X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=6e2ceff3f9c74f4d118cdbd3db5c3cfbc7240d29;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=f45681783825752683d153040a664df9171c3688;hpb=9e31b7ef69779d6d6a162b92900ee639d0f6cd95;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index f456817..6e2ceff 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 (2.9.0b1) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -39,7 +38,6 @@ 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 +45,7 @@ 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 +74,6 @@ public class StructureChooser extends GStructureChooser private boolean isValidPBDEntry; - private static Hashtable cachedEntryMap; - public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) { @@ -170,7 +165,6 @@ public class StructureChooser extends GStructureChooser && !resultList.getSearchSummary().isEmpty()) { discoveredStructuresSet.addAll(resultList.getSearchSummary()); - updateSequencePDBEntries(seq, resultList.getSearchSummary()); } } @@ -184,94 +178,49 @@ 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() - { - @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(); + 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(); - Object[] pdbEntryRowData = new Object[] - { seq, 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); } /** @@ -297,9 +246,9 @@ public class StructureChooser extends GStructureChooser } } - if (seq.getPDBId() != null) + if (seq.getAllPDBEntries() != null) { - for (PDBEntry entry : seq.getPDBId()) + for (PDBEntry entry : seq.getAllPDBEntries()) { if (isValidSeqName(entry.getId())) { @@ -331,6 +280,11 @@ 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; } @@ -433,14 +387,13 @@ 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(); @@ -448,8 +401,11 @@ 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); } } @@ -461,7 +417,6 @@ public class StructureChooser extends GStructureChooser filterThread.start(); } - /** * Handles action event for btn_pdbFromFile */ @@ -471,11 +426,11 @@ 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) @@ -536,7 +491,8 @@ 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(); } @@ -588,9 +544,10 @@ 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) @@ -628,8 +585,7 @@ 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); @@ -692,19 +648,20 @@ 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; } @@ -713,7 +670,8 @@ 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; @@ -724,11 +682,10 @@ public class StructureChooser extends GStructureChooser 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_summary.getValueAt(row, + PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row, + pdbIdColIndex); + pdbEntriesToView[count++] = pdbEntry; + SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row, refSeqColIndex); selectedSeqsToView.add(selectedSeq); } @@ -747,20 +704,18 @@ 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) { @@ -771,33 +726,42 @@ 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[] 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) + final StructureViewer sViewer = new StructureViewer(ssm); + new Thread(new Runnable() { - sViewer.viewStructures(pdbEntriesToView, alignPanel.av.collateForPDB(pdbEntriesToView), - alignPanel); - } - else - { - 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(); } /** @@ -810,7 +774,6 @@ 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) { @@ -847,39 +810,45 @@ 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 + 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 @@ -901,4 +870,102 @@ 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; + } + + } }