X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=347c1b2d8ed7b4ec91480bf97acb76b74b7763a3;hb=1b06ffc30dc430351081ecf4bc1515f9448e7ec4;hp=5c86ce26e6fcaded633fe0b8d24aebfc1be452a5;hpb=bca294a4376fbe2087f03ca2c44bd591edc61aed;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 5c86ce2..347c1b2 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -39,15 +39,14 @@ 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; import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JLabel; -import javax.swing.table.DefaultTableModel; - +import javax.swing.JOptionPane; +import javax.swing.table.AbstractTableModel; /** * Provides the behaviors for the Structure chooser Panel @@ -76,8 +75,6 @@ public class StructureChooser extends GStructureChooser private boolean isValidPBDEntry; - private static Hashtable cachedEntryMap; - public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) { @@ -99,9 +96,13 @@ public class StructureChooser extends GStructureChooser public void run() { long startTime = System.currentTimeMillis(); - String msg = MessageManager.getString("status.fetching_db_refs"); - updateProgressIndicator(msg, startTime); + updateProgressIndicator(MessageManager + .getString("status.loading_cached_pdb_entries"), startTime); loadLocalCachedPDBEntries(); + updateProgressIndicator(null, startTime); + updateProgressIndicator(MessageManager + .getString("status.searching_for_pdb_structures"), + startTime); fetchStructuresMetaData(); populateFilterComboBox(); updateProgressIndicator(null, startTime); @@ -139,6 +140,7 @@ public class StructureChooser extends GStructureChooser .getStructureSummaryFields(); discoveredStructuresSet = new LinkedHashSet(); + HashSet errors = new HashSet(); for (SequenceI seq : selectedSequences) { PDBRestRequest pdbRequest = new PDBRestRequest(); @@ -147,19 +149,29 @@ public class StructureChooser extends GStructureChooser pdbRequest.setFieldToSearchBy("(text:"); pdbRequest.setWantedFields(wantedFields); pdbRequest.setSearchTerm(buildQuery(seq) + ")"); - pdbRequest.setAssociatedSequence(seq.getName()); + pdbRequest.setAssociatedSequence(seq); pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest); + PDBRestResponse resultList; + try + { + resultList = pdbRestCleint.executeRequest(pdbRequest); + } catch (Exception e) + { + e.printStackTrace(); + errors.add(e.getMessage()); + continue; + } lastPdbRequest = pdbRequest; if (resultList.getSearchSummary() != null && !resultList.getSearchSummary().isEmpty()) { discoveredStructuresSet.addAll(resultList.getSearchSummary()); - updateSequenceDbRef(seq, resultList.getSearchSummary()); } } int noOfStructuresFound = 0; + String totalTime = (System.currentTimeMillis() - startTime) + + " milli secs"; if (discoveredStructuresSet != null && !discoveredStructuresSet.isEmpty()) { @@ -167,59 +179,49 @@ public class StructureChooser extends GStructureChooser discoveredStructuresSet)); structuresDiscovered = true; noOfStructuresFound = discoveredStructuresSet.size(); + mainFrame.setTitle(MessageManager.formatMessage( + "label.structure_chooser_no_of_structures", + noOfStructuresFound, totalTime)); + } + else + { + mainFrame.setTitle(MessageManager + .getString("label.structure_chooser_manual_association")); + if (errors.size() > 0) + { + StringBuilder errorMsg = new StringBuilder(); + for (String error : errors) + { + errorMsg.append(error).append("\n"); + } + JOptionPane.showMessageDialog(this, errorMsg.toString(), + MessageManager.getString("label.pdb_web-service_error"), + JOptionPane.ERROR_MESSAGE); + } } - String totalTime = (System.currentTimeMillis() - startTime) - + " milli secs"; - mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound - + " Found (" + totalTime + ")"); } public void loadLocalCachedPDBEntries() { - DefaultTableModel tableModel = new DefaultTableModel(); - tableModel.addColumn("Sequence"); - tableModel.addColumn("PDB Id"); - 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[] pdbEntryRowData = new String[] - { seq.getDisplayId(false), pdbEntry.getId(), pdbEntry.getType(), - pdbEntry.getFile() }; - tableModel.addRow(pdbEntryRowData); - cachedEntryMap.put(seq.getDisplayId(false) + pdbEntry.getId(), - pdbEntry); + if (pdbEntry.getFile() != null) + { + entries.add(new CachedPDB(seq, pdbEntry)); + } } } } - tbl_local_pdb.setModel(tableModel); - } - /** - * Update the DBRef entry 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 updateSequenceDbRef(SequenceI seq, - Collection responseSummaries) - { - for (PDBResponseSummary response : responseSummaries) - { - PDBEntry newEntry = new PDBEntry(); - newEntry.setId(response.getPdbId()); - newEntry.setType("PDB"); - seq.getDatasetSequence().addPDBId(newEntry); - } + PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries); + tbl_local_pdb.setModel(tableModelx); } /** @@ -232,38 +234,99 @@ public class StructureChooser extends GStructureChooser public static String buildQuery(SequenceI seq) { - String query = seq.getName(); - StringBuilder queryBuilder = new StringBuilder(); - int count = 0; + 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()) { - queryBuilder.append("text:").append(entry.getId()).append(" OR "); + if (isValidSeqName(entry.getId())) + { + seqRefs.add(entry.getId()); + } } } if (seq.getDBRef() != null && seq.getDBRef().length != 0) { + int count = 0; for (DBRefEntry dbRef : seq.getDBRef()) { - queryBuilder.append("text:") - .append(dbRef.getAccessionId().replaceAll("GO:", "")) - .append(" OR "); + if (isValidSeqName(getDBRefId(dbRef))) + { + seqRefs.add(getDBRefId(dbRef)); + } ++count; if (count > 10) { break; } } - int endIndex = queryBuilder.lastIndexOf(" OR "); - query = queryBuilder.toString().substring(5, endIndex); } + + StringBuilder queryBuilder = new StringBuilder(); + for (String seqRef : seqRefs) + { + queryBuilder.append("text:").append(seqRef).append(" OR "); + } + int endIndex = queryBuilder.lastIndexOf(" OR "); + + if (queryBuilder.toString().length() < 6) + { + return null; + } + String query = queryBuilder.toString().substring(5, endIndex); return query; } /** + * Ensures sequence ref names are not less than 3 characters and does not + * contain a database name + * + * @param seqName + * @return + */ + public static boolean isValidSeqName(String seqName) + { + // System.out.println("seqName : " + seqName); + String ignoreList = "pdb,uniprot,swiss-prot"; + if (seqName.length() < 3) + { + return false; + } + if (seqName.contains(":")) + { + return false; + } + seqName = seqName.toLowerCase(); + for (String ignoredEntry : ignoreList.split(",")) + { + if (seqName.contains(ignoredEntry)) + { + return false; + } + } + return true; + } + + public static String getDBRefId(DBRefEntry dbRef) + { + String ref = dbRef.getAccessionId().replaceAll("GO:", ""); + return ref; + } + + /** * Filters a given list of discovered structures based on supplied argument * * @param fieldToFilterBy @@ -277,66 +340,84 @@ public class StructureChooser extends GStructureChooser public void run() { long startTime = System.currentTimeMillis(); - try + lbl_loading.setVisible(true); + Collection wantedFields = PDBDocFieldPreferences + .getStructureSummaryFields(); + Collection filteredResponse = new HashSet(); + HashSet errors = new HashSet(); + for (SequenceI seq : selectedSequences) { - lbl_loading.setVisible(true); - - Collection wantedFields = PDBDocFieldPreferences - .getStructureSummaryFields(); - Collection filteredResponse = 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; + try { - 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.getName()); - pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList = pdbRestCleint - .executeRequest(pdbRequest); - lastPdbRequest = pdbRequest; - if (resultList.getSearchSummary() != null - && !resultList.getSearchSummary().isEmpty()) - { - filteredResponse.addAll(resultList.getSearchSummary()); - } + resultList = pdbRestCleint.executeRequest(pdbRequest); + } catch (Exception e) + { + e.printStackTrace(); + errors.add(e.getMessage()); + continue; } - - if (!filteredResponse.isEmpty()) + lastPdbRequest = pdbRequest; + if (resultList.getSearchSummary() != null + && !resultList.getSearchSummary().isEmpty()) { - final int filterResponseCount = filteredResponse.size(); - Collection reorderedStructuresSet = new LinkedHashSet(); - reorderedStructuresSet.addAll(filteredResponse); - reorderedStructuresSet.addAll(discoveredStructuresSet); - tbl_summary.setModel(PDBRestResponse.getTableModel( - lastPdbRequest, reorderedStructuresSet)); - - // Update table selection model here - tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1); - + filteredResponse.addAll(resultList.getSearchSummary()); } + } - lbl_loading.setVisible(false); - String totalTime = (System.currentTimeMillis() - startTime) - + " milli secs"; - mainFrame.setTitle("Structure Chooser - Filter time (" - + totalTime + ")"); - - validateSelections(); - } catch (Exception e) + String totalTime = (System.currentTimeMillis() - startTime) + + " milli secs"; + if (!filteredResponse.isEmpty()) { - e.printStackTrace(); + final int filterResponseCount = filteredResponse.size(); + Collection reorderedStructuresSet = new LinkedHashSet(); + reorderedStructuresSet.addAll(filteredResponse); + reorderedStructuresSet.addAll(discoveredStructuresSet); + tbl_summary.setModel(PDBRestResponse.getTableModel( + lastPdbRequest, reorderedStructuresSet)); + + // Update table selection model here + tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1); + mainFrame.setTitle(MessageManager.formatMessage( + "label.structure_chooser_filter_time", totalTime)); } + else + { + mainFrame.setTitle(MessageManager.formatMessage( + "label.structure_chooser_filter_time", totalTime)); + if (errors.size() > 0) + { + StringBuilder errorMsg = new StringBuilder(); + for (String error : errors) + { + errorMsg.append(error).append("\n"); + } + JOptionPane.showMessageDialog( + null, + errorMsg.toString(), + MessageManager.getString("label.pdb_web-service_error"), + JOptionPane.ERROR_MESSAGE); + } + } + + lbl_loading.setVisible(false); + + validateSelections(); } }); filterThread.start(); } - /** * Handles action event for btn_pdbFromFile */ @@ -346,11 +427,11 @@ public class StructureChooser extends GStructureChooser 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) @@ -411,6 +492,8 @@ public class StructureChooser extends GStructureChooser else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID || selectedFilterOpt.getView() == VIEWS_FROM_FILE) { + mainFrame.setTitle(MessageManager + .getString("label.structure_chooser_manual_association")); idInputAssSeqPanel.loadCmbAssSeq(); fileChooserAssSeqPanel.loadCmbAssSeq(); } @@ -459,6 +542,22 @@ public class StructureChooser extends GStructureChooser AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel .getCmb_assSeq().getSelectedItem(); lbl_pdbManualFetchStatus.setIcon(errorImage); + lbl_pdbManualFetchStatus.setToolTipText(""); + if (txt_search.getText().length() > 0) + { + lbl_pdbManualFetchStatus + .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager + .formatMessage("info.no_pdb_entry_found_for", + txt_search.getText()))); + } + + if (errorWarning.length() > 0) + { + lbl_pdbManualFetchStatus.setIcon(warningImage); + lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip( + true, errorWarning.toString())); + } + if (selectedSequences.length == 1 || !assSeqOpt.getName().equalsIgnoreCase( "-Select Associated Seq-")) @@ -467,6 +566,7 @@ public class StructureChooser extends GStructureChooser if (isValidPBDEntry) { btn_view.setEnabled(true); + lbl_pdbManualFetchStatus.setToolTipText(""); lbl_pdbManualFetchStatus.setIcon(goodImage); } } @@ -486,8 +586,7 @@ 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); @@ -542,35 +641,59 @@ public class StructureChooser extends GStructureChooser String currentView = selectedFilterOpt.getView(); if (currentView == VIEWS_FILTER) { - int pdbIdCol = PDBRestClient.getPDBIdColumIndex( - lastPdbRequest.getWantedFields(), true); + 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; - for (int summaryRow : selectedRows) + ArrayList selectedSeqsToView = new ArrayList(); + for (int row : selectedRows) { - String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol) + String pdbIdStr = tbl_summary.getValueAt(row, pdbIdColIndex) .toString(); - PDBEntry pdbEntry = new PDBEntry(); - pdbEntry.setId(pdbIdStr); - pdbEntry.setType("PDB"); + SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(row, + refSeqColIndex); + selectedSeqsToView.add(selectedSeq); + 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, selectedSequences); + 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, 0).toString() + tbl_local_pdb.getValueAt(row, 1).toString(); - 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) { @@ -580,15 +703,20 @@ public class StructureChooser extends GStructureChooser { selectedSequence = userSelectedSeq; } - PDBEntry pdbEntry = new PDBEntry(); - pdbEntry.setId(txt_search.getText()); - pdbEntry.setType("PDB"); - selectedSequence.getDatasetSequence().addPDBId(pdbEntry); - PDBEntry[] pdbEntriesToView = new PDBEntry[] - { 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(ap.getStructureSelectionManager(), - pdbEntriesToView, ap, new SequenceI[] - { selectedSequence }); + pdbEntriesToView, ap, new SequenceI[] { selectedSequence }); } else if (currentView == VIEWS_FROM_FILE) { @@ -599,33 +727,42 @@ 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[] selectedSequences) + 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(alignPanel, pdbEntriesToView, - alignPanel.av.collateForPDB(pdbEntriesToView)); - } - else + final StructureViewer sViewer = new StructureViewer(ssm); + new Thread(new Runnable() { - sViewer.viewStructures(pdbEntriesToView[0], selectedSequences, null, - alignPanel); - } + 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(); } /** @@ -638,7 +775,6 @@ public class StructureChooser extends GStructureChooser 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) { @@ -675,27 +811,45 @@ public class StructureChooser extends GStructureChooser @Override protected void txt_search_ActionPerformed() { - 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.getName()); - pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest); - if (resultList.getSearchSummary() != null - && resultList.getSearchSummary().size() > 0) + public void run() { - isValidPBDEntry = true; + 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(); } - } - validateSelections(); + }.start(); } @Override @@ -717,4 +871,102 @@ 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; + } + + } }