X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;fp=src%2Fjalview%2Fgui%2FStructureChooser.java;h=510ce782e83017a02a2f2ab6a74c768c57e339e4;hb=f06554784411ddbf871d642e66c8dcb7f147d4a8;hp=2e3b37ab56bc29b704a629cf60a22b4d5cb97583;hpb=cf06ee5d732af6cc874115aece1138adafca8ad7;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 2e3b37a..510ce78 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -22,20 +22,6 @@ package jalview.gui; -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.JOptionPane; -import javax.swing.table.DefaultTableModel; - import jalview.datamodel.DBRefEntry; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; @@ -49,6 +35,18 @@ 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; +import java.util.HashSet; +import java.util.LinkedHashSet; +import java.util.List; + +import javax.swing.JCheckBox; +import javax.swing.JComboBox; +import javax.swing.JLabel; +import javax.swing.JOptionPane; +import javax.swing.table.AbstractTableModel; /** * Provides the behaviors for the Structure chooser Panel @@ -77,7 +75,6 @@ public class StructureChooser extends GStructureChooser private boolean isValidPBDEntry; - private static Hashtable cachedEntryMap; public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) @@ -153,7 +150,7 @@ 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; try @@ -161,6 +158,7 @@ public class StructureChooser extends GStructureChooser resultList = pdbRestCleint.executeRequest(pdbRequest); } catch (Exception e) { + e.printStackTrace(); errors.add(e.getMessage()); continue; } @@ -169,7 +167,6 @@ public class StructureChooser extends GStructureChooser && !resultList.getSearchSummary().isEmpty()) { discoveredStructuresSet.addAll(resultList.getSearchSummary()); - updateSequencePDBEntries(seq, resultList.getSearchSummary()); } } @@ -183,89 +180,51 @@ 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 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); + 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); } + /** * Builds a query string for a given sequences using its DBRef entries * @@ -289,11 +248,14 @@ public class StructureChooser extends GStructureChooser } } - if (seq.getPDBId() != null) + if (seq.getAllPDBEntries() != null) { - for (PDBEntry entry : seq.getPDBId()) + for (PDBEntry entry : seq.getAllPDBEntries()) { - seqRefs.add(entry.getId()); + if (isValidSeqName(entry.getId())) + { + seqRefs.add(entry.getId()); + } } } @@ -302,7 +264,10 @@ public class StructureChooser extends GStructureChooser int count = 0; for (DBRefEntry dbRef : seq.getDBRef()) { - seqRefs.add(getDBRefId(dbRef)); + if (isValidSeqName(getDBRefId(dbRef))) + { + seqRefs.add(getDBRefId(dbRef)); + } ++count; if (count > 10) { @@ -317,6 +282,11 @@ public class StructureChooser extends GStructureChooser 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; } @@ -330,14 +300,20 @@ public class StructureChooser extends GStructureChooser */ public static boolean isValidSeqName(String seqName) { - String ignoreList = "pdb,uniprot"; + // 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.equalsIgnoreCase(ignoredEntry)) + if (seqName.contains(ignoredEntry)) { return false; } @@ -380,7 +356,7 @@ public class StructureChooser extends GStructureChooser !chk_invertFilter.isSelected()); pdbRequest.setSearchTerm(buildQuery(seq) + ")"); pdbRequest.setWantedFields(wantedFields); - pdbRequest.setAssociatedSequence(seq.getName()); + pdbRequest.setAssociatedSequence(seq); pdbRestCleint = new PDBRestClient(); PDBRestResponse resultList; try @@ -388,6 +364,7 @@ public class StructureChooser extends GStructureChooser resultList = pdbRestCleint.executeRequest(pdbRequest); } catch (Exception e) { + e.printStackTrace(); errors.add(e.getMessage()); continue; } @@ -412,14 +389,15 @@ 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(); @@ -428,7 +406,8 @@ public class StructureChooser extends GStructureChooser errorMsg.append(error).append("\n"); } JOptionPane.showMessageDialog(null, errorMsg.toString(), - "PDB Web-service Error", JOptionPane.ERROR_MESSAGE); + MessageManager.getString("label.pdb_web-service_error"), + JOptionPane.ERROR_MESSAGE); } } @@ -440,7 +419,6 @@ public class StructureChooser extends GStructureChooser filterThread.start(); } - /** * Handles action event for btn_pdbFromFile */ @@ -450,11 +428,11 @@ 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) @@ -515,7 +493,8 @@ 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(); } @@ -568,8 +547,9 @@ public class StructureChooser extends GStructureChooser if (txt_search.getText().length() > 0) { lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip( - true, "No PDB entry found for \'" + txt_search.getText() - + "\'")); + true, MessageManager.formatMessage( + "info.no_pdb_entry_found_for", + txt_search.getText()))); } if (errorWarning.length() > 0) @@ -607,8 +587,7 @@ 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); @@ -663,40 +642,59 @@ 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 = cachedEntryMap.get(pdbIdStr.toLowerCase()); + 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, 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) { @@ -708,15 +706,15 @@ 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(), @@ -732,9 +730,9 @@ 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[] @@ -744,21 +742,32 @@ public class StructureChooser extends GStructureChooser 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); - } + 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(); } /** @@ -771,7 +780,6 @@ 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) { @@ -808,6 +816,10 @@ public class StructureChooser extends GStructureChooser @Override protected void txt_search_ActionPerformed() { + new Thread() + { + public void run() + { errorWarning.setLength(0); isValidPBDEntry = false; if (txt_search.getText().length() > 0) @@ -820,7 +832,7 @@ 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; try @@ -841,6 +853,8 @@ public class StructureChooser extends GStructureChooser } } validateSelections(); + } + }.start(); } @Override @@ -862,4 +876,103 @@ 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; + } + + } }