diff --git a/uk/ac/sanger/artemis/components/FeatureEdit.java b/uk/ac/sanger/artemis/components/FeatureEdit.java
index 9fb8152762790418ca66a6651fe0d3d2d877f85f..613999b3bb6fccde456432f911bcb18239b549e0 100644
--- a/uk/ac/sanger/artemis/components/FeatureEdit.java
+++ b/uk/ac/sanger/artemis/components/FeatureEdit.java
@@ -166,6 +166,8 @@ public class FeatureEdit extends JPanel
private GeneEditorPanel editorPanel;
+ private static UserDefinedQualifier userDefinedQualifierFrame;
+
/**
* Create a new FeatureEdit object from the given Feature.
* @param entry_group The EntryGroup that contains this Feature.
@@ -215,6 +217,8 @@ public class FeatureEdit extends JPanel
{
stopListening();
frame.dispose();
+ if(userDefinedQualifierFrame != null)
+ userDefinedQualifierFrame.setVisible(false);
}
});
}
@@ -510,6 +514,7 @@ public class FeatureEdit extends JPanel
location_panel.add(location_text, "Center");
final JButton complement_button = new JButton("Complement");
+ complement_button.setToolTipText("Complement position");
location_button_panel.add(complement_button);
complement_button.addActionListener(new ActionListener ()
{
@@ -533,6 +538,7 @@ public class FeatureEdit extends JPanel
}
final JButton grab_button = new JButton("Grab Range");
+ grab_button.setToolTipText("Add selected base range from feature coordinates");
location_button_panel.add(grab_button);
grab_button.addActionListener(new ActionListener()
{
@@ -543,6 +549,7 @@ public class FeatureEdit extends JPanel
});
final JButton remove_button = new JButton("Remove Range");
+ remove_button.setToolTipText("Remove selected base range from feature coordinates");
location_button_panel.add(remove_button);
remove_button.addActionListener(new ActionListener()
{
@@ -553,16 +560,18 @@ public class FeatureEdit extends JPanel
});
final JButton goto_button = new JButton("Goto Feature");
+ goto_button.setToolTipText("Goto and select this feature");
location_button_panel.add(goto_button);
goto_button.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
goto_event_source.gotoBase(getFeature().getFirstBaseMarker());
+ getSelection().set(getFeature());
}
});
- final JButton select_button = new JButton("Select Feature");
+/* final JButton select_button = new JButton("Select Feature");
location_button_panel.add(select_button);
select_button.addActionListener(new ActionListener()
{
@@ -570,7 +579,7 @@ public class FeatureEdit extends JPanel
{
getSelection().set(getFeature());
}
- });
+ });*/
if(Options.getOptions().getPropertyTruthValue("sanger_options"))
{
@@ -588,10 +597,9 @@ public class FeatureEdit extends JPanel
}
catch(QualifierParseException exception)
{
- final String error_string = exception.getMessage();
new MessageDialog(frame,
- "Cannot tidy - qualifier error: " +
- error_string);
+ "Cannot tidy - qualifier error: " +
+ exception.getMessage());
}
}
});
@@ -771,6 +779,33 @@ public class FeatureEdit extends JPanel
});
}
+ final JButton userQualifiers = new JButton("User Qualifiers");
+ userQualifiers.setToolTipText("User defined qualifier selection");
+ location_button_panel.add(userQualifiers);
+ userQualifiers.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ if(userDefinedQualifierFrame == null)
+ {
+ userDefinedQualifierFrame = new UserDefinedQualifier();
+ userDefinedQualifierFrame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);
+ }
+
+ userDefinedQualifierFrame.pack();
+ final JFrame topFrame =
+ (JFrame) SwingUtilities.getWindowAncestor(FeatureEdit.this);
+ Point p = topFrame.getLocationOnScreen();
+ p.x -= userDefinedQualifierFrame.getWidth();
+ if(p.x < 10)
+ p.x = 10;
+ userDefinedQualifierFrame.setLocation(p);
+
+ userDefinedQualifierFrame.setQualifierTextArea(qualifier_text_area);
+ userDefinedQualifierFrame.setVisible(true);
+ }
+ });
+
middle_panel.add(location_panel, "North");
add(key_and_qualifier_panel, "North");
@@ -781,6 +816,8 @@ public class FeatureEdit extends JPanel
if(edit_feature.getEntry() != null)
stopListening();
frame.dispose();
+ if(userDefinedQualifierFrame != null)
+ userDefinedQualifierFrame.setVisible(false);
}
});
@@ -798,6 +835,8 @@ public class FeatureEdit extends JPanel
propertiesPanel.updateSettings();
frame.dispose();
+ if(userDefinedQualifierFrame != null)
+ userDefinedQualifierFrame.setVisible(false);
}
}
});
@@ -1125,43 +1164,30 @@ public class FeatureEdit extends JPanel
private void tidy() throws QualifierParseException
{
final StringBuffer buffer = new StringBuffer();
-
final QualifierVector qualifiers =
qualifier_text_area.getParsedQualifiers(getEntryInformation());
-
- for(int qualifier_index = 0; qualifier_index < qualifiers.size();
- ++qualifier_index)
+
+ for(Qualifier this_qualifier: qualifiers)
{
- final Qualifier this_qualifier = (Qualifier)qualifiers.elementAt(qualifier_index);
-
final QualifierInfo qualifier_info =
getEntryInformation().getQualifierInfo(this_qualifier.getName());
-
final StringVector qualifier_strings =
StreamQualifier.toStringVector(qualifier_info, this_qualifier);
- for(int value_index = 0; value_index < qualifier_strings.size();
- ++value_index)
- {
- final String qualifier_string =
- (String)qualifier_strings.elementAt(value_index);
-
+ for(String qualifier_string: qualifier_strings)
buffer.append(tidyHelper(qualifier_string) + "\n");
- }
}
-
qualifier_text_area.setText(buffer.toString());
}
private void tidyGO() throws QualifierParseException
{
String qualifier_txt = qualifier_text_area.getText();
- StringReader strRead = new StringReader(qualifier_txt);
- BufferedReader buff = new BufferedReader(strRead);
- String line;
+ BufferedReader buff = new BufferedReader(new StringReader(qualifier_txt));
final Vector<String> qual_str = new Vector<String>();
try
{
+ String line;
while((line = buff.readLine()) != null)
qual_str.add(line);
}
@@ -1180,12 +1206,8 @@ public class FeatureEdit extends JPanel
Collections.sort(qual_str, comparator);
StringBuffer buffer = new StringBuffer();
- for(int i = 0; i < qual_str.size(); i++)
- {
- final String qualifier_string =
- qual_str.elementAt(i);
+ for(String qualifier_string: qual_str)
buffer.append(tidyHelper(qualifier_string) + "\n");
- }
qualifier_text_area.setText(buffer.toString());
}
@@ -1597,11 +1619,8 @@ public class FeatureEdit extends JPanel
final StringBuffer buffer = new StringBuffer();
final QualifierVector qualifiers = getFeature().getQualifiers();
- for(int qualifier_index = 0; qualifier_index < qualifiers.size();
- ++qualifier_index)
+ for(Qualifier this_qualifier: qualifiers)
{
- final Qualifier this_qualifier = (Qualifier)qualifiers.elementAt(qualifier_index);
-
//
// strip out CV qualifiers
//
@@ -1621,12 +1640,8 @@ public class FeatureEdit extends JPanel
final StringVector qualifier_strings =
StreamQualifier.toStringVector(qualifier_info, this_qualifier);
- for(int value_index = 0; value_index < qualifier_strings.size();
- ++value_index)
- {
- final String qualifier_string = (String)qualifier_strings.elementAt(value_index);
- buffer.append(qualifier_string + "\n");
- }
+ for(String qualStr: qualifier_strings)
+ buffer.append(qualStr + "\n");
}
return buffer.toString();