X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=3350f6cc62327c338415713360233537290d1a83;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=11fb9433703b4444d0fdf962924a7344d9cf3796;hpb=e4a49e444d89dc2d8d35913813bddc3a0dabcad6;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 11fb943..3350f6c 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -1,278 +1,1175 @@ +/* + * 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.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.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.JCheckBox; +import javax.swing.JComboBox; +import javax.swing.JLabel; import javax.swing.JOptionPane; +import javax.swing.table.AbstractTableModel; +/** + * Provides the behaviors for the Structure chooser Panel + * + * @author tcnofoegbu + * + */ @SuppressWarnings("serial") -public class StructureChooser extends GStructureChooser +public class StructureChooser extends GStructureChooser implements + IProgressIndicator { - - private boolean structuresWereFound = false; - 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; + + 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 + */ + public void init() { - // TODO code to load selected structures to jmol or chimera + 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(); + 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); + updateProgressIndicator(null, startTime); + mainFrame.setVisible(true); + updateCurrentView(); + } + }); + discoverPDBStructuresThread.start(); } - protected void populateFilterOptions() + /** + * Updates the progress indicator with the specified message + * + * @param message + * displayed message for the operation + * @param id + * unique handle for this indicator + */ + public void updateProgressIndicator(String message, long id) { - if (structuresWereFound) - { - 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)); - - // "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( - } - filterOptionsComboBox.addItem(new FilterOptions("Enter PDB Id", "-", - VIEWS_ENTER_ID)); - filterOptionsComboBox.addItem(new FilterOptions("From File", "-", - VIEWS_FROM_FILE)); + if (progressIndicator != null) + { + progressIndicator.setProgressBar(message, id); + } } - private void fetchStructures() + /** + * Retrieve meta-data for all the structure(s) for a given sequence(s) in a + * selection group + */ + public 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"); + } + JOptionPane.showMessageDialog(this, errorMsg.toString(), + MessageManager.getString("label.pdb_web-service_error"), + JOptionPane.ERROR_MESSAGE); + } + } + } + + public 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 + */ + + public 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(); + + if (seq.getAllPDBEntries() != null) + { + for (PDBEntry entry : seq.getAllPDBEntries()) + { + if (isValidSeqName(entry.getId())) + { + queryBuilder.append("pdb_id:") + .append(entry.getId().toLowerCase()).append(" OR "); + isPDBRefsFound = true; + // seqRefs.add(entry.getId()); + } + } + } + + if (seq.getDBRefs() != null && seq.getDBRefs().length != 0) + { + for (DBRefEntry dbRef : seq.getDBRefs()) + { + if (isValidSeqName(getDBRefId(dbRef))) + { + 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 (!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 + */ + 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 + * the field to filter by + */ + public 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"); + } + JOptionPane.showMessageDialog( + null, + errorMsg.toString(), + MessageManager.getString("label.pdb_web-service_error"), + JOptionPane.ERROR_MESSAGE); + } + } + + lbl_loading.setVisible(false); + + validateSelections(); + } + }); + filterThread.start(); + } + + /** + * Handles action event for btn_pdbFromFile + */ @Override - protected void stateChanged() + public void pdbFromFile_actionPerformed() { - updateCurrentView(); + 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(); + } } - int debounceCount = 0; + /** + * Populates the filter combo-box options dynamically depending on discovered + * structures + */ + protected void populateFilterComboBox(boolean haveData, + boolean cachedPDBExists) + { + /* + * temporarily suspend the change listener behaviour + */ + cmb_filterOption.removeItemListener(this); + + cmb_filterOption.removeAllItems(); + if (haveData) + { + cmb_filterOption.addItem(new FilterOption("Best Quality", + "overall_quality", VIEWS_FILTER)); + cmb_filterOption.addItem(new FilterOption("Best Resolution", + "resolution", VIEWS_FILTER)); + cmb_filterOption.addItem(new FilterOption("Most Protein Chain", + "number_of_protein_chains", VIEWS_FILTER)); + cmb_filterOption.addItem(new FilterOption("Most Bound Molecules", + "number_of_bound_molecules", VIEWS_FILTER)); + cmb_filterOption.addItem(new FilterOption("Most Polymer Residues", + "number_of_polymer_residues", VIEWS_FILTER)); + } + cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-", + VIEWS_ENTER_ID)); + cmb_filterOption.addItem(new FilterOption("From File", "-", + VIEWS_FROM_FILE)); + FilterOption cachedOption = new FilterOption("Cached PDB Entries", "-", + VIEWS_LOCAL_PDB); + cmb_filterOption.addItem(cachedOption); + + if (/*!haveData &&*/cachedPDBExists) + { + cmb_filterOption.setSelectedItem(cachedOption); + } + + cmb_filterOption.addItemListener(this); + } + + /** + * 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) { - filterResultSet(currentOption.getValue()); + mainFrame.setTitle(filterTitle); + chk_invertFilter.setVisible(true); + filterResultSet(selectedFilterOpt.getValue()); } + else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID + || selectedFilterOpt.getView() == VIEWS_FROM_FILE) + { + mainFrame.setTitle(MessageManager + .getString("label.structure_chooser_manual_association")); + idInputAssSeqPanel.loadCmbAssSeq(); + fileChooserAssSeqPanel.loadCmbAssSeq(); + } + validateSelections(); } - public void filterResultSet(String filterTarget) + /** + * Validates user selection and activates the view button if all parameters + * are correct + */ + @Override + public void validateSelections() { - System.out.println("-----------------> Filter by : " + filterTarget); + 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(); + } + } - 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); + /** + * Validates inputs from the Manual PDB entry panel + */ + public 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()))); + } - PDBSearchRequest request = new PDBSearchRequest(); - request.setAllowEmptySeq(false); - request.setResponseSize(1); - request.setSearchTarget("(text:"); - request.setSortTarget(filterTarget, true); + if (errorWarning.length() > 0) + { + lbl_pdbManualFetchStatus.setIcon(warningImage); + lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip( + true, errorWarning.toString())); + } - request.setWantedFields(wantedFields); + 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); + } + } - Collection searchSummaries = new HashSet(); - for (SequenceI seq : selectedSequences) + /** + * 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-"))) { - request.setSearchTerm(buildQuery(seq) + ")"); - PDBRestClient pdbRestCleint = new PDBRestClient(); - PDBSearchResponse resultList = pdbRestCleint.executeRequest(request); - if (resultList.getSearchSummary() != null - && !resultList.getSearchSummary().isEmpty()) + btn_pdbFromFile.setEnabled(true); + if (selectedPdbFileName != null && selectedPdbFileName.length() > 0) { - searchSummaries.addAll(resultList.getSearchSummary()); + btn_view.setEnabled(true); + lbl_fromFileStatus.setIcon(goodImage); + } + } + else + { + btn_pdbFromFile.setEnabled(false); + lbl_fromFileStatus.setIcon(errorImage); + } + } + @Override + public 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) + { + updateCurrentView(); + } + else + { + if (e.getStateChange() == ItemEvent.SELECTED) + { + updateCurrentView(); } } - for (PDBResponseSummary summary : searchSummaries) + } + + /** + * Handles action event for btn_ok + */ + @Override + public void ok_ActionPerformed() + { + final long progressSessionId = System.currentTimeMillis(); + final StructureSelectionManager ssm = ap.getStructureSelectionManager(); + final int preferredHeight = pnl_filter.getHeight(); + ssm.setProgressIndicator(this); + ssm.setProgressSessionId(progressSessionId); + 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; + ArrayList 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(); + ArrayList 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, + jalview.io.AppletFormatAdapter.FILE, + selectedSequence, true, Desktop.instance); + + launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, + new SequenceI[] { selectedSequence }); + } + closeAction(preferredHeight); + } + }).start(); + } + + private PDBEntry getFindEntry(String id, Vector pdbEntries) + { + Objects.requireNonNull(id); + Objects.requireNonNull(pdbEntries); + PDBEntry foundEntry = null; + for (PDBEntry entry : pdbEntries) { - jListFoundStructures.setSelectedValue(summary, true); - // jListFoundStructures. - break; + if (entry.getId().equalsIgnoreCase(id)) + { + return entry; + } } - System.out.println("Found item count : " + searchSummaries.size()); + return foundEntry; } - public void pdbFromFile_actionPerformed() + private void launchStructureViewer(StructureSelectionManager ssm, + final PDBEntry[] pdbEntriesToView, + final AlignmentPanel alignPanel, SequenceI[] sequences) { - 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) })); + ssm.setProgressBar(MessageManager + .getString("status.launching_3d_structure_viewer")); + final StructureViewer sViewer = new StructureViewer(ssm); - int value = chooser.showOpenDialog(null); + 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(); + ssm.setProgressBar(null); + ssm.setProgressBar(MessageManager.formatMessage( + "status.fetching_dbrefs_for_sequences_without_valid_refs", + y)); + SequenceI[] seqWithoutSrcDBRef = new SequenceI[y]; + int x = 0; + for (SequenceI fSeq : seqsWithoutSourceDBRef) + { + seqWithoutSrcDBRef[x++] = fSeq; + } + DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef); + dbRefFetcher.fetchDBRefs(true); + } + } + if (pdbEntriesToView.length > 1) + { + ArrayList seqsMap = new ArrayList(); + for (SequenceI seq : sequences) + { + seqsMap.add(new SequenceI[] { seq }); + } + SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]); + ssm.setProgressBar(null); + ssm.setProgressBar(MessageManager + .getString("status.fetching_3d_structures_for_selected_entries")); + sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel); + } + else + { + ssm.setProgressBar(null); + ssm.setProgressBar(MessageManager.formatMessage( + "status.fetching_3d_structures_for", + pdbEntriesToView[0].getId())); + sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); + } + } - if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) + /** + * 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) { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, - jalview.io.AppletFormatAdapter.FILE, selectedSequence, true, - Desktop.instance); + 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 boolean isStructuresDiscovered() + { + return discoveredStructuresSet != null + && !discoveredStructuresSet.isEmpty(); } + public Collection getDiscoveredStructuresSet() + { + return discoveredStructuresSet; + } - // rpdbview.addActionListener(new ActionListener() - // { - // - // @Override - // public void actionPerformed(ActionEvent e) - // { - // new StructureViewer(ap.getStructureSelectionManager()) - // .viewStructures(ap, pr, ap.av.collateForPDB(pr)); - // } - // }); + @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(); + } - public void enterPDB_actionPerformed() + @Override + public void tabRefresh() { - 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) + if (selectedSequences != null) { - PDBEntry entry = new PDBEntry(); - entry.setId(id.toUpperCase()); - selectedSequence.getDatasetSequence().addPDBId(entry); + Thread refreshThread = new Thread(new Runnable() + { + @Override + public void run() + { + fetchStructuresMetaData(); + filterResultSet(((FilterOption) cmb_filterOption + .getSelectedItem()).getValue()); + } + }); + refreshThread.start(); } } - // public static void main(String[] args) - // { - // SwingUtilities.invokeLater(new Runnable() - // { - // public void run() - // { - // new StructureChooser(null, null); - // } - // }); - // } + 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(); + } }