*/
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 com.stevesoft.pat.Regex;
-
-import jalview.datamodel.*;
-import jalview.io.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
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.Iterator;
+import java.util.List;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.SwingConstants;
+import javax.swing.tree.DefaultMutableTreeNode;
+
+import com.stevesoft.pat.Regex;
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();
+
+ 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 Thread initingThread = null;
+ int debounceTrap = 0;
/**
* Blocking method that initialises and returns the shared instance of the
* SequenceFetcher client
return sfetch;
}
+ private IProgressIndicator progressIndicator;
public SequenceFetcher(IProgressIndicator guiIndic)
{
- final IProgressIndicator guiWindow = guiIndic;
+ 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);
}
else
{
public void keyPressed(KeyEvent e)
{
if (e.getKeyCode() == KeyEvent.VK_ENTER)
+ {
ok_actionPerformed();
+ }
}
});
jPanel3.setLayout(borderLayout1);
databaseButt.setFont(JvSwingUtils.getLabelFont());
database.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
- 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 }));
- 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);
+ debounceTrap++;
+ String currentSelection = database.getSelectedItem();
- } catch (Exception ex)
+ if (!currentSelection.equalsIgnoreCase("pdb"))
{
- dbeg.setText("");
- replacePunctuation.setEnabled(true);
+ otherSourceAction();
}
- jPanel2.repaint();
+ if (currentSelection.equalsIgnoreCase("pdb") && ((debounceTrap % 2) == 0))
+ {
+ pdbSourceAction();
+ }
+
}
});
dbeg.setText("");
}
+ private void pdbSourceAction()
+ {
+ databaseButt.setText(database.getSelectedItem());
+ new PDBSearchPanel(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 }));
+ 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("");
+ replacePunctuation.setEnabled(true);
+ }
+ jPanel2.repaint();
+ }
+
protected void example_actionPerformed()
{
DbSourceProxy db = null;
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)
{
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;
List<SequenceI> alsqs;
synchronized (alsqs = al.getSequences())
{
for (SequenceI sq : alsqs)
{
- if ((sfs = (sq).getDatasetSequence().getSequenceFeatures()) != null)
+ if ((sfs = sq.getSequenceFeatures()) != null)
{
if (sfs.length > 0)
{
}
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;
}
});
}
+
+ public IProgressIndicator getProgressIndicator()
+ {
+ return progressIndicator;
+ }
+
+ public void setProgressIndicator(IProgressIndicator progressIndicator)
+ {
+ this.progressIndicator = progressIndicator;
+ }
}
git://source.jalview.org / jalview.git / blobdiff