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Commit e83db98a authored by tjc's avatar tjc
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options for searching and deleting duplicate qualifiers 

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8268 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent 71864a4d
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uk/ac/sanger/artemis/components/FindAndReplace.java
+ 182
− 25
View file @ e83db98a
......@@ -22,23 +22,24 @@
package uk.ac.sanger.artemis.components;
import java.awt.BorderLayout;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.util.regex.Pattern;
import javax.swing.ButtonGroup;
import javax.swing.Box;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
import javax.swing.JRadioButton;
import javax.swing.JSeparator;
import javax.swing.JPanel;
import javax.swing.JTabbedPane;
import javax.swing.JTextField;
import javax.swing.SwingConstants;
import uk.ac.sanger.artemis.Entry;
import uk.ac.sanger.artemis.EntryGroup;
......@@ -46,6 +47,7 @@ import uk.ac.sanger.artemis.EntryGroupChangeEvent;
import uk.ac.sanger.artemis.EntryGroupChangeListener;
import uk.ac.sanger.artemis.Feature;
import uk.ac.sanger.artemis.FeatureKeyQualifierPredicate;
import uk.ac.sanger.artemis.FeaturePredicate;
import uk.ac.sanger.artemis.FeatureVector;
import uk.ac.sanger.artemis.FilteredEntryGroup;
import uk.ac.sanger.artemis.GotoEventSource;
......@@ -58,21 +60,84 @@ import uk.ac.sanger.artemis.io.QualifierVector;
import uk.ac.sanger.artemis.util.ReadOnlyException;
import uk.ac.sanger.artemis.util.StringVector;
public class FindAndReplace extends JFrame
implements EntryGroupChangeListener
{
private static final long serialVersionUID = 1L;
private EntryGroup entry_group;
/**
* Find, replace and delete qualifiers
* @param selection
* @param goto_event_source
* @param entry_group
* @param base_plot_group
*/
public FindAndReplace(final Selection selection,
final GotoEventSource goto_event_source,
final EntryGroup entry_group,
final BasePlotGroup base_plot_group)
{
super("Find/Replace Qualifier Text");
super("Find/Replace/Delete");
this.entry_group = entry_group;
final JTabbedPane tabPane = new JTabbedPane();
getContentPane().add(tabPane, BorderLayout.CENTER);
addFindReplaceTab(selection, goto_event_source,
base_plot_group, tabPane);
addFindDeleteDuplicateTab(selection, goto_event_source,
entry_group, base_plot_group, tabPane);
addWindowListener(new WindowAdapter()
{
public void windowClosing(WindowEvent event)
{
entry_group.removeEntryGroupChangeListener(FindAndReplace.this);
FindAndReplace.this.dispose();
}
});
final Box xbox = Box.createHorizontalBox();
final JButton closeButton = new JButton("Close");
closeButton.setHorizontalAlignment(SwingConstants.LEFT);
closeButton.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
entry_group.removeEntryGroupChangeListener(FindAndReplace.this);
FindAndReplace.this.dispose();
}
});
xbox.add(closeButton);
xbox.add(Box.createHorizontalGlue());
getContentPane().add(xbox, BorderLayout.SOUTH);
pack();
Utilities.centreFrame(this);
setVisible(true);
}
/**
* Find and replace option for qualifier text
* @param selection
* @param goto_event_source
* @param base_plot_group
* @param tabPane
*/
private void addFindReplaceTab(final Selection selection,
final GotoEventSource goto_event_source,
final BasePlotGroup base_plot_group,
final JTabbedPane tabPane)
{
GridBagLayout gridbag = new GridBagLayout();
getContentPane().setLayout(gridbag);
JPanel panel = new JPanel(gridbag);
tabPane.addTab("Qualifier Text", panel);
GridBagConstraints c = new GridBagConstraints();
......@@ -105,20 +170,20 @@ public class FindAndReplace extends JFrame
final JTextField findTextField = new JTextField(15);
c.gridx = 0;
c.gridy = ++ypos;
getContentPane().add(new JLabel("Find:"),c);
panel.add(new JLabel("Find:"),c);
c.gridx = 1;
getContentPane().add(findTextField, c);
panel.add(findTextField, c);
final JTextField replaceTextField = new JTextField(15);
c.gridx = 0;
c.gridy = ++ypos;
getContentPane().add(new JLabel("Replace with:"), c);
panel.add(new JLabel("Replace with:"), c);
c.gridx = 1;
getContentPane().add(replaceTextField, c);
panel.add(replaceTextField, c);
c.gridx = 0;
c.gridy = ++ypos;
getContentPane().add(key_selector,c);
panel.add(key_selector,c);
final JCheckBox selectedKeyButton = new JCheckBox("Restrict to Selected Key", false);
selectedKeyButton.addActionListener(new ActionListener()
......@@ -132,18 +197,18 @@ public class FindAndReplace extends JFrame
}
});
c.gridx = 1;
getContentPane().add(selectedKeyButton,c);
panel.add(selectedKeyButton,c);
final JCheckBox caseSensitive = new JCheckBox("Case sensitive", true);
c.gridx = 0;
c.gridy = ++ypos;
getContentPane().add(caseSensitive, c);
panel.add(caseSensitive, c);
final JCheckBox qualifierValueSubString = new JCheckBox("Match substring", true);
c.gridy = ++ypos;
getContentPane().add(qualifierValueSubString, c);
panel.add(qualifierValueSubString, c);
final JButton findButton = new JButton("Find");
findButton.addActionListener(new ActionListener()
......@@ -178,7 +243,7 @@ public class FindAndReplace extends JFrame
});
c.gridx = 0;
c.gridy = ++ypos;
getContentPane().add(findButton, c);
panel.add(findButton, c);
final JButton replaceButton = new JButton("Replace");
replaceButton.addActionListener(new ActionListener()
......@@ -221,7 +286,102 @@ public class FindAndReplace extends JFrame
}
});
c.gridx = 1;
getContentPane().add(replaceButton, c);
panel.add(replaceButton, c);
}
/**
* Search and delete options for duplicate qualifiers on features
* @param selection
* @param goto_event_source
* @param entry_group
* @param base_plot_group
* @param tabPane
*/
public void addFindDeleteDuplicateTab(final Selection selection,
final GotoEventSource goto_event_source,
final EntryGroup entry_group,
final BasePlotGroup base_plot_group,
final JTabbedPane tabPane)
{
GridBagLayout gridbag = new GridBagLayout();
final JPanel panel = new JPanel(gridbag);
tabPane.addTab("Duplicate Qualifiers", panel);
panel.setLayout(gridbag);
GridBagConstraints c = new GridBagConstraints();
c.fill = GridBagConstraints.HORIZONTAL;
c.anchor = GridBagConstraints.WEST;
c.ipadx = 5;
c.ipady = 5;
c.gridx = 0;
c.gridy = 0;
c.gridwidth = 3;
panel.add(new JLabel("Search for duplicate qualifiers:"), c);
c.gridwidth = 1;
final JButton findButton = new JButton("Find");
findButton.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
final FeaturePredicate predicate = new FeaturePredicate ()
{
public boolean testPredicate (final Feature feature)
{
return findOrDeleteDuplicate(feature, false);
}
};
final FilteredEntryGroup filtered_entry_group =
new FilteredEntryGroup(entry_group, predicate, "Features with duplicate qualifiers");
final FeatureListFrame feature_list_frame =
new FeatureListFrame("Features Found",
selection,
goto_event_source, filtered_entry_group,
base_plot_group);
feature_list_frame.setVisible(true);
}
});
c.gridx = 0;
c.gridy = 1;
panel.add(findButton, c);
final JButton deleteButton = new JButton("Delete");
deleteButton.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
final FeaturePredicate predicate = new FeaturePredicate ()
{
public boolean testPredicate(final Feature feature)
{
return findOrDeleteDuplicate(feature, true);
}
};
int ncount = 0;
final FeatureVector features = entry_group.getAllFeatures();
for(int i=0; i<features.size(); i++)
{
if(predicate.testPredicate(features.elementAt(i)))
ncount++;
}
JOptionPane.showMessageDialog(FindAndReplace.this,
( (ncount>0) ? "Duplicate qualifiers in "+ncount+" feature(s) deleted." :
"No duplicate qualifiers found."),
"Duplicate Qualifiers",
JOptionPane.INFORMATION_MESSAGE);
}
});
c.gridx = 1;
panel.add(deleteButton, c);
addWindowListener(new WindowAdapter()
{
......@@ -231,10 +391,7 @@ public class FindAndReplace extends JFrame
FindAndReplace.this.dispose();
}
});
pack();
Utilities.centreFrame(this);
setVisible(true);
}
/**
......@@ -288,12 +445,13 @@ public class FindAndReplace extends JFrame
return true;
}
if(values.size() != newValues.size())
newQualifiers.setQualifier(
new Qualifier(this_qualifier.getName(),newValues));
}
}
if(!delete)
if(!delete || newQualifiers.size() == 0)
return false;
for(int i = 0; i < newQualifiers.size(); i++)
......@@ -311,8 +469,7 @@ public class FindAndReplace extends JFrame
e.printStackTrace();
}
}
return false;
return true;
}
}
\ No newline at end of file
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