/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ 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.api.FeatureSettingsModelI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
import jalview.fts.core.GFTSPanel;
import jalview.fts.service.pdb.PDBFTSPanel;
import jalview.fts.service.uniprot.UniprotFTSPanel;
import jalview.io.FileFormatI;
import jalview.io.gff.SequenceOntologyI;
import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.awt.BorderLayout;
import java.awt.Font;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTextArea;
import javax.swing.SwingConstants;
/**
* A panel where the use may choose a database source, and enter one or more
* accessions, to retrieve entries from the database.
*
* If the selected source is Uniprot or PDB, a free text search panel is opened
* instead to perform the search and selection.
*/
public class SequenceFetcher extends JPanel implements Runnable
{
private static jalview.ws.SequenceFetcher sfetch = null;
JLabel exampleAccession;
JComboBox database;
JCheckBox replacePunctuation;
JButton okBtn;
JButton exampleBtn;
JButton closeBtn;
JButton backBtn;
JTextArea textArea;
JInternalFrame frame;
IProgressIndicator guiWindow;
AlignFrame alignFrame;
GFTSPanel parentSearchPanel;
IProgressIndicator progressIndicator;
volatile boolean _isConstructing = false;
/**
* Returns the shared instance of the SequenceFetcher client
*
* @return
*/
public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton()
{
if (sfetch == null)
{
sfetch = new jalview.ws.SequenceFetcher();
}
return sfetch;
}
/**
* Constructor given a client to receive any status or progress messages
* (currently either the Desktop, or an AlignFrame panel)
*
* @param guiIndic
*/
public SequenceFetcher(IProgressIndicator guiIndic)
{
this(guiIndic, null, null);
}
/**
* Constructor with specified database and accession(s) to retrieve
*
* @param guiIndic
* @param selectedDb
* @param queryString
*/
public SequenceFetcher(IProgressIndicator guiIndic,
final String selectedDb, final String queryString)
{
this.progressIndicator = guiIndic;
getSequenceFetcherSingleton();
this.guiWindow = progressIndicator;
if (progressIndicator instanceof AlignFrame)
{
alignFrame = (AlignFrame) progressIndicator;
}
jbInit(selectedDb);
textArea.setText(queryString);
frame = new JInternalFrame();
frame.setContentPane(this);
Desktop.addInternalFrame(frame, getFrameTitle(), true, 400,
Platform.isAMacAndNotJS() ? 240 : 180);
}
private String getFrameTitle()
{
return ((alignFrame == null)
? MessageManager.getString("label.new_sequence_fetcher")
: MessageManager
.getString("label.additional_sequence_fetcher"));
}
private void jbInit(String selectedDb)
{
this.setLayout(new BorderLayout());
database = new JComboBox<>();
database.setFont(JvSwingUtils.getLabelFont());
database.setPrototypeDisplayValue("ENSEMBLGENOMES ");
String[] sources = new jalview.ws.SequenceFetcher().getSupportedDb();
Arrays.sort(sources, String.CASE_INSENSITIVE_ORDER);
database.addItem(MessageManager.getString("action.select_ddbb"));
for (String source : sources)
{
database.addItem(source);
}
database.setSelectedItem(selectedDb);
if (database.getSelectedIndex() == -1)
{
database.setSelectedIndex(0);
}
database.setMaximumRowCount(database.getItemCount());
database.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
String currentSelection = (String) database.getSelectedItem();
updateExampleQuery(currentSelection);
if ("pdb".equalsIgnoreCase(currentSelection))
{
frame.dispose();
new PDBFTSPanel(SequenceFetcher.this);
}
else if ("uniprot".equalsIgnoreCase(currentSelection))
{
frame.dispose();
new UniprotFTSPanel(SequenceFetcher.this);
}
else
{
otherSourceAction();
}
}
});
exampleAccession = new JLabel("");
exampleAccession.setFont(new Font("Verdana", Font.BOLD, 11));
JLabel jLabel1 = new JLabel(MessageManager
.getString("label.separate_multiple_accession_ids"));
jLabel1.setFont(new Font("Verdana", Font.ITALIC, 11));
jLabel1.setHorizontalAlignment(SwingConstants.LEFT);
replacePunctuation = new JCheckBox(
MessageManager.getString("label.replace_commas_semicolons"));
replacePunctuation.setHorizontalAlignment(SwingConstants.LEFT);
replacePunctuation.setFont(new Font("Verdana", Font.ITALIC, 11));
okBtn = new JButton(MessageManager.getString("action.ok"));
okBtn.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
ok_actionPerformed();
}
});
JButton clear = new JButton(MessageManager.getString("action.clear"));
clear.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
clear_actionPerformed();
}
});
exampleBtn = new JButton(MessageManager.getString("label.example"));
exampleBtn.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
example_actionPerformed();
}
});
closeBtn = new JButton(MessageManager.getString("action.cancel"));
closeBtn.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
close_actionPerformed(e);
}
});
backBtn = new JButton(MessageManager.getString("action.back"));
backBtn.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
parentSearchPanel.btn_back_ActionPerformed();
}
});
// back not visible unless embedded
backBtn.setVisible(false);
textArea = new JTextArea();
textArea.setFont(JvSwingUtils.getLabelFont());
textArea.setLineWrap(true);
textArea.addKeyListener(new KeyAdapter()
{
@Override
public void keyPressed(KeyEvent e)
{
if (e.getKeyCode() == KeyEvent.VK_ENTER)
{
ok_actionPerformed();
}
}
});
JPanel actionPanel = new JPanel();
actionPanel.add(backBtn);
actionPanel.add(exampleBtn);
actionPanel.add(clear);
actionPanel.add(okBtn);
actionPanel.add(closeBtn);
JPanel databasePanel = new JPanel();
databasePanel.setLayout(new BorderLayout());
databasePanel.add(database, BorderLayout.NORTH);
databasePanel.add(exampleAccession, BorderLayout.CENTER);
JPanel jPanel2a = new JPanel(new BorderLayout());
jPanel2a.add(jLabel1, BorderLayout.NORTH);
jPanel2a.add(replacePunctuation, BorderLayout.SOUTH);
databasePanel.add(jPanel2a, BorderLayout.SOUTH);
JPanel idsPanel = new JPanel();
idsPanel.setLayout(new BorderLayout(0, 5));
JScrollPane jScrollPane1 = new JScrollPane();
jScrollPane1.getViewport().add(textArea);
idsPanel.add(jScrollPane1, BorderLayout.CENTER);
this.add(actionPanel, BorderLayout.SOUTH);
this.add(idsPanel, BorderLayout.CENTER);
this.add(databasePanel, BorderLayout.NORTH);
}
/**
* Answers a semi-colon-delimited string with the example query or queries for
* the selected database
*
* @param db
* @return
*/
protected String getExampleQueries(String db)
{
StringBuilder sb = new StringBuilder();
HashSet hs = new HashSet<>();
for (DbSourceProxy dbs : sfetch.getSourceProxy(db))
{
String tq = dbs.getTestQuery();
if (hs.add(tq)) // not a duplicate source
{
if (sb.length() > 0)
{
sb.append(";");
}
sb.append(tq);
}
}
return sb.toString();
}
/**
* Action on selecting a database other than Uniprot or PDB is to enable or
* disable 'Replace commas', and await input in the query field
*/
protected void otherSourceAction()
{
try
{
String eq = exampleAccession.getText();
// TODO this should be a property of the SequenceFetcher whether commas
// are allowed in the IDs...
boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
replacePunctuation.setEnabled(enablePunct);
} catch (Exception ex)
{
exampleAccession.setText("");
replacePunctuation.setEnabled(true);
}
repaint();
}
/**
* Sets the text of the example query to incorporate the example accession
* provided by the selected database source
*
* @param selectedDatabase
* @return
*/
protected String updateExampleQuery(String selectedDatabase)
{
String eq = getExampleQueries(selectedDatabase);
exampleAccession.setText(MessageManager
.formatMessage("label.example_query_param", new String[]
{ eq }));
return eq;
}
/**
* Action on clicking the 'Example' button is to write the example accession
* as the query text field value
*/
protected void example_actionPerformed()
{
String eq = getExampleQueries((String) database.getSelectedItem());
textArea.setText(eq);
repaint();
}
/**
* Clears the query input field
*/
protected void clear_actionPerformed()
{
textArea.setText("");
repaint();
}
/**
* Action on Close button is to close this frame, and also (if it is embedded
* in a search panel) to close the search panel
*
* @param e
*/
protected void close_actionPerformed(ActionEvent e)
{
try
{
frame.setClosed(true);
if (parentSearchPanel != null)
{
parentSearchPanel.btn_cancel_ActionPerformed();
}
} catch (Exception ex)
{
}
}
/**
* Action on OK is to start the fetch for entered accession(s)
*/
public void ok_actionPerformed()
{
/*
* tidy inputs and check there is something to search for
*/
String t0 = textArea.getText();
String text = t0.trim();
if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
{
text = text.replace(",", ";");
}
text = text.replaceAll("(\\s|[; ])+", ";");
if (!t0.equals(text))
{
textArea.setText(text);
}
if (text.isEmpty())
{
// todo i18n
showErrorMessage(
"Please enter a (semi-colon separated list of) database id(s)");
resetDialog();
return;
}
if (database.getSelectedIndex() == 0)
{
// todo i18n
showErrorMessage("Please choose a database");
resetDialog();
return;
}
exampleBtn.setEnabled(false);
textArea.setEnabled(false);
okBtn.setEnabled(false);
closeBtn.setEnabled(false);
backBtn.setEnabled(false);
Thread worker = new Thread(this);
worker.start();
}
private void resetDialog()
{
exampleBtn.setEnabled(true);
textArea.setEnabled(true);
okBtn.setEnabled(true);
closeBtn.setEnabled(true);
backBtn.setEnabled(parentSearchPanel != null);
}
@Override
public void run()
{
boolean addToLast = false;
List aresultq = new ArrayList<>();
List presultTitle = new ArrayList<>();
List presult = new ArrayList<>();
List aresult = new ArrayList<>();
List sources = sfetch
.getSourceProxy((String) database.getSelectedItem());
Iterator proxies = sources.iterator();
String[] qries = textArea.getText().trim().split(";");
List nextFetch = Arrays.asList(qries);
Iterator en = Arrays.asList(new String[0]).iterator();
int nqueries = qries.length;
FeatureSettingsModelI preferredFeatureColours = null;
while (proxies.hasNext() && (en.hasNext() || nextFetch.size() > 0))
{
if (!en.hasNext() && nextFetch.size() > 0)
{
en = nextFetch.iterator();
nqueries = nextFetch.size();
// save the remaining queries in the original array
qries = nextFetch.toArray(new String[nqueries]);
nextFetch = new ArrayList<>();
}
DbSourceProxy proxy = proxies.next();
try
{
// update status
guiWindow.setProgressBar(MessageManager.formatMessage(
"status.fetching_sequence_queries_from", new String[]
{ Integer.valueOf(nqueries).toString(),
proxy.getDbName() }),
Thread.currentThread().hashCode());
if (proxy.getMaximumQueryCount() == 1)
{
/*
* proxy only handles one accession id at a time
*/
while (en.hasNext())
{
String acc = en.next();
if (!fetchSingleAccession(proxy, acc, aresultq, aresult))
{
nextFetch.add(acc);
}
}
}
else
{
/*
* proxy can fetch multiple accessions at one time
*/
fetchMultipleAccessions(proxy, en, aresultq, aresult, nextFetch);
}
} catch (Exception e)
{
showErrorMessage("Error retrieving " + textArea.getText() + " from "
+ database.getSelectedItem());
// error
// +="Couldn't retrieve sequences from "+database.getSelectedItem();
System.err.println("Retrieval failed for source ='"
+ database.getSelectedItem() + "' and query\n'"
+ textArea.getText() + "'\n");
e.printStackTrace();
} catch (OutOfMemoryError e)
{
showErrorMessage("Out of Memory when retrieving "
+ textArea.getText() + " from " + database.getSelectedItem()
+ "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
e.printStackTrace();
} catch (Error e)
{
showErrorMessage("Serious Error retrieving " + textArea.getText()
+ " from " + database.getSelectedItem());
e.printStackTrace();
}
// Stack results ready for opening in alignment windows
if (aresult != null && aresult.size() > 0)
{
FeatureSettingsModelI proxyColourScheme = proxy
.getFeatureColourScheme();
if (proxyColourScheme != null)
{
preferredFeatureColours = proxyColourScheme;
}
AlignmentI ar = null;
if (proxy.isAlignmentSource())
{
addToLast = false;
// new window for each result
while (aresult.size() > 0)
{
presult.add(aresult.remove(0));
presultTitle.add(
aresultq.remove(0) + " " + getDefaultRetrievalTitle());
}
}
else
{
String titl = null;
if (addToLast && presult.size() > 0)
{
ar = presult.remove(presult.size() - 1);
titl = presultTitle.remove(presultTitle.size() - 1);
}
// concatenate all results in one window
while (aresult.size() > 0)
{
if (ar == null)
{
ar = aresult.remove(0);
}
else
{
ar.append(aresult.remove(0));
}
}
addToLast = true;
presult.add(ar);
presultTitle.add(titl);
}
}
guiWindow.setProgressBar(
MessageManager.getString("status.finshed_querying"),
Thread.currentThread().hashCode());
}
guiWindow
.setProgressBar(
(presult.size() > 0)
? MessageManager
.getString("status.parsing_results")
: MessageManager.getString("status.processing"),
Thread.currentThread().hashCode());
// process results
while (presult.size() > 0)
{
parseResult(presult.remove(0), presultTitle.remove(0), null,
preferredFeatureColours);
}
// only remove visual delay after we finished parsing.
guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
if (nextFetch.size() > 0)
{
StringBuffer sb = new StringBuffer();
sb.append("Didn't retrieve the following "
+ (nextFetch.size() == 1 ? "query"
: nextFetch.size() + " queries")
+ ": \n");
int l = sb.length(), lr = 0;
for (String s : nextFetch)
{
if (l != sb.length())
{
sb.append("; ");
}
if (lr - sb.length() > 40)
{
sb.append("\n");
}
sb.append(s);
}
showErrorMessage(sb.toString());
}
resetDialog();
}
/**
* Tries to fetch one or more accession ids from the database proxy
*
* @param proxy
* @param accessions
* the queries to fetch
* @param aresultq
* a successful queries list to add to
* @param aresult
* a list of retrieved alignments to add to
* @param nextFetch
* failed queries are added to this list
* @throws Exception
*/
void fetchMultipleAccessions(DbSourceProxy proxy,
Iterator accessions, List aresultq,
List aresult, List nextFetch) throws Exception
{
StringBuilder multiacc = new StringBuilder();
List tosend = new ArrayList<>();
while (accessions.hasNext())
{
String nel = accessions.next();
tosend.add(nel);
multiacc.append(nel);
if (accessions.hasNext())
{
multiacc.append(proxy.getAccessionSeparator());
}
}
try
{
String query = multiacc.toString();
AlignmentI rslt = proxy.getSequenceRecords(query);
if (rslt == null || rslt.getHeight() == 0)
{
// no results - pass on all queries to next source
nextFetch.addAll(tosend);
}
else
{
aresultq.add(query);
aresult.add(rslt);
if (tosend.size() > 1)
{
checkResultForQueries(rslt, tosend, nextFetch, proxy);
}
}
} catch (OutOfMemoryError oome)
{
new OOMWarning("fetching " + multiacc + " from "
+ database.getSelectedItem(), oome, this);
}
}
/**
* Query for a single accession id via the database proxy
*
* @param proxy
* @param accession
* @param aresultq
* a list of successful queries to add to
* @param aresult
* a list of retrieved alignments to add to
* @return true if the fetch was successful, else false
*/
boolean fetchSingleAccession(DbSourceProxy proxy, String accession,
List aresultq, List aresult)
{
boolean success = false;
try
{
if (aresult != null)
{
try
{
// give the server a chance to breathe
Thread.sleep(5);
} catch (Exception e)
{
//
}
}
AlignmentI indres = null;
try
{
indres = proxy.getSequenceRecords(accession);
} catch (OutOfMemoryError oome)
{
new OOMWarning(
"fetching " + accession + " from " + proxy.getDbName(),
oome, this);
}
if (indres != null)
{
aresultq.add(accession);
aresult.add(indres);
success = true;
}
} catch (Exception e)
{
Cache.log.info("Error retrieving " + accession + " from "
+ proxy.getDbName(), e);
}
return success;
}
/**
* Checks which of the queries were successfully retrieved by searching the
* DBRefs of the retrieved sequences for a match. Any not found are added to
* the 'nextFetch' list.
*
* @param rslt
* @param queries
* @param nextFetch
* @param proxy
*/
void checkResultForQueries(AlignmentI rslt, List queries,
List nextFetch, DbSourceProxy proxy)
{
SequenceI[] rs = rslt.getSequencesArray();
for (String q : queries)
{
// BH 2019.01.25 dbr is never used.
// DBRefEntry dbr = new DBRefEntry();
// dbr.setSource(proxy.getDbSource());
// dbr.setVersion(null);
String accId = proxy.getAccessionIdFromQuery(q);
// dbr.setAccessionId(accId);
boolean rfound = false;
for (int r = 0, nr = rs.length; r < nr; r++)
{
if (rs[r] != null)
{
List found = DBRefUtils.searchRefs(rs[r].getDBRefs(),
accId);
if (!found.isEmpty())
{
rfound = true;
break;
}
}
}
if (!rfound)
{
nextFetch.add(q);
}
}
}
/**
*
* @return a standard title for any results retrieved using the currently
* selected source and settings
*/
public String getDefaultRetrievalTitle()
{
return "Retrieved from " + database.getSelectedItem();
}
AlignmentI parseResult(AlignmentI al, String title,
FileFormatI currentFileFormat,
FeatureSettingsModelI preferredFeatureColours)
{
if (al != null && al.getHeight() > 0)
{
if (title == null)
{
title = getDefaultRetrievalTitle();
}
if (alignFrame == null)
{
AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
if (currentFileFormat != null)
{
af.currentFileFormat = currentFileFormat;
}
List alsqs = al.getSequences();
synchronized (alsqs)
{
for (SequenceI sq : alsqs)
{
if (sq.getFeatures().hasFeatures())
{
af.setShowSeqFeatures(true);
break;
}
}
}
if (preferredFeatureColours != null)
{
af.getViewport().applyFeaturesStyle(preferredFeatureColours);
}
if (Cache.getDefault("HIDE_INTRONS", true))
{
af.hideFeatureColumns(SequenceOntologyI.EXON, false);
}
Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
af.setStatus(MessageManager
.getString("label.successfully_pasted_alignment_file"));
try
{
af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (Exception ex)
{
}
}
else
{
alignFrame.viewport.addAlignment(al, title);
}
}
return al;
}
void showErrorMessage(final String error)
{
resetDialog();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop, error,
MessageManager.getString("label.error_retrieving_data"),
JvOptionPane.WARNING_MESSAGE);
}
});
}
public IProgressIndicator getProgressIndicator()
{
return progressIndicator;
}
public void setProgressIndicator(IProgressIndicator progressIndicator)
{
this.progressIndicator = progressIndicator;
}
/**
* Hide this panel (on clicking the database button to open the database
* chooser)
*/
void hidePanel()
{
frame.setVisible(false);
}
public void setQuery(String ids)
{
textArea.setText(ids);
}
/**
* Called to modify the search panel for embedding as an alternative tab of a
* free text search panel. The database choice list is hidden (since the
* choice has been made), and a Back button is made visible (which reopens the
* Sequence Fetcher panel).
*
* @param parentPanel
*/
public void embedIn(GFTSPanel parentPanel)
{
database.setVisible(false);
backBtn.setVisible(true);
parentSearchPanel = parentPanel;
}
}