X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=217f653bf5e403979f0ebedc0890895288499262;hb=6c118f968f6e8f726fdbb6ce6c24d870b22419bb;hp=4b3f5dea989484dc80aa19849f94f900fdbb8175;hpb=d9cedb863c0d5b665b8cdde3f8791d8a96030c6b;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 4b3f5de..217f653 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -21,27 +21,39 @@ package jalview.gui; +import jalview.bin.Jalview; import jalview.datamodel.DBRefEntry; +import jalview.datamodel.DBRefSource; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; +import jalview.fts.api.FTSData; +import jalview.fts.api.FTSDataColumnI; +import jalview.fts.api.FTSRestClientI; +import jalview.fts.core.FTSRestRequest; +import jalview.fts.core.FTSRestResponse; +import jalview.fts.service.pdb.PDBFTSRestClient; +import jalview.io.DataSourceType; import jalview.jbgui.GStructureChooser; +import jalview.structure.StructureMapping; +import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; -import jalview.ws.dbsources.PDBRestClient; -import jalview.ws.dbsources.PDBRestClient.PDBDocField; -import jalview.ws.uimodel.PDBRestRequest; -import jalview.ws.uimodel.PDBRestResponse; -import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary; +import jalview.ws.DBRefFetcher; +import jalview.ws.sifts.SiftsSettings; import java.awt.event.ItemEvent; import java.util.ArrayList; import java.util.Collection; import java.util.HashSet; +import java.util.LinkedHashSet; import java.util.List; +import java.util.Objects; +import java.util.Set; import java.util.Vector; import javax.swing.JCheckBox; -import javax.swing.JOptionPane; -import javax.swing.ListSelectionModel; +import javax.swing.JComboBox; +import javax.swing.JLabel; +import javax.swing.table.AbstractTableModel; /** * Provides the behaviors for the Structure chooser Panel @@ -51,8 +63,9 @@ import javax.swing.ListSelectionModel; */ @SuppressWarnings("serial") public class StructureChooser extends GStructureChooser + implements IProgressIndicator { - private boolean structuresDiscovered = false; + private static int MAX_QLENGTH = 7820; private SequenceI selectedSequence; @@ -60,12 +73,17 @@ public class StructureChooser extends GStructureChooser private IProgressIndicator progressIndicator; - private Collection discoveredStructuresSet = new HashSet(); + private Collection discoveredStructuresSet; - private PDBRestRequest pdbRequest; + private FTSRestRequest lastPdbRequest; - private PDBRestClient pdbRestCleint; + private FTSRestClientI pdbRestCleint; + private String selectedPdbFileName; + + private boolean isValidPBDEntry; + + private boolean cachedPDBExists; public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) @@ -82,16 +100,28 @@ public class StructureChooser extends GStructureChooser */ public void init() { + if (!Jalview.isHeadlessMode()) + { + progressBar = new ProgressBar(this.statusPanel, this.statusBar); + } + + // ensure a filter option is in force for search + populateFilterComboBox(true, cachedPDBExists); Thread discoverPDBStructuresThread = new Thread(new Runnable() { @Override public void run() { long startTime = System.currentTimeMillis(); - String msg = MessageManager.getString("status.fetching_db_refs"); - updateProgressIndicator(msg, startTime); + updateProgressIndicator(MessageManager + .getString("status.loading_cached_pdb_entries"), startTime); + loadLocalCachedPDBEntries(); + updateProgressIndicator(null, startTime); + updateProgressIndicator(MessageManager.getString( + "status.searching_for_pdb_structures"), startTime); fetchStructuresMetaData(); - populateFilterComboBox(); + // revise filter options if no results were found + populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists); updateProgressIndicator(null, startTime); mainFrame.setVisible(true); updateCurrentView(); @@ -123,68 +153,95 @@ public class StructureChooser extends GStructureChooser public void fetchStructuresMetaData() { long startTime = System.currentTimeMillis(); - List wantedFields = new ArrayList(); - // wantedFields.add(PDBDocField.MOLECULE_TYPE); - wantedFields.add(PDBDocField.PDB_ID); - // wantedFields.add(PDBDocField.GENUS); - // wantedFields.add(PDBDocField.GENE_NAME); - wantedFields.add(PDBDocField.TITLE); - pdbRequest = new PDBRestRequest(); - pdbRequest.setAllowEmptySeq(false); - pdbRequest.setResponseSize(500); - pdbRequest.setFieldToSearchBy("(text:"); - pdbRequest.setWantedFields(wantedFields); + pdbRestCleint = PDBFTSRestClient.getInstance(); + Collection wantedFields = pdbDocFieldPrefs + .getStructureSummaryFields(); + + discoveredStructuresSet = new LinkedHashSet<>(); + HashSet errors = new HashSet<>(); for (SequenceI seq : selectedSequences) { + FTSRestRequest pdbRequest = new FTSRestRequest(); + pdbRequest.setAllowEmptySeq(false); + pdbRequest.setResponseSize(500); + pdbRequest.setFieldToSearchBy("("); + FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption + .getSelectedItem()); + pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(), + !chk_invertFilter.isSelected()); + pdbRequest.setWantedFields(wantedFields); pdbRequest.setSearchTerm(buildQuery(seq) + ")"); - pdbRequest.setAssociatedSequence(seq.getName()); - pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest); + pdbRequest.setAssociatedSequence(seq); + FTSRestResponse resultList; + try + { + resultList = pdbRestCleint.executeRequest(pdbRequest); + } catch (Exception e) + { + e.printStackTrace(); + errors.add(e.getMessage()); + continue; + } + lastPdbRequest = pdbRequest; if (resultList.getSearchSummary() != null && !resultList.getSearchSummary().isEmpty()) { discoveredStructuresSet.addAll(resultList.getSearchSummary()); - updateSequenceDbRef(seq, resultList.getSearchSummary()); } } int noOfStructuresFound = 0; + String totalTime = (System.currentTimeMillis() - startTime) + + " milli secs"; if (discoveredStructuresSet != null && !discoveredStructuresSet.isEmpty()) { - jList_FoundStructures.setModel(PDBRestResponse - .getListModel(discoveredStructuresSet)); - tbl_summary.setModel(PDBRestResponse.getTableModel(pdbRequest, - discoveredStructuresSet)); - // resizeColumnWidth(summaryTable); - structuresDiscovered = true; + getResultTable().setModel(FTSRestResponse + .getTableModel(lastPdbRequest, discoveredStructuresSet)); noOfStructuresFound = discoveredStructuresSet.size(); + mainFrame.setTitle(MessageManager.formatMessage( + "label.structure_chooser_no_of_structures", + noOfStructuresFound, totalTime)); + } + else + { + mainFrame.setTitle(MessageManager + .getString("label.structure_chooser_manual_association")); + if (errors.size() > 0) + { + StringBuilder errorMsg = new StringBuilder(); + for (String error : errors) + { + errorMsg.append(error).append("\n"); + } + JvOptionPane.showMessageDialog(this, errorMsg.toString(), + MessageManager.getString("label.pdb_web-service_error"), + JvOptionPane.ERROR_MESSAGE); + } } - String totalTime = (System.currentTimeMillis() - startTime) - + " milli secs"; - mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound - + " Found (" + totalTime + ")"); } - /** - * Update the DBRef entry for a given sequence with values retrieved from - * PDBResponseSummary - * - * @param seq - * the Sequence to update its DBRef entry - * @param responseSummaries - * a collection of PDBResponseSummary - */ - public void updateSequenceDbRef(SequenceI seq, - Collection responseSummaries) + public void loadLocalCachedPDBEntries() { - for (PDBResponseSummary response : responseSummaries) + ArrayList entries = new ArrayList<>(); + for (SequenceI seq : selectedSequences) { - PDBEntry newEntry = new PDBEntry(); - newEntry.setId(response.getPdbId()); - newEntry.setType("PDB"); - seq.getDatasetSequence().addPDBId(newEntry); + if (seq.getDatasetSequence() != null + && seq.getDatasetSequence().getAllPDBEntries() != null) + { + for (PDBEntry pdbEntry : seq.getDatasetSequence() + .getAllPDBEntries()) + { + if (pdbEntry.getFile() != null) + { + entries.add(new CachedPDB(seq, pdbEntry)); + } + } + } } + cachedPDBExists = !entries.isEmpty(); + PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries); + tbl_local_pdb.setModel(tableModelx); } /** @@ -194,42 +251,139 @@ public class StructureChooser extends GStructureChooser * the sequences to build a query for * @return the built query string */ - @SuppressWarnings("unchecked") + public static String buildQuery(SequenceI seq) { - String query = seq.getName(); + boolean isPDBRefsFound = false; + boolean isUniProtRefsFound = false; StringBuilder queryBuilder = new StringBuilder(); - int count = 0; + Set seqRefs = new LinkedHashSet<>(); + + if (seq.getAllPDBEntries() != null + && queryBuilder.length() < MAX_QLENGTH) + { + for (PDBEntry entry : seq.getAllPDBEntries()) + { + if (isValidSeqName(entry.getId())) + { + queryBuilder.append("pdb_id:").append(entry.getId().toLowerCase()) + .append(" OR "); + isPDBRefsFound = true; + } + } + } - if (seq.getPDBId() != null) + if (seq.getDBRefs() != null && seq.getDBRefs().length != 0) { - for (PDBEntry entry : (Vector) seq.getPDBId()) + for (DBRefEntry dbRef : seq.getDBRefs()) { - queryBuilder.append("text:").append(entry.getId()).append(" OR "); + if (isValidSeqName(getDBRefId(dbRef)) + && queryBuilder.length() < MAX_QLENGTH) + { + if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT)) + { + queryBuilder.append("uniprot_accession:") + .append(getDBRefId(dbRef)).append(" OR "); + queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef)) + .append(" OR "); + isUniProtRefsFound = true; + } + else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB)) + { + + queryBuilder.append("pdb_id:") + .append(getDBRefId(dbRef).toLowerCase()).append(" OR "); + isPDBRefsFound = true; + } + else + { + seqRefs.add(getDBRefId(dbRef)); + } + } } } - if (seq.getDBRef() != null && seq.getDBRef().length != 0) + if (!isPDBRefsFound && !isUniProtRefsFound) { - for (DBRefEntry dbRef : seq.getDBRef()) + String seqName = seq.getName(); + seqName = sanitizeSeqName(seqName); + String[] names = seqName.toLowerCase().split("\\|"); + for (String name : names) { - queryBuilder.append("text:") - .append(dbRef.getAccessionId().replaceAll("GO:", "")) - .append(" OR "); - ++count; - if (count > 10) + // System.out.println("Found name : " + name); + name.trim(); + if (isValidSeqName(name)) { - break; + seqRefs.add(name); } } - int endIndex = queryBuilder.lastIndexOf(" OR "); - query = queryBuilder.toString().substring(5, endIndex); + + for (String seqRef : seqRefs) + { + queryBuilder.append("text:").append(seqRef).append(" OR "); + } + } + + int endIndex = queryBuilder.lastIndexOf(" OR "); + if (queryBuilder.toString().length() < 6) + { + return null; } - // System.out.println("Query -----> " + query); + String query = queryBuilder.toString().substring(0, endIndex); return query; } /** + * Remove the following special characters from input string +, -, &, !, (, ), + * {, }, [, ], ^, ", ~, *, ?, :, \ + * + * @param seqName + * @return + */ + static String sanitizeSeqName(String seqName) + { + Objects.requireNonNull(seqName); + return seqName.replaceAll("\\[\\d*\\]", "") + .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+"); + } + + /** + * Ensures sequence ref names are not less than 3 characters and does not + * contain a database name + * + * @param seqName + * @return + */ + public static boolean isValidSeqName(String seqName) + { + // System.out.println("seqName : " + seqName); + String ignoreList = "pdb,uniprot,swiss-prot"; + if (seqName.length() < 3) + { + return false; + } + if (seqName.contains(":")) + { + return false; + } + seqName = seqName.toLowerCase(); + for (String ignoredEntry : ignoreList.split(",")) + { + if (seqName.contains(ignoredEntry)) + { + return false; + } + } + return true; + } + + public static String getDBRefId(DBRefEntry dbRef) + { + String ref = dbRef.getAccessionId().replaceAll("GO:", ""); + return ref; + } + + /** * Filters a given list of discovered structures based on supplied argument * * @param fieldToFilterBy @@ -242,202 +396,314 @@ public class StructureChooser extends GStructureChooser @Override public void run() { - try - { - lbl_loading.setVisible(true); - pdbRequest.setResponseSize(1); - pdbRequest.setFieldToSearchBy("(text:"); - pdbRequest.setFieldToSortBy(fieldToFilterBy, - !chk_invertFilter.isSelected()); + long startTime = System.currentTimeMillis(); + pdbRestCleint = PDBFTSRestClient.getInstance(); + lbl_loading.setVisible(true); + Collection wantedFields = pdbDocFieldPrefs + .getStructureSummaryFields(); + Collection filteredResponse = new HashSet<>(); + HashSet errors = new HashSet<>(); - Collection filteredResponse = new HashSet(); - for (SequenceI seq : selectedSequences) + for (SequenceI seq : selectedSequences) + { + FTSRestRequest pdbRequest = new FTSRestRequest(); + if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage")) { + pdbRequest.setAllowEmptySeq(false); + pdbRequest.setResponseSize(1); + pdbRequest.setFieldToSearchBy("("); pdbRequest.setSearchTerm(buildQuery(seq) + ")"); - pdbRequest.setAssociatedSequence(seq.getName()); - pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList = pdbRestCleint - .executeRequest(pdbRequest); - if (resultList.getSearchSummary() != null - && !resultList.getSearchSummary().isEmpty()) - { - filteredResponse.addAll(resultList.getSearchSummary()); - } + pdbRequest.setWantedFields(wantedFields); + pdbRequest.setAssociatedSequence(seq); + pdbRequest.setFacet(true); + pdbRequest.setFacetPivot(fieldToFilterBy + ",entry_entity"); + pdbRequest.setFacetPivotMinCount(1); + } + else + { + pdbRequest.setAllowEmptySeq(false); + pdbRequest.setResponseSize(1); + pdbRequest.setFieldToSearchBy("("); + pdbRequest.setFieldToSortBy(fieldToFilterBy, + !chk_invertFilter.isSelected()); + pdbRequest.setSearchTerm(buildQuery(seq) + ")"); + pdbRequest.setWantedFields(wantedFields); + pdbRequest.setAssociatedSequence(seq); + } + FTSRestResponse resultList; + try + { + resultList = pdbRestCleint.executeRequest(pdbRequest); + } catch (Exception e) + { + e.printStackTrace(); + errors.add(e.getMessage()); + continue; } + lastPdbRequest = pdbRequest; + if (resultList.getSearchSummary() != null + && !resultList.getSearchSummary().isEmpty()) + { + filteredResponse.addAll(resultList.getSearchSummary()); + } + } - if (filteredResponse != null) + String totalTime = (System.currentTimeMillis() - startTime) + + " milli secs"; + if (!filteredResponse.isEmpty()) + { + final int filterResponseCount = filteredResponse.size(); + Collection reorderedStructuresSet = new LinkedHashSet<>(); + reorderedStructuresSet.addAll(filteredResponse); + reorderedStructuresSet.addAll(discoveredStructuresSet); + getResultTable().setModel(FTSRestResponse + .getTableModel(lastPdbRequest, reorderedStructuresSet)); + + FTSRestResponse.configureTableColumn(getResultTable(), + wantedFields, tempUserPrefs); + getResultTable().getColumn("Ref Sequence").setPreferredWidth(120); + getResultTable().getColumn("Ref Sequence").setMinWidth(100); + getResultTable().getColumn("Ref Sequence").setMaxWidth(200); + // Update table selection model here + getResultTable().addRowSelectionInterval(0, + filterResponseCount - 1); + mainFrame.setTitle(MessageManager.formatMessage( + "label.structure_chooser_filter_time", totalTime)); + } + else + { + mainFrame.setTitle(MessageManager.formatMessage( + "label.structure_chooser_filter_time", totalTime)); + if (errors.size() > 0) { - int filterResponseCount = filteredResponse.size(); - List originalDiscoveredStructuresList = new ArrayList( - discoveredStructuresSet); - originalDiscoveredStructuresList.removeAll(filteredResponse); - - Collection reorderedStructuresSet = new ArrayList(); - reorderedStructuresSet.addAll(filteredResponse); - reorderedStructuresSet.addAll(originalDiscoveredStructuresList); - - jList_FoundStructures.setModel(PDBRestResponse - .getListModel(reorderedStructuresSet)); - tbl_summary.setModel(PDBRestResponse.getTableModel(pdbRequest, - reorderedStructuresSet)); - - // int[] filterIndice = new int[filterResponseCount]; - ListSelectionModel model = tbl_summary.getSelectionModel(); - model.clearSelection(); - for (int x = 0; x < filterResponseCount; x++) + StringBuilder errorMsg = new StringBuilder(); + for (String error : errors) { - // filterIndice[x] = x; - model.addSelectionInterval(x, x); + errorMsg.append(error).append("\n"); } - - // Discard unwanted objects to make them eligible for garbage - // collection - originalDiscoveredStructuresList = null; - reorderedStructuresSet = null; - - // jListFoundStructures.setSelectedIndices(filterIndice); + JvOptionPane.showMessageDialog(null, errorMsg.toString(), + MessageManager.getString("label.pdb_web-service_error"), + JvOptionPane.ERROR_MESSAGE); } - - lbl_loading.setVisible(false); - } catch (Exception e) - { - e.printStackTrace(); } + + lbl_loading.setVisible(false); + + validateSelections(); } }); filterThread.start(); } /** - * Determines the column index for the pdb id in the summary table. The pdb id - * serves as a unique identifier for a given row in the summary table - * - * @param wantedFeilds - * the available table columns in no particular order - * @return the pdb id field column index - */ - public static int getPDBIdColumIndex(Collection wantedFeilds) - { - int pdbFeildIndex = 1; - for (PDBDocField feild : wantedFeilds) - { - if (feild.equals(PDBDocField.PDB_ID)) - { - break; - } - ++pdbFeildIndex; - } - return pdbFeildIndex; - } - - /** * Handles action event for btn_pdbFromFile */ + @Override public void pdbFromFile_actionPerformed() { jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle(MessageManager.formatMessage( - "label.select_pdb_file_for", new String[] - { selectedSequence.getDisplayId(false) })); + chooser.setDialogTitle( + MessageManager.formatMessage("label.select_pdb_file_for", + selectedSequence.getDisplayId(false))); chooser.setToolTipText(MessageManager.formatMessage( - "label.load_pdb_file_associate_with_sequence", new String[] - { selectedSequence.getDisplayId(false) })); + "label.load_pdb_file_associate_with_sequence", + selectedSequence.getDisplayId(false))); int value = chooser.showOpenDialog(null); if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, - jalview.io.AppletFormatAdapter.FILE, selectedSequence, true, - Desktop.instance); + selectedPdbFileName = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName); + validateSelections(); } } /** - * Handles action event for btn_ok + * Populates the filter combo-box options dynamically depending on discovered + * structures */ - @Override - public void ok_ActionPerformed() + protected void populateFilterComboBox(boolean haveData, + boolean cachedPDBExist) { - int pdbIdCol = getPDBIdColumIndex(pdbRequest.getWantedFields()); - int[] selectedRows = tbl_summary.getSelectedRows(); - PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; - int count = 0; - for (int summaryRow : selectedRows) - { - String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol) - .toString(); - PDBEntry pdbEntry = new PDBEntry(); - pdbEntry.setId(pdbIdStr); - pdbEntry.setType("PDB"); - pdbEntriesToView[count++] = pdbEntry; - } - new StructureViewer(ap.getStructureSelectionManager()).viewStructures( - ap, pdbEntriesToView, ap.av.collateForPDB(pdbEntriesToView)); + /* + * temporarily suspend the change listener behaviour + */ + cmb_filterOption.removeItemListener(this); + + cmb_filterOption.removeAllItems(); + if (haveData) + { + cmb_filterOption.addItem(new FilterOption( + MessageManager.getString("label.best_quality"), + "overall_quality", VIEWS_FILTER, false)); + cmb_filterOption.addItem(new FilterOption( + MessageManager.getString("label.best_resolution"), + "resolution", VIEWS_FILTER, false)); + cmb_filterOption.addItem(new FilterOption( + MessageManager.getString("label.most_protein_chain"), + "number_of_protein_chains", VIEWS_FILTER, false)); + cmb_filterOption.addItem(new FilterOption( + MessageManager.getString("label.most_bound_molecules"), + "number_of_bound_molecules", VIEWS_FILTER, false)); + cmb_filterOption.addItem(new FilterOption( + MessageManager.getString("label.most_polymer_residues"), + "number_of_polymer_residues", VIEWS_FILTER, true)); + } + cmb_filterOption.addItem( + new FilterOption(MessageManager.getString("label.enter_pdb_id"), + "-", VIEWS_ENTER_ID, false)); + cmb_filterOption.addItem( + new FilterOption(MessageManager.getString("label.from_file"), + "-", VIEWS_FROM_FILE, false)); + + if (cachedPDBExist) + { + FilterOption cachedOption = new FilterOption( + MessageManager.getString("label.cached_structures"), + "-", VIEWS_LOCAL_PDB, false); + cmb_filterOption.addItem(cachedOption); + cmb_filterOption.setSelectedItem(cachedOption); + } + + cmb_filterOption.addItemListener(this); } /** - * Handles action event for manual entry of pdb ids + * Updates the displayed view based on the selected filter option */ - public void enterPDB_actionPerformed() + protected void updateCurrentView() { - String id = JOptionPane.showInternalInputDialog(Desktop.desktop, - MessageManager.getString("label.enter_pdb_id"), - MessageManager.getString("label.enter_pdb_id"), - JOptionPane.QUESTION_MESSAGE); - if (id != null && id.length() > 0) + FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption + .getSelectedItem()); + layout_switchableViews.show(pnl_switchableViews, + selectedFilterOpt.getView()); + String filterTitle = mainFrame.getTitle(); + mainFrame.setTitle(frameTitle); + chk_invertFilter.setVisible(false); + if (selectedFilterOpt.getView() == VIEWS_FILTER) + { + mainFrame.setTitle(filterTitle); + chk_invertFilter.setVisible(true); + filterResultSet(selectedFilterOpt.getValue()); + } + else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID + || selectedFilterOpt.getView() == VIEWS_FROM_FILE) { - PDBEntry entry = new PDBEntry(); - entry.setId(id.toUpperCase()); - selectedSequence.getDatasetSequence().addPDBId(entry); + mainFrame.setTitle(MessageManager + .getString("label.structure_chooser_manual_association")); + idInputAssSeqPanel.loadCmbAssSeq(); + fileChooserAssSeqPanel.loadCmbAssSeq(); } + validateSelections(); } /** - * Populates the filter combo-box options dynamically depending on discovered - * structures + * Validates user selection and activates the view button if all parameters + * are correct */ - protected void populateFilterComboBox() + @Override + public void validateSelections() { - if (isStructuresDiscovered()) - { - cmb_filterOption.addItem(new FilterOption("Best Quality", - PDBDocField.OVERALL_QUALITY.getCode(), VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Best UniProt Coverage", - PDBDocField.UNIPROT_COVERAGE.getCode(), VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Highest Resolution", - PDBDocField.RESOLUTION.getCode(), VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Highest Protein Chain", - PDBDocField.PROTEIN_CHAIN_COUNT.getCode(), VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Highest Bound Molecules", - PDBDocField.BOUND_MOLECULE_COUNT.getCode(), VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Highest Polymer Residues", - PDBDocField.POLYMER_RESIDUE_COUNT.getCode(), VIEWS_FILTER)); - } - cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-", - VIEWS_ENTER_ID)); - cmb_filterOption.addItem(new FilterOption("From File", "-", - VIEWS_FROM_FILE)); + FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption + .getSelectedItem()); + btn_view.setEnabled(false); + String currentView = selectedFilterOpt.getView(); + if (currentView == VIEWS_FILTER) + { + if (getResultTable().getSelectedRows().length > 0) + { + btn_view.setEnabled(true); + } + } + else if (currentView == VIEWS_LOCAL_PDB) + { + if (tbl_local_pdb.getSelectedRows().length > 0) + { + btn_view.setEnabled(true); + } + } + else if (currentView == VIEWS_ENTER_ID) + { + validateAssociationEnterPdb(); + } + else if (currentView == VIEWS_FROM_FILE) + { + validateAssociationFromFile(); + } } /** - * Updates the displayed view based on the selected filter option + * Validates inputs from the Manual PDB entry panel */ - protected void updateCurrentView() + public void validateAssociationEnterPdb() { - FilterOption selectedOption = ((FilterOption) cmb_filterOption - .getSelectedItem()); - layout_switchableViews.show(pnl_switchableViews, - selectedOption.getView()); - chk_invertFilter.setEnabled(false); - if (selectedOption.getView() == VIEWS_FILTER) + AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel + .getCmb_assSeq().getSelectedItem(); + lbl_pdbManualFetchStatus.setIcon(errorImage); + lbl_pdbManualFetchStatus.setToolTipText(""); + if (txt_search.getText().length() > 0) { - chk_invertFilter.setEnabled(true); - filterResultSet(selectedOption.getValue()); + lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true, + MessageManager.formatMessage("info.no_pdb_entry_found_for", + txt_search.getText()))); } + + if (errorWarning.length() > 0) + { + lbl_pdbManualFetchStatus.setIcon(warningImage); + lbl_pdbManualFetchStatus.setToolTipText( + JvSwingUtils.wrapTooltip(true, errorWarning.toString())); + } + + if (selectedSequences.length == 1 || !assSeqOpt.getName() + .equalsIgnoreCase("-Select Associated Seq-")) + { + txt_search.setEnabled(true); + if (isValidPBDEntry) + { + btn_view.setEnabled(true); + lbl_pdbManualFetchStatus.setToolTipText(""); + lbl_pdbManualFetchStatus.setIcon(goodImage); + } + } + else + { + txt_search.setEnabled(false); + lbl_pdbManualFetchStatus.setIcon(errorImage); + } + } + + /** + * Validates inputs for the manual PDB file selection options + */ + public void validateAssociationFromFile() + { + AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel + .getCmb_assSeq().getSelectedItem(); + lbl_fromFileStatus.setIcon(errorImage); + if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt + .getName().equalsIgnoreCase("-Select Associated Seq-"))) + { + btn_pdbFromFile.setEnabled(true); + if (selectedPdbFileName != null && selectedPdbFileName.length() > 0) + { + btn_view.setEnabled(true); + lbl_fromFileStatus.setIcon(goodImage); + } + } + else + { + btn_pdbFromFile.setEnabled(false); + lbl_fromFileStatus.setIcon(errorImage); + } + } + + @Override + public void cmbAssSeqStateChanged() + { + validateSelections(); } /** @@ -461,19 +727,455 @@ public class StructureChooser extends GStructureChooser } + /** + * Handles action event for btn_ok + */ + @Override + public void ok_ActionPerformed() + { + final StructureSelectionManager ssm = ap.getStructureSelectionManager(); - public boolean isStructuresDiscovered() + final int preferredHeight = pnl_filter.getHeight(); + + new Thread(new Runnable() + { + @Override + public void run() + { + FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption + .getSelectedItem()); + String currentView = selectedFilterOpt.getView(); + if (currentView == VIEWS_FILTER) + { + int pdbIdColIndex = getResultTable().getColumn("PDB Id") + .getModelIndex(); + int refSeqColIndex = getResultTable().getColumn("Ref Sequence") + .getModelIndex(); + int[] selectedRows = getResultTable().getSelectedRows(); + PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; + int count = 0; + List selectedSeqsToView = new ArrayList<>(); + for (int row : selectedRows) + { + String pdbIdStr = getResultTable() + .getValueAt(row, pdbIdColIndex).toString(); + SequenceI selectedSeq = (SequenceI) getResultTable() + .getValueAt(row, refSeqColIndex); + selectedSeqsToView.add(selectedSeq); + PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr); + if (pdbEntry == null) + { + pdbEntry = getFindEntry(pdbIdStr, + selectedSeq.getAllPDBEntries()); + } + + if (pdbEntry == null) + { + pdbEntry = new PDBEntry(); + pdbEntry.setId(pdbIdStr); + pdbEntry.setType(PDBEntry.Type.PDB); + selectedSeq.getDatasetSequence().addPDBId(pdbEntry); + } + pdbEntriesToView[count++] = pdbEntry; + } + SequenceI[] selectedSeqs = selectedSeqsToView + .toArray(new SequenceI[selectedSeqsToView.size()]); + launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs); + } + else if (currentView == VIEWS_LOCAL_PDB) + { + int[] selectedRows = tbl_local_pdb.getSelectedRows(); + PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; + int count = 0; + int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id") + .getModelIndex(); + int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence") + .getModelIndex(); + List selectedSeqsToView = new ArrayList<>(); + for (int row : selectedRows) + { + PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row, + pdbIdColIndex); + pdbEntriesToView[count++] = pdbEntry; + SequenceI selectedSeq = (SequenceI) tbl_local_pdb + .getValueAt(row, refSeqColIndex); + selectedSeqsToView.add(selectedSeq); + } + SequenceI[] selectedSeqs = selectedSeqsToView + .toArray(new SequenceI[selectedSeqsToView.size()]); + launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs); + } + else if (currentView == VIEWS_ENTER_ID) + { + SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel + .getCmb_assSeq().getSelectedItem()).getSequence(); + if (userSelectedSeq != null) + { + selectedSequence = userSelectedSeq; + } + String pdbIdStr = txt_search.getText(); + PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr); + if (pdbEntry == null) + { + pdbEntry = new PDBEntry(); + if (pdbIdStr.split(":").length > 1) + { + pdbEntry.setId(pdbIdStr.split(":")[0]); + pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase()); + } + else + { + pdbEntry.setId(pdbIdStr); + } + pdbEntry.setType(PDBEntry.Type.PDB); + selectedSequence.getDatasetSequence().addPDBId(pdbEntry); + } + + PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; + launchStructureViewer(ssm, pdbEntriesToView, ap, + new SequenceI[] + { selectedSequence }); + } + else if (currentView == VIEWS_FROM_FILE) + { + SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel + .getCmb_assSeq().getSelectedItem()).getSequence(); + if (userSelectedSeq != null) + { + selectedSequence = userSelectedSeq; + } + PDBEntry fileEntry = new AssociatePdbFileWithSeq() + .associatePdbWithSeq(selectedPdbFileName, + DataSourceType.FILE, selectedSequence, true, + Desktop.instance); + + launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, + new SequenceI[] + { selectedSequence }); + } + closeAction(preferredHeight); + mainFrame.dispose(); + } + }).start(); + } + + private PDBEntry getFindEntry(String id, Vector pdbEntries) + { + Objects.requireNonNull(id); + Objects.requireNonNull(pdbEntries); + PDBEntry foundEntry = null; + for (PDBEntry entry : pdbEntries) + { + if (entry.getId().equalsIgnoreCase(id)) + { + return entry; + } + } + return foundEntry; + } + + private void launchStructureViewer(StructureSelectionManager ssm, + final PDBEntry[] pdbEntriesToView, + final AlignmentPanel alignPanel, SequenceI[] sequences) { - return structuresDiscovered; + long progressId = sequences.hashCode(); + setProgressBar(MessageManager + .getString("status.launching_3d_structure_viewer"), progressId); + final StructureViewer sViewer = new StructureViewer(ssm); + setProgressBar(null, progressId); + + if (SiftsSettings.isMapWithSifts()) + { + List seqsWithoutSourceDBRef = new ArrayList<>(); + int p = 0; + // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a + // real PDB ID. For moment, we can also safely do this if there is already + // a known mapping between the PDBEntry and the sequence. + for (SequenceI seq : sequences) + { + PDBEntry pdbe = pdbEntriesToView[p++]; + if (pdbe != null && pdbe.getFile() != null) + { + StructureMapping[] smm = ssm.getMapping(pdbe.getFile()); + if (smm != null && smm.length > 0) + { + for (StructureMapping sm : smm) + { + if (sm.getSequence() == seq) + { + continue; + } + } + } + } + if (seq.getPrimaryDBRefs().size() == 0) + { + seqsWithoutSourceDBRef.add(seq); + continue; + } + } + if (!seqsWithoutSourceDBRef.isEmpty()) + { + int y = seqsWithoutSourceDBRef.size(); + setProgressBar(MessageManager.formatMessage( + "status.fetching_dbrefs_for_sequences_without_valid_refs", + y), progressId); + SequenceI[] seqWithoutSrcDBRef = new SequenceI[y]; + int x = 0; + for (SequenceI fSeq : seqsWithoutSourceDBRef) + { + seqWithoutSrcDBRef[x++] = fSeq; + } + + DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef); + dbRefFetcher.fetchDBRefs(true); + + setProgressBar("Fetch complete.", progressId); // todo i18n + } + } + if (pdbEntriesToView.length > 1) + { + setProgressBar(MessageManager.getString( + "status.fetching_3d_structures_for_selected_entries"), + progressId); + sViewer.viewStructures(pdbEntriesToView, sequences, alignPanel); + } + else + { + setProgressBar(MessageManager.formatMessage( + "status.fetching_3d_structures_for", + pdbEntriesToView[0].getId()),progressId); + sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); + } + setProgressBar(null, progressId); + } + + /** + * Populates the combo-box used in associating manually fetched structures to + * a unique sequence when more than one sequence selection is made. + */ + @Override + public void populateCmbAssociateSeqOptions( + JComboBox cmb_assSeq, + JLabel lbl_associateSeq) + { + cmb_assSeq.removeAllItems(); + cmb_assSeq.addItem( + new AssociateSeqOptions("-Select Associated Seq-", null)); + lbl_associateSeq.setVisible(false); + if (selectedSequences.length > 1) + { + for (SequenceI seq : selectedSequences) + { + cmb_assSeq.addItem(new AssociateSeqOptions(seq)); + } + } + else + { + String seqName = selectedSequence.getDisplayId(false); + seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39); + lbl_associateSeq.setText(seqName); + lbl_associateSeq.setVisible(true); + cmb_assSeq.setVisible(false); + } } - public void setStructuresDiscovered(boolean structuresDiscovered) + public boolean isStructuresDiscovered() { - this.structuresDiscovered = structuresDiscovered; + return discoveredStructuresSet != null + && !discoveredStructuresSet.isEmpty(); } - public Collection getDiscoveredStructuresSet() + public Collection getDiscoveredStructuresSet() { return discoveredStructuresSet; } + + @Override + protected void txt_search_ActionPerformed() + { + new Thread() + { + @Override + public void run() + { + errorWarning.setLength(0); + isValidPBDEntry = false; + if (txt_search.getText().length() > 0) + { + String searchTerm = txt_search.getText().toLowerCase(); + searchTerm = searchTerm.split(":")[0]; + // System.out.println(">>>>> search term : " + searchTerm); + List wantedFields = new ArrayList<>(); + FTSRestRequest pdbRequest = new FTSRestRequest(); + pdbRequest.setAllowEmptySeq(false); + pdbRequest.setResponseSize(1); + pdbRequest.setFieldToSearchBy("(pdb_id:"); + pdbRequest.setWantedFields(wantedFields); + pdbRequest.setSearchTerm(searchTerm + ")"); + pdbRequest.setAssociatedSequence(selectedSequence); + pdbRestCleint = PDBFTSRestClient.getInstance(); + wantedFields.add(pdbRestCleint.getPrimaryKeyColumn()); + FTSRestResponse resultList; + try + { + resultList = pdbRestCleint.executeRequest(pdbRequest); + } catch (Exception e) + { + errorWarning.append(e.getMessage()); + return; + } finally + { + validateSelections(); + } + if (resultList.getSearchSummary() != null + && resultList.getSearchSummary().size() > 0) + { + isValidPBDEntry = true; + } + } + validateSelections(); + } + }.start(); + } + + @Override + public void tabRefresh() + { + if (selectedSequences != null) + { + Thread refreshThread = new Thread(new Runnable() + { + @Override + public void run() + { + fetchStructuresMetaData(); + filterResultSet( + ((FilterOption) cmb_filterOption.getSelectedItem()) + .getValue()); + } + }); + refreshThread.start(); + } + } + + public class PDBEntryTableModel extends AbstractTableModel + { + String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", + "File" }; + + private List pdbEntries; + + public PDBEntryTableModel(List pdbEntries) + { + this.pdbEntries = new ArrayList<>(pdbEntries); + } + + @Override + public String getColumnName(int columnIndex) + { + return columns[columnIndex]; + } + + @Override + public int getRowCount() + { + return pdbEntries.size(); + } + + @Override + public int getColumnCount() + { + return columns.length; + } + + @Override + public boolean isCellEditable(int row, int column) + { + return false; + } + + @Override + public Object getValueAt(int rowIndex, int columnIndex) + { + Object value = "??"; + CachedPDB entry = pdbEntries.get(rowIndex); + switch (columnIndex) + { + case 0: + value = entry.getSequence(); + break; + case 1: + value = entry.getPdbEntry(); + break; + case 2: + value = entry.getPdbEntry().getChainCode() == null ? "_" + : entry.getPdbEntry().getChainCode(); + break; + case 3: + value = entry.getPdbEntry().getType(); + break; + case 4: + value = entry.getPdbEntry().getFile(); + break; + } + return value; + } + + @Override + public Class getColumnClass(int columnIndex) + { + return columnIndex == 0 ? SequenceI.class : PDBEntry.class; + } + + public CachedPDB getPDBEntryAt(int row) + { + return pdbEntries.get(row); + } + + } + + private class CachedPDB + { + private SequenceI sequence; + + private PDBEntry pdbEntry; + + public CachedPDB(SequenceI sequence, PDBEntry pdbEntry) + { + this.sequence = sequence; + this.pdbEntry = pdbEntry; + } + + public SequenceI getSequence() + { + return sequence; + } + + public PDBEntry getPdbEntry() + { + return pdbEntry; + } + + } + + private IProgressIndicator progressBar; + + @Override + public void setProgressBar(String message, long id) + { + progressBar.setProgressBar(message, id); + } + + @Override + public void registerHandler(long id, IProgressIndicatorHandler handler) + { + progressBar.registerHandler(id, handler); + } + + @Override + public boolean operationInProgress() + { + return progressBar.operationInProgress(); + } }