/*
* 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 .
* 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.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;
import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Vector;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JLabel;
/**
* 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 discoveredStructuresSet;
private PDBRestRequest lastPdbRequest;
private PDBRestClient pdbRestCleint;
private String selectedPdbFileName;
private boolean isValidPBDEntry;
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
{
this.ap = ap;
this.selectedSequence = selectedSeq;
this.selectedSequences = selectedSeqs;
this.progressIndicator = (ap == null) ? null : ap.alignFrame;
init();
}
/**
* Initializes parameters used by the Structure Chooser Panel
*/
public void init()
{
Thread discoverPDBStructuresThread = new Thread(new Runnable()
{
@Override
public void run()
{
long startTime = System.currentTimeMillis();
String msg = MessageManager.getString("status.fetching_db_refs");
updateProgressIndicator(msg, startTime);
fetchStructuresMetaData();
populateFilterComboBox();
updateProgressIndicator(null, startTime);
mainFrame.setVisible(true);
updateCurrentView();
}
});
discoverPDBStructuresThread.start();
}
/**
* 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)
{
if (progressIndicator != null)
{
progressIndicator.setProgressBar(message, id);
}
}
/**
* 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 wantedFields = PDBDocFieldPreferences
.getStructureSummaryFields();
discoveredStructuresSet = new LinkedHashSet();
for (SequenceI seq : selectedSequences)
{
PDBRestRequest pdbRequest = new PDBRestRequest();
pdbRequest.setAllowEmptySeq(false);
pdbRequest.setResponseSize(500);
pdbRequest.setFieldToSearchBy("(text:");
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setSearchTerm(buildQuery(seq) + ")");
pdbRequest.setAssociatedSequence(seq.getName());
pdbRestCleint = new PDBRestClient();
PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
lastPdbRequest = pdbRequest;
if (resultList.getSearchSummary() != null
&& !resultList.getSearchSummary().isEmpty())
{
discoveredStructuresSet.addAll(resultList.getSearchSummary());
updateSequenceDbRef(seq, resultList.getSearchSummary());
}
}
int noOfStructuresFound = 0;
if (discoveredStructuresSet != null
&& !discoveredStructuresSet.isEmpty())
{
tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest,
discoveredStructuresSet));
structuresDiscovered = true;
noOfStructuresFound = discoveredStructuresSet.size();
}
String totalTime = (System.currentTimeMillis() - startTime)
+ " milli secs";
mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound
+ " Found (" + totalTime + ")");
}
/**
* Update the DBRef entry 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 updateSequenceDbRef(SequenceI seq,
Collection responseSummaries)
{
for (PDBResponseSummary response : responseSummaries)
{
PDBEntry newEntry = new PDBEntry();
newEntry.setId(response.getPdbId());
newEntry.setType("PDB");
seq.getDatasetSequence().addPDBId(newEntry);
}
}
/**
* 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
*/
@SuppressWarnings("unchecked")
public static String buildQuery(SequenceI seq)
{
String query = seq.getName();
StringBuilder queryBuilder = new StringBuilder();
int count = 0;
if (seq.getPDBId() != null)
{
for (PDBEntry entry : (Vector) seq.getPDBId())
{
queryBuilder.append("text:").append(entry.getId()).append(" OR ");
}
}
if (seq.getDBRef() != null && seq.getDBRef().length != 0)
{
for (DBRefEntry dbRef : seq.getDBRef())
{
queryBuilder.append("text:")
.append(dbRef.getAccessionId().replaceAll("GO:", ""))
.append(" OR ");
++count;
if (count > 10)
{
break;
}
}
int endIndex = queryBuilder.lastIndexOf(" OR ");
query = queryBuilder.toString().substring(5, endIndex);
}
return query;
}
/**
* Filters a given list of discovered structures based on supplied argument
*
* @param fieldToFilterBy
* the field to filter by
*/
public void filterResultSet(final String fieldToFilterBy)
{
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();
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 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)
{
e.printStackTrace();
}
}
});
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();
}
}
/**
* Populates the filter combo-box options dynamically depending on discovered
* structures
*/
protected void populateFilterComboBox()
{
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));
}
/**
* Updates the displayed view based on the selected filter option
*/
protected void updateCurrentView()
{
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
{
idInputAssSeqPanel.loadCmbAssSeq();
fileChooserAssSeqPanel.loadCmbAssSeq();
}
validateSelections();
}
/**
* Validates user selection and activates the view button if all parameters
* are correct
*/
public void validateSelections()
{
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
.getSelectedItem());
btn_view.setEnabled(false);
String currentView = selectedFilterOpt.getView();
if (currentView == VIEWS_FILTER)
{
if (tbl_summary.getSelectedRows().length > 0)
{
btn_view.setEnabled(true);
}
}
else if (currentView == VIEWS_ENTER_ID)
{
validateAssociationEnterPdb();
}
else if (currentView == VIEWS_FROM_FILE)
{
validateAssociationFromFile();
}
}
/**
* Validates inputs from the Manual PDB entry panel
*/
public void validateAssociationEnterPdb()
{
AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
.getCmb_assSeq().getSelectedItem();
lbl_pdbManualFetchStatus.setIcon(errorImage);
if (selectedSequences.length == 1
|| !assSeqOpt.getName().equalsIgnoreCase(
"-Select Associated Seq-"))
{
txt_search.setEnabled(true);
if (isValidPBDEntry)
{
btn_view.setEnabled(true);
lbl_pdbManualFetchStatus.setIcon(goodImage);
}
}
else
{
txt_search.setEnabled(false);
lbl_pdbManualFetchStatus.setIcon(errorImage);
}
}
/**
* Validates inputs for the manual PDB file selection options
*/
public void validateAssociationFromFile()
{
AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
.getCmb_assSeq().getSelectedItem();
lbl_fromFileStatus.setIcon(errorImage);
if (selectedSequences.length == 1
|| (assSeqOpt != null
&& !assSeqOpt.getName().equalsIgnoreCase(
"-Select Associated Seq-")))
{
btn_pdbFromFile.setEnabled(true);
if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
{
btn_view.setEnabled(true);
lbl_fromFileStatus.setIcon(goodImage);
}
}
else
{
btn_pdbFromFile.setEnabled(false);
lbl_fromFileStatus.setIcon(errorImage);
}
}
@Override
public void cmbAssSeqStateChanged()
{
validateSelections();
}
/**
* 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();
}
}
}
/**
* 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)
{
int pdbIdCol = PDBRestClient.getPDBIdColumIndex(
lastPdbRequest.getWantedFields(), true);
int[] selectedRows = tbl_summary.getSelectedRows();
PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
int count = 0;
for (int summaryRow : selectedRows)
{
String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
.toString();
PDBEntry pdbEntry = new PDBEntry();
pdbEntry.setId(pdbIdStr);
pdbEntry.setType("PDB");
pdbEntriesToView[count++] = pdbEntry;
}
new StructureViewer(ap.getStructureSelectionManager())
.viewStructures(ap, pdbEntriesToView,
ap.av.collateForPDB(pdbEntriesToView));
}
else if (currentView == VIEWS_ENTER_ID)
{
selectedSequence = ((AssociateSeqOptions) idInputAssSeqPanel
.getCmb_assSeq().getSelectedItem()).getSequence();
PDBEntry pdbEntry = new PDBEntry();
pdbEntry.setId(txt_search.getText());
pdbEntry.setType("PDB");
selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
PDBEntry[] pdbEntriesToView = new PDBEntry[]
{ pdbEntry };
new StructureViewer(ap.getStructureSelectionManager())
.viewStructures(ap, pdbEntriesToView,
ap.av.collateForPDB(pdbEntriesToView));
}
else if (currentView == VIEWS_FROM_FILE)
{
selectedSequence = ((AssociateSeqOptions) fileChooserAssSeqPanel
.getCmb_assSeq().getSelectedItem()).getSequence();
new AssociatePdbFileWithSeq().associatePdbWithSeq(
selectedPdbFileName, jalview.io.AppletFormatAdapter.FILE,
selectedSequence, true, Desktop.instance);
}
mainFrame.dispose();
}
/**
* 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 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)
{
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 setStructuresDiscovered(boolean structuresDiscovered)
{
this.structuresDiscovered = structuresDiscovered;
}
public Collection getDiscoveredStructuresSet()
{
return discoveredStructuresSet;
}
@Override
protected void txt_search_ActionPerformed()
{
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.getName());
pdbRestCleint = new PDBRestClient();
PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
if (resultList.getSearchSummary() != null
&& resultList.getSearchSummary().size() > 0)
{
isValidPBDEntry = true;
}
}
validateSelections();
}
@Override
public void tabRefresh()
{
if (selectedSequences != null)
{
Thread refreshThread = new Thread(new Runnable()
{
@Override
public void run()
{
fetchStructuresMetaData();
filterResultSet(((FilterOption) cmb_filterOption
.getSelectedItem()).getValue());
}
});
refreshThread.start();
}
}
}