X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=ec2ebe3355b58eedce3aa77f3a0963bad1eb1a73;hb=9c16178c0601ea3169d7a5d5d623dafa45c54f85;hp=11fb9433703b4444d0fdf962924a7344d9cf3796;hpb=e4a49e444d89dc2d8d35913813bddc3a0dabcad6;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 11fb943..ec2ebe3 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -1,278 +1,1395 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ + package jalview.gui; +import jalview.api.structures.JalviewStructureDisplayI; +import jalview.bin.Cache; +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.PDBSearchRequest; -import jalview.ws.uimodel.PDBSearchResponse; -import jalview.ws.uimodel.PDBSearchResponse.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.JOptionPane; +import javax.swing.JCheckBox; +import javax.swing.JComboBox; +import javax.swing.JLabel; +import javax.swing.JTable; +import javax.swing.SwingUtilities; +import javax.swing.table.AbstractTableModel; +/** + * Provides the behaviors for the Structure chooser Panel + * + * @author tcnofoegbu + * + */ @SuppressWarnings("serial") public class StructureChooser extends GStructureChooser + implements IProgressIndicator { + private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE"; - private boolean structuresWereFound = false; + private static int MAX_QLENGTH = 7820; private SequenceI selectedSequence; private SequenceI[] selectedSequences; - public StructureChooser(AlignmentPanel ap, final SequenceI sequence) + private IProgressIndicator progressIndicator; + + private Collection discoveredStructuresSet; + + private FTSRestRequest lastPdbRequest; + + private FTSRestClientI pdbRestCleint; + + private String selectedPdbFileName; + + private boolean isValidPBDEntry; + + private boolean cachedPDBExists; + + private static StructureViewer lastTargetedView = null; + + public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, + AlignmentPanel ap) { this.ap = ap; - this.selectedSequence = sequence; - selectedSequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[] - { sequence } : ap.av.getSequenceSelection()); - fetchStructures(); - populateFilterOptions(); - updateCurrentView(); + this.selectedSequence = selectedSeq; + this.selectedSequences = selectedSeqs; + this.progressIndicator = (ap == null) ? null : ap.alignFrame; + init(); } - @Override - public void ok_ActionPerformed() + /** + * Initializes parameters used by the Structure Chooser Panel + */ + protected void init() { - // TODO code to load selected structures to jmol or chimera + if (!Jalview.isHeadlessMode()) + { + progressBar = new ProgressBar(this.statusPanel, this.statusBar); + } + + chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true)); + + // 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(); + updateProgressIndicator(MessageManager + .getString("status.loading_cached_pdb_entries"), startTime); + loadLocalCachedPDBEntries(); + updateProgressIndicator(null, startTime); + updateProgressIndicator(MessageManager.getString( + "status.searching_for_pdb_structures"), startTime); + fetchStructuresMetaData(); + // revise filter options if no results were found + populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists); + discoverStructureViews(); + updateProgressIndicator(null, startTime); + mainFrame.setVisible(true); + updateCurrentView(); + } + }); + discoverPDBStructuresThread.start(); } - protected void populateFilterOptions() + /** + * Builds a drop-down choice list of existing structure viewers to which new + * structures may be added. If this list is empty then it, and the 'Add' + * button, are hidden. + */ + private void discoverStructureViews() { - if (structuresWereFound) + if (Desktop.instance != null) { - filterOptionsComboBox.addItem(new FilterOptions( - "- Filter Criteria -", "", - VIEWS_FILTER)); - filterOptionsComboBox.addItem(new FilterOptions("All", "all", - VIEWS_FILTER)); - filterOptionsComboBox.addItem(new FilterOptions("Best Coverage", - "coverage", - VIEWS_FILTER)); - filterOptionsComboBox.addItem(new FilterOptions("Best Resolution", - PDBDocField.RESOLUTION.getCode(), - VIEWS_FILTER)); - filterOptionsComboBox.addItem(new FilterOptions("Best Quality", - PDBDocField.OVERALL_QUALITY.getCode(), - VIEWS_FILTER)); + targetView.removeAllItems(); + if (lastTargetedView != null && !lastTargetedView.isVisible()) + { + lastTargetedView = null; + } + int linkedViewsAt = 0; + for (StructureViewerBase view : Desktop.instance + .getStructureViewers(null, null)) + { + StructureViewer viewHandler = (lastTargetedView != null + && lastTargetedView.sview == view) ? lastTargetedView + : StructureViewer.reconfigure(view); + + if (view.isLinkedWith(ap)) + { + targetView.insertItemAt(viewHandler, + linkedViewsAt++); + } + else + { + targetView.addItem(viewHandler); + } + } + + /* + * show option to Add to viewer if at least 1 viewer found + */ + targetView.setVisible(false); + if (targetView.getItemCount() > 0) + { + targetView.setVisible(true); + if (lastTargetedView != null) + { + targetView.setSelectedItem(lastTargetedView); + } + else + { + targetView.setSelectedIndex(0); + } + } + btn_add.setVisible(targetView.isVisible()); + } + } - // "number_of_polymers"), PROTEIN_CHAIN_COUNT( - // "Protein Chain Count", "number_of_protein_chains"), - // BOUND_MOLECULE_COUNT( - // "Bound Molecule Count", "number_of_bound_molecules"), - // POLYMER_RESIDUE_COUNT( - // "Polymer Residue Count", "number_of_polymer_residues"), - // UNIPROT_COVERAGE( + /** + * Updates the progress indicator with the specified message + * + * @param message + * displayed message for the operation + * @param id + * unique handle for this indicator + */ + protected void updateProgressIndicator(String message, long id) + { + if (progressIndicator != null) + { + progressIndicator.setProgressBar(message, id); } - filterOptionsComboBox.addItem(new FilterOptions("Enter PDB Id", "-", - VIEWS_ENTER_ID)); - filterOptionsComboBox.addItem(new FilterOptions("From File", "-", - VIEWS_FROM_FILE)); } - private void fetchStructures() + /** + * Retrieve meta-data for all the structure(s) for a given sequence(s) in a + * selection group + */ + void fetchStructuresMetaData() { long startTime = System.currentTimeMillis(); - // final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new - // SequenceI[] - // { sequence } - // : ap.av.getSequenceSelection()); - - int foundStructures = 0; - 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); - - PDBSearchRequest request = new PDBSearchRequest(); - request.setAllowEmptySeq(false); - request.setResponseSize(500); - request.setSearchTarget("(text:"); - request.setWantedFields(wantedFields); - - Collection searchSummaries = new HashSet(); + pdbRestCleint = PDBFTSRestClient.getInstance(); + Collection wantedFields = pdbDocFieldPrefs + .getStructureSummaryFields(); + + discoveredStructuresSet = new LinkedHashSet<>(); + HashSet errors = new HashSet<>(); for (SequenceI seq : selectedSequences) { - request.setSearchTerm(buildQuery(seq) + ")"); - PDBRestClient pdbRestCleint = new PDBRestClient(); - PDBSearchResponse resultList = pdbRestCleint - .executeRequest(request); + 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); + 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()) { - searchSummaries.addAll(resultList.getSearchSummary()); + discoveredStructuresSet.addAll(resultList.getSearchSummary()); } } - foundStructures = searchSummaries.size(); - if (searchSummaries != null) - { - jListFoundStructures.setModel(PDBSearchResponse - .getListModel(searchSummaries)); - structuresWereFound = true; - } + int noOfStructuresFound = 0; String totalTime = (System.currentTimeMillis() - startTime) + " milli secs"; - mainFrame.setTitle("Structure Chooser - " + foundStructures - + " Found (" + totalTime + ")"); + if (discoveredStructuresSet != null + && !discoveredStructuresSet.isEmpty()) + { + 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); + } + } + } + + protected void loadLocalCachedPDBEntries() + { + ArrayList entries = new ArrayList<>(); + for (SequenceI seq : selectedSequences) + { + 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); } - private String buildQuery(SequenceI seq) + /** + * Builds a query string for a given sequences using its DBRef entries + * + * @param seq + * the sequences to build a query for + * @return the built query string + */ + + static String buildQuery(SequenceI seq) { - String query = seq.getName(); + boolean isPDBRefsFound = false; + boolean isUniProtRefsFound = false; StringBuilder queryBuilder = new StringBuilder(); - int count = 0; - if (seq.getDBRef() != null && seq.getDBRef().length != 0) + Set seqRefs = new LinkedHashSet<>(); + + /* + * note PDBs as DBRefEntry so they are not duplicated in query + */ + Set pdbids = new HashSet<>(); + + if (seq.getAllPDBEntries() != null + && queryBuilder.length() < MAX_QLENGTH) + { + for (PDBEntry entry : seq.getAllPDBEntries()) + { + if (isValidSeqName(entry.getId())) + { + String id = entry.getId().toLowerCase(); + queryBuilder.append("pdb_id:").append(id).append(" OR "); + isPDBRefsFound = true; + pdbids.add(id); + } + } + } + + if (seq.getDBRefs() != null && seq.getDBRefs().length != 0) + { + for (DBRefEntry dbRef : seq.getDBRefs()) + { + 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)) + { + + String id = getDBRefId(dbRef).toLowerCase(); + if (!pdbids.contains(id)) + { + queryBuilder.append("pdb_id:").append(id).append(" OR "); + isPDBRefsFound = true; + pdbids.add(id); + } + } + else + { + seqRefs.add(getDBRefId(dbRef)); + } + } + } + } + + 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()) - .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; + } + 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 + */ + 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; + } + + 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 + * the field to filter by + */ + void filterResultSet(final String fieldToFilterBy) + { + Thread filterThread = new Thread(new Runnable() + { + @Override + public void run() + { + long startTime = System.currentTimeMillis(); + pdbRestCleint = PDBFTSRestClient.getInstance(); + lbl_loading.setVisible(true); + Collection wantedFields = pdbDocFieldPrefs + .getStructureSummaryFields(); + Collection filteredResponse = new HashSet<>(); + HashSet errors = new HashSet<>(); + + 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.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()); + } + } + + 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) + { + StringBuilder errorMsg = new StringBuilder(); + for (String error : errors) + { + errorMsg.append(error).append("\n"); + } + JvOptionPane.showMessageDialog(null, errorMsg.toString(), + MessageManager.getString("label.pdb_web-service_error"), + JvOptionPane.ERROR_MESSAGE); + } + } + + lbl_loading.setVisible(false); + + validateSelections(); + } + }); + filterThread.start(); + } + + /** + * Handles action event for btn_pdbFromFile + */ @Override - protected void stateChanged() + protected 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", + selectedSequence.getDisplayId(false))); + chooser.setToolTipText(MessageManager.formatMessage( + "label.load_pdb_file_associate_with_sequence", + selectedSequence.getDisplayId(false))); + + int value = chooser.showOpenDialog(null); + if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) + { + selectedPdbFileName = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName); + validateSelections(); + } + } + + /** + * Populates the filter combo-box options dynamically depending on discovered + * structures + */ + protected void populateFilterComboBox(boolean haveData, + boolean cachedPDBExist) { - updateCurrentView(); + /* + * 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); } - int debounceCount = 0; + /** + * Updates the displayed view based on the selected filter option + */ protected void updateCurrentView() { - FilterOptions currentOption = ((FilterOptions) filterOptionsComboBox + FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption .getSelectedItem()); - switchableViewsLayout.show(switchableViewsPanel, - currentOption.getView()); - ++debounceCount; - if (currentOption.getView() == VIEWS_FILTER && debounceCount % 2 == 0) + 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) { - filterResultSet(currentOption.getValue()); + mainFrame.setTitle(MessageManager + .getString("label.structure_chooser_manual_association")); + idInputAssSeqPanel.loadCmbAssSeq(); + fileChooserAssSeqPanel.loadCmbAssSeq(); } + validateSelections(); } - public void filterResultSet(String filterTarget) + /** + * Validates user selection and enables the 'Add' and 'New View' buttons if + * all parameters are correct (the Add button will only be visible if there is + * at least one existing structure viewer open). This basically means at least + * one structure selected and no error messages. + *

+ * The 'Superpose Structures' option is enabled if either more than one + * structure is selected, or the 'Add' to existing view option is enabled, and + * disabled if the only option is to open a new view of a single structure. + */ + @Override + protected void validateSelections() { - System.out.println("-----------------> Filter by : " + filterTarget); + FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption + .getSelectedItem()); + btn_add.setEnabled(false); + String currentView = selectedFilterOpt.getView(); + int selectedCount = 0; + if (currentView == VIEWS_FILTER) + { + selectedCount = getResultTable().getSelectedRows().length; + if (selectedCount > 0) + { + btn_add.setEnabled(true); + } + } + else if (currentView == VIEWS_LOCAL_PDB) + { + selectedCount = tbl_local_pdb.getSelectedRows().length; + if (selectedCount > 0) + { + btn_add.setEnabled(true); + } + } + else if (currentView == VIEWS_ENTER_ID) + { + validateAssociationEnterPdb(); + } + else if (currentView == VIEWS_FROM_FILE) + { + validateAssociationFromFile(); + } - 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); + btn_newView.setEnabled(btn_add.isEnabled()); - PDBSearchRequest request = new PDBSearchRequest(); - request.setAllowEmptySeq(false); - request.setResponseSize(1); - request.setSearchTarget("(text:"); - request.setSortTarget(filterTarget, true); + /* + * enable 'Superpose' option if more than one structure is selected, + * or there are view(s) available to add structure(s) to + */ + chk_superpose + .setEnabled(selectedCount > 1 || targetView.getItemCount() > 0); + } - request.setWantedFields(wantedFields); + /** + * Validates inputs from the Manual PDB entry panel + */ + protected void validateAssociationEnterPdb() + { + AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel + .getCmb_assSeq().getSelectedItem(); + lbl_pdbManualFetchStatus.setIcon(errorImage); + lbl_pdbManualFetchStatus.setToolTipText(""); + if (txt_search.getText().length() > 0) + { + lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true, + MessageManager.formatMessage("info.no_pdb_entry_found_for", + txt_search.getText()))); + } - Collection searchSummaries = new HashSet(); - for (SequenceI seq : selectedSequences) + if (errorWarning.length() > 0) { - request.setSearchTerm(buildQuery(seq) + ")"); - PDBRestClient pdbRestCleint = new PDBRestClient(); - PDBSearchResponse resultList = pdbRestCleint.executeRequest(request); - if (resultList.getSearchSummary() != null - && !resultList.getSearchSummary().isEmpty()) + 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) { - searchSummaries.addAll(resultList.getSearchSummary()); + btn_add.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 + */ + protected 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_add.setEnabled(true); + lbl_fromFileStatus.setIcon(goodImage); } } + else + { + btn_pdbFromFile.setEnabled(false); + lbl_fromFileStatus.setIcon(errorImage); + } + } - for (PDBResponseSummary summary : searchSummaries) + @Override + protected void cmbAssSeqStateChanged() + { + validateSelections(); + } + + /** + * Handles the state change event for the 'filter' combo-box and 'invert' + * check-box + */ + @Override + protected void stateChanged(ItemEvent e) + { + if (e.getSource() instanceof JCheckBox) { - jListFoundStructures.setSelectedValue(summary, true); - // jListFoundStructures. - break; + updateCurrentView(); } - System.out.println("Found item count : " + searchSummaries.size()); + else + { + if (e.getStateChange() == ItemEvent.SELECTED) + { + updateCurrentView(); + } + } + } - public void pdbFromFile_actionPerformed() + /** + * select structures for viewing by their PDB IDs + * + * @param pdbids + * @return true if structures were found and marked as selected + */ + public boolean selectStructure(String... pdbids) { - 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.setToolTipText(MessageManager.formatMessage( - "label.load_pdb_file_associate_with_sequence", new String[] - { selectedSequence.getDisplayId(false) })); + boolean found = false; - int value = chooser.showOpenDialog(null); + FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption + .getSelectedItem()); + String currentView = selectedFilterOpt.getView(); + JTable restable = (currentView == VIEWS_FILTER) ? getResultTable() + : (currentView == VIEWS_LOCAL_PDB) ? tbl_local_pdb : null; - if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) + if (restable == null) { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, - jalview.io.AppletFormatAdapter.FILE, selectedSequence, true, - Desktop.instance); + // can't select (enter PDB ID, or load file - need to also select which + // sequence to associate with) + return false; + } + + int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex(); + for (int r = 0; r < restable.getRowCount(); r++) + { + for (int p = 0; p < pdbids.length; p++) + { + if (String.valueOf(restable.getValueAt(r, pdbIdColIndex)) + .equalsIgnoreCase(pdbids[p])) + { + restable.setRowSelectionInterval(r, r); + found = true; + } + } } + return found; + } + + /** + * Handles the 'New View' action + */ + @Override + protected void newView_ActionPerformed() + { + targetView.setSelectedItem(null); + showStructures(false); + } + /** + * Handles the 'Add to existing viewer' action + */ + @Override + protected void add_ActionPerformed() + { + showStructures(false); } + /** + * structure viewer opened by this dialog, or null + */ + private StructureViewer sViewer = null; + + public void showStructures(boolean waitUntilFinished) + { + + final StructureSelectionManager ssm = ap.getStructureSelectionManager(); + + final int preferredHeight = pnl_filter.getHeight(); + + Runnable viewStruc = new Runnable() + { + @Override + public void run() + { + FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption + .getSelectedItem()); + String currentView = selectedFilterOpt.getView(); + JTable restable = (currentView == VIEWS_FILTER) ? getResultTable() + : tbl_local_pdb; + + if (currentView == VIEWS_FILTER) + { + int pdbIdColIndex = restable.getColumn("PDB Id") + .getModelIndex(); + int refSeqColIndex = restable.getColumn("Ref Sequence") + .getModelIndex(); + int[] selectedRows = restable.getSelectedRows(); + PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; + int count = 0; + List selectedSeqsToView = new ArrayList<>(); + for (int row : selectedRows) + { + String pdbIdStr = restable + .getValueAt(row, pdbIdColIndex).toString(); + SequenceI selectedSeq = (SequenceI) restable + .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()]); + sViewer = 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()]); + sViewer = 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 }; + sViewer = 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); + + sViewer = launchStructureViewer( + ssm, new PDBEntry[] + { fileEntry }, ap, + new SequenceI[] + { selectedSequence }); + } + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + closeAction(preferredHeight); + mainFrame.dispose(); + } + }); + } + }; + Thread runner = new Thread(viewStruc); + runner.start(); + if (waitUntilFinished) + { + while (sViewer == null ? runner.isAlive() + : (sViewer.sview == null ? true + : !sViewer.sview.hasMapping())) + { + try + { + Thread.sleep(300); + } catch (InterruptedException ie) + { - // rpdbview.addActionListener(new ActionListener() - // { - // - // @Override - // public void actionPerformed(ActionEvent e) - // { - // new StructureViewer(ap.getStructureSelectionManager()) - // .viewStructures(ap, pr, ap.av.collateForPDB(pr)); - // } - // }); + } + } + } + } - public void enterPDB_actionPerformed() + private PDBEntry getFindEntry(String id, Vector pdbEntries) { - 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) + Objects.requireNonNull(id); + Objects.requireNonNull(pdbEntries); + PDBEntry foundEntry = null; + for (PDBEntry entry : pdbEntries) { - PDBEntry entry = new PDBEntry(); - entry.setId(id.toUpperCase()); - selectedSequence.getDatasetSequence().addPDBId(entry); + if (entry.getId().equalsIgnoreCase(id)) + { + return entry; + } } + return foundEntry; + } + + /** + * Answers a structure viewer (new or existing) configured to superimpose + * added structures or not according to the user's choice + * + * @param ssm + * @return + */ + StructureViewer getTargetedStructureViewer( + StructureSelectionManager ssm) + { + Object sv = targetView.getSelectedItem(); + + return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv; } - // public static void main(String[] args) - // { - // SwingUtilities.invokeLater(new Runnable() - // { - // public void run() - // { - // new StructureChooser(null, null); - // } - // }); - // } + /** + * Adds PDB structures to a new or existing structure viewer + * + * @param ssm + * @param pdbEntriesToView + * @param alignPanel + * @param sequences + * @return + */ + private StructureViewer launchStructureViewer( + StructureSelectionManager ssm, + final PDBEntry[] pdbEntriesToView, + final AlignmentPanel alignPanel, SequenceI[] sequences) + { + long progressId = sequences.hashCode(); + setProgressBar(MessageManager + .getString("status.launching_3d_structure_viewer"), progressId); + final StructureViewer theViewer = getTargetedStructureViewer(ssm); + boolean superimpose = chk_superpose.isSelected(); + theViewer.setSuperpose(superimpose); + + /* + * remember user's choice of superimpose or not + */ + Cache.setProperty(AUTOSUPERIMPOSE, + Boolean.valueOf(superimpose).toString()); + + 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().isEmpty()) + { + 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 = seqsWithoutSourceDBRef + .toArray(new SequenceI[y]); + 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); + theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel); + } + else + { + setProgressBar(MessageManager.formatMessage( + "status.fetching_3d_structures_for", + pdbEntriesToView[0].getId()),progressId); + theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); + } + setProgressBar(null, progressId); + // remember the last viewer we used... + lastTargetedView = theViewer; + return theViewer; + } + /** + * Populates the combo-box used in associating manually fetched structures to + * a unique sequence when more than one sequence selection is made. + */ + @Override + protected 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); + } + } + + protected boolean isStructuresDiscovered() + { + return discoveredStructuresSet != null + && !discoveredStructuresSet.isEmpty(); + } + + @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 + protected 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(); + } + + public JalviewStructureDisplayI getOpenedStructureViewer() + { + return sViewer == null ? null : sViewer.sview; + } }