diff --git a/uk/ac/sanger/artemis/components/FindAndReplace.java b/uk/ac/sanger/artemis/components/FindAndReplace.java
index 5f25f2408580ea38917c72d55dd40054836e8c6e..a85e127e97c9ec4fae3262794be987b7f414c5de 100644
--- a/uk/ac/sanger/artemis/components/FindAndReplace.java
+++ b/uk/ac/sanger/artemis/components/FindAndReplace.java
@@ -23,6 +23,7 @@
package uk.ac.sanger.artemis.components;
import java.awt.BorderLayout;
+import java.awt.Cursor;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.event.ActionEvent;
@@ -54,6 +55,7 @@ import uk.ac.sanger.artemis.GotoEventSource;
import uk.ac.sanger.artemis.Selection;
import uk.ac.sanger.artemis.io.EntryInformation;
import uk.ac.sanger.artemis.io.EntryInformationException;
+import uk.ac.sanger.artemis.io.GFFDocumentEntry;
import uk.ac.sanger.artemis.io.Key;
import uk.ac.sanger.artemis.io.Qualifier;
import uk.ac.sanger.artemis.io.QualifierVector;
@@ -155,37 +157,56 @@ public class FindAndReplace extends JFrame
Entry default_entry = entry_group.getDefaultEntry();
if(default_entry == null)
default_entry = entry_group.elementAt(0);
-
+
+ boolean isGFF = false;
+ if(default_entry.getEMBLEntry() instanceof GFFDocumentEntry)
+ isGFF = true;
+
final EntryInformation default_entry_information =
default_entry.getEntryInformation();
final KeyChoice key_selector = new KeyChoice(default_entry_information);
key_selector.setEnabled(false);
-
- //final StringVector qualifierNames =
- // Feature.getAllQualifierNames (selected_features);
-
+ final QualifierChoice qualifier_selector = new QualifierChoice(
+ default_entry_information, null, null, isGFF);
+ qualifier_selector.setEnabled(false);
+
+ // column 1
int ypos = 0;
-
final JTextField findTextField = new JTextField(15);
c.gridx = 0;
- c.gridy = ++ypos;
+ c.gridy = ypos;
+ c.anchor = GridBagConstraints.EAST;
+ c.fill = GridBagConstraints.NONE;
panel.add(new JLabel("Find:"),c);
- c.gridx = 1;
- panel.add(findTextField, c);
-
final JTextField replaceTextField = new JTextField(15);
- c.gridx = 0;
c.gridy = ++ypos;
panel.add(new JLabel("Replace with:"), c);
+ c.gridy = ++ypos;
+ panel.add(key_selector,c);
+ c.gridy = ++ypos;
+ panel.add(qualifier_selector,c);
+ final JCheckBox caseSensitive = new JCheckBox("Case sensitive", true);
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.gridy = ++ypos;
+ panel.add(caseSensitive, c);
+
+ final JCheckBox qualifierValueSubString = new JCheckBox("Match substring", true);
+ c.gridy = ++ypos;
+ panel.add(qualifierValueSubString, c);
+
+
+ // column 2
+ ypos = 0;
+ c.anchor = GridBagConstraints.WEST;
c.gridx = 1;
- panel.add(replaceTextField, c);
+ c.gridy = ypos;
+ panel.add(findTextField, c);
- c.gridx = 0;
c.gridy = ++ypos;
- panel.add(key_selector,c);
+ panel.add(replaceTextField, c);
- final JCheckBox selectedKeyButton = new JCheckBox("Restrict to Selected Key", false);
+ final JCheckBox selectedKeyButton = new JCheckBox("Restrict to a Key", false);
selectedKeyButton.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -196,19 +217,24 @@ public class FindAndReplace extends JFrame
key_selector.setEnabled(false);
}
});
- c.gridx = 1;
+ c.gridy = ++ypos;
panel.add(selectedKeyButton,c);
-
-
- final JCheckBox caseSensitive = new JCheckBox("Case sensitive", true);
- c.gridx = 0;
+ final JCheckBox selectedQualifierButton = new JCheckBox("Restrict to a Qualifier", false);
+ selectedQualifierButton.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ if(selectedQualifierButton.isSelected())
+ qualifier_selector.setEnabled(true);
+ else
+ qualifier_selector.setEnabled(false);
+ }
+ });
c.gridy = ++ypos;
- panel.add(caseSensitive, c);
+ panel.add(selectedQualifierButton,c);
+
- final JCheckBox qualifierValueSubString = new JCheckBox("Match substring", true);
- c.gridy = ++ypos;
- panel.add(qualifierValueSubString, c);
final JButton findButton = new JButton("Find");
findButton.addActionListener(new ActionListener()
@@ -218,13 +244,17 @@ public class FindAndReplace extends JFrame
if(findTextField.getText().equals(""))
JOptionPane.showMessageDialog(FindAndReplace.this,
"No text entered!", "No Text", JOptionPane.WARNING_MESSAGE);
-
+ setCursor(new Cursor(Cursor.WAIT_CURSOR));
Key key = null;
if(selectedKeyButton.isSelected())
key = key_selector.getSelectedItem();
+ String qualifierName = null;
+ if(selectedQualifierButton.isSelected())
+ qualifierName = (String) qualifier_selector.getSelectedItem();
+
FeatureKeyQualifierPredicate predicate =
- new FeatureKeyQualifierPredicate(key, null,
+ new FeatureKeyQualifierPredicate(key, qualifierName,
findTextField.getText(),
qualifierValueSubString.isSelected(),
!caseSensitive.isSelected());
@@ -237,10 +267,12 @@ public class FindAndReplace extends JFrame
selection,
goto_event_source, filtered_entry_group,
base_plot_group);
+ setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
feature_list_frame.setVisible(true);
}
});
+ ypos+=3;
c.gridx = 0;
c.gridy = ++ypos;
panel.add(findButton, c);
@@ -250,12 +282,22 @@ public class FindAndReplace extends JFrame
{
public void actionPerformed(ActionEvent e)
{
+ setCursor(new Cursor(Cursor.WAIT_CURSOR));
Key key = null;
if(selectedKeyButton.isSelected())
key = key_selector.getSelectedItem();
+ String qualifierName = null;
+ StringVector qualifierStrings = null;
+ if(selectedQualifierButton.isSelected())
+ {
+ qualifierName = (String) qualifier_selector.getSelectedItem();
+ qualifierStrings = new StringVector();
+ qualifierStrings.add(qualifierName);
+ }
+
FeatureKeyQualifierPredicate predicate =
- new FeatureKeyQualifierPredicate(key, null,
+ new FeatureKeyQualifierPredicate(key, qualifierName,
findTextField.getText(),
qualifierValueSubString.isSelected(),
!caseSensitive.isSelected());
@@ -266,16 +308,17 @@ public class FindAndReplace extends JFrame
entry_group.getActionController().startAction();
FeatureVector features = filtered_entry_group.getAllFeatures();
+
for(int i=0; i<features.size(); i++)
{
final Feature feature = features.elementAt(i);
feature.findOrReplaceText(findTextField.getText(),
!caseSensitive.isSelected(), qualifierValueSubString.isSelected(),
- null, replaceTextField.getText());
+ qualifierStrings, replaceTextField.getText());
}
entry_group.getActionController().endAction();
-
+ setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
/* final FeatureListFrame feature_list_frame =
new FeatureListFrame("Features Found and Text Replaced",
selection,