X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=3df7e0c8c3a08df73b704ade978d604ab3cc349b;hb=0611a46a5652c852426da0d024bb43e0756501c7;hp=3db26f3865ccb18cd91f485026f8fbfdfe45934f;hpb=c394157681d10261bd6f7883b19eaf88d6784609;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 3db26f3..3df7e0c 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. * @@ -23,6 +22,7 @@ package jalview.gui; import jalview.datamodel.DBRefEntry; +import jalview.datamodel.DBRefSource; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.jbgui.GStructureChooser; @@ -39,7 +39,6 @@ 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; @@ -47,8 +46,7 @@ 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 @@ -77,8 +75,6 @@ public class StructureChooser extends GStructureChooser private boolean isValidPBDEntry; - private static Hashtable cachedEntryMap; - public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) { @@ -150,7 +146,7 @@ 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); @@ -170,7 +166,6 @@ public class StructureChooser extends GStructureChooser && !resultList.getSearchSummary().isEmpty()) { discoveredStructuresSet.addAll(resultList.getSearchSummary()); - updateSequencePDBEntries(seq, resultList.getSearchSummary()); } } @@ -184,87 +179,49 @@ 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(); - tableModel.addColumn("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(); - String[] pdbEntryRowData = new String[] - { seq.getDisplayId(false), 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); } /** @@ -277,54 +234,88 @@ 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; } @@ -388,7 +379,7 @@ public class StructureChooser extends GStructureChooser PDBRestRequest pdbRequest = new PDBRestRequest(); pdbRequest.setAllowEmptySeq(false); pdbRequest.setResponseSize(1); - pdbRequest.setFieldToSearchBy("(text:"); + pdbRequest.setFieldToSearchBy("("); pdbRequest.setFieldToSortBy(fieldToFilterBy, !chk_invertFilter.isSelected()); pdbRequest.setSearchTerm(buildQuery(seq) + ")"); @@ -426,14 +417,13 @@ 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(); @@ -441,8 +431,11 @@ 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); } } @@ -454,21 +447,21 @@ public class StructureChooser extends GStructureChooser filterThread.start(); } - /** * 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) @@ -483,6 +476,7 @@ public class StructureChooser extends GStructureChooser * Populates the filter combo-box options dynamically depending on discovered * structures */ + @Override protected void populateFilterComboBox() { if (isStructuresDiscovered()) @@ -511,6 +505,7 @@ public class StructureChooser extends GStructureChooser /** * Updates the displayed view based on the selected filter option */ + @Override protected void updateCurrentView() { FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption @@ -529,7 +524,8 @@ 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(); } @@ -540,6 +536,7 @@ 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 @@ -581,9 +578,10 @@ 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) @@ -621,8 +619,7 @@ public class StructureChooser extends GStructureChooser .getCmb_assSeq().getSelectedItem(); lbl_fromFileStatus.setIcon(errorImage); if (selectedSequences.length == 1 - || (assSeqOpt != null - && !assSeqOpt.getName().equalsIgnoreCase( + || (assSeqOpt != null && !assSeqOpt.getName().equalsIgnoreCase( "-Select Associated Seq-"))) { btn_pdbFromFile.setEnabled(true); @@ -685,19 +682,20 @@ 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; } @@ -706,18 +704,29 @@ public class StructureChooser extends GStructureChooser launchStructureViewer(ap.getStructureSelectionManager(), pdbEntriesToView, ap, selectedSeqs); } - else if(currentView == VIEWS_LOCAL_PDB){ + 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) { - String entryKey = tbl_local_pdb.getValueAt(row, 1).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, selectedSequences); + pdbEntriesToView, ap, selectedSeqs); } else if (currentView == VIEWS_ENTER_ID) { @@ -729,20 +738,18 @@ 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 }; + PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; launchStructureViewer(ap.getStructureSelectionManager(), - pdbEntriesToView, ap, new SequenceI[] - { selectedSequence }); + pdbEntriesToView, ap, new SequenceI[] { selectedSequence }); } else if (currentView == VIEWS_FROM_FILE) { @@ -753,46 +760,56 @@ public class StructureChooser extends GStructureChooser selectedSequence = userSelectedSeq; } PDBEntry fileEntry = new AssociatePdbFileWithSeq() - .associatePdbWithSeq( - selectedPdbFileName, jalview.io.AppletFormatAdapter.FILE, - selectedSequence, true, Desktop.instance); + .associatePdbWithSeq(selectedPdbFileName, + jalview.io.AppletFormatAdapter.FILE, + selectedSequence, true, Desktop.instance); launchStructureViewer(ap.getStructureSelectionManager(), - new PDBEntry[] - { fileEntry }, ap, new SequenceI[] - { selectedSequence }); + new PDBEntry[] { fileEntry }, ap, + new SequenceI[] { selectedSequence }); } mainFrame.dispose(); } - private void launchStructureViewer(StructureSelectionManager ssm, - PDBEntry[] pdbEntriesToView, AlignmentPanel alignPanel, - SequenceI[] sequences) + private void launchStructureViewer(final StructureSelectionManager ssm, + final PDBEntry[] pdbEntriesToView, + final AlignmentPanel alignPanel, final SequenceI[] sequences) { - StructureViewer sViewer = new StructureViewer(ssm); - if (pdbEntriesToView.length > 1) - { - sViewer.viewStructures(pdbEntriesToView, alignPanel.av.collateForPDB(pdbEntriesToView), - alignPanel); - } - else + final StructureViewer sViewer = new StructureViewer(ssm); + new Thread(new Runnable() { - sViewer.viewStructures(pdbEntriesToView[0], sequences, - alignPanel); - } + @Override + public void run() + { + if (pdbEntriesToView.length > 1) + { + ArrayList seqsMap = new ArrayList(); + for (SequenceI seq : sequences) + { + seqsMap.add(new SequenceI[] { seq }); + } + SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]); + sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel); + } + else + { + 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) { @@ -829,39 +846,46 @@ 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 @@ -883,4 +907,102 @@ 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; + } + + } }