X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=2e3b37ab56bc29b704a629cf60a22b4d5cb97583;hb=fd1c6fd67abdd50ff0d77410d3da9be66be315ce;hp=cd4faf62f691dcba35feb23e7b5dbbe0b79b2fe2;hpb=c9764f63ef34188eee34d2a6958efdc3d2f74e71;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index cd4faf6..2e3b37a 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -22,19 +22,6 @@ package jalview.gui; -import jalview.datamodel.DBRefEntry; -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; -import jalview.ws.uimodel.PDBRestRequest; -import jalview.ws.uimodel.PDBRestResponse; -import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary; - import java.awt.event.ItemEvent; import java.util.ArrayList; import java.util.Collection; @@ -46,8 +33,22 @@ import java.util.List; import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JLabel; +import javax.swing.JOptionPane; import javax.swing.table.DefaultTableModel; +import jalview.datamodel.DBRefEntry; +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; +import jalview.ws.uimodel.PDBRestRequest; +import jalview.ws.uimodel.PDBRestResponse; +import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary; + /** * Provides the behaviors for the Structure chooser Panel @@ -99,9 +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); @@ -139,6 +144,7 @@ public class StructureChooser extends GStructureChooser .getStructureSummaryFields(); discoveredStructuresSet = new LinkedHashSet(); + HashSet errors = new HashSet(); for (SequenceI seq : selectedSequences) { PDBRestRequest pdbRequest = new PDBRestRequest(); @@ -149,17 +155,27 @@ public class StructureChooser extends GStructureChooser pdbRequest.setSearchTerm(buildQuery(seq) + ")"); pdbRequest.setAssociatedSequence(seq.getName()); pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest); + PDBRestResponse resultList; + try + { + resultList = pdbRestCleint.executeRequest(pdbRequest); + } catch (Exception e) + { + 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()) { @@ -167,11 +183,25 @@ public class StructureChooser extends GStructureChooser discoveredStructuresSet)); structuresDiscovered = true; noOfStructuresFound = discoveredStructuresSet.size(); + mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound + + " Found (" + totalTime + ")"); + } + else + { + mainFrame +.setTitle("Structure Chooser - Manual association"); + if (errors.size() > 0) + { + StringBuilder errorMsg = new StringBuilder(); + // "Operation was unsucessful 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); + } } - String totalTime = (System.currentTimeMillis() - startTime) - + " milli secs"; - mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound - + " Found (" + totalTime + ")"); } public void loadLocalCachedPDBEntries() @@ -179,6 +209,7 @@ public class StructureChooser extends GStructureChooser DefaultTableModel tableModel = new DefaultTableModel(); tableModel.addColumn("Sequence"); tableModel.addColumn("PDB Id"); + tableModel.addColumn("Chain"); tableModel.addColumn("Type"); tableModel.addColumn("File"); cachedEntryMap = new Hashtable(); @@ -189,11 +220,19 @@ public class StructureChooser extends GStructureChooser { for (PDBEntry pdbEntry : seq.getDatasetSequence().getPDBId()) { + + String chain = pdbEntry.getChainCode() == null ? "_" : pdbEntry + .getChainCode(); String[] pdbEntryRowData = new String[] - { seq.getDisplayId(false), pdbEntry.getId(), pdbEntry.getType(), + { seq.getDisplayId(false), pdbEntry.getId(), + chain, + pdbEntry.getType(), pdbEntry.getFile() }; - tableModel.addRow(pdbEntryRowData); - cachedEntryMap.put(seq.getDisplayId(false) + pdbEntry.getId(), + if (pdbEntry.getFile() != null) + { + tableModel.addRow(pdbEntryRowData); + } + cachedEntryMap.put(pdbEntry.getId().toLowerCase(), pdbEntry); } } @@ -202,7 +241,7 @@ public class StructureChooser extends GStructureChooser } /** - * 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 @@ -210,15 +249,20 @@ 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); } } @@ -321,60 +365,76 @@ 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.getName()); + 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) + { + 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)); + filteredResponse.addAll(resultList.getSearchSummary()); + } + } - // Update table selection model here - tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1); + 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(); @@ -455,6 +515,7 @@ public class StructureChooser extends GStructureChooser else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID || selectedFilterOpt.getView() == VIEWS_FROM_FILE) { + mainFrame.setTitle(filterTitle); idInputAssSeqPanel.loadCmbAssSeq(); fileChooserAssSeqPanel.loadCmbAssSeq(); } @@ -503,6 +564,21 @@ 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-")) @@ -511,6 +587,7 @@ public class StructureChooser extends GStructureChooser if (isValidPBDEntry) { btn_view.setEnabled(true); + lbl_pdbManualFetchStatus.setToolTipText(""); lbl_pdbManualFetchStatus.setIcon(goodImage); } } @@ -595,12 +672,16 @@ public class StructureChooser extends GStructureChooser { String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol) .toString(); - PDBEntry pdbEntry = new PDBEntry(); - pdbEntry.setId(pdbIdStr); - pdbEntry.setType("PDB"); + + PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase()); + if (pdbEntry == null) + { + pdbEntry = new PDBEntry(); + pdbEntry.setId(pdbIdStr); + pdbEntry.setType(PDBEntry.Type.PDB); + } pdbEntriesToView[count++] = pdbEntry; } - launchStructureViewer(ap.getStructureSelectionManager(), pdbEntriesToView, ap, selectedSequences); } @@ -610,7 +691,8 @@ public class StructureChooser extends GStructureChooser int count = 0; for (int row : selectedRows) { - String entryKey = tbl_local_pdb.getValueAt(row, 0).toString() + tbl_local_pdb.getValueAt(row, 1).toString(); + String entryKey = tbl_local_pdb.getValueAt(row, 1).toString() + .toLowerCase(); pdbEntriesToView[count++] = cachedEntryMap.get(entryKey); } launchStructureViewer(ap.getStructureSelectionManager(), @@ -624,9 +706,16 @@ public class StructureChooser extends GStructureChooser { selectedSequence = userSelectedSeq; } - PDBEntry pdbEntry = new PDBEntry(); - pdbEntry.setId(txt_search.getText()); - pdbEntry.setType("PDB"); + + 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 }; @@ -657,17 +746,17 @@ public class StructureChooser extends GStructureChooser private void launchStructureViewer(StructureSelectionManager ssm, PDBEntry[] pdbEntriesToView, AlignmentPanel alignPanel, - SequenceI[] selectedSequences) + SequenceI[] sequences) { StructureViewer sViewer = new StructureViewer(ssm); if (pdbEntriesToView.length > 1) { - sViewer.viewStructures(alignPanel, pdbEntriesToView, - alignPanel.av.collateForPDB(pdbEntriesToView)); + sViewer.viewStructures(pdbEntriesToView, alignPanel.av.collateForPDB(pdbEntriesToView), + alignPanel); } else { - sViewer.viewStructures(pdbEntriesToView[0], selectedSequences, null, + sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); } } @@ -719,6 +808,7 @@ public class StructureChooser extends GStructureChooser @Override protected void txt_search_ActionPerformed() { + errorWarning.setLength(0); isValidPBDEntry = false; if (txt_search.getText().length() > 0) { @@ -732,7 +822,18 @@ public class StructureChooser extends GStructureChooser pdbRequest.setSearchTerm(txt_search.getText() + ")"); pdbRequest.setAssociatedSequence(selectedSequence.getName()); 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) {