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
863   {
864     Objects.requireNonNull(id);
865     Objects.requireNonNull(pdbEntries);
866     PDBEntry foundEntry = null;
867     for (PDBEntry entry : pdbEntries)
868     {
869       if (entry.getId().equalsIgnoreCase(id))
870       {
871         return entry;
872       }
873     }
874     return foundEntry;
875   }
876
877   private void launchStructureViewer(StructureSelectionManager ssm,
878           final PDBEntry[] pdbEntriesToView,
879           final AlignmentPanel alignPanel, SequenceI[] sequences)
880   {
881     long progressId = sequences.hashCode();
882     setProgressBar(MessageManager
883             .getString("status.launching_3d_structure_viewer"), progressId);
884     final StructureViewer sViewer = new StructureViewer(ssm);
885     setProgressBar(null, progressId);
886
887     if (SiftsSettings.isMapWithSifts())
888     {
889       List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
890       int p = 0;
891       // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
892       // real PDB ID. For moment, we can also safely do this if there is already
893       // a known mapping between the PDBEntry and the sequence.
894       for (SequenceI seq : sequences)
895       {
896         PDBEntry pdbe = pdbEntriesToView[p++];
897         if (pdbe != null && pdbe.getFile() != null)
898         {
899           StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
900           if (smm != null && smm.length > 0)
901           {
902             for (StructureMapping sm : smm)
903             {
904               if (sm.getSequence() == seq)
905               {
906                 continue;
907               }
908             }
909           }
910         }
911         if (seq.getPrimaryDBRefs().size() == 0)
912         {
913           seqsWithoutSourceDBRef.add(seq);
914           continue;
915         }
916       }
917       if (!seqsWithoutSourceDBRef.isEmpty())
918       {
919         int y = seqsWithoutSourceDBRef.size();
920         setProgressBar(MessageManager.formatMessage(
921                 "status.fetching_dbrefs_for_sequences_without_valid_refs",
922                 y), progressId);
923         SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
924         int x = 0;
925         for (SequenceI fSeq : seqsWithoutSourceDBRef)
926         {
927           seqWithoutSrcDBRef[x++] = fSeq;
928         }
929
930         DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
931         dbRefFetcher.fetchDBRefs(true);
932
933         setProgressBar("Fetch complete.", progressId); // todo i18n
934       }
935     }
936     if (pdbEntriesToView.length > 1)
937     {
938       setProgressBar(MessageManager.getString(
939               "status.fetching_3d_structures_for_selected_entries"),
940               progressId);
941       sViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
942     }
943     else
944     {
945       setProgressBar(MessageManager.formatMessage(
946               "status.fetching_3d_structures_for",
947               pdbEntriesToView[0].getId()),progressId);
948       sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
949     }
950     setProgressBar(null, progressId);
951   }
952
953   /**
954    * Populates the combo-box used in associating manually fetched structures to
955    * a unique sequence when more than one sequence selection is made.
956    */
957   @Override
958   public void populateCmbAssociateSeqOptions(
959           JComboBox<AssociateSeqOptions> cmb_assSeq,
960           JLabel lbl_associateSeq)
961   {
962     cmb_assSeq.removeAllItems();
963     cmb_assSeq.addItem(
964             new AssociateSeqOptions("-Select Associated Seq-", null));
965     lbl_associateSeq.setVisible(false);
966     if (selectedSequences.length > 1)
967     {
968       for (SequenceI seq : selectedSequences)
969       {
970         cmb_assSeq.addItem(new AssociateSeqOptions(seq));
971       }
972     }
973     else
974     {
975       String seqName = selectedSequence.getDisplayId(false);
976       seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
977       lbl_associateSeq.setText(seqName);
978       lbl_associateSeq.setVisible(true);
979       cmb_assSeq.setVisible(false);
980     }
981   }
982
983   public boolean isStructuresDiscovered()
984   {
985     return discoveredStructuresSet != null
986             && !discoveredStructuresSet.isEmpty();
987   }
988
989   public Collection<FTSData> getDiscoveredStructuresSet()
990   {
991     return discoveredStructuresSet;
992   }
993
994   @Override
995   protected void txt_search_ActionPerformed()
996   {
997     new Thread()
998     {
999       @Override
1000       public void run()
1001       {
1002         errorWarning.setLength(0);
1003         isValidPBDEntry = false;
1004         if (txt_search.getText().length() > 0)
1005         {
1006           String searchTerm = txt_search.getText().toLowerCase();
1007           searchTerm = searchTerm.split(":")[0];
1008           // System.out.println(">>>>> search term : " + searchTerm);
1009           List<FTSDataColumnI> wantedFields = new ArrayList<>();
1010           FTSRestRequest pdbRequest = new FTSRestRequest();
1011           pdbRequest.setAllowEmptySeq(false);
1012           pdbRequest.setResponseSize(1);
1013           pdbRequest.setFieldToSearchBy("(pdb_id:");
1014           pdbRequest.setWantedFields(wantedFields);
1015           pdbRequest.setSearchTerm(searchTerm + ")");
1016           pdbRequest.setAssociatedSequence(selectedSequence);
1017           pdbRestCleint = PDBFTSRestClient.getInstance();
1018           wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
1019           FTSRestResponse resultList;
1020           try
1021           {
1022             resultList = pdbRestCleint.executeRequest(pdbRequest);
1023           } catch (Exception e)
1024           {
1025             errorWarning.append(e.getMessage());
1026             return;
1027           } finally
1028           {
1029             validateSelections();
1030           }
1031           if (resultList.getSearchSummary() != null
1032                   && resultList.getSearchSummary().size() > 0)
1033           {
1034             isValidPBDEntry = true;
1035           }
1036         }
1037         validateSelections();
1038       }
1039     }.start();
1040   }
1041
1042   @Override
1043   public void tabRefresh()
1044   {
1045     if (selectedSequences != null)
1046     {
1047       Thread refreshThread = new Thread(new Runnable()
1048       {
1049         @Override
1050         public void run()
1051         {
1052           fetchStructuresMetaData();
1053           filterResultSet(
1054                   ((FilterOption) cmb_filterOption.getSelectedItem())
1055                           .getValue());
1056         }
1057       });
1058       refreshThread.start();
1059     }
1060   }
1061
1062   public class PDBEntryTableModel extends AbstractTableModel
1063   {
1064     String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type",
1065         "File" };
1066
1067     private List<CachedPDB> pdbEntries;
1068
1069     public PDBEntryTableModel(List<CachedPDB> pdbEntries)
1070     {
1071       this.pdbEntries = new ArrayList<>(pdbEntries);
1072     }
1073
1074     @Override
1075     public String getColumnName(int columnIndex)
1076     {
1077       return columns[columnIndex];
1078     }
1079
1080     @Override
1081     public int getRowCount()
1082     {
1083       return pdbEntries.size();
1084     }
1085
1086     @Override
1087     public int getColumnCount()
1088     {
1089       return columns.length;
1090     }
1091
1092     @Override
1093     public boolean isCellEditable(int row, int column)
1094     {
1095       return false;
1096     }
1097
1098     @Override
1099     public Object getValueAt(int rowIndex, int columnIndex)
1100     {
1101       Object value = "??";
1102       CachedPDB entry = pdbEntries.get(rowIndex);
1103       switch (columnIndex)
1104       {
1105       case 0:
1106         value = entry.getSequence();
1107         break;
1108       case 1:
1109         value = entry.getPdbEntry();
1110         break;
1111       case 2:
1112         value = entry.getPdbEntry().getChainCode() == null ? "_"
1113                 : entry.getPdbEntry().getChainCode();
1114         break;
1115       case 3:
1116         value = entry.getPdbEntry().getType();
1117         break;
1118       case 4:
1119         value = entry.getPdbEntry().getFile();
1120         break;
1121       }
1122       return value;
1123     }
1124
1125     @Override
1126     public Class<?> getColumnClass(int columnIndex)
1127     {
1128       return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
1129     }
1130
1131     public CachedPDB getPDBEntryAt(int row)
1132     {
1133       return pdbEntries.get(row);
1134     }
1135
1136   }
1137
1138   private class CachedPDB
1139   {
1140     private SequenceI sequence;
1141
1142     private PDBEntry pdbEntry;
1143
1144     public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
1145     {
1146       this.sequence = sequence;
1147       this.pdbEntry = pdbEntry;
1148     }
1149
1150     public SequenceI getSequence()
1151     {
1152       return sequence;
1153     }
1154
1155     public PDBEntry getPdbEntry()
1156     {
1157       return pdbEntry;
1158     }
1159
1160   }
1161
1162   private IProgressIndicator progressBar;
1163
1164   @Override
1165   public void setProgressBar(String message, long id)
1166   {
1167     progressBar.setProgressBar(message, id);
1168   }
1169
1170   @Override
1171   public void registerHandler(long id, IProgressIndicatorHandler handler)
1172   {
1173     progressBar.registerHandler(id, handler);
1174   }
1175
1176   @Override
1177   public boolean operationInProgress()
1178   {
1179     return progressBar.operationInProgress();
1180   }
1181 }