/*
- * 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 ($$Version-Rel$$)
+ * 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.
- *
+ * 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/>.
+ * 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 java.util.*;
-
-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 jalview.datamodel.*;
-import jalview.io.*;
-import jalview.ws.dbsources.das.api.DasSourceRegistryI;
+import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceFeature;
+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.Collections;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.SwingConstants;
+import javax.swing.tree.DefaultMutableTreeNode;
public class SequenceFetcher extends JPanel implements Runnable
{
- // ASequenceFetcher sfetch;
+ JLabel dbeg = new JLabel();
+
+ JDatabaseTree database;
+
+ JButton databaseButt;
+
+ JLabel jLabel1 = new JLabel();
+
+ JCheckBox replacePunctuation = new JCheckBox();
+
+ JButton ok = new JButton();
+
+ JButton clear = new JButton();
+
+ JButton example = new JButton();
+
+ JButton close = new JButton();
+
+ JButton back = new JButton();
+
+ JPanel jPanel1 = new JPanel();
+
+ JTextArea textArea = new JTextArea();
+
+ JScrollPane jScrollPane1 = new JScrollPane();
+
+ JPanel jPanel2 = new JPanel();
+
+ JPanel jPanel3 = new JPanel();
+
+ JPanel jPanel4 = new JPanel();
+
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ BorderLayout borderLayout2 = new BorderLayout();
+
+ BorderLayout borderLayout3 = new BorderLayout();
+
JInternalFrame frame;
IProgressIndicator guiWindow;
private static jalview.ws.SequenceFetcher sfetch = null;
- private static long lastDasSourceRegistry = -3;
-
- private static DasSourceRegistryI dasRegistry = null;
-
private static boolean _initingFetcher = false;
private static Thread initingThread = null;
+ public JTextArea getTextArea()
+ {
+ return textArea;
+ }
+
/**
* Blocking method that initialises and returns the shared instance of the
* SequenceFetcher client
if (guiWindow != null)
{
guiWindow.setProgressBar(
- "Waiting for Sequence Database Fetchers to initialise",
+ MessageManager.getString(
+ "status.waiting_sequence_database_fetchers_init"),
Thread.currentThread().hashCode());
}
// initting happening on another thread - so wait around to see if it
if (guiWindow != null)
{
guiWindow.setProgressBar(
- "Waiting for Sequence Database Fetchers to initialise",
+ MessageManager.getString(
+ "status.waiting_sequence_database_fetchers_init"),
Thread.currentThread().hashCode());
}
}
- if (sfetch == null
- || dasRegistry != jalview.bin.Cache.getDasSourceRegistry()
- || lastDasSourceRegistry != (jalview.bin.Cache
- .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache
- .getDasSourceRegistry().getLocalSourceString())
- .hashCode())
+ if (sfetch == null)
{
_initingFetcher = true;
initingThread = Thread.currentThread();
*/
if (guiWindow != null)
{
- guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
+ guiWindow.setProgressBar(
+ MessageManager.getString(
+ "status.init_sequence_database_fetchers"),
Thread.currentThread().hashCode());
}
- dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
- dasRegistry.refreshSources();
jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
if (guiWindow != null)
{
- guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
- Thread.currentThread().hashCode());
+ guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
}
- lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
- .getLocalSourceString()).hashCode();
sfetch = sf;
_initingFetcher = false;
initingThread = null;
return sfetch;
}
+ private IProgressIndicator progressIndicator;
+
+ private volatile boolean _isConstructing = false;
+
+ private List<AlignFrame> newAlframes = null;
+
public SequenceFetcher(IProgressIndicator guiIndic)
{
- final IProgressIndicator guiWindow = guiIndic;
+ this(guiIndic, null, null);
+ }
+
+ public SequenceFetcher(IProgressIndicator guiIndic,
+ final String selectedDb, final String queryString)
+ {
+ this._isConstructing = true;
+ this.progressIndicator = guiIndic;
final SequenceFetcher us = this;
// launch initialiser thread
Thread sf = new Thread(new Runnable()
{
+ @Override
public void run()
{
- if (getSequenceFetcherSingleton(guiWindow) != null)
+ if (getSequenceFetcherSingleton(progressIndicator) != null)
{
- us.initGui(guiWindow);
+ us.initGui(progressIndicator, selectedDb, queryString);
+ us._isConstructing = false;
}
else
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- "Could not create the sequence fetcher client. Check error logs for details.",
- "Couldn't create SequenceFetcher",
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString(
+ "warn.couldnt_create_sequence_fetcher_client"),
+ MessageManager.getString(
+ "label.couldnt_create_sequence_fetcher"),
+ JvOptionPane.ERROR_MESSAGE);
}
});
sf.start();
}
+ /**
+ * blocking call which creates a new sequence fetcher panel, configures it and
+ * presses the OK button with the given database and query.
+ *
+ * @param database
+ * @param query
+ */
+ public static List<AlignFrame> fetchAndShow(String database, String query)
+ {
+ final SequenceFetcher sf = new SequenceFetcher(Desktop.instance,
+ database, query);
+ while (sf._isConstructing)
+ {
+ try
+ {
+ Thread.sleep(50);
+ } catch (Exception q)
+ {
+ return Collections.emptyList();
+ }
+ }
+ sf.newAlframes = new ArrayList<>();
+ sf.run();
+ return sf.newAlframes;
+ }
+
private class DatabaseAuthority extends DefaultMutableTreeNode
{
};
/**
+ * initialise the database and query for this fetcher panel
+ *
+ * @param selectedDb
+ * - string that should correspond to a sequence fetcher
+ * @param queryString
+ * - string that will be entered in the query dialog
+ * @return true if UI was configured with valid database and query string
+ */
+ protected boolean setInitialQuery(String selectedDb, String queryString)
+ {
+ if (selectedDb == null || selectedDb.trim().length() == 0)
+ {
+ return false;
+ }
+ try
+ {
+ List<DbSourceProxy> sp = sfetch.getSourceProxy(selectedDb);
+ for (DbSourceProxy sourcep : sp)
+ {
+ if (sourcep.getTier() == 0)
+ {
+ database.selection = Arrays
+ .asList(new DbSourceProxy[]
+ { sourcep });
+ break;
+ }
+ }
+ if (database.selection == null || database.selection.size() == 0)
+ {
+ System.err.println(
+ "Ignoring fetch parameter db='" + selectedDb + "'");
+ return false;
+ }
+ textArea.setText(queryString);
+ } catch (Exception q)
+ {
+ System.err.println("Ignoring fetch parameter db='" + selectedDb
+ + "' and query='" + queryString + "'");
+ return false;
+ }
+ return true;
+ }
+
+ /**
* called by thread spawned by constructor
*
* @param guiWindow
+ * @param queryString
+ * @param selectedDb
*/
- private void initGui(IProgressIndicator guiWindow)
+ private void initGui(IProgressIndicator guiWindow, String selectedDb,
+ String queryString)
{
this.guiWindow = guiWindow;
if (guiWindow instanceof AlignFrame)
try
{
jbInit();
+ /*
+ * configure the UI with any query parameters we were called with
+ */
+ if (!setInitialQuery(selectedDb, queryString))
+ {
+ /*
+ * none provided, so show the database chooser
+ */
+ database.waitForInput();
+ }
} catch (Exception ex)
{
ex.printStackTrace();
frame = new JInternalFrame();
frame.setContentPane(this);
- if (new jalview.util.Platform().isAMac())
+ if (Platform.isAMac())
{
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
+ Desktop.addInternalFrame(frame, getFrameTitle(), false, 400, 240);
}
else
{
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
+ Desktop.addInternalFrame(frame, getFrameTitle(), false, 400, 180);
}
}
private String getFrameTitle()
{
- return ((alignFrame == null) ? "New " : "Additional ")
- + "Sequence Fetcher";
+ return ((alignFrame == null)
+ ? MessageManager.getString("label.new_sequence_fetcher")
+ : MessageManager
+ .getString("label.additional_sequence_fetcher"));
}
+ GFTSPanel parentFTSframe = null;
+ /**
+ * change the buttons so they fit with the FTS panel.
+ */
+ public void embedWithFTSPanel(GFTSPanel toClose)
+ {
+ back.setVisible(true);
+ parentFTSframe = toClose;
+ }
private void jbInit() throws Exception
{
this.setLayout(borderLayout2);
dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
- jLabel1.setText("Separate multiple accession ids with semi colon \";\"");
+ jLabel1.setText(MessageManager
+ .getString("label.separate_multiple_accession_ids"));
replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
replacePunctuation
.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
- replacePunctuation.setText("Replace commas with semi-colons");
- ok.setText("OK");
+ replacePunctuation.setText(
+ MessageManager.getString("label.replace_commas_semicolons"));
+ ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
ok_actionPerformed();
}
});
- clear.setText("Clear");
+ clear.setText(MessageManager.getString("action.clear"));
clear.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
clear_actionPerformed();
}
});
- example.setText("Example");
+ example.setText(MessageManager.getString("label.example"));
example.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
example_actionPerformed();
}
});
- close.setText("Close");
+ close.setText(MessageManager.getString("action.cancel"));
close.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
close_actionPerformed(e);
}
});
+ back.setText(MessageManager.getString("action.back"));
+ back.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ parentFTSframe.btn_back_ActionPerformed();
+ }
+ });
+ // back not visible unless embedded
+ back.setVisible(false);
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();
+ }
}
});
jPanel3.setLayout(borderLayout1);
borderLayout1.setVgap(5);
- jPanel1.add(ok);
+ jPanel1.add(back);
jPanel1.add(example);
jPanel1.add(clear);
+ jPanel1.add(ok);
jPanel1.add(close);
- jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
jPanel2.setLayout(borderLayout3);
- databaseButt = database.getDatabaseSelectorButton();
+ databaseButt = /*database.getDatabaseSelectorButton();
+ final JButton viewdbs =*/new JButton(
+ MessageManager.getString("action.select_ddbb"));
+ databaseButt.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ hidePanel();
+ database.showDialog();
+ }
+ });
databaseButt.setFont(JvSwingUtils.getLabelFont());
database.addActionListener(new ActionListener()
{
-
+ @Override
public void actionPerformed(ActionEvent e)
{
- DbSourceProxy db = null;
- try
+ String currentSelection = database.getSelectedItem();
+ if (currentSelection == null)
{
- databaseButt.setText(database.getSelectedItem()
- + (database.getSelectedSources().size() > 1 ? " (and "
- + database.getSelectedSources().size()
- + " others)" : ""));
- String eq = database.getExampleQueries();
- dbeg.setText("Example query: " + eq);
- replacePunctuation.setEnabled(!(eq != null && eq.indexOf(",") > -1));
- } catch (Exception ex)
+ close_actionPerformed(null);
+ }
+
+ showPanel();
+
+ if ("pdb".equalsIgnoreCase(currentSelection))
{
- dbeg.setText("");
- replacePunctuation.setEnabled(true);
+ pdbSourceAction();
}
- jPanel2.repaint();
+ else if ("uniprot".equalsIgnoreCase(currentSelection))
+ {
+ uniprotSourceAction();
+ }
+ else
+ {
+ otherSourceAction();
+ }
+ database.action = -1;
}
});
+
dbeg.setText("");
jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
this.add(jPanel3, java.awt.BorderLayout.CENTER);
this.add(jPanel2, java.awt.BorderLayout.NORTH);
jScrollPane1.getViewport().add(textArea);
+ }
+ private void pdbSourceAction()
+ {
+ databaseButt.setText(database.getSelectedItem());
+ new PDBFTSPanel(this);
+ frame.dispose();
+ }
+
+ private void uniprotSourceAction()
+ {
+ databaseButt.setText(database.getSelectedItem());
+ new UniprotFTSPanel(this);
+ frame.dispose();
+ }
+
+ private void otherSourceAction()
+ {
+ try
+ {
+ databaseButt.setText(database.getSelectedItem()
+ + (database.getSelectedSources().size() > 1 ? " (and "
+ + database.getSelectedSources().size() + " others)"
+ : ""));
+ String eq = database.getExampleQueries();
+ dbeg.setText(MessageManager.formatMessage("label.example_query_param",
+ new String[]
+ { eq }));
+ // TODO this should be a property of the SequenceFetcher whether commas are and
+ // colons are allowed in the IDs...
+
+ boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
+ replacePunctuation.setEnabled(enablePunct);
+
+ } catch (Exception ex)
+ {
+ dbeg.setText("");
+ replacePunctuation.setEnabled(true);
+ }
+ jPanel2.repaint();
}
protected void example_actionPerformed()
jPanel3.repaint();
}
- JLabel dbeg = new JLabel();
-
- JDatabaseTree database;
-
- JButton databaseButt;
-
- JLabel jLabel1 = new JLabel();
-
- JCheckBox replacePunctuation = new JCheckBox();
-
- JButton ok = new JButton();
-
- JButton clear = new JButton();
-
- JButton example = new JButton();
-
- JButton close = new JButton();
-
- JPanel jPanel1 = new JPanel();
-
- JTextArea textArea = new JTextArea();
-
- JScrollPane jScrollPane1 = new JScrollPane();
-
- JPanel jPanel2 = new JPanel();
-
- JPanel jPanel3 = new JPanel();
-
- JPanel jPanel4 = new JPanel();
-
- BorderLayout borderLayout1 = new BorderLayout();
-
- BorderLayout borderLayout2 = new BorderLayout();
-
- BorderLayout borderLayout3 = new BorderLayout();
-
public void close_actionPerformed(ActionEvent e)
{
try
{
frame.setClosed(true);
+ if (parentFTSframe!=null)
+ {
+ parentFTSframe.btn_cancel_ActionPerformed();
+ }
} catch (Exception ex)
{
}
public void ok_actionPerformed()
{
- database.setEnabled(false);
+ databaseButt.setEnabled(false);
+ example.setEnabled(false);
textArea.setEnabled(false);
ok.setEnabled(false);
close.setEnabled(false);
-
+ back.setEnabled(false);
Thread worker = new Thread(this);
worker.start();
}
private void resetDialog()
{
- database.setEnabled(true);
+ databaseButt.setEnabled(true);
+ example.setEnabled(true);
textArea.setEnabled(true);
ok.setEnabled(true);
close.setEnabled(true);
+ back.setEnabled(parentFTSframe != null);
}
+ @Override
public void run()
{
String error = "";
if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
{
empty = new com.stevesoft.pat.Regex(
- // replace commas and spaces with a semicolon
+ // replace commas and spaces with a semicolon
"(\\s|[,; ])+", ";");
}
else
}
textArea.setText(empty.replaceAll(textArea.getText()));
// see if there's anthing to search with
- if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
- .getText()))
+ if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]")
+ .search(textArea.getText()))
{
error += "Please enter a (semi-colon separated list of) database id(s)";
}
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
+ // TODO: Refactor to GUI independent code and write tests.
+ // indicate if successive sources should be merged into one alignment.
+ boolean addToLast = false;
+ List<String> aresultq = new ArrayList<>();
+ List<String> presultTitle = new ArrayList<>();
+ List<AlignmentI> presult = new ArrayList<>();
+ List<AlignmentI> aresult = new ArrayList<>();
+ 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;
+
+ FeatureSettingsModelI preferredFeatureColours = null;
+ while (proxies.hasNext() && (en.hasNext() || nextFetch.size() > 0))
{
- guiWindow.setProgressBar(
- "Fetching Sequences from " + proxy.getDbName(), Thread
- .currentThread().hashCode());
- isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
- if (proxy.getAccessionSeparator() == null)
+ 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
{
- while (en.hasMoreElements())
+ // 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)
{
- String item = (String) en.nextElement();
- try
+ /*
+ * proxy only handles one accession id at a time
+ */
+ while (en.hasNext())
{
- if (aresult != null)
+ String acc = en.next();
+ if (!fetchSingleAccession(proxy, acc, aresultq, aresult))
{
- try
- {
- // give the server a chance to breathe
- Thread.sleep(5);
- } catch (Exception e)
- {
- //
- }
-
+ 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();
+ }
- AlignmentI indres = null;
- try
- {
- indres = proxy.getSequenceRecords(item);
- } catch (OutOfMemoryError oome)
+ // 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)
{
- new OOMWarning("fetching " + item + " from "
- + proxy.getDbName(), oome, this);
+ ar = aresult.remove(0);
}
- if (indres != null)
+ else
{
- aresultq.add(item);
- aresult.add(indres);
+ ar.append(aresult.remove(0));
}
- } catch (Exception e)
- {
- jalview.bin.Cache.log.info("Error retrieving " + item
- + " from " + proxy.getDbName(), e);
}
+ addToLast = true;
+ presult.add(ar);
+ presultTitle.add(titl);
}
}
- else
+ 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)
{
- StringBuffer multiacc = new StringBuffer();
- while (en.hasMoreElements())
+ if (l != sb.length())
{
- multiacc.append(en.nextElement());
- if (en.hasMoreElements())
- {
- multiacc.append(proxy.getAccessionSeparator());
- }
+ sb.append("; ");
}
- try
- {
- aresultq.add(multiacc.toString());
- aresult.add(proxy.getSequenceRecords(multiacc.toString()));
- } catch (OutOfMemoryError oome)
+ if (lr - sb.length() > 40)
{
- new OOMWarning("fetching " + multiacc + " from "
- + database.getSelectedItem(), oome, this);
+ sb.append("\n");
}
-
+ sb.append(s);
}
+ showErrorMessage(sb.toString());
+ }
+ resetDialog();
+ }
- } catch (Exception e)
+ /**
+ * 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<String> accessions, List<String> aresultq,
+ List<AlignmentI> aresult, List<String> nextFetch) throws Exception
+ {
+ StringBuilder multiacc = new StringBuilder();
+ List<String> tosend = new ArrayList<>();
+ while (accessions.hasNext())
{
- 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();
+ String nel = accessions.next();
+ tosend.add(nel);
+ multiacc.append(nel);
+ if (accessions.hasNext())
+ {
+ multiacc.append(proxy.getAccessionSeparator());
+ }
}
- if (aresult != null && aresult.size() > 0)
+
+ try
{
- AlignmentI ar = null;
- if (isAliSource)
+ String query = multiacc.toString();
+ AlignmentI rslt = proxy.getSequenceRecords(query);
+ if (rslt == null || rslt.getHeight() == 0)
{
- // new window for each result
- while (aresult.size() > 0)
- {
- parseResult(aresult.remove(0), aresultq.remove(0) + " "
- + getDefaultRetrievalTitle(), null);
- }
+ // no results - pass on all queries to next source
+ nextFetch.addAll(tosend);
}
else
{
- // concatenate all results in one window
- while (aresult.size() > 0)
+ aresultq.add(query);
+ aresult.add(rslt);
+ if (tosend.size() > 1)
{
- if (ar == null)
- {
- ar = aresult.remove(0);
- }
- else
- {
- ar.append(aresult.remove(0));
- }
- ;
+ checkResultForQueries(rslt, tosend, nextFetch, proxy);
}
- parseResult(ar, null, null);
}
+ } catch (OutOfMemoryError oome)
+ {
+ new OOMWarning("fetching " + multiacc + " from "
+ + database.getSelectedItem(), oome, this);
}
- // only remove visual delay after we finished parsing.
- guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
- resetDialog();
}
- AlignmentI parseResult(String result, String title)
+ /**
+ * 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<String> aresultq, List<AlignmentI> aresult)
{
- String format = new IdentifyFile().Identify(result, "Paste");
- Alignment sequences = null;
- if (FormatAdapter.isValidFormat(format))
+ boolean success = false;
+ try
{
- sequences = null;
+ if (aresult != null)
+ {
+ try
+ {
+ // give the server a chance to breathe
+ Thread.sleep(5);
+ } catch (Exception e)
+ {
+ //
+ }
+ }
+
+ AlignmentI indres = null;
try
{
- sequences = new FormatAdapter().readFile(result.toString(),
- "Paste", format);
- } catch (Exception ex)
+ indres = proxy.getSequenceRecords(accession);
+ } catch (OutOfMemoryError oome)
{
+ new OOMWarning(
+ "fetching " + accession + " from " + proxy.getDbName(),
+ oome, this);
}
-
- if (sequences != null)
+ if (indres != null)
{
- return parseResult(sequences, title, format);
+ aresultq.add(accession);
+ aresult.add(indres);
+ success = true;
}
- }
- else
+ } catch (Exception e)
{
- showErrorMessage("Error retrieving " + textArea.getText() + " from "
- + database.getSelectedItem());
+ Cache.log.info("Error retrieving " + accession + " from "
+ + proxy.getDbName(), e);
}
+ return success;
+ }
- return null;
+ /**
+ * 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<String> queries,
+ List<String> nextFetch, DbSourceProxy proxy)
+ {
+ SequenceI[] rs = rslt.getSequencesArray();
+
+ for (String q : queries)
+ {
+ 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; r < rs.length; r++)
+ {
+ if (rs[r] != null)
+ {
+ List<DBRefEntry> found = DBRefUtils.searchRefs(rs[r].getDBRefs(),
+ accId);
+ if (!found.isEmpty())
+ {
+ rfound = true;
+ break;
+ }
+ }
+ }
+ if (!rfound)
+ {
+ nextFetch.add(q);
+ }
+ }
}
/**
}
AlignmentI parseResult(AlignmentI al, String title,
- String currentFileFormat)
+ 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,
// Alignments?
}
- if (title == null)
- {
- 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 (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);
+ }
+ if (newAlframes != null)
+ {
+ newAlframes.add(af);
}
Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- af.statusBar.setText("Successfully pasted alignment file");
+ af.setStatus(MessageManager
+ .getString("label.successfully_pasted_alignment_file"));
try
{
- af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
- false));
+ af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (Exception ex)
{
}
}
else
{
- for (int i = 0; i < al.getHeight(); i++)
- {
- alignFrame.viewport.getAlignment().addSequence(
- al.getSequenceAt(i)); // this
- // also
- // creates
- // dataset
- // sequence
- // entries
- }
- alignFrame.viewport.setEndSeq(alignFrame.viewport.getAlignment()
- .getHeight());
- alignFrame.viewport.getAlignment().getWidth();
- alignFrame.viewport.firePropertyChange("alignment", null,
- alignFrame.viewport.getAlignment().getSequences());
+ alignFrame.viewport.addAlignment(al, title);
}
}
return al;
resetDialog();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
- "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);
+ 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;
+ }
+
+ /**
+ * Make this panel visible (after a selection has been made in the database
+ * chooser)
+ */
+ void showPanel()
+ {
+ frame.setVisible(true);
+ }
+
+ /**
+ * Hide this panel (on clicking the database button to open the database
+ * chooser)
+ */
+ void hidePanel()
+ {
+ frame.setVisible(false);
+ }
+
+ public void setDatabaseChooserVisible(boolean b)
+ {
+ databaseButt.setVisible(b);
+ }
}