X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=7c386f1a8cf63bd953e20adcaa2d22f2b871ae83;hb=bf97c293ad31f6ed5006a97d3a7d079c032652e8;hp=6e2ceff3f9c74f4d118cdbd3db5c3cfbc7240d29;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 6e2ceff..7c386f1 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (2.9.0b1) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -21,18 +21,24 @@ package jalview.gui; +import jalview.bin.Jalview; import jalview.datamodel.DBRefEntry; +import jalview.datamodel.DBRefSource; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; +import jalview.fts.api.FTSData; +import jalview.fts.api.FTSDataColumnI; +import jalview.fts.api.FTSRestClientI; +import jalview.fts.core.FTSRestRequest; +import jalview.fts.core.FTSRestResponse; +import jalview.fts.service.pdb.PDBFTSRestClient; +import jalview.io.DataSourceType; import jalview.jbgui.GStructureChooser; -import jalview.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.uimodel.PDBRestRequest; -import jalview.ws.uimodel.PDBRestResponse; -import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary; +import jalview.ws.DBRefFetcher; +import jalview.ws.sifts.SiftsSettings; import java.awt.event.ItemEvent; import java.util.ArrayList; @@ -40,11 +46,13 @@ 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; /** @@ -55,8 +63,9 @@ import javax.swing.table.AbstractTableModel; */ @SuppressWarnings("serial") public class StructureChooser extends GStructureChooser + implements IProgressIndicator { - private boolean structuresDiscovered = false; + private static int MAX_QLENGTH = 7820; private SequenceI selectedSequence; @@ -64,16 +73,18 @@ public class StructureChooser extends GStructureChooser 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) { @@ -89,6 +100,13 @@ public class StructureChooser extends GStructureChooser */ public void init() { + if (!Jalview.isHeadlessMode()) + { + progressBar = new ProgressBar(this.statusPanel, this.statusBar); + } + + // ensure a filter option is in force for search + populateFilterComboBox(true, cachedPDBExists); Thread discoverPDBStructuresThread = new Thread(new Runnable() { @Override @@ -99,11 +117,11 @@ public class StructureChooser extends GStructureChooser .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(); @@ -135,22 +153,26 @@ public class StructureChooser extends GStructureChooser 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("(text:"); + 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); @@ -174,9 +196,8 @@ public class StructureChooser extends GStructureChooser 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", @@ -193,16 +214,16 @@ public class StructureChooser extends GStructureChooser { 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 @@ -218,7 +239,7 @@ public class StructureChooser extends GStructureChooser } } } - + cachedPDBExists = !entries.isEmpty(); PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries); tbl_local_pdb.setModel(tableModelx); } @@ -233,63 +254,100 @@ public class StructureChooser extends GStructureChooser public static String buildQuery(SequenceI seq) { - HashSet seqRefs = new LinkedHashSet(); - String seqName = seq.getName(); - String[] names = seqName.toLowerCase().split("\\|"); - for (String name : names) - { - // System.out.println("Found name : " + name); - name.trim(); - if (isValidSeqName(name)) - { - seqRefs.add(name); - } - } + boolean isPDBRefsFound = false; + boolean isUniProtRefsFound = false; + StringBuilder queryBuilder = new StringBuilder(); + 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())) { - seqRefs.add(entry.getId()); + queryBuilder.append("pdb_id:").append(entry.getId().toLowerCase()) + .append(" OR "); + isPDBRefsFound = true; } } } - if (seq.getDBRef() != null && seq.getDBRef().length != 0) + if (seq.getDBRefs() != null && seq.getDBRefs().length != 0) { - int count = 0; - for (DBRefEntry dbRef : seq.getDBRef()) + for (DBRefEntry dbRef : seq.getDBRefs()) { - if (isValidSeqName(getDBRefId(dbRef))) - { - seqRefs.add(getDBRefId(dbRef)); - } - ++count; - if (count > 10) + if (isValidSeqName(getDBRefId(dbRef)) + && queryBuilder.length() < MAX_QLENGTH) { - break; + 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)); + } } } } - StringBuilder queryBuilder = new StringBuilder(); - for (String seqRef : seqRefs) + if (!isPDBRefsFound && !isUniProtRefsFound) { - queryBuilder.append("text:").append(seqRef).append(" OR "); + String seqName = seq.getName(); + seqName = sanitizeSeqName(seqName); + String[] names = seqName.toLowerCase().split("\\|"); + for (String name : names) + { + // System.out.println("Found name : " + name); + name.trim(); + if (isValidSeqName(name)) + { + seqRefs.add(name); + } + } + + for (String seqRef : seqRefs) + { + queryBuilder.append("text:").append(seqRef).append(" OR "); + } } - int endIndex = queryBuilder.lastIndexOf(" OR "); + int endIndex = queryBuilder.lastIndexOf(" OR "); if (queryBuilder.toString().length() < 6) { return null; } - String query = queryBuilder.toString().substring(5, endIndex); + 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 * @@ -339,24 +397,40 @@ public class StructureChooser extends GStructureChooser 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(); - pdbRequest.setAllowEmptySeq(false); - pdbRequest.setResponseSize(1); - pdbRequest.setFieldToSearchBy("(text:"); - pdbRequest.setFieldToSortBy(fieldToFilterBy, - !chk_invertFilter.isSelected()); - pdbRequest.setSearchTerm(buildQuery(seq) + ")"); - pdbRequest.setWantedFields(wantedFields); - pdbRequest.setAssociatedSequence(seq); - pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList; + 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); @@ -379,14 +453,20 @@ public class StructureChooser extends GStructureChooser 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)); } @@ -401,11 +481,9 @@ public class StructureChooser extends GStructureChooser { 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); } } @@ -420,14 +498,15 @@ public class StructureChooser extends GStructureChooser /** * Handles action event for btn_pdbFromFile */ + @Override public void pdbFromFile_actionPerformed() { jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle(MessageManager.formatMessage( - "label.select_pdb_file_for", - 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))); @@ -445,29 +524,42 @@ public class StructureChooser extends GStructureChooser * Populates the filter combo-box options dynamically depending on discovered * structures */ - protected void populateFilterComboBox() + protected void populateFilterComboBox(boolean haveData, + boolean cachedPDBExists) { - if (isStructuresDiscovered()) + /* + * temporarily suspend the change listener behaviour + */ + cmb_filterOption.removeItemListener(this); + + cmb_filterOption.removeAllItems(); + if (haveData) { cmb_filterOption.addItem(new FilterOption("Best Quality", - PDBDocField.OVERALL_QUALITY.getCode(), VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Best UniProt Coverage", - PDBDocField.UNIPROT_COVERAGE.getCode(), VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Highest Resolution", - PDBDocField.RESOLUTION.getCode(), VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Highest Protein Chain", - PDBDocField.PROTEIN_CHAIN_COUNT.getCode(), VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Highest Bound Molecules", - PDBDocField.BOUND_MOLECULE_COUNT.getCode(), VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Highest Polymer Residues", - PDBDocField.POLYMER_RESIDUE_COUNT.getCode(), VIEWS_FILTER)); - } - cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-", - VIEWS_ENTER_ID)); - cmb_filterOption.addItem(new FilterOption("From File", "-", - VIEWS_FROM_FILE)); - cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-", - VIEWS_LOCAL_PDB)); + "overall_quality", VIEWS_FILTER, false)); + cmb_filterOption.addItem(new FilterOption("Best Resolution", + "resolution", VIEWS_FILTER, false)); + cmb_filterOption.addItem(new FilterOption("Most Protein Chain", + "number_of_protein_chains", VIEWS_FILTER, false)); + cmb_filterOption.addItem(new FilterOption("Most Bound Molecules", + "number_of_bound_molecules", VIEWS_FILTER, false)); + cmb_filterOption.addItem(new FilterOption("Most Polymer Residues", + "number_of_polymer_residues", VIEWS_FILTER, true)); + } + cmb_filterOption.addItem( + new FilterOption("Enter PDB Id", "-", VIEWS_ENTER_ID, false)); + cmb_filterOption.addItem( + new FilterOption("From File", "-", VIEWS_FROM_FILE, false)); + + if (cachedPDBExists) + { + FilterOption cachedOption = new FilterOption("Cached Structures", + "-", VIEWS_LOCAL_PDB, false); + cmb_filterOption.addItem(cachedOption); + cmb_filterOption.setSelectedItem(cachedOption); + } + + cmb_filterOption.addItemListener(this); } /** @@ -503,6 +595,7 @@ public class StructureChooser extends GStructureChooser * Validates user selection and activates the view button if all parameters * are correct */ + @Override public void validateSelections() { FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption @@ -511,7 +604,7 @@ public class StructureChooser extends GStructureChooser String currentView = selectedFilterOpt.getView(); if (currentView == VIEWS_FILTER) { - if (tbl_summary.getSelectedRows().length > 0) + if (getResultTable().getSelectedRows().length > 0) { btn_view.setEnabled(true); } @@ -544,22 +637,20 @@ public class StructureChooser extends GStructureChooser 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) @@ -584,9 +675,8 @@ public class StructureChooser extends GStructureChooser 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) @@ -635,145 +725,235 @@ public class StructureChooser extends GStructureChooser @Override public void ok_ActionPerformed() { - FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption - .getSelectedItem()); - String currentView = selectedFilterOpt.getView(); - if (currentView == VIEWS_FILTER) + final StructureSelectionManager ssm = ap.getStructureSelectionManager(); + + final int preferredHeight = pnl_filter.getHeight(); + + new Thread(new Runnable() { - 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) + @Override + public void run() { - 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) + FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption + .getSelectedItem()); + String currentView = selectedFilterOpt.getView(); + if (currentView == VIEWS_FILTER) { - pdbEntry = new PDBEntry(); - pdbEntry.setId(pdbIdStr); - pdbEntry.setType(PDBEntry.Type.PDB); - selectedSeq.getDatasetSequence().addPDBId(pdbEntry); + int pdbIdColIndex = getResultTable().getColumn("PDB Id") + .getModelIndex(); + int refSeqColIndex = getResultTable().getColumn("Ref Sequence") + .getModelIndex(); + int[] selectedRows = getResultTable().getSelectedRows(); + PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; + int count = 0; + List selectedSeqsToView = new ArrayList<>(); + for (int row : selectedRows) + { + String pdbIdStr = getResultTable() + .getValueAt(row, pdbIdColIndex).toString(); + SequenceI selectedSeq = (SequenceI) getResultTable() + .getValueAt(row, refSeqColIndex); + selectedSeqsToView.add(selectedSeq); + PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr); + if (pdbEntry == null) + { + pdbEntry = getFindEntry(pdbIdStr, + selectedSeq.getAllPDBEntries()); + } + + if (pdbEntry == null) + { + pdbEntry = new PDBEntry(); + pdbEntry.setId(pdbIdStr); + pdbEntry.setType(PDBEntry.Type.PDB); + selectedSeq.getDatasetSequence().addPDBId(pdbEntry); + } + pdbEntriesToView[count++] = pdbEntry; + } + SequenceI[] selectedSeqs = selectedSeqsToView + .toArray(new SequenceI[selectedSeqsToView.size()]); + launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs); } - pdbEntriesToView[count++] = pdbEntry; - } - SequenceI[] selectedSeqs = selectedSeqsToView - .toArray(new SequenceI[selectedSeqsToView.size()]); - launchStructureViewer(ap.getStructureSelectionManager(), - 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( - PDBRestClient.PDBDocField.PDB_ID.getName()).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(ap.getStructureSelectionManager(), - pdbEntriesToView, ap, selectedSeqs); - } - else if (currentView == VIEWS_ENTER_ID) - { - SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel - .getCmb_assSeq().getSelectedItem()).getSequence(); - if (userSelectedSeq != null) - { - selectedSequence = userSelectedSeq; - } + else if (currentView == VIEWS_LOCAL_PDB) + { + int[] selectedRows = tbl_local_pdb.getSelectedRows(); + PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; + int count = 0; + int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id") + .getModelIndex(); + int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence") + .getModelIndex(); + List selectedSeqsToView = new ArrayList<>(); + for (int row : selectedRows) + { + PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row, + pdbIdColIndex); + pdbEntriesToView[count++] = pdbEntry; + SequenceI selectedSeq = (SequenceI) tbl_local_pdb + .getValueAt(row, refSeqColIndex); + selectedSeqsToView.add(selectedSeq); + } + SequenceI[] selectedSeqs = selectedSeqsToView + .toArray(new SequenceI[selectedSeqsToView.size()]); + launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs); + } + else if (currentView == VIEWS_ENTER_ID) + { + SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel + .getCmb_assSeq().getSelectedItem()).getSequence(); + if (userSelectedSeq != null) + { + selectedSequence = userSelectedSeq; + } + String pdbIdStr = txt_search.getText(); + PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr); + if (pdbEntry == null) + { + pdbEntry = new PDBEntry(); + if (pdbIdStr.split(":").length > 1) + { + pdbEntry.setId(pdbIdStr.split(":")[0]); + pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase()); + } + else + { + pdbEntry.setId(pdbIdStr); + } + pdbEntry.setType(PDBEntry.Type.PDB); + selectedSequence.getDatasetSequence().addPDBId(pdbEntry); + } - 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) + { + SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel + .getCmb_assSeq().getSelectedItem()).getSequence(); + if (userSelectedSeq != null) + { + selectedSequence = userSelectedSeq; + } + PDBEntry fileEntry = new AssociatePdbFileWithSeq() + .associatePdbWithSeq(selectedPdbFileName, + DataSourceType.FILE, selectedSequence, true, + Desktop.instance); + + launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, + new SequenceI[] + { selectedSequence }); + } + closeAction(preferredHeight); + mainFrame.dispose(); } + }).start(); + } - PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; - launchStructureViewer(ap.getStructureSelectionManager(), - 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(ap.getStructureSelectionManager(), - new PDBEntry[] { fileEntry }, ap, - new SequenceI[] { selectedSequence }); } - mainFrame.dispose(); + return foundEntry; } - private void launchStructureViewer(final StructureSelectionManager ssm, + private void launchStructureViewer(StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView, - final AlignmentPanel alignPanel, final SequenceI[] sequences) + final AlignmentPanel alignPanel, SequenceI[] sequences) { + long progressId = sequences.hashCode(); + setProgressBar(MessageManager + .getString("status.launching_3d_structure_viewer"), progressId); final StructureViewer sViewer = new StructureViewer(ssm); - new Thread(new Runnable() + setProgressBar(null, progressId); + + if (SiftsSettings.isMapWithSifts()) { - public void run() + 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 (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]); - sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel); } - else + if (seq.getPrimaryDBRefs().size() == 0) { - sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); + seqsWithoutSourceDBRef.add(seq); + continue; } } - }).start(); + if (!seqsWithoutSourceDBRef.isEmpty()) + { + int y = seqsWithoutSourceDBRef.size(); + setProgressBar(MessageManager.formatMessage( + "status.fetching_dbrefs_for_sequences_without_valid_refs", + y), progressId); + SequenceI[] seqWithoutSrcDBRef = new SequenceI[y]; + int x = 0; + for (SequenceI fSeq : seqsWithoutSourceDBRef) + { + seqWithoutSrcDBRef[x++] = fSeq; + } + + DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef); + dbRefFetcher.fetchDBRefs(true); + + setProgressBar("Fetch complete.", progressId); // todo i18n + } + } + if (pdbEntriesToView.length > 1) + { + setProgressBar(MessageManager.getString( + "status.fetching_3d_structures_for_selected_entries"), + progressId); + sViewer.viewStructures(pdbEntriesToView, sequences, alignPanel); + } + else + { + setProgressBar(MessageManager.formatMessage( + "status.fetching_3d_structures_for", + pdbEntriesToView[0].getId()),progressId); + sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); + } + setProgressBar(null, progressId); } /** * Populates the combo-box used in associating manually fetched structures to * a unique sequence when more than one sequence selection is made. */ + @Override public void populateCmbAssociateSeqOptions( - JComboBox cmb_assSeq, JLabel lbl_associateSeq) + 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) { @@ -794,15 +974,11 @@ public class StructureChooser extends GStructureChooser public boolean isStructuresDiscovered() { - return structuresDiscovered; + return discoveredStructuresSet != null + && !discoveredStructuresSet.isEmpty(); } - public void setStructuresDiscovered(boolean structuresDiscovered) - { - this.structuresDiscovered = structuresDiscovered; - } - - public Collection getDiscoveredStructuresSet() + public Collection getDiscoveredStructuresSet() { return discoveredStructuresSet; } @@ -812,23 +988,27 @@ public class StructureChooser extends GStructureChooser { new Thread() { + @Override public void run() { errorWarning.setLength(0); 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); @@ -862,8 +1042,9 @@ public class StructureChooser extends GStructureChooser public void run() { fetchStructuresMetaData(); - filterResultSet(((FilterOption) cmb_filterOption - .getSelectedItem()).getValue()); + filterResultSet( + ((FilterOption) cmb_filterOption.getSelectedItem()) + .getValue()); } }); refreshThread.start(); @@ -872,13 +1053,14 @@ public class StructureChooser extends GStructureChooser 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 @@ -919,8 +1101,8 @@ public class StructureChooser extends GStructureChooser 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(); @@ -968,4 +1150,24 @@ public class StructureChooser extends GStructureChooser } } + + 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(); + } }