/*
- * 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.io.*;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-
-import MCview.*;
-import jalview.datamodel.*;
-import jalview.datamodel.xdb.embl.*;
-import java.io.File;
-import jalview.io.*;
-import jalview.ws.DBRefFetcher;
-import jalview.ws.ebi.EBIFetchClient;
-import jalview.ws.seqfetcher.ASequenceFetcher;
+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.Rectangle;
import java.awt.BorderLayout;
-import java.awt.Dimension;
-
+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.
+ * <p>
+ * 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
{
- // ASequenceFetcher sfetch;
- JInternalFrame frame;
+ private static jalview.ws.SequenceFetcher sfetch = null;
- IProgressIndicator guiWindow;
+ JLabel exampleAccession;
- AlignFrame alignFrame;
+ JComboBox<String> database;
- StringBuffer result;
+ JCheckBox replacePunctuation;
- final String noDbSelected = "-- Select Database --";
+ JButton okBtn;
- Hashtable sources = new Hashtable();
+ JButton exampleBtn;
- private static jalview.ws.SequenceFetcher sfetch = null;
+ JButton closeBtn;
- private static String dasRegistry = null;
+ JButton backBtn;
- private static boolean _initingFetcher = false;
+ JTextArea textArea;
- private static Thread initingThread = null;
+ JInternalFrame frame;
+
+ IProgressIndicator guiWindow;
+
+ AlignFrame alignFrame;
+
+ GFTSPanel parentSearchPanel;
+
+ IProgressIndicator progressIndicator;
+
+ volatile boolean _isConstructing = false;
/**
- * Blocking method that initialises and returns the shared instance of the
- * SequenceFetcher client
+ * Returns the shared instance of the SequenceFetcher client
*
- * @param guiWindow
- * - where the initialisation delay message should be shown
- * @return the singleton instance of the sequence fetcher client
+ * @return
*/
- public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
- final IProgressIndicator guiWindow)
+ public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton()
{
- if (_initingFetcher && initingThread != null && initingThread.isAlive())
- {
- if (guiWindow != null)
- {
- guiWindow.setProgressBar(
- "Waiting for Sequence Database Fetchers to initialise",
- Thread.currentThread().hashCode());
- }
- // initting happening on another thread - so wait around to see if it
- // finishes.
- while (_initingFetcher && initingThread != null
- && initingThread.isAlive())
- {
- try
- {
- Thread.sleep(10);
- } catch (Exception e)
- {
- }
- ;
- }
- if (guiWindow != null)
- {
- guiWindow.setProgressBar(
- "Waiting for Sequence Database Fetchers to initialise",
- Thread.currentThread().hashCode());
- }
- }
- if (sfetch == null
- || dasRegistry != DasSourceBrowser.getDasRegistryURL())
+ if (sfetch == null)
{
- _initingFetcher = true;
- initingThread = Thread.currentThread();
- /**
- * give a visual indication that sequence fetcher construction is occuring
- */
- if (guiWindow != null)
- {
- guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
- Thread.currentThread().hashCode());
- }
- dasRegistry = DasSourceBrowser.getDasRegistryURL();
- jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
- if (guiWindow != null)
- {
- guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
- Thread.currentThread().hashCode());
- }
- sfetch = sf;
- _initingFetcher = false;
- initingThread = 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)
{
- final IProgressIndicator guiWindow = guiIndic;
- final SequenceFetcher us = this;
- // launch initialiser thread
- Thread sf = new Thread(new Runnable()
- {
-
- public void run()
- {
- if (getSequenceFetcherSingleton(guiWindow) != null)
- {
- us.initGui(guiWindow);
- }
- else
- {
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- 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);
- }
- });
-
- // raise warning dialog
- }
- }
- });
- sf.start();
+ this(guiIndic, null, null);
}
/**
- * called by thread spawned by constructor
+ * Constructor with specified database and accession(s) to retrieve
*
- * @param guiWindow
+ * @param guiIndic
+ * @param selectedDb
+ * @param queryString
*/
- private void initGui(IProgressIndicator guiWindow)
+ public SequenceFetcher(IProgressIndicator guiIndic,
+ final String selectedDb, final String queryString)
{
- this.guiWindow = guiWindow;
- if (guiWindow instanceof AlignFrame)
- {
- alignFrame = (AlignFrame) guiWindow;
- }
+ this.progressIndicator = guiIndic;
+ getSequenceFetcherSingleton();
+ this.guiWindow = progressIndicator;
- database.addItem(noDbSelected);
- /*
- * Dynamically generated database list will need a translation function from
- * internal source to externally distinct names. UNIPROT and UP_NAME are
- * identical DB sources, and should be collapsed.
- */
-
- String dbs[] = sfetch.getOrderedSupportedSources();
- for (int i = 0; i < dbs.length; i++)
+ if (progressIndicator instanceof AlignFrame)
{
- if (!sources.containsValue(dbs[i]))
- {
- String name = sfetch.getSourceProxy(dbs[i]).getDbName();
- // duplicate source names are thrown away, here.
- if (!sources.containsKey(name))
- {
- database.addItem(name);
- }
- // overwrite with latest version of the retriever for this source
- sources.put(name, dbs[i]);
- }
- }
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- ex.printStackTrace();
+ alignFrame = (AlignFrame) progressIndicator;
}
+ jbInit(selectedDb);
+ textArea.setText(queryString);
+
frame = new JInternalFrame();
frame.setContentPane(this);
- if (new jalview.util.Platform().isAMac())
- {
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
- }
- else
- {
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
- }
+ int height = Platform.isAMac() ? 240 : 180;
+ Desktop.addInternalFrame(frame, getFrameTitle(), true, 400, height);
}
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"));
}
- private void jbInit() throws Exception
+ private void jbInit(String selectedDb)
{
- this.setLayout(borderLayout2);
+ this.setLayout(new BorderLayout());
+ database = new JComboBox<>();
database.setFont(JvSwingUtils.getLabelFont());
- dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
- jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
+ 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))
+ {
+ new PDBFTSPanel(SequenceFetcher.this);
+ frame.dispose();
+ }
+ else if ("uniprot".equalsIgnoreCase(currentSelection))
+ {
+ new UniprotFTSPanel(SequenceFetcher.this);
+ frame.dispose();
+ }
+ 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.CENTER);
- jLabel1.setText("Separate multiple accession ids with semi colon \";\"");
+ replacePunctuation = new JCheckBox(
+ MessageManager.getString("label.replace_commas_semicolons"));
replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
- replacePunctuation
- .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
- replacePunctuation.setText("Replace commas with semi-colons");
- ok.setText("OK");
- ok.addActionListener(new ActionListener()
+ 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();
}
});
- clear.setText("Clear");
+ JButton clear = new JButton(MessageManager.getString("action.clear"));
clear.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
clear_actionPerformed();
}
});
- example.setText("Example");
- example.addActionListener(new ActionListener()
+ exampleBtn = new JButton(MessageManager.getString("label.example"));
+ exampleBtn.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
example_actionPerformed();
}
});
- close.setText("Close");
- close.addActionListener(new ActionListener()
+ 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();
+ }
}
});
- jPanel3.setLayout(borderLayout1);
- borderLayout1.setVgap(5);
- jPanel1.add(ok);
- jPanel1.add(example);
- jPanel1.add(clear);
- jPanel1.add(close);
- jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
- jPanel2.setLayout(borderLayout3);
- database.addActionListener(new ActionListener()
- {
+ 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);
- public void actionPerformed(ActionEvent e)
+ 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<String> hs = new HashSet<>();
+ for (DbSourceProxy dbs : sfetch.getSourceProxy(db))
+ {
+ String tq = dbs.getTestQuery();
+ if (hs.add(tq)) // not a duplicate source
{
- DbSourceProxy db = null;
- try
- {
- db = sfetch.getSourceProxy((String) sources.get(database
- .getSelectedItem()));
- String eq = db.getTestQuery();
- dbeg.setText("Example query: " + eq);
- replacePunctuation.setEnabled(!(eq != null && eq.indexOf(",") > -1));
- } catch (Exception ex)
+ if (sb.length() > 0)
{
- dbeg.setText("");
- replacePunctuation.setEnabled(true);
+ sb.append(";");
}
- jPanel2.repaint();
+ sb.append(tq);
}
- });
- dbeg.setText("");
- jPanel2.add(database, java.awt.BorderLayout.NORTH);
- jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
- JPanel jPanel2a = new JPanel(new BorderLayout());
- jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
- jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
- jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
- // jPanel2.setPreferredSize(new Dimension())
- jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
- this.add(jPanel1, java.awt.BorderLayout.SOUTH);
- this.add(jPanel3, java.awt.BorderLayout.CENTER);
- this.add(jPanel2, java.awt.BorderLayout.NORTH);
- jScrollPane1.getViewport().add(textArea);
-
+ }
+ return sb.toString();
}
- protected void example_actionPerformed()
+ /**
+ * 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()
{
- DbSourceProxy db = null;
try
{
- db = sfetch.getSourceProxy((String) sources.get(database
- .getSelectedItem()));
- textArea.setText(db.getTestQuery());
+ 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);
}
- jPanel3.repaint();
+ repaint();
}
- protected void clear_actionPerformed()
+ /**
+ * 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)
{
- textArea.setText("");
- jPanel3.repaint();
+ String eq = getExampleQueries(selectedDatabase);
+ exampleAccession.setText(MessageManager
+ .formatMessage("label.example_query_param", new String[]
+ { eq }));
+ return eq;
}
- JLabel dbeg = new JLabel();
-
- JComboBox database = new JComboBox();
-
- 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();
+ /**
+ * 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();
+ }
- BorderLayout borderLayout3 = new BorderLayout();
+ /**
+ * Clears the query input field
+ */
+ protected void clear_actionPerformed()
+ {
+ textArea.setText("");
+ repaint();
+ }
- public void close_actionPerformed(ActionEvent e)
+ /**
+ * 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()
{
- database.setEnabled(false);
+ /*
+ * tidy inputs and check there is something to search for
+ */
+ String text = textArea.getText();
+ if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
+ {
+ text = text.replace(",", ";");
+ }
+ text = text.replaceAll("(\\s|[,; ])+", ";");
+ textArea.setText(text);
+ if (text.isEmpty())
+ {
+ // todo i18n
+ showErrorMessage(
+ "Please enter a (semi-colon separated list of) database id(s)");
+ resetDialog();
+ return;
+ }
+ exampleBtn.setEnabled(false);
textArea.setEnabled(false);
- ok.setEnabled(false);
- close.setEnabled(false);
+ okBtn.setEnabled(false);
+ closeBtn.setEnabled(false);
+ backBtn.setEnabled(false);
Thread worker = new Thread(this);
worker.start();
private void resetDialog()
{
- database.setEnabled(true);
+ exampleBtn.setEnabled(true);
textArea.setEnabled(true);
- ok.setEnabled(true);
- close.setEnabled(true);
+ okBtn.setEnabled(true);
+ closeBtn.setEnabled(true);
+ backBtn.setEnabled(parentSearchPanel != null);
}
+ @Override
public void run()
{
- String error = "";
- if (database.getSelectedItem().equals(noDbSelected))
- {
- error += "Please select the source database\n";
- }
- // TODO: make this transformation more configurable
- com.stevesoft.pat.Regex empty;
- if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
- {
- empty = new com.stevesoft.pat.Regex(
- // replace commas and spaces with a semicolon
- "(\\s|[,; ])+", ";");
- }
- else
- {
- // just turn spaces and semicolons into single semicolons
- empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
- }
- 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()))
- {
- error += "Please enter a (semi-colon separated list of) database id(s)";
- }
- if (error.length() > 0)
- {
- showErrorMessage(error);
- resetDialog();
- return;
- }
- ArrayList<String> aresultq=new ArrayList<String>();
- ArrayList<AlignmentI> aresult = new ArrayList<AlignmentI>();
- Object source = database.getSelectedItem();
- Enumeration en = new StringTokenizer(textArea.getText(), ";");
- boolean isAliSource=false;
- try
- {
- guiWindow.setProgressBar(
- "Fetching Sequences from " + database.getSelectedItem(),
- Thread.currentThread().hashCode());
- DbSourceProxy proxy = sfetch.getSourceProxy((String) sources
- .get(source));
- isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
- if (proxy.getAccessionSeparator() == null)
+ boolean addToLast = false;
+ List<String> aresultq = new ArrayList<>();
+ List<String> presultTitle = new ArrayList<>();
+ List<AlignmentI> presult = new ArrayList<>();
+ List<AlignmentI> aresult = new ArrayList<>();
+ List<DbSourceProxy> sources = sfetch
+ .getSourceProxy((String) database.getSelectedItem());
+ Iterator<DbSourceProxy> proxies = sources.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))
+ {
+ 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 "
- + database.getSelectedItem(), 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 " + source, 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
+ if (lr - sb.length() > 40)
{
- aresultq.add(multiacc.toString());
- aresult.add(proxy.getSequenceRecords(multiacc.toString()));
- } catch (OutOfMemoryError oome)
- {
- new OOMWarning("fetching " + multiacc + " from "
- + database.getSelectedItem(), oome, this);
+ sb.append("\n");
}
-
+ sb.append(s);
}
+ showErrorMessage(sb.toString());
+ }
+ resetDialog();
+ }
- } 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();
+ /**
+ * 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())
+ {
+ 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) {
- // new window for each result
- while (aresult.size()>0)
- {
- parseResult(aresult.remove(0), aresultq.remove(0)+" "+getDefaultRetrievalTitle(), null);
- }
- } else {
- // concatenate all results in one window
- while (aresult.size()>0)
+ 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)
{
- 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();
}
- /*
- * result = new StringBuffer(); if
- * (database.getSelectedItem().equals("Uniprot")) {
- * getUniprotFile(textArea.getText()); } else if
- * (database.getSelectedItem().equals("EMBL") ||
- * database.getSelectedItem().equals("EMBLCDS")) { String DBRefSource =
- * database.getSelectedItem().equals("EMBLCDS") ?
- * jalview.datamodel.DBRefSource.EMBLCDS : jalview.datamodel.DBRefSource.EMBL;
- *
- * StringTokenizer st = new StringTokenizer(textArea.getText(), ";");
- * SequenceI[] seqs = null; while(st.hasMoreTokens()) { EBIFetchClient dbFetch
- * = new EBIFetchClient(); String qry =
- * database.getSelectedItem().toString().toLowerCase( ) + ":" +
- * st.nextToken(); File reply = dbFetch.fetchDataAsFile( qry, "emblxml",null);
- *
- * jalview.datamodel.xdb.embl.EmblFile efile=null; if (reply != null &&
- * reply.exists()) { efile =
- * jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply); } if (efile!=null)
- * { for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) { EmblEntry
- * entry = (EmblEntry) i.next(); SequenceI[] seqparts =
- * entry.getSequences(false,true, DBRefSource); if (seqparts!=null) {
- * SequenceI[] newseqs = null; int si=0; if (seqs==null) { newseqs = new
- * SequenceI[seqparts.length]; } else { newseqs = new
- * SequenceI[seqs.length+seqparts.length];
- *
- * for (;si<seqs.length; si++) { newseqs[si] = seqs[si]; seqs[si] = null; } }
- * for (int j=0;j<seqparts.length; si++, j++) { newseqs[si] =
- * seqparts[j].deriveSequence(); // place DBReferences on dataset and refer }
- * seqs=newseqs; } } } else { result.append("# no response for "+qry); } } if
- * (seqs!=null && seqs.length>0) { if (parseResult(new Alignment(seqs), null,
- * null)!=null) { result.append("# Successfully parsed the
- * "+database.getSelectedItem()+" Queries into an Alignment"); } } } else if
- * (database.getSelectedItem().equals("PDB")) { StringTokenizer qset = new
- * StringTokenizer(textArea.getText(), ";"); String query; SequenceI[] seqs =
- * null; while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null)) {
- * SequenceI[] seqparts = getPDBFile(query.toUpperCase()); if (seqparts !=
- * null) { if (seqs == null) { seqs = seqparts; } else { SequenceI[] newseqs =
- * new SequenceI[seqs.length+seqparts.length]; int i=0; for (; i <
- * seqs.length; i++) { newseqs[i] = seqs[i]; seqs[i] = null; } for (int
- * j=0;j<seqparts.length; i++, j++) { newseqs[i] = seqparts[j]; }
- * seqs=newseqs; } result.append("# Success for "+query.toUpperCase()+"\n"); }
- * } if (seqs != null && seqs.length > 0) { if (parseResult(new
- * Alignment(seqs), null, null)!=null) { result.append( "# Successfully parsed
- * the PDB File Queries into an
- * Alignment"); } } } else if( database.getSelectedItem().equals("PFAM")) {
- * try { result.append(new FastaFile(
- * "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc=" +
- * textArea.getText().toUpperCase(), "URL").print() );
- *
- * if(result.length()>0) { parseResult( result.toString(),
- * textArea.getText().toUpperCase() ); } } catch (java.io.IOException ex) {
- * result = null; } }
- *
- * if (result == null || result.length() == 0) { showErrorMessage("Error
- * retrieving " + textArea.getText() + " from " + database.getSelectedItem());
- * }
- *
- * resetDialog(); return; }
- *
- * void getUniprotFile(String id) { EBIFetchClient ebi = new EBIFetchClient();
- * File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
- *
- * DBRefFetcher dbref = new DBRefFetcher(); Vector entries =
- * dbref.getUniprotEntries(file);
- *
- * if (entries != null) { //First, make the new sequences Enumeration en =
- * entries.elements(); while (en.hasMoreElements()) { UniprotEntry entry =
- * (UniprotEntry) en.nextElement();
- *
- * StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot"); Enumeration
- * en2 = entry.getAccession().elements(); while (en2.hasMoreElements()) {
- * name.append("|"); name.append(en2.nextElement()); } en2 =
- * entry.getName().elements(); while (en2.hasMoreElements()) {
- * name.append("|"); name.append(en2.nextElement()); }
- *
- * if (entry.getProtein() != null) { name.append(" " +
- * entry.getProtein().getName().elementAt(0)); }
- *
- * result.append(name + "\n" + entry.getUniprotSequence().getContent() +
- * "\n"); }
- *
- * //Then read in the features and apply them to the dataset Alignment al =
- * parseResult(result.toString(), null); for (int i = 0; i < entries.size();
- * i++) { UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
- * Enumeration e = entry.getDbReference().elements(); Vector onlyPdbEntries =
- * new Vector(); while (e.hasMoreElements()) { PDBEntry pdb = (PDBEntry)
- * e.nextElement(); if (!pdb.getType().equals("PDB")) { continue; }
- *
- * onlyPdbEntries.addElement(pdb); }
- *
- * Enumeration en2 = entry.getAccession().elements(); while
- * (en2.hasMoreElements()) {
- * al.getSequenceAt(i).getDatasetSequence().addDBRef(new DBRefEntry(
- * DBRefSource.UNIPROT, "0", en2.nextElement().toString())); }
- *
- *
- *
- *
- * al.getSequenceAt(i).getDatasetSequence().setPDBId(onlyPdbEntries); if
- * (entry.getFeature() != null) { e = entry.getFeature().elements(); while
- * (e.hasMoreElements()) { SequenceFeature sf = (SequenceFeature)
- * e.nextElement(); sf.setFeatureGroup("Uniprot");
- * al.getSequenceAt(i).getDatasetSequence().addSequenceFeature( sf ); } } } }
- * }
- *
- * SequenceI[] getPDBFile(String id) { Vector result = new Vector(); String
- * chain = null; if (id.indexOf(":") > -1) { chain =
- * id.substring(id.indexOf(":") + 1); id = id.substring(0, id.indexOf(":")); }
- *
- * EBIFetchClient ebi = new EBIFetchClient(); String file =
- * ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw"). getAbsolutePath(); if (file
- * == null) { return null; } try { PDBfile pdbfile = new PDBfile(file,
- * jalview.io.AppletFormatAdapter.FILE); for (int i = 0; i <
- * pdbfile.chains.size(); i++) { if (chain == null || ( (PDBChain)
- * pdbfile.chains.elementAt(i)).id. toUpperCase().equals(chain)) { PDBChain
- * pdbchain = (PDBChain) pdbfile.chains.elementAt(i); // Get the Chain's
- * Sequence - who's dataset includes any special features added from the PDB
- * file SequenceI sq = pdbchain.sequence; // Specially formatted name for the
- * PDB chain sequences retrieved from the PDB
- * sq.setName("PDB|"+id+"|"+sq.getName()); // Might need to add more metadata
- * to the PDBEntry object // like below /* PDBEntry entry = new PDBEntry(); //
- * Construct the PDBEntry entry.setId(id); if (entry.getProperty() == null)
- * entry.setProperty(new Hashtable()); entry.getProperty().put("chains",
- * pdbchain.id + "=" + sq.getStart() + "-" + sq.getEnd());
- * sq.getDatasetSequence().addPDBId(entry); // Add PDB DB Refs // We make a
- * DBRefEtntry because we have obtained the PDB file from a verifiable source
- * // JBPNote - PDB DBRefEntry should also carry the chain and mapping
- * information DBRefEntry dbentry = new
- * DBRefEntry(jalview.datamodel.DBRefSource.PDB, "0", id + pdbchain.id);
- * sq.addDBRef(dbentry); // and add seuqence to the retrieved set
- * result.addElement(sq.deriveSequence()); } }
- *
- * if (result.size() < 1) { throw new Exception("WsDBFetch for PDB id resulted
- * in zero result size"); } } catch (Exception ex) // Problem parsing PDB file
- * { jalview.bin.Cache.log.warn("Exception when retrieving " +
- * textArea.getText() + " from " + database.getSelectedItem(), ex); return
- * null; }
- *
+ /**
+ * Query for a single accession id via the database proxy
*
- * SequenceI[] results = new SequenceI[result.size()]; for (int i = 0, j =
- * result.size(); i < j; i++) { results[i] = (SequenceI) result.elementAt(i);
- * result.setElementAt(null,i); } return results; }
+ * @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
*/
- AlignmentI parseResult(String result, String title)
+ 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;
+ }
+
+ /**
+ * 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();
- return null;
+ 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);
+ }
+ }
}
/**
*
- * @return a standard title for any results retrieved using the currently selected source and settings
+ * @return a standard title for any results retrieved using the currently
+ * selected source and settings
*/
- public String getDefaultRetrievalTitle() {
+ public String getDefaultRetrievalTitle()
+ {
return "Retrieved from " + database.getSelectedItem();
}
+
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,
AlignFrame.DEFAULT_HEIGHT);
if (currentFileFormat != null)
{
- af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
- // FORMAT FOR
- // NON-FormatAdapter Sourced
- // Alignments?
+ af.currentFileFormat = currentFileFormat;
}
- if (title == null)
- {
- title = getDefaultRetrievalTitle();
- }
- SequenceFeature[] sfs = null;
- for (Enumeration sq = al.getSequences().elements(); sq
- .hasMoreElements();)
+ List<SequenceI> alsqs = al.getSequences();
+ synchronized (alsqs)
{
- 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);
}
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;
+ }
+
+ /**
+ * 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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff