/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* 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
package jalview.gui;
import java.util.*;
+import java.util.List;
import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
import javax.swing.tree.DefaultMutableTreeNode;
-import javax.swing.tree.MutableTreeNode;
-import javax.swing.tree.TreeModel;
+
+import com.stevesoft.pat.Regex;
import jalview.datamodel.*;
import jalview.io.*;
+import jalview.util.DBRefUtils;
+import jalview.util.MessageManager;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import jalview.ws.seqfetcher.DbSourceProxy;
-
import java.awt.BorderLayout;
public class SequenceFetcher extends JPanel implements Runnable
Thread sf = new Thread(new Runnable()
{
+ @Override
public void run()
{
if (getSequenceFetcherSingleton(guiWindow) != null)
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
JOptionPane
ok.setText("OK");
ok.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
ok_actionPerformed();
clear.setText("Clear");
clear.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
clear_actionPerformed();
example.setText("Example");
example.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
example_actionPerformed();
close.setText("Close");
close.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
close_actionPerformed(e);
textArea.setLineWrap(true);
textArea.addKeyListener(new KeyAdapter()
{
+ @Override
public void keyPressed(KeyEvent e)
{
if (e.getKeyCode() == KeyEvent.VK_ENTER)
database.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- DbSourceProxy db = null;
try
{
databaseButt.setText(database.getSelectedItem()
+ " others)" : ""));
String eq = database.getExampleQueries();
dbeg.setText("Example query: " + eq);
- replacePunctuation.setEnabled(!(eq != null && eq.indexOf(",") > -1));
+ boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
+ for (DbSourceProxy dbs : database.getSelectedSources())
+ {
+ if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
+ {
+ enablePunct = false;
+ break;
+ }
+ }
+ replacePunctuation.setEnabled(enablePunct);
+
} catch (Exception ex)
{
dbeg.setText("");
public void ok_actionPerformed()
{
- database.setEnabled(false);
+ databaseButt.setEnabled(false);
+ example.setEnabled(false);
textArea.setEnabled(false);
ok.setEnabled(false);
close.setEnabled(false);
private void resetDialog()
{
- database.setEnabled(true);
+ databaseButt.setEnabled(true);
+ example.setEnabled(true);
textArea.setEnabled(true);
ok.setEnabled(true);
close.setEnabled(true);
}
+ @Override
public void run()
{
String error = "";
resetDialog();
return;
}
- ArrayList<String> aresultq = new ArrayList<String>();
- ArrayList<AlignmentI> aresult = new ArrayList<AlignmentI>();
- DbSourceProxy proxy = database.getSelectedSources().get(0);
- Enumeration en = new StringTokenizer(textArea.getText(), ";");
- boolean isAliSource = false;
- try
- {
- guiWindow.setProgressBar(
- "Fetching Sequences from " + proxy.getDbName(), Thread
- .currentThread().hashCode());
- isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
- if (proxy.getAccessionSeparator() == null)
+ // indicate if successive sources should be merged into one alignment.
+ boolean addToLast = false;
+ ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
+ ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
+ Iterator<DbSourceProxy> proxies = database.getSelectedSources()
+ .iterator();
+ String[] qries;
+ List<String> nextfetch = Arrays.asList(qries = textArea.getText()
+ .split(";"));
+ Iterator<String> en = Arrays.asList(new String[0]).iterator();
+ int nqueries = qries.length;
+ 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<String>();
+ }
+
+ DbSourceProxy proxy = proxies.next();
+ boolean isAliSource = false;
+ try
{
- while (en.hasMoreElements())
+ // update status
+ guiWindow.setProgressBar("Fetching " + nqueries
+ + " sequence queries from " + proxy.getDbName(), Thread
+ .currentThread().hashCode());
+ isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
+ if (proxy.getAccessionSeparator() == null)
{
- String item = (String) en.nextElement();
- try
+ while (en.hasNext())
{
- if (aresult != null)
+ String item = en.next();
+ try
{
+ if (aresult != null)
+ {
+ try
+ {
+ // give the server a chance to breathe
+ Thread.sleep(5);
+ } catch (Exception e)
+ {
+ //
+ }
+
+ }
+
+ AlignmentI indres = null;
try
{
- // give the server a chance to breathe
- Thread.sleep(5);
- } catch (Exception e)
+ indres = proxy.getSequenceRecords(item);
+ } catch (OutOfMemoryError oome)
{
- //
+ new OOMWarning("fetching " + item + " from "
+ + proxy.getDbName(), oome, this);
}
-
+ if (indres != null)
+ {
+ aresultq.add(item);
+ aresult.add(indres);
+ }
+ else
+ {
+ nextfetch.add(item);
+ }
+ } catch (Exception e)
+ {
+ jalview.bin.Cache.log.info("Error retrieving " + item
+ + " from " + proxy.getDbName(), e);
+ nextfetch.add(item);
}
-
- AlignmentI indres = null;
- try
+ }
+ }
+ else
+ {
+ StringBuffer multiacc = new StringBuffer();
+ ArrayList<String> tosend = new ArrayList<String>();
+ while (en.hasNext())
+ {
+ String nel = en.next();
+ tosend.add(nel);
+ multiacc.append(nel);
+ if (en.hasNext())
{
- indres = proxy.getSequenceRecords(item);
- } catch (OutOfMemoryError oome)
+ multiacc.append(proxy.getAccessionSeparator());
+ }
+ }
+ try
+ {
+ AlignmentI rslt;
+ SequenceI[] rs;
+ List<String> nores = new ArrayList<String>();
+ rslt = proxy.getSequenceRecords(multiacc.toString());
+ if (rslt == null || rslt.getHeight() == 0)
{
- new OOMWarning("fetching " + item + " from "
- + proxy.getDbName(), oome, this);
+ // no results - pass on all queries to next source
+ nextfetch.addAll(tosend);
}
- if (indres != null)
+ else
{
- aresultq.add(item);
- aresult.add(indres);
+ aresultq.add(multiacc.toString());
+ aresult.add(rslt);
+
+ rs = rslt.getSequencesArray();
+ // search for each query in the dbrefs associated with each
+ // sequence
+ // returned.
+ // ones we do not find will be used to query next source (if any)
+ for (String q : tosend)
+ {
+ DBRefEntry dbr = new DBRefEntry(), found[] = null;
+ dbr.setSource(proxy.getDbSource());
+ dbr.setVersion(null);
+ if (proxy.getAccessionValidator() != null)
+ {
+ Regex vgr = proxy.getAccessionValidator();
+ vgr.search(q);
+ if (vgr.numSubs() > 0)
+ {
+ dbr.setAccessionId(vgr.stringMatched(1));
+ }
+ else
+ {
+ dbr.setAccessionId(vgr.stringMatched());
+ }
+ }
+ else
+ {
+ dbr.setAccessionId(q);
+ }
+ boolean rfound = false;
+ for (int r = 0; r < rs.length; r++)
+ {
+ if (rs[r] != null
+ && (found = DBRefUtils.searchRefs(
+ rs[r].getDBRef(), dbr)) != null
+ && found.length > 0)
+ {
+ rfound = true;
+ rs[r] = null;
+ continue;
+ }
+ }
+ if (!rfound)
+ {
+ nextfetch.add(q);
+ }
+ }
}
- } catch (Exception e)
+ } catch (OutOfMemoryError oome)
{
- jalview.bin.Cache.log.info("Error retrieving " + item
- + " from " + proxy.getDbName(), e);
+ new OOMWarning("fetching " + multiacc + " from "
+ + database.getSelectedItem(), oome, this);
}
}
+
+ } 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)
+ {
+ // resets dialog box - so we don't use OOMwarning here.
+ 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();
}
- else
+ // Stack results ready for opening in alignment windows
+ if (aresult != null && aresult.size() > 0)
{
- StringBuffer multiacc = new StringBuffer();
- while (en.hasMoreElements())
+ AlignmentI ar = null;
+ if (isAliSource)
{
- multiacc.append(en.nextElement());
- if (en.hasMoreElements())
+ addToLast = false;
+ // new window for each result
+ while (aresult.size() > 0)
{
- multiacc.append(proxy.getAccessionSeparator());
+ presult.add(aresult.remove(0));
+ presultTitle.add(aresultq.remove(0) + " "
+ + getDefaultRetrievalTitle());
}
}
- try
- {
- aresultq.add(multiacc.toString());
- aresult.add(proxy.getSequenceRecords(multiacc.toString()));
- } catch (OutOfMemoryError oome)
+ else
{
- new OOMWarning("fetching " + multiacc + " from "
- + database.getSelectedItem(), oome, this);
+ 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);
}
-
}
-
- } 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)
- {
- // resets dialog box - so we don't use OOMwarning here.
- 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();
+ guiWindow.setProgressBar("Finished querying", Thread.currentThread()
+ .hashCode());
}
- if (aresult != null && aresult.size() > 0)
+ guiWindow.setProgressBar((presult.size() > 0) ? "Parsing results."
+ : "Processing ..", Thread.currentThread().hashCode());
+ // process results
+ while (presult.size() > 0)
{
- AlignmentI ar = null;
- if (isAliSource)
+ parseResult(presult.remove(0), presultTitle.remove(0), null);
+ }
+ // 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)
{
- // new window for each result
- while (aresult.size() > 0)
+ if (l != sb.length())
{
- parseResult(aresult.remove(0), aresultq.remove(0) + " "
- + getDefaultRetrievalTitle(), null);
+ sb.append("; ");
}
- }
- else
- {
- // concatenate all results in one window
- while (aresult.size() > 0)
+ if (lr - sb.length() > 40)
{
- if (ar == null)
- {
- ar = aresult.remove(0);
- }
- else
- {
- ar.append(aresult.remove(0));
- }
- ;
+ sb.append("\n");
}
- parseResult(ar, null, null);
+ sb.append(s);
}
+ showErrorMessage(sb.toString());
}
- // only remove visual delay after we finished parsing.
- guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
resetDialog();
}
title = getDefaultRetrievalTitle();
}
SequenceFeature[] sfs = null;
- for (Enumeration sq = al.getSequences().elements(); sq
- .hasMoreElements();)
+ List<SequenceI> alsqs;
+ synchronized (alsqs = al.getSequences())
{
- if ((sfs = ((SequenceI) sq.nextElement()).getDatasetSequence()
- .getSequenceFeatures()) != null)
+ for (SequenceI sq : alsqs)
{
- if (sfs.length > 0)
+ if ((sfs = (sq).getDatasetSequence().getSequenceFeatures()) != null)
{
- af.setShowSeqFeatures(true);
- break;
+ if (sfs.length > 0)
+ {
+ af.setShowSeqFeatures(true);
+ break;
+ }
}
- }
+ }
}
Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
resetDialog();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
- "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.error_retrieving_data"), JOptionPane.WARNING_MESSAGE);
}
});
}