+/*
+
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
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.uimodel.PDBSearchRequest;
-import jalview.ws.uimodel.PDBSearchResponse;
-import jalview.ws.uimodel.PDBSummaryListModel;
-import jalview.ws.uimodel.PDBSummaryListModel.PDBDocField;
+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;
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.SwingUtilities;
+import javax.swing.table.DefaultTableModel;
+
+/**
+ * Provides the behaviors for the Structure chooser Panel
+ *
+ * @author tcnofoegbu
+ *
+ */
@SuppressWarnings("serial")
public class StructureChooser extends GStructureChooser
{
+ private boolean structuresDiscovered = false;
+
+ private SequenceI selectedSequence;
+
+ private SequenceI[] selectedSequences;
+
+ private IProgressIndicator progressIndicator;
+
+ private Collection<PDBResponseSummary> discoveredStructuresSet;
+
+ private PDBRestRequest lastPdbRequest;
+
+ private PDBRestClient pdbRestCleint;
+ private String selectedPdbFileName;
- private SequenceI sequence;
+ private boolean isValidPBDEntry;
+ private static Hashtable<String, PDBEntry> cachedEntryMap;
- public StructureChooser(AlignmentPanel ap, final SequenceI sequence)
+ public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
+ AlignmentPanel ap)
{
this.ap = ap;
- this.sequence = sequence;
- fetchStructures();
+ this.selectedSequence = selectedSeq;
+ this.selectedSequences = selectedSeqs;
+ this.progressIndicator = (ap == null) ? null : ap.alignFrame;
+ init();
}
- @Override
- public void ok_ActionPerformed()
+ /**
+ * Initializes parameters used by the Structure Chooser Panel
+ */
+ public void init()
{
- jListFoundStructures.setSelectedValue("op1x", true);
+ Thread discoverPDBStructuresThread = new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ long startTime = System.currentTimeMillis();
+ 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);
+ mainFrame.setVisible(true);
+ updateCurrentView();
+ }
+ });
+ discoverPDBStructuresThread.start();
}
- public void pdbFromFile_actionPerformed()
+ /**
+ * Updates the progress indicator with the specified message
+ *
+ * @param message
+ * displayed message for the operation
+ * @param id
+ * unique handle for this indicator
+ */
+ public void updateProgressIndicator(String message, long id)
{
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
- chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager.formatMessage(
- "label.select_pdb_file_for", new String[]
- { sequence.getDisplayId(false) }));
- chooser.setToolTipText(MessageManager.formatMessage(
- "label.load_pdb_file_associate_with_sequence", new String[]
- { sequence.getDisplayId(false) }));
+ if (progressIndicator != null)
+ {
+ progressIndicator.setProgressBar(message, id);
+ }
+ }
- int value = chooser.showOpenDialog(null);
+ /**
+ * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
+ * selection group
+ */
+ public void fetchStructuresMetaData()
+ {
+ long startTime = System.currentTimeMillis();
+ Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
+ .getStructureSummaryFields();
- if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+ discoveredStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+ HashSet<String> errors = new HashSet<String>();
+ for (SequenceI seq : selectedSequences)
{
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
- jalview.io.AppletFormatAdapter.FILE, sequence, true,
- Desktop.instance);
+ PDBRestRequest pdbRequest = new PDBRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(500);
+ pdbRequest.setFieldToSearchBy("(text:");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ pdbRequest.setAssociatedSequence(seq);
+ pdbRestCleint = new PDBRestClient();
+ 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());
+ updateSequencePDBEntries(seq, resultList.getSearchSummary());
+ }
}
+ int noOfStructuresFound = 0;
+ String totalTime = (System.currentTimeMillis() - startTime)
+ + " milli secs";
+ if (discoveredStructuresSet != null
+ && !discoveredStructuresSet.isEmpty())
+ {
+ tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest,
+ 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 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 discoverPDB_actionPerformed()
+ public void loadLocalCachedPDBEntries()
{
-
- final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
- { sequence }
- : ap.av.getSequenceSelection());
- Thread discpdb = new Thread(new Runnable()
+ DefaultTableModel tableModel = new DefaultTableModel()
{
@Override
- public void run()
+ 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<String, PDBEntry>();
+ for (SequenceI seq : selectedSequences)
+ {
+ if (seq.getDatasetSequence() != null
+ && seq.getDatasetSequence().getPDBId() != null)
+ {
+ for (PDBEntry pdbEntry : seq.getDatasetSequence().getPDBId())
+ {
- new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
- .fetchDBRefs(false);
+ 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);
+ }
- });
- discpdb.start();
+ /**
+ * 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<PDBResponseSummary> 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);
+ }
+ }
+
+ /**
+ * Builds a query string for a given sequences using its DBRef entries
+ *
+ * @param seq
+ * the sequences to build a query for
+ * @return the built query string
+ */
+
+ public static String buildQuery(SequenceI seq)
+ {
+ HashSet<String> seqRefs = new LinkedHashSet<String>();
+ 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 : seq.getPDBId())
+ {
+ if (isValidSeqName(entry.getId()))
+ {
+ seqRefs.add(entry.getId());
+ }
+ }
+ }
+
+ if (seq.getDBRef() != null && seq.getDBRef().length != 0)
+ {
+ int count = 0;
+ for (DBRefEntry dbRef : seq.getDBRef())
+ {
+ if (isValidSeqName(getDBRefId(dbRef)))
+ {
+ seqRefs.add(getDBRefId(dbRef));
+ }
+ ++count;
+ if (count > 10)
+ {
+ break;
+ }
+ }
+ }
+
+ 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;
}
- // rpdbview.addActionListener(new ActionListener()
- // {
- //
- // @Override
- // public void actionPerformed(ActionEvent e)
- // {
- // new StructureViewer(ap.getStructureSelectionManager())
- // .viewStructures(ap, pr, ap.av.collateForPDB(pr));
- // }
- // });
-
- public void enterPDB_actionPerformed()
+ /**
+ * 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)
{
- String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
- MessageManager.getString("label.enter_pdb_id"),
- MessageManager.getString("label.enter_pdb_id"),
- JOptionPane.QUESTION_MESSAGE);
- if (id != null && id.length() > 0)
+ // System.out.println("seqName : " + seqName);
+ String ignoreList = "pdb,uniprot,swiss-prot";
+ if (seqName.length() < 3)
+ {
+ return false;
+ }
+ if (seqName.contains(":"))
{
- PDBEntry entry = new PDBEntry();
- entry.setId(id.toUpperCase());
- sequence.getDatasetSequence().addPDBId(entry);
+ 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;
}
- public static void main(String[] args)
+ /**
+ * Filters a given list of discovered structures based on supplied argument
+ *
+ * @param fieldToFilterBy
+ * the field to filter by
+ */
+ public void filterResultSet(final String fieldToFilterBy)
{
- SwingUtilities.invokeLater(new Runnable()
+ Thread filterThread = new Thread(new Runnable()
{
+ @Override
public void run()
{
- new StructureChooser(null, null);
+ long startTime = System.currentTimeMillis();
+ lbl_loading.setVisible(true);
+ Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
+ .getStructureSummaryFields();
+ Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
+ HashSet<String> errors = new HashSet<String>();
+ 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
+ {
+ resultList = pdbRestCleint.executeRequest(pdbRequest);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ errors.add(e.getMessage());
+ continue;
+ }
+ lastPdbRequest = pdbRequest;
+ if (resultList.getSearchSummary() != null
+ && !resultList.getSearchSummary().isEmpty())
+ {
+ filteredResponse.addAll(resultList.getSearchSummary());
+ }
+ }
+
+ String totalTime = (System.currentTimeMillis() - startTime)
+ + " milli secs";
+ if (!filteredResponse.isEmpty())
+ {
+ final int filterResponseCount = filteredResponse.size();
+ Collection<PDBResponseSummary> reorderedStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+ 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("Structure Chooser - Filter time ("
+ + totalTime + ")");
+ }
+ else
+ {
+ 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();
+ }
+
+
+ /**
+ * Handles action event for btn_pdbFromFile
+ */
+ public void pdbFromFile_actionPerformed()
+ {
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
+ 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) }));
+ chooser.setToolTipText(MessageManager.formatMessage(
+ "label.load_pdb_file_associate_with_sequence", new String[]
+ { selectedSequence.getDisplayId(false) }));
+
+ int value = chooser.showOpenDialog(null);
+ if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+ {
+ selectedPdbFileName = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+ validateSelections();
+ }
}
- @SuppressWarnings("unchecked")
- protected void populateFilterOptions()
+ /**
+ * Populates the filter combo-box options dynamically depending on discovered
+ * structures
+ */
+ protected void populateFilterComboBox()
{
- filterOptions.addItem(new FilterOptions("- Filter Criteria -", "",
- VIEWS_AUTO));
- filterOptions.addItem(new FilterOptions("All", "all", VIEWS_AUTO));
- filterOptions
- .addItem(new FilterOptions("Best Coverage", "", VIEWS_AUTO));
- filterOptions.addItem(new FilterOptions("Best Resolution", "",
- VIEWS_AUTO));
- filterOptions
- .addItem(new FilterOptions("Best Quality", "", VIEWS_AUTO));
- filterOptions.addItem(new FilterOptions("Enter PDB Id", "", VIEWS_ID));
- filterOptions.addItem(new FilterOptions("From File", "", VIEWS_FILE));
+ if (isStructuresDiscovered())
+ {
+ cmb_filterOption.addItem(new FilterOption("Best Quality",
+ PDBDocField.OVERALL_QUALITY.getCode(), VIEWS_FILTER));
+ cmb_filterOption.addItem(new FilterOption("Best UniProt Coverage",
+ PDBDocField.UNIPROT_COVERAGE.getCode(), VIEWS_FILTER));
+ cmb_filterOption.addItem(new FilterOption("Highest Resolution",
+ PDBDocField.RESOLUTION.getCode(), VIEWS_FILTER));
+ cmb_filterOption.addItem(new FilterOption("Highest Protein Chain",
+ PDBDocField.PROTEIN_CHAIN_COUNT.getCode(), VIEWS_FILTER));
+ cmb_filterOption.addItem(new FilterOption("Highest Bound Molecules",
+ PDBDocField.BOUND_MOLECULE_COUNT.getCode(), VIEWS_FILTER));
+ cmb_filterOption.addItem(new FilterOption("Highest Polymer Residues",
+ PDBDocField.POLYMER_RESIDUE_COUNT.getCode(), VIEWS_FILTER));
+ }
+ cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-",
+ VIEWS_ENTER_ID));
+ cmb_filterOption.addItem(new FilterOption("From File", "-",
+ VIEWS_FROM_FILE));
+ cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-",
+ VIEWS_LOCAL_PDB));
}
+ /**
+ * Updates the displayed view based on the selected filter option
+ */
protected void updateCurrentView()
{
- String currentView = ((FilterOptions) filterOptions.getSelectedItem())
- .getView();
- switchableViewsLayout.show(switchableViewsPanel, currentView);
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ layout_switchableViews.show(pnl_switchableViews,
+ selectedFilterOpt.getView());
+ String filterTitle = mainFrame.getTitle();
+ mainFrame.setTitle(frameTitle);
+ chk_invertFilter.setVisible(false);
+ if (selectedFilterOpt.getView() == VIEWS_FILTER)
+ {
+ mainFrame.setTitle(filterTitle);
+ chk_invertFilter.setVisible(true);
+ filterResultSet(selectedFilterOpt.getValue());
+ }
+ else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
+ || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
+ {
+ mainFrame.setTitle(filterTitle);
+ idInputAssSeqPanel.loadCmbAssSeq();
+ fileChooserAssSeqPanel.loadCmbAssSeq();
+ }
+ validateSelections();
}
- private void fetchStructures()
+ /**
+ * Validates user selection and activates the view button if all parameters
+ * are correct
+ */
+ public void validateSelections()
{
- long startTime = System.currentTimeMillis();
- final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
- { sequence }
- : ap.av.getSequenceSelection());
- int foundStructures = 0;
- PDBSearchRequest request = new PDBSearchRequest();
- request.setAllowEmptySeq(false);
- request.setResponseSize(500);
- request.setSearchTarget("(text:");
- List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
- wantedFields.add(PDBDocField.MOLECULE_TYPE);
- wantedFields.add(PDBDocField.PDB_ID);
- wantedFields.add(PDBDocField.GENUS);
- wantedFields.add(PDBDocField.GENE_NAME);
- wantedFields.add(PDBDocField.TITLE);
- request.setWantedFields(wantedFields);
-
- Collection<PDBSummaryListModel> searchSummaries = new HashSet<PDBSummaryListModel>();
- // searchSummaries.
- for (SequenceI seq : sequences)
- {
- // System.out.println("Selected : " + seq.getName());
- request.setSearchTerm(buildQuery(seq) + ")");
-
- PDBRestClient pdbRestCleint = new PDBRestClient();
-
- PDBSearchResponse resultList = pdbRestCleint
- .executeRequest(request);
- if (resultList.getSearchSummary() != null
- && !resultList.getSearchSummary().isEmpty())
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ btn_view.setEnabled(false);
+ String currentView = selectedFilterOpt.getView();
+ if (currentView == VIEWS_FILTER)
+ {
+ if (tbl_summary.getSelectedRows().length > 0)
{
- searchSummaries.addAll(resultList.getSearchSummary());
+ 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();
+ }
+ else if (currentView == VIEWS_FROM_FILE)
+ {
+ validateAssociationFromFile();
+ }
+ }
- foundStructures = searchSummaries.size();
- if (searchSummaries != null)
+ /**
+ * Validates inputs from the Manual PDB entry panel
+ */
+ public void validateAssociationEnterPdb()
+ {
+ AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem();
+ lbl_pdbManualFetchStatus.setIcon(errorImage);
+ lbl_pdbManualFetchStatus.setToolTipText("");
+ if (txt_search.getText().length() > 0)
{
- jListFoundStructures.setModel(PDBSearchResponse
- .getListModel(searchSummaries));
+ lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
+ true, "No PDB entry found for \'" + txt_search.getText()
+ + "\'"));
}
- String totalTime = (System.currentTimeMillis() - startTime)
- + " milli secs";
- mainFrame.setTitle("Structure Chooser - " + foundStructures
- + " Found (" + totalTime + ")");
+ 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-"))
+ {
+ txt_search.setEnabled(true);
+ if (isValidPBDEntry)
+ {
+ btn_view.setEnabled(true);
+ lbl_pdbManualFetchStatus.setToolTipText("");
+ lbl_pdbManualFetchStatus.setIcon(goodImage);
+ }
+ }
+ else
+ {
+ txt_search.setEnabled(false);
+ lbl_pdbManualFetchStatus.setIcon(errorImage);
+ }
}
- private String buildQuery(SequenceI seq)
+ /**
+ * Validates inputs for the manual PDB file selection options
+ */
+ public void validateAssociationFromFile()
{
- String query = seq.getName();
- StringBuilder queryBuilder = new StringBuilder();
- int count = 0;
- if (seq.getDBRef() != null && seq.getDBRef().length != 0)
+ AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
+ .getCmb_assSeq().getSelectedItem();
+ lbl_fromFileStatus.setIcon(errorImage);
+ if (selectedSequences.length == 1
+ || (assSeqOpt != null
+ && !assSeqOpt.getName().equalsIgnoreCase(
+ "-Select Associated Seq-")))
{
- for (DBRefEntry dbRef : seq.getDBRef())
+ btn_pdbFromFile.setEnabled(true);
+ if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
{
- System.out.println("dbref : " + dbRef.getAccessionId());
- queryBuilder.append("text:").append(dbRef.getAccessionId())
- .append(" OR ");
- ++count;
- if (count > 10)
- {
- break;
- }
+ btn_view.setEnabled(true);
+ lbl_fromFileStatus.setIcon(goodImage);
}
- // int beginIndex = queryBuilder. firstIndexOf("text");
- int endIndex = queryBuilder.lastIndexOf(" OR ");
- query = queryBuilder.toString().substring(5, endIndex);
}
- System.out.println("------------> " + query);
- return query;
+ else
+ {
+ btn_pdbFromFile.setEnabled(false);
+ lbl_fromFileStatus.setIcon(errorImage);
+ }
}
- public class FilterOptions
+ @Override
+ public void cmbAssSeqStateChanged()
{
- private String name;
+ validateSelections();
+ }
- private String value;
+ /**
+ * Handles the state change event for the 'filter' combo-box and 'invert'
+ * check-box
+ */
+ @Override
+ protected void stateChanged(ItemEvent e)
+ {
+ if (e.getSource() instanceof JCheckBox)
+ {
+ updateCurrentView();
+ }
+ else
+ {
+ if (e.getStateChange() == ItemEvent.SELECTED)
+ {
+ updateCurrentView();
+ }
+ }
- private String view;
+ }
- public FilterOptions(String name, String value, String view)
+ /**
+ * Handles action event for btn_ok
+ */
+ @Override
+ public void ok_ActionPerformed()
+ {
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ String currentView = selectedFilterOpt.getView();
+ if (currentView == VIEWS_FILTER)
{
- this.name = name;
- this.value = value;
- this.view = view;
+ 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<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+ for (int summaryRow : selectedRows)
+ {
+ String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdColIndex)
+ .toString();
+ 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;
+ }
+ 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<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+ 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);
- public String getName()
- {
- return name;
+ }
+ SequenceI[] selectedSeqs = selectedSeqsToView
+ .toArray(new SequenceI[selectedSeqsToView.size()]);
+ launchStructureViewer(ap.getStructureSelectionManager(),
+ pdbEntriesToView, ap, selectedSeqs);
}
+ else if (currentView == VIEWS_ENTER_ID)
+ {
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ 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);
+ }
- public void setName(String name)
+ selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
+ PDBEntry[] pdbEntriesToView = new PDBEntry[]
+ { pdbEntry };
+ launchStructureViewer(ap.getStructureSelectionManager(),
+ pdbEntriesToView, ap, new SequenceI[]
+ { selectedSequence });
+ }
+ else if (currentView == VIEWS_FROM_FILE)
{
- this.name = name;
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ 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();
+ }
- public String getValue()
+ private void launchStructureViewer(StructureSelectionManager ssm,
+ PDBEntry[] pdbEntriesToView, AlignmentPanel alignPanel,
+ SequenceI[] sequences)
+ {
+ StructureViewer sViewer = new StructureViewer(ssm);
+ if (pdbEntriesToView.length > 1)
{
- return value;
+ ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
+ 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);
}
-
- public void setValue(String value)
+ else
{
- this.value = value;
+ sViewer.viewStructures(pdbEntriesToView[0], sequences,
+ alignPanel);
}
+ }
- public String getView()
+ /**
+ * Populates the combo-box used in associating manually fetched structures to
+ * a unique sequence when more than one sequence selection is made.
+ */
+ public void populateCmbAssociateSeqOptions(
+ JComboBox<AssociateSeqOptions> cmb_assSeq, JLabel lbl_associateSeq)
+ {
+ 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)
{
- return view;
+ for (SequenceI seq : selectedSequences)
+ {
+ cmb_assSeq.addItem(new AssociateSeqOptions(seq));
+ }
+ }
+ else
+ {
+ String seqName = selectedSequence.getDisplayId(false);
+ seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
+ lbl_associateSeq.setText(seqName);
+ lbl_associateSeq.setVisible(true);
+ cmb_assSeq.setVisible(false);
}
+ }
+
+ public boolean isStructuresDiscovered()
+ {
+ return structuresDiscovered;
+ }
- public void setView(String view)
+ public void setStructuresDiscovered(boolean structuresDiscovered)
+ {
+ this.structuresDiscovered = structuresDiscovered;
+ }
+
+ public Collection<PDBResponseSummary> getDiscoveredStructuresSet()
+ {
+ return discoveredStructuresSet;
+ }
+
+ @Override
+ protected void txt_search_ActionPerformed()
+ {
+ errorWarning.setLength(0);
+ isValidPBDEntry = false;
+ if (txt_search.getText().length() > 0)
{
- this.view = view;
+ List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
+ 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();
+ }
- public String toString()
+ @Override
+ public void tabRefresh()
+ {
+ if (selectedSequences != null)
{
- return this.name;
+ Thread refreshThread = new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ fetchStructuresMetaData();
+ filterResultSet(((FilterOption) cmb_filterOption
+ .getSelectedItem()).getValue());
+ }
+ });
+ refreshThread.start();
}
}
+
}
git://source.jalview.org / jalview.git / blobdiff