X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=976b77b9c89227e3995c2a4cd095e2802729cfef;hb=7a1a7eea9501cd9e3841e996f4926cf1686be76a;hp=35c5791176f96f977c471fca96abf101d5ab2d4a;hpb=5dc62d509b6d0f90f3545bf40b272390410eda45;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 35c5791..976b77b 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -27,6 +27,7 @@ import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.jbgui.GStructureChooser; import jalview.jbgui.PDBDocFieldPreferences; +import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; import jalview.ws.dbsources.PDBRestClient; import jalview.ws.dbsources.PDBRestClient.PDBDocField; @@ -38,13 +39,16 @@ 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 java.util.Vector; import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JLabel; +import javax.swing.JOptionPane; +import javax.swing.table.DefaultTableModel; + /** * Provides the behaviors for the Structure chooser Panel @@ -73,6 +77,8 @@ public class StructureChooser extends GStructureChooser private boolean isValidPBDEntry; + private static Hashtable cachedEntryMap; + public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) { @@ -94,8 +100,13 @@ 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); @@ -133,6 +144,7 @@ public class StructureChooser extends GStructureChooser .getStructureSummaryFields(); discoveredStructuresSet = new LinkedHashSet(); + HashSet errors = new HashSet(); for (SequenceI seq : selectedSequences) { PDBRestRequest pdbRequest = new PDBRestRequest(); @@ -141,19 +153,30 @@ 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()); + updateSequencePDBEntries(seq, resultList.getSearchSummary()); } } int noOfStructuresFound = 0; + String totalTime = (System.currentTimeMillis() - startTime) + + " milli secs"; if (discoveredStructuresSet != null && !discoveredStructuresSet.isEmpty()) { @@ -161,15 +184,72 @@ public class StructureChooser extends GStructureChooser discoveredStructuresSet)); structuresDiscovered = true; noOfStructuresFound = discoveredStructuresSet.size(); + mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound + + " Found (" + totalTime + ")"); } - String totalTime = (System.currentTimeMillis() - startTime) - + " milli secs"; - mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound - + " Found (" + totalTime + ")"); + else + { + mainFrame +.setTitle("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); + } + } + } + + 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(); + for (SequenceI seq : selectedSequences) + { + if (seq.getDatasetSequence() != null + && seq.getDatasetSequence().getPDBId() != null) + { + for (PDBEntry pdbEntry : seq.getDatasetSequence().getPDBId()) + { + + 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); + } + cachedEntryMap.put(pdbEntry.getId().toLowerCase(), + pdbEntry); + } + } + } + tbl_local_pdb.setModel(tableModel); } /** - * Update the DBRef entry for a given sequence with values retrieved from + * Update the PDBEntry for a given sequence with values retrieved from * PDBResponseSummary * * @param seq @@ -177,15 +257,20 @@ public class StructureChooser extends GStructureChooser * @param responseSummaries * a collection of PDBResponseSummary */ - public void updateSequenceDbRef(SequenceI seq, + public void updateSequencePDBEntries(SequenceI seq, Collection responseSummaries) { for (PDBResponseSummary response : responseSummaries) { - PDBEntry newEntry = new PDBEntry(); - newEntry.setId(response.getPdbId()); - newEntry.setType("PDB"); - seq.getDatasetSequence().addPDBId(newEntry); + 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); } } @@ -196,41 +281,97 @@ public class StructureChooser extends GStructureChooser * the sequences to build a query for * @return the built query string */ - @SuppressWarnings("unchecked") + 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) { - for (PDBEntry entry : (Vector) seq.getPDBId()) + for (PDBEntry entry : seq.getPDBId()) { - 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 "); + 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 @@ -238,156 +379,83 @@ public class StructureChooser extends GStructureChooser */ public void filterResultSet(final String fieldToFilterBy) { - - // SwingWorker aWorker = new SwingWorker() - // { - // long startTime = System.currentTimeMillis(); - // - // @Override - // protected Object doInBackground() throws Exception - // { - // 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.getName()); - // pdbRestCleint = new PDBRestClient(); - // PDBRestResponse resultList = pdbRestCleint - // .executeRequest(pdbRequest); - // lastPdbRequest = pdbRequest; - // if (resultList.getSearchSummary() != null - // && !resultList.getSearchSummary().isEmpty()) - // { - // filteredResponse.addAll(resultList.getSearchSummary()); - // } - // } - // - // if (!filteredResponse.isEmpty()) - // { - // final int filterResponseCount = filteredResponse.size(); - // Collection reorderedStructuresSet = new - // LinkedHashSet(); - // reorderedStructuresSet.addAll(filteredResponse); - // reorderedStructuresSet.addAll(discoveredStructuresSet); - // tbl_summary.setModel(PDBRestResponse.getTableModel( - // lastPdbRequest, reorderedStructuresSet)); - // - // // Update the model here - // // ListSelectionModel model = tbl_summary.getSelectionModel(); - // // model.clearSelection(); - // // model.addSelectionInterval(0, filterResponseCount - 1); - // // EventQueue.invokeLater(new Runnable() - // // { - // // public void run() - // // { - // // tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1); - // - // // } - // // }); - // // Discard unwanted objects to make them eligible for garbage - // // collection - // reorderedStructuresSet = null; - // } - // return null; - // } - // - // public void done() - // { - // lbl_loading.setVisible(false); - // tbl_summary.addRowSelectionInterval(0, 2); - // String totalTime = (System.currentTimeMillis() - startTime) - // + " milli secs"; - // mainFrame.setTitle("Structure Chooser - Filter time (" + totalTime - // + ")"); - // validateSelections(); - // } - // }; - // aWorker.execute(); - Thread filterThread = new Thread(new Runnable() { @Override 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 the model here - // ListSelectionModel model = tbl_summary.getSelectionModel(); - // model.clearSelection(); - // model.addSelectionInterval(0, filterResponseCount - 1); - // EventQueue.invokeLater(new Runnable() - // { - // public void run() - // { - tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1); - - // } - // }); - // Discard unwanted objects to make them eligible for garbage - // collection - reorderedStructuresSet = null; + filteredResponse.addAll(resultList.getSearchSummary()); } + } + + String totalTime = (System.currentTimeMillis() - startTime) + + " milli secs"; + if (!filteredResponse.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); - lbl_loading.setVisible(false); - String totalTime = (System.currentTimeMillis() - startTime) - + " milli secs"; mainFrame.setTitle("Structure Chooser - Filter time (" + totalTime + ")"); - - validateSelections(); - } catch (Exception e) + } + else { - e.printStackTrace(); + mainFrame.setTitle("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(), + "PDB Web-service Error", JOptionPane.ERROR_MESSAGE); + } } + + lbl_loading.setVisible(false); + + validateSelections(); } }); filterThread.start(); @@ -443,6 +511,8 @@ public class StructureChooser extends GStructureChooser VIEWS_ENTER_ID)); cmb_filterOption.addItem(new FilterOption("From File", "-", VIEWS_FROM_FILE)); + cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-", + VIEWS_LOCAL_PDB)); } /** @@ -463,8 +533,10 @@ public class StructureChooser extends GStructureChooser chk_invertFilter.setVisible(true); filterResultSet(selectedFilterOpt.getValue()); } - else + else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID + || selectedFilterOpt.getView() == VIEWS_FROM_FILE) { + mainFrame.setTitle(filterTitle); idInputAssSeqPanel.loadCmbAssSeq(); fileChooserAssSeqPanel.loadCmbAssSeq(); } @@ -488,6 +560,13 @@ public class StructureChooser extends GStructureChooser btn_view.setEnabled(true); } } + else if (currentView == VIEWS_LOCAL_PDB) + { + if (tbl_local_pdb.getSelectedRows().length > 0) + { + btn_view.setEnabled(true); + } + } else if (currentView == VIEWS_ENTER_ID) { validateAssociationEnterPdb(); @@ -506,6 +585,21 @@ 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, "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-")) @@ -514,6 +608,7 @@ public class StructureChooser extends GStructureChooser if (isValidPBDEntry) { btn_view.setEnabled(true); + lbl_pdbManualFetchStatus.setToolTipText(""); lbl_pdbManualFetchStatus.setIcon(goodImage); } } @@ -589,49 +684,133 @@ 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; + ArrayList selectedSeqsToView = new ArrayList(); for (int summaryRow : selectedRows) { - String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol) + String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdColIndex) .toString(); - PDBEntry pdbEntry = new PDBEntry(); - pdbEntry.setId(pdbIdStr); - pdbEntry.setType("PDB"); + SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt( + summaryRow, refSeqColIndex); + selectedSeqsToView.add(selectedSeq); + PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase()); + if (pdbEntry == null) + { + pdbEntry = new PDBEntry(); + pdbEntry.setId(pdbIdStr); + pdbEntry.setType(PDBEntry.Type.PDB); + } pdbEntriesToView[count++] = pdbEntry; } - new StructureViewer(ap.getStructureSelectionManager()) - .viewStructures(ap, pdbEntriesToView, - ap.av.collateForPDB(pdbEntriesToView)); + 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) + { + String entryKey = tbl_local_pdb.getValueAt(row, pdbIdColIndex) + .toString() + .toLowerCase(); + pdbEntriesToView[count++] = cachedEntryMap.get(entryKey); + 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) { - selectedSequence = ((AssociateSeqOptions) idInputAssSeqPanel + SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel .getCmb_assSeq().getSelectedItem()).getSequence(); - PDBEntry pdbEntry = new PDBEntry(); - pdbEntry.setId(txt_search.getText()); - pdbEntry.setType("PDB"); + if (userSelectedSeq != null) + { + selectedSequence = userSelectedSeq; + } + + String pdbIdStr = txt_search.getText(); + PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase()); + if (pdbEntry == null) + { + pdbEntry = new PDBEntry(); + pdbEntry.setId(txt_search.getText()); + pdbEntry.setType(PDBEntry.Type.PDB); + } + selectedSequence.getDatasetSequence().addPDBId(pdbEntry); PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; - new StructureViewer(ap.getStructureSelectionManager()) - .viewStructures(ap, pdbEntriesToView, - ap.av.collateForPDB(pdbEntriesToView)); + launchStructureViewer(ap.getStructureSelectionManager(), + pdbEntriesToView, ap, new SequenceI[] + { selectedSequence }); } else if (currentView == VIEWS_FROM_FILE) { - selectedSequence = ((AssociateSeqOptions) fileChooserAssSeqPanel + SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel .getCmb_assSeq().getSelectedItem()).getSequence(); - new AssociatePdbFileWithSeq().associatePdbWithSeq( + if (userSelectedSeq != null) + { + selectedSequence = userSelectedSeq; + } + 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(); } + private void launchStructureViewer(StructureSelectionManager ssm, + PDBEntry[] pdbEntriesToView, AlignmentPanel alignPanel, + SequenceI[] sequences) + { + StructureViewer sViewer = new StructureViewer(ssm); + 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); + // sViewer.viewStructures(pdbEntriesToView, + // alignPanel.av.collateForPDB(pdbEntriesToView), + // alignPanel); + } + else + { + sViewer.viewStructures(pdbEntriesToView[0], sequences, + alignPanel); + } + } + /** * Populates the combo-box used in associating manually fetched structures to * a unique sequence when more than one sequence selection is made. @@ -679,6 +858,7 @@ public class StructureChooser extends GStructureChooser @Override protected void txt_search_ActionPerformed() { + errorWarning.setLength(0); isValidPBDEntry = false; if (txt_search.getText().length() > 0) { @@ -690,9 +870,20 @@ public class StructureChooser extends GStructureChooser pdbRequest.setFieldToSearchBy("(pdb_id:"); pdbRequest.setWantedFields(wantedFields); pdbRequest.setSearchTerm(txt_search.getText() + ")"); - pdbRequest.setAssociatedSequence(selectedSequence.getName()); + pdbRequest.setAssociatedSequence(selectedSequence); pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest); + 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) {