X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=5d381b9bf84f1aaa0d10d8fc461ad95a25810212;hb=782d4f5f28a6d138378b74ce74f4dbf14a49333f;hp=765c214b769344bf3f0a6cf7b3d34cdf6b0d2038;hpb=2d03102b7c6af888fda6676a90497b8d71a14f11;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 765c214..5d381b9 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -1,7 +1,6 @@ /* - - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -22,7 +21,9 @@ 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.jbgui.GStructureChooser; @@ -31,6 +32,7 @@ import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; import jalview.ws.dbsources.PDBRestClient; import jalview.ws.dbsources.PDBRestClient.PDBDocField; +import jalview.ws.sifts.SiftsSettings; import jalview.ws.uimodel.PDBRestRequest; import jalview.ws.uimodel.PDBRestResponse; import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary; @@ -39,7 +41,6 @@ import java.awt.event.ItemEvent; import java.util.ArrayList; import java.util.Collection; import java.util.HashSet; -import java.util.Hashtable; import java.util.LinkedHashSet; import java.util.List; @@ -47,7 +48,7 @@ import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JLabel; import javax.swing.JOptionPane; -import javax.swing.table.DefaultTableModel; +import javax.swing.table.AbstractTableModel; /** * Provides the behaviors for the Structure chooser Panel @@ -56,7 +57,8 @@ import javax.swing.table.DefaultTableModel; * */ @SuppressWarnings("serial") -public class StructureChooser extends GStructureChooser +public class StructureChooser extends GStructureChooser implements + IProgressIndicator { private boolean structuresDiscovered = false; @@ -76,8 +78,6 @@ public class StructureChooser extends GStructureChooser private boolean isValidPBDEntry; - private static Hashtable cachedEntryMap; - public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) { @@ -93,6 +93,11 @@ public class StructureChooser extends GStructureChooser */ public void init() { + if (!Jalview.isHeadlessMode()) + { + progressBar = new ProgressBar(this.statusPanel, this.statusBar); + } + Thread discoverPDBStructuresThread = new Thread(new Runnable() { @Override @@ -149,7 +154,7 @@ public class StructureChooser extends GStructureChooser PDBRestRequest pdbRequest = new PDBRestRequest(); pdbRequest.setAllowEmptySeq(false); pdbRequest.setResponseSize(500); - pdbRequest.setFieldToSearchBy("(text:"); + pdbRequest.setFieldToSearchBy("("); pdbRequest.setWantedFields(wantedFields); pdbRequest.setSearchTerm(buildQuery(seq) + ")"); pdbRequest.setAssociatedSequence(seq); @@ -169,7 +174,6 @@ public class StructureChooser extends GStructureChooser && !resultList.getSearchSummary().isEmpty()) { discoveredStructuresSet.addAll(resultList.getSearchSummary()); - updateSequencePDBEntries(seq, resultList.getSearchSummary()); } } @@ -183,90 +187,49 @@ public class StructureChooser extends GStructureChooser discoveredStructuresSet)); structuresDiscovered = true; noOfStructuresFound = discoveredStructuresSet.size(); - mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound - + " Found (" + totalTime + ")"); + mainFrame.setTitle(MessageManager.formatMessage( + "label.structure_chooser_no_of_structures", + noOfStructuresFound, totalTime)); } else { - mainFrame.setTitle("Structure Chooser - Manual association"); + mainFrame.setTitle(MessageManager + .getString("label.structure_chooser_manual_association")); if (errors.size() > 0) { StringBuilder errorMsg = new StringBuilder(); - // "Operation was unsuccessful due to the following: \n"); for (String error : errors) { errorMsg.append(error).append("\n"); } JOptionPane.showMessageDialog(this, errorMsg.toString(), - "PDB Web-service Error", JOptionPane.ERROR_MESSAGE); + MessageManager.getString("label.pdb_web-service_error"), + JOptionPane.ERROR_MESSAGE); } } } public void loadLocalCachedPDBEntries() { - DefaultTableModel tableModel = new DefaultTableModel() - { - @Override - public boolean isCellEditable(int row, int column) - { - return false; - } - }; - tableModel.addColumn("Ref Sequence"); - tableModel.addColumn("PDB Id"); - tableModel.addColumn("Chain"); - tableModel.addColumn("Type"); - tableModel.addColumn("File"); - cachedEntryMap = new Hashtable(); + ArrayList entries = new ArrayList(); for (SequenceI seq : selectedSequences) { if (seq.getDatasetSequence() != null - && seq.getDatasetSequence().getPDBId() != null) + && seq.getDatasetSequence().getAllPDBEntries() != null) { - for (PDBEntry pdbEntry : seq.getDatasetSequence().getPDBId()) + for (PDBEntry pdbEntry : seq.getDatasetSequence() + .getAllPDBEntries()) { - - String chain = pdbEntry.getChainCode() == null ? "_" : pdbEntry - .getChainCode(); - Object[] pdbEntryRowData = new Object[] - { seq, pdbEntry.getId(), chain, pdbEntry.getType(), - pdbEntry.getFile() }; if (pdbEntry.getFile() != null) { - tableModel.addRow(pdbEntryRowData); + entries.add(new CachedPDB(seq, pdbEntry)); } - cachedEntryMap.put(pdbEntry.getId().toLowerCase(), pdbEntry); } } } - tbl_local_pdb.setModel(tableModel); - } - /** - * Update the PDBEntry for a given sequence with values retrieved from - * PDBResponseSummary - * - * @param seq - * the Sequence to update its DBRef entry - * @param responseSummaries - * a collection of PDBResponseSummary - */ - public void updateSequencePDBEntries(SequenceI seq, - Collection responseSummaries) - { - for (PDBResponseSummary response : responseSummaries) - { - String pdbIdStr = response.getPdbId(); - PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase()); - if (pdbEntry == null) - { - pdbEntry = new PDBEntry(); - pdbEntry.setId(pdbIdStr); - pdbEntry.setType(PDBEntry.Type.PDB); - } - seq.getDatasetSequence().addPDBId(pdbEntry); - } + PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries); + tbl_local_pdb.setModel(tableModelx); } /** @@ -279,54 +242,88 @@ public class StructureChooser extends GStructureChooser public static String buildQuery(SequenceI seq) { + boolean isPDBRefsFound = false; + boolean isUniProtRefsFound = false; + StringBuilder queryBuilder = new StringBuilder(); 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); - } - } - if (seq.getPDBId() != null) + if (seq.getAllPDBEntries() != null) { - for (PDBEntry entry : seq.getPDBId()) + for (PDBEntry entry : seq.getAllPDBEntries()) { if (isValidSeqName(entry.getId())) { - seqRefs.add(entry.getId()); + queryBuilder.append(PDBRestClient.PDBDocField.PDB_ID.getCode()) + .append(":") +.append(entry.getId().toLowerCase()) + .append(" OR "); + isPDBRefsFound = true; + // seqRefs.add(entry.getId()); } } } - 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)); + 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(":") + .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 "); + isPDBRefsFound = true; + } + else + { + seqRefs.add(getDBRefId(dbRef)); + } } - ++count; - if (count > 10) + } + } + + if (!isPDBRefsFound && !isUniProtRefsFound) + { + String seqName = seq.getName(); + String[] names = seqName.toLowerCase().split("\\|"); + for (String name : names) + { + // System.out.println("Found name : " + name); + name.trim(); + if (isValidSeqName(name)) { - break; + seqRefs.add(name); } } + + for (String seqRef : seqRefs) + { + queryBuilder.append("text:").append(seqRef).append(" OR "); + } } - StringBuilder queryBuilder = new StringBuilder(); - for (String seqRef : seqRefs) + int endIndex = queryBuilder.lastIndexOf(" OR "); + if (queryBuilder.toString().length() < 6) { - queryBuilder.append("text:").append(seqRef).append(" OR "); + return null; } - int endIndex = queryBuilder.lastIndexOf(" OR "); - String query = queryBuilder.toString().substring(5, endIndex); + String query = queryBuilder.toString().substring(0, endIndex); return query; } @@ -385,17 +382,46 @@ public class StructureChooser extends GStructureChooser .getStructureSummaryFields(); Collection filteredResponse = new HashSet(); HashSet errors = new HashSet(); + // try + // { + // PDBDocField fiterField = PDBRestClient + // .getPDBDocFieldByCode(fieldToFilterBy); + // if (!wantedFields.contains(fiterField)) + // { + // wantedFields.add(fiterField); + // } + // } catch (Exception e) + // { + // e.printStackTrace(); + // } + 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); + if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage")) + { + System.out.println(">>>>>> Filtering with uniprot coverate"); + 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); + } pdbRestCleint = new PDBRestClient(); PDBRestResponse resultList; try @@ -428,14 +454,13 @@ public class StructureChooser extends GStructureChooser // Update table selection model here tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1); - - mainFrame.setTitle("Structure Chooser - Filter time (" - + totalTime + ")"); + mainFrame.setTitle(MessageManager.formatMessage( + "label.structure_chooser_filter_time", totalTime)); } else { - mainFrame.setTitle("Structure Chooser - Filter time (" - + totalTime + ")"); + mainFrame.setTitle(MessageManager.formatMessage( + "label.structure_chooser_filter_time", totalTime)); if (errors.size() > 0) { StringBuilder errorMsg = new StringBuilder(); @@ -443,8 +468,11 @@ public class StructureChooser extends GStructureChooser { errorMsg.append(error).append("\n"); } - JOptionPane.showMessageDialog(null, errorMsg.toString(), - "PDB Web-service Error", JOptionPane.ERROR_MESSAGE); + JOptionPane.showMessageDialog( + null, + errorMsg.toString(), + MessageManager.getString("label.pdb_web-service_error"), + JOptionPane.ERROR_MESSAGE); } } @@ -459,17 +487,18 @@ 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", new String[] - { selectedSequence.getDisplayId(false) })); + "label.select_pdb_file_for", + selectedSequence.getDisplayId(false))); chooser.setToolTipText(MessageManager.formatMessage( - "label.load_pdb_file_associate_with_sequence", new String[] - { selectedSequence.getDisplayId(false) })); + "label.load_pdb_file_associate_with_sequence", + selectedSequence.getDisplayId(false))); int value = chooser.showOpenDialog(null); if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) @@ -484,21 +513,22 @@ public class StructureChooser extends GStructureChooser * Populates the filter combo-box options dynamically depending on discovered * structures */ + @Override protected void populateFilterComboBox() { if (isStructuresDiscovered()) { cmb_filterOption.addItem(new FilterOption("Best Quality", PDBDocField.OVERALL_QUALITY.getCode(), VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Best UniProt Coverage", + cmb_filterOption.addItem(new FilterOption("Most UniProt Coverage", PDBDocField.UNIPROT_COVERAGE.getCode(), VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Highest Resolution", + cmb_filterOption.addItem(new FilterOption("Best Resolution", PDBDocField.RESOLUTION.getCode(), VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Highest Protein Chain", + cmb_filterOption.addItem(new FilterOption("Most Protein Chain", PDBDocField.PROTEIN_CHAIN_COUNT.getCode(), VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Highest Bound Molecules", + cmb_filterOption.addItem(new FilterOption("Most Bound Molecules", PDBDocField.BOUND_MOLECULE_COUNT.getCode(), VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Highest Polymer Residues", + cmb_filterOption.addItem(new FilterOption("Most Polymer Residues", PDBDocField.POLYMER_RESIDUE_COUNT.getCode(), VIEWS_FILTER)); } cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-", @@ -512,6 +542,7 @@ public class StructureChooser extends GStructureChooser /** * Updates the displayed view based on the selected filter option */ + @Override protected void updateCurrentView() { FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption @@ -530,7 +561,8 @@ public class StructureChooser extends GStructureChooser else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID || selectedFilterOpt.getView() == VIEWS_FROM_FILE) { - mainFrame.setTitle(filterTitle); + mainFrame.setTitle(MessageManager + .getString("label.structure_chooser_manual_association")); idInputAssSeqPanel.loadCmbAssSeq(); fileChooserAssSeqPanel.loadCmbAssSeq(); } @@ -541,6 +573,7 @@ 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 @@ -582,9 +615,10 @@ public class StructureChooser extends GStructureChooser lbl_pdbManualFetchStatus.setToolTipText(""); if (txt_search.getText().length() > 0) { - lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip( - true, "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) @@ -672,6 +706,15 @@ public class StructureChooser extends GStructureChooser @Override public void ok_ActionPerformed() { + final long progressSessionId = System.currentTimeMillis(); + final StructureSelectionManager ssm = ap.getStructureSelectionManager(); + ssm.setProgressIndicator(this); + ssm.setProgressSessionId(progressSessionId); + new Thread(new Runnable() + { + @Override + public void run() + { FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption .getSelectedItem()); String currentView = selectedFilterOpt.getView(); @@ -685,26 +728,26 @@ public class StructureChooser extends GStructureChooser PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; int count = 0; ArrayList selectedSeqsToView = new ArrayList(); - for (int summaryRow : selectedRows) + for (int row : selectedRows) { - String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdColIndex) + String pdbIdStr = tbl_summary.getValueAt(row, pdbIdColIndex) .toString(); - SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt( - summaryRow, refSeqColIndex); + SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(row, + refSeqColIndex); selectedSeqsToView.add(selectedSeq); - PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase()); + PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr); 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(ap.getStructureSelectionManager(), - pdbEntriesToView, ap, selectedSeqs); + launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs); } else if (currentView == VIEWS_LOCAL_PDB) { @@ -718,18 +761,16 @@ public class StructureChooser extends GStructureChooser ArrayList selectedSeqsToView = new ArrayList(); for (int row : selectedRows) { - String entryKey = tbl_local_pdb.getValueAt(row, pdbIdColIndex) - .toString().toLowerCase(); - pdbEntriesToView[count++] = cachedEntryMap.get(entryKey); + 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); + launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs); } else if (currentView == VIEWS_ENTER_ID) { @@ -741,20 +782,18 @@ public class StructureChooser extends GStructureChooser } String pdbIdStr = txt_search.getText(); - PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase()); + PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr); if (pdbEntry == null) { pdbEntry = new PDBEntry(); - pdbEntry.setId(txt_search.getText()); + pdbEntry.setId(pdbIdStr); pdbEntry.setType(PDBEntry.Type.PDB); + selectedSequence.getDatasetSequence().addPDBId(pdbEntry); } - selectedSequence.getDatasetSequence().addPDBId(pdbEntry); - PDBEntry[] pdbEntriesToView = new PDBEntry[] - { pdbEntry }; - launchStructureViewer(ap.getStructureSelectionManager(), - pdbEntriesToView, ap, new SequenceI[] - { selectedSequence }); + PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; + launchStructureViewer(ssm, pdbEntriesToView, ap, + new SequenceI[] { selectedSequence }); } else if (currentView == VIEWS_FROM_FILE) { @@ -769,56 +808,67 @@ public class StructureChooser extends GStructureChooser jalview.io.AppletFormatAdapter.FILE, selectedSequence, true, Desktop.instance); - launchStructureViewer(ap.getStructureSelectionManager(), - new PDBEntry[] - { fileEntry }, ap, new SequenceI[] - { selectedSequence }); + launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, + new SequenceI[] { selectedSequence }); } mainFrame.dispose(); + } + }).start(); } - 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) { + ssm.setProgressBar("Launching PDB structure viewer.."); final StructureViewer sViewer = new StructureViewer(ssm); - new Thread(new Runnable() + + if (SiftsSettings.isMapWithSifts()) { - public void run() + 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) { ArrayList seqsMap = new ArrayList(); for (SequenceI seq : sequences) { - seqsMap.add(new SequenceI[] - { seq }); + seqsMap.add(new SequenceI[] { seq }); } SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]); + ssm.setProgressBar(null); + ssm.setProgressBar("Fetching PDB Structures for selected entries.."); sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel); - // sViewer.viewStructures(pdbEntriesToView, - // alignPanel.av.collateForPDB(pdbEntriesToView), - // alignPanel); } else { + ssm.setProgressBar(null); + ssm.setProgressBar("Fetching PDB Structure for " + + pdbEntriesToView[0].getId()); sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); } - } - }).start(); } /** * 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)); - // cmb_assSeq.addItem(new AssociateSeqOptions("Auto Detect", null)); lbl_associateSeq.setVisible(false); if (selectedSequences.length > 1) { @@ -855,39 +905,46 @@ public class StructureChooser extends GStructureChooser @Override protected void txt_search_ActionPerformed() { - errorWarning.setLength(0); - isValidPBDEntry = false; - if (txt_search.getText().length() > 0) + new Thread() { - List wantedFields = new ArrayList(); - wantedFields.add(PDBDocField.PDB_ID); - PDBRestRequest pdbRequest = new PDBRestRequest(); - pdbRequest.setAllowEmptySeq(false); - pdbRequest.setResponseSize(1); - pdbRequest.setFieldToSearchBy("(pdb_id:"); - pdbRequest.setWantedFields(wantedFields); - pdbRequest.setSearchTerm(txt_search.getText() + ")"); - pdbRequest.setAssociatedSequence(selectedSequence); - pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList; - try - { - resultList = pdbRestCleint.executeRequest(pdbRequest); - } catch (Exception e) - { - errorWarning.append(e.getMessage()); - return; - } finally + @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(); + pdbRequest.setAllowEmptySeq(false); + pdbRequest.setResponseSize(1); + pdbRequest.setFieldToSearchBy("(pdb_id:"); + pdbRequest.setWantedFields(wantedFields); + pdbRequest.setSearchTerm(txt_search.getText() + ")"); + pdbRequest.setAssociatedSequence(selectedSequence); + pdbRestCleint = new PDBRestClient(); + PDBRestResponse 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(); } - if (resultList.getSearchSummary() != null - && resultList.getSearchSummary().size() > 0) - { - isValidPBDEntry = true; - } - } - validateSelections(); + }.start(); } @Override @@ -909,4 +966,122 @@ public class StructureChooser extends GStructureChooser } } + 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(); + } }