X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=198aa626baa97f7b4e470ebcb59396cac130cb1f;hb=f8eadd61b07375a6aada36b2b4b2aa8c3423510e;hp=7d0d76ad00d7aa0a92c34bd65f0a32a773b05844;hpb=e6438a4c2df8713e8acc65b1625f7446b6e76416;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 7d0d76a..198aa62 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -21,21 +21,25 @@ package jalview.gui; +import jalview.api.structures.JalviewStructureDisplayI; 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.jbgui.PDBDocFieldPreferences; +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.DBRefFetcher; import jalview.ws.sifts.SiftsSettings; -import jalview.ws.uimodel.PDBRestRequest; -import jalview.ws.uimodel.PDBRestResponse; -import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary; import java.awt.event.ItemEvent; import java.util.ArrayList; @@ -43,11 +47,15 @@ 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.JTable; +import javax.swing.SwingUtilities; import javax.swing.table.AbstractTableModel; /** @@ -57,10 +65,10 @@ import javax.swing.table.AbstractTableModel; * */ @SuppressWarnings("serial") -public class StructureChooser extends GStructureChooser implements - IProgressIndicator +public class StructureChooser extends GStructureChooser + implements IProgressIndicator { - private boolean structuresDiscovered = false; + private static int MAX_QLENGTH = 7820; private SequenceI selectedSequence; @@ -68,16 +76,18 @@ public class StructureChooser extends GStructureChooser implements private IProgressIndicator progressIndicator; - private Collection discoveredStructuresSet; + private Collection discoveredStructuresSet; - private PDBRestRequest lastPdbRequest; + 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) { @@ -98,6 +108,8 @@ public class StructureChooser extends GStructureChooser implements 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 @@ -108,11 +120,11 @@ public class StructureChooser extends GStructureChooser implements .getString("status.loading_cached_pdb_entries"), startTime); loadLocalCachedPDBEntries(); updateProgressIndicator(null, startTime); - updateProgressIndicator(MessageManager - .getString("status.searching_for_pdb_structures"), - 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(); @@ -144,22 +156,26 @@ public class StructureChooser extends GStructureChooser implements public void fetchStructuresMetaData() { long startTime = System.currentTimeMillis(); - Collection wantedFields = PDBDocFieldPreferences + pdbRestCleint = PDBFTSRestClient.getInstance(); + Collection wantedFields = pdbDocFieldPrefs .getStructureSummaryFields(); - discoveredStructuresSet = new LinkedHashSet(); - HashSet errors = new HashSet(); + discoveredStructuresSet = new LinkedHashSet<>(); + HashSet errors = new HashSet<>(); for (SequenceI seq : selectedSequences) { - PDBRestRequest pdbRequest = new PDBRestRequest(); + 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); - pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList; + FTSRestResponse resultList; try { resultList = pdbRestCleint.executeRequest(pdbRequest); @@ -183,9 +199,8 @@ public class StructureChooser extends GStructureChooser implements if (discoveredStructuresSet != null && !discoveredStructuresSet.isEmpty()) { - tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest, - discoveredStructuresSet)); - structuresDiscovered = true; + getResultTable().setModel(FTSRestResponse + .getTableModel(lastPdbRequest, discoveredStructuresSet)); noOfStructuresFound = discoveredStructuresSet.size(); mainFrame.setTitle(MessageManager.formatMessage( "label.structure_chooser_no_of_structures", @@ -202,16 +217,16 @@ public class StructureChooser extends GStructureChooser implements { errorMsg.append(error).append("\n"); } - JOptionPane.showMessageDialog(this, errorMsg.toString(), + JvOptionPane.showMessageDialog(this, errorMsg.toString(), MessageManager.getString("label.pdb_web-service_error"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } } } public void loadLocalCachedPDBEntries() { - ArrayList entries = new ArrayList(); + ArrayList entries = new ArrayList<>(); for (SequenceI seq : selectedSequences) { if (seq.getDatasetSequence() != null @@ -227,7 +242,7 @@ public class StructureChooser extends GStructureChooser implements } } } - + cachedPDBExists = !entries.isEmpty(); PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries); tbl_local_pdb.setModel(tableModelx); } @@ -245,20 +260,18 @@ public class StructureChooser extends GStructureChooser implements boolean isPDBRefsFound = false; boolean isUniProtRefsFound = false; StringBuilder queryBuilder = new StringBuilder(); - HashSet seqRefs = new LinkedHashSet(); + Set seqRefs = new LinkedHashSet<>(); - if (seq.getAllPDBEntries() != null) + if (seq.getAllPDBEntries() != null + && queryBuilder.length() < MAX_QLENGTH) { for (PDBEntry entry : seq.getAllPDBEntries()) { if (isValidSeqName(entry.getId())) { - queryBuilder.append(PDBRestClient.PDBDocField.PDB_ID.getCode()) - .append(":") -.append(entry.getId().toLowerCase()) + queryBuilder.append("pdb_id:").append(entry.getId().toLowerCase()) .append(" OR "); isPDBRefsFound = true; - // seqRefs.add(entry.getId()); } } } @@ -267,27 +280,22 @@ public class StructureChooser extends GStructureChooser implements { for (DBRefEntry dbRef : seq.getDBRefs()) { - if (isValidSeqName(getDBRefId(dbRef))) + if (isValidSeqName(getDBRefId(dbRef)) + && queryBuilder.length() < MAX_QLENGTH) { if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT)) { - queryBuilder - .append(PDBRestClient.PDBDocField.UNIPROT_ACCESSION - .getCode()).append(":") - .append(getDBRefId(dbRef)) - .append(" OR "); - queryBuilder - .append(PDBRestClient.PDBDocField.UNIPROT_ID.getCode()) - .append(":") + 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(PDBRestClient.PDBDocField.PDB_ID.getCode()) - .append(":").append(getDBRefId(dbRef).toLowerCase()) - .append(" OR "); + queryBuilder.append("pdb_id:") + .append(getDBRefId(dbRef).toLowerCase()).append(" OR "); isPDBRefsFound = true; } else @@ -301,6 +309,7 @@ public class StructureChooser extends GStructureChooser implements if (!isPDBRefsFound && !isUniProtRefsFound) { String seqName = seq.getName(); + seqName = sanitizeSeqName(seqName); String[] names = seqName.toLowerCase().split("\\|"); for (String name : names) { @@ -328,6 +337,20 @@ public class StructureChooser extends GStructureChooser implements } /** + * 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 * @@ -377,17 +400,18 @@ public class StructureChooser extends GStructureChooser implements public void run() { long startTime = System.currentTimeMillis(); + pdbRestCleint = PDBFTSRestClient.getInstance(); lbl_loading.setVisible(true); - Collection wantedFields = PDBDocFieldPreferences + Collection wantedFields = pdbDocFieldPrefs .getStructureSummaryFields(); - Collection filteredResponse = new HashSet(); - HashSet errors = new HashSet(); + Collection filteredResponse = new HashSet<>(); + HashSet errors = new HashSet<>(); + for (SequenceI seq : selectedSequences) { - PDBRestRequest pdbRequest = new PDBRestRequest(); + FTSRestRequest pdbRequest = new FTSRestRequest(); if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage")) { - System.out.println(">>>>>> Filtering with uniprot coverate"); pdbRequest.setAllowEmptySeq(false); pdbRequest.setResponseSize(1); pdbRequest.setFieldToSearchBy("("); @@ -409,8 +433,7 @@ public class StructureChooser extends GStructureChooser implements pdbRequest.setWantedFields(wantedFields); pdbRequest.setAssociatedSequence(seq); } - pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList; + FTSRestResponse resultList; try { resultList = pdbRestCleint.executeRequest(pdbRequest); @@ -433,14 +456,20 @@ public class StructureChooser extends GStructureChooser implements if (!filteredResponse.isEmpty()) { final int filterResponseCount = filteredResponse.size(); - Collection reorderedStructuresSet = new LinkedHashSet(); + Collection reorderedStructuresSet = new LinkedHashSet<>(); reorderedStructuresSet.addAll(filteredResponse); reorderedStructuresSet.addAll(discoveredStructuresSet); - tbl_summary.setModel(PDBRestResponse.getTableModel( - lastPdbRequest, reorderedStructuresSet)); - + 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 - tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1); + getResultTable().addRowSelectionInterval(0, + filterResponseCount - 1); mainFrame.setTitle(MessageManager.formatMessage( "label.structure_chooser_filter_time", totalTime)); } @@ -455,11 +484,9 @@ public class StructureChooser extends GStructureChooser implements { errorMsg.append(error).append("\n"); } - JOptionPane.showMessageDialog( - null, - errorMsg.toString(), + JvOptionPane.showMessageDialog(null, errorMsg.toString(), MessageManager.getString("label.pdb_web-service_error"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } } @@ -480,9 +507,9 @@ public class StructureChooser extends GStructureChooser implements 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.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))); @@ -500,36 +527,55 @@ public class StructureChooser extends GStructureChooser implements * Populates the filter combo-box options dynamically depending on discovered * structures */ - @Override - protected void populateFilterComboBox() + protected void populateFilterComboBox(boolean haveData, + boolean cachedPDBExist) { - if (isStructuresDiscovered()) + /* + * 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) { - 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)); + FilterOption cachedOption = new FilterOption( + MessageManager.getString("label.cached_structures"), + "-", VIEWS_LOCAL_PDB, false); + cmb_filterOption.addItem(cachedOption); + cmb_filterOption.setSelectedItem(cachedOption); } - cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-", - VIEWS_ENTER_ID)); - cmb_filterOption.addItem(new FilterOption("From File", "-", - VIEWS_FROM_FILE)); - cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-", - VIEWS_LOCAL_PDB)); + + cmb_filterOption.addItemListener(this); } /** * Updates the displayed view based on the selected filter option */ - @Override protected void updateCurrentView() { FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption @@ -569,7 +615,7 @@ public class StructureChooser extends GStructureChooser implements String currentView = selectedFilterOpt.getView(); if (currentView == VIEWS_FILTER) { - if (tbl_summary.getSelectedRows().length > 0) + if (getResultTable().getSelectedRows().length > 0) { btn_view.setEnabled(true); } @@ -602,22 +648,20 @@ public class StructureChooser extends GStructureChooser implements 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()))); + 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())); + lbl_pdbManualFetchStatus.setToolTipText( + JvSwingUtils.wrapTooltip(true, errorWarning.toString())); } - if (selectedSequences.length == 1 - || !assSeqOpt.getName().equalsIgnoreCase( - "-Select Associated Seq-")) + if (selectedSequences.length == 1 || !assSeqOpt.getName() + .equalsIgnoreCase("-Select Associated Seq-")) { txt_search.setEnabled(true); if (isValidPBDEntry) @@ -642,9 +686,8 @@ public class StructureChooser extends GStructureChooser implements AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel .getCmb_assSeq().getSelectedItem(); lbl_fromFileStatus.setIcon(errorImage); - if (selectedSequences.length == 1 - || (assSeqOpt != null && !assSeqOpt.getName().equalsIgnoreCase( - "-Select Associated Seq-"))) + if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt + .getName().equalsIgnoreCase("-Select Associated Seq-"))) { btn_pdbFromFile.setEnabled(true); if (selectedPdbFileName != null && selectedPdbFileName.length() > 0) @@ -688,161 +731,308 @@ public class StructureChooser extends GStructureChooser implements } /** - * Handles action event for btn_ok + * select structures for viewing by their PDB IDs + * + * @param pdbids + * @return true if structures were found and marked as selected */ - @Override - public void ok_ActionPerformed() + public boolean selectStructure(String... pdbids) { - final long progressSessionId = System.currentTimeMillis(); - final StructureSelectionManager ssm = ap.getStructureSelectionManager(); - ssm.setProgressIndicator(this); - ssm.setProgressSessionId(progressSessionId); - new Thread(new Runnable() - { - @Override - public void run() - { + boolean found = false; + FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption .getSelectedItem()); String currentView = selectedFilterOpt.getView(); - if (currentView == VIEWS_FILTER) + JTable restable = (currentView == VIEWS_FILTER) ? getResultTable() + : (currentView == VIEWS_LOCAL_PDB) ? tbl_local_pdb : null; + + if (restable == null) { - int pdbIdColIndex = tbl_summary.getColumn( - PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex(); - int refSeqColIndex = tbl_summary.getColumn("Ref Sequence") - .getModelIndex(); - int[] selectedRows = tbl_summary.getSelectedRows(); - PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; - int count = 0; - ArrayList selectedSeqsToView = new ArrayList(); - for (int row : selectedRows) + // 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++) { - String pdbIdStr = tbl_summary.getValueAt(row, pdbIdColIndex) - .toString(); - SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(row, - refSeqColIndex); - selectedSeqsToView.add(selectedSeq); - PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr); - if (pdbEntry == null) + if (String.valueOf(restable.getValueAt(r, pdbIdColIndex)) + .equalsIgnoreCase(pdbids[p])) { - pdbEntry = new PDBEntry(); - pdbEntry.setId(pdbIdStr); - pdbEntry.setType(PDBEntry.Type.PDB); - selectedSeq.getDatasetSequence().addPDBId(pdbEntry); + restable.setRowSelectionInterval(r, r); + found = true; } - pdbEntriesToView[count++] = pdbEntry; } - SequenceI[] selectedSeqs = selectedSeqsToView - .toArray(new SequenceI[selectedSeqsToView.size()]); - launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs); } - else if (currentView == VIEWS_LOCAL_PDB) + return found; + } + /** + * Handles action event for btn_ok + */ + @Override + public void ok_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() { - int[] selectedRows = tbl_local_pdb.getSelectedRows(); - PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; - int count = 0; - int pdbIdColIndex = tbl_local_pdb.getColumn( - PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex(); - int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence") - .getModelIndex(); - ArrayList selectedSeqsToView = new ArrayList(); - for (int row : selectedRows) + @Override + public void run() { - PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row, - pdbIdColIndex); - pdbEntriesToView[count++] = pdbEntry; - SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row, - refSeqColIndex); - selectedSeqsToView.add(selectedSeq); + 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(); + } + }); } - SequenceI[] selectedSeqs = selectedSeqsToView - .toArray(new SequenceI[selectedSeqsToView.size()]); - launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs); - } - else if (currentView == VIEWS_ENTER_ID) + }; + Thread runner = new Thread(viewStruc); + runner.start(); + if (waitUntilFinished) { - SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel - .getCmb_assSeq().getSelectedItem()).getSequence(); - if (userSelectedSeq != null) + while (sViewer == null ? runner.isAlive() + : (sViewer.sview == null ? true + : !sViewer.sview.hasMapping())) { - selectedSequence = userSelectedSeq; - } + try + { + Thread.sleep(300); + } catch (InterruptedException ie) + { - String pdbIdStr = txt_search.getText(); - PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr); - if (pdbEntry == null) - { - pdbEntry = new PDBEntry(); - 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) + } + + private PDBEntry getFindEntry(String id, Vector pdbEntries) + { + Objects.requireNonNull(id); + Objects.requireNonNull(pdbEntries); + PDBEntry foundEntry = null; + for (PDBEntry entry : pdbEntries) { - SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel - .getCmb_assSeq().getSelectedItem()).getSequence(); - if (userSelectedSeq != null) + if (entry.getId().equalsIgnoreCase(id)) { - selectedSequence = userSelectedSeq; + return entry; } - PDBEntry fileEntry = new AssociatePdbFileWithSeq() - .associatePdbWithSeq(selectedPdbFileName, - jalview.io.AppletFormatAdapter.FILE, - selectedSequence, true, Desktop.instance); - - launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, - new SequenceI[] { selectedSequence }); } - mainFrame.dispose(); - } - }).start(); + return foundEntry; } - private void launchStructureViewer(StructureSelectionManager ssm, + private StructureViewer launchStructureViewer( + StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView, final AlignmentPanel alignPanel, SequenceI[] sequences) { - ssm.setProgressBar("Launching PDB structure viewer.."); + 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) { - if (seq.getSourceDBRef() == null) - { - ssm.setProgressBar(null); - ssm.setProgressBar("Fetching Database refs.."); - new jalview.ws.DBRefFetcher(sequences, null, null, null, false) - .fetchDBRefs(true); - break; - } - } - } - if (pdbEntriesToView.length > 1) + PDBEntry pdbe = pdbEntriesToView[p++]; + if (pdbe != null && pdbe.getFile() != null) { - ArrayList seqsMap = new ArrayList(); - for (SequenceI seq : sequences) + StructureMapping[] smm = ssm.getMapping(pdbe.getFile()); + if (smm != null && smm.length > 0) { - seqsMap.add(new SequenceI[] { seq }); + for (StructureMapping sm : smm) + { + if (sm.getSequence() == seq) + { + continue; + } + } } - SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]); - ssm.setProgressBar(null); - ssm.setProgressBar("Fetching PDB Structures for selected entries.."); - sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel); } - else + 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) { - ssm.setProgressBar(null); - ssm.setProgressBar("Fetching PDB Structure for " - + pdbEntriesToView[0].getId()); - sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); + 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); + return sViewer; } /** @@ -851,11 +1041,12 @@ public class StructureChooser extends GStructureChooser implements */ @Override public void populateCmbAssociateSeqOptions( - JComboBox cmb_assSeq, JLabel lbl_associateSeq) + JComboBox cmb_assSeq, + JLabel lbl_associateSeq) { cmb_assSeq.removeAllItems(); - cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-", - null)); + cmb_assSeq.addItem( + new AssociateSeqOptions("-Select Associated Seq-", null)); lbl_associateSeq.setVisible(false); if (selectedSequences.length > 1) { @@ -876,15 +1067,11 @@ public class StructureChooser extends GStructureChooser implements public boolean isStructuresDiscovered() { - return structuresDiscovered; - } - - public void setStructuresDiscovered(boolean structuresDiscovered) - { - this.structuresDiscovered = structuresDiscovered; + return discoveredStructuresSet != null + && !discoveredStructuresSet.isEmpty(); } - public Collection getDiscoveredStructuresSet() + public Collection getDiscoveredStructuresSet() { return discoveredStructuresSet; } @@ -901,17 +1088,20 @@ public class StructureChooser extends GStructureChooser implements isValidPBDEntry = false; if (txt_search.getText().length() > 0) { - List wantedFields = new ArrayList(); - wantedFields.add(PDBDocField.PDB_ID); - PDBRestRequest pdbRequest = new PDBRestRequest(); + 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(txt_search.getText() + ")"); + pdbRequest.setSearchTerm(searchTerm + ")"); pdbRequest.setAssociatedSequence(selectedSequence); - pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList; + pdbRestCleint = PDBFTSRestClient.getInstance(); + wantedFields.add(pdbRestCleint.getPrimaryKeyColumn()); + FTSRestResponse resultList; try { resultList = pdbRestCleint.executeRequest(pdbRequest); @@ -945,8 +1135,9 @@ public class StructureChooser extends GStructureChooser implements public void run() { fetchStructuresMetaData(); - filterResultSet(((FilterOption) cmb_filterOption - .getSelectedItem()).getValue()); + filterResultSet( + ((FilterOption) cmb_filterOption.getSelectedItem()) + .getValue()); } }); refreshThread.start(); @@ -955,13 +1146,14 @@ public class StructureChooser extends GStructureChooser implements public class PDBEntryTableModel extends AbstractTableModel { - String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", "File" }; + String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", + "File" }; private List pdbEntries; public PDBEntryTableModel(List pdbEntries) { - this.pdbEntries = new ArrayList(pdbEntries); + this.pdbEntries = new ArrayList<>(pdbEntries); } @Override @@ -1002,8 +1194,8 @@ public class StructureChooser extends GStructureChooser implements value = entry.getPdbEntry(); break; case 2: - value = entry.getPdbEntry().getChainCode() == null ? "_" : entry - .getPdbEntry().getChainCode(); + value = entry.getPdbEntry().getChainCode() == null ? "_" + : entry.getPdbEntry().getChainCode(); break; case 3: value = entry.getPdbEntry().getType(); @@ -1071,4 +1263,9 @@ public class StructureChooser extends GStructureChooser implements { return progressBar.operationInProgress(); } + + public JalviewStructureDisplayI getOpenedStructureViewer() + { + return sViewer == null ? null : sViewer.sview; + } }