diff --git a/uk/ac/sanger/artemis/components/SelectMenu.java b/uk/ac/sanger/artemis/components/SelectMenu.java
index 8c4a36587bfac261b010e722e74b0e561bbf7468..4d801fa1f5029a0f9751b3ea55b28de0d39c4900 100644
--- a/uk/ac/sanger/artemis/components/SelectMenu.java
+++ b/uk/ac/sanger/artemis/components/SelectMenu.java
@@ -60,7 +60,6 @@ import javax.swing.KeyStroke;
* "Select by key".
*
* @author Kim Rutherford
- * @version $Id: SelectMenu.java,v 1.13 2008-05-21 14:14:04 tjc Exp $
**/
public class SelectMenu extends SelectionMenu
@@ -78,21 +77,6 @@ public class SelectMenu extends SelectionMenu
**/
private GotoEventSource goto_event_source;
- private JMenuItem selector_item = null;
- private JMenuItem all_item = null;
- private JMenuItem all_bases_item = null;
- private JMenuItem none_item = null;
- private JMenuItem selection_toggle_item = null;
- private JMenuItem select_same_type_item = null;
- private JMenuItem select_matching_qualifiers_item = null;
- private JMenuItem select_features_in_range_item = null;
- private JMenuItem select_base_range_item = null;
- private JMenuItem select_aa_range_in_feature_item = null;
- private JMenuItem select_orf_item = null;
- private JMenuItem select_by_key_item = null;
- private JMenuItem select_non_pseudo_cds_item = null;
- private JMenuItem select_all_cds_item = null;
-
/**
* The shortcut for Select All
**/
@@ -170,7 +154,7 @@ public class SelectMenu extends SelectionMenu
this.entry_group = entry_group;
this.goto_event_source = goto_event_source;
- selector_item = new JMenuItem("Feature Selector ...");
+ JMenuItem selector_item = new JMenuItem("Feature Selector ...");
selector_item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent event)
@@ -179,12 +163,11 @@ public class SelectMenu extends SelectionMenu
base_plot_group);
}
});
-
add(selector_item);
addSeparator();
- all_item = new JMenuItem("All");
+ JMenuItem all_item = new JMenuItem("All");
all_item.setAccelerator(SELECT_ALL_KEY);
all_item.addActionListener(new ActionListener()
{
@@ -195,10 +178,9 @@ public class SelectMenu extends SelectionMenu
frame.setCursor(cdone);
}
});
-
add(all_item);
- all_bases_item = new JMenuItem("All Bases");
+ JMenuItem all_bases_item = new JMenuItem("All Bases");
all_bases_item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent event)
@@ -208,7 +190,6 @@ public class SelectMenu extends SelectionMenu
frame.setCursor(cdone);
}
});
-
add(all_bases_item);
@@ -255,7 +236,7 @@ public class SelectMenu extends SelectionMenu
}
- none_item = new JMenuItem("None");
+ JMenuItem none_item = new JMenuItem("None");
none_item.setAccelerator(SELECT_NONE_KEY);
none_item.addActionListener(new ActionListener()
{
@@ -264,10 +245,9 @@ public class SelectMenu extends SelectionMenu
clearSelection();
}
});
-
add(none_item);
- select_by_key_item = new JMenuItem("By Key");
+ JMenuItem select_by_key_item = new JMenuItem("By Key");
select_by_key_item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent event)
@@ -278,7 +258,7 @@ public class SelectMenu extends SelectionMenu
add(select_by_key_item);
- select_non_pseudo_cds_item =
+ JMenuItem select_non_pseudo_cds_item =
new JMenuItem("CDS Features without /pseudogene");
select_non_pseudo_cds_item.addActionListener(new ActionListener()
{
@@ -295,12 +275,11 @@ public class SelectMenu extends SelectionMenu
selectFeaturesByPredicate(predicate);
}
});
-
add(select_non_pseudo_cds_item);
final boolean isDatabaseGroup = GeneUtils.isDatabaseEntry( getEntryGroup() );
-
+ final JMenuItem select_all_cds_item;
if(isDatabaseGroup)
{
select_non_pseudo_cds_item.setEnabled(false);
@@ -324,10 +303,9 @@ public class SelectMenu extends SelectionMenu
selectFeaturesByPredicate(predicate);
}
});
-
add(select_all_cds_item);
- select_same_type_item = new JMenuItem("Same Key");
+ JMenuItem select_same_type_item = new JMenuItem("Same Key");
select_same_type_item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent event)
@@ -335,10 +313,9 @@ public class SelectMenu extends SelectionMenu
selectSameKey();
}
});
-
add(select_same_type_item);
- select_matching_qualifiers_item =
+ JMenuItem select_matching_qualifiers_item =
new JMenuItem("Features Matching Qualifier");
select_matching_qualifiers_item.addActionListener(new ActionListener()
{
@@ -347,10 +324,9 @@ public class SelectMenu extends SelectionMenu
selectMatchingQualifiers();
}
});
-
add(select_matching_qualifiers_item);
- select_orf_item = new JMenuItem("Open Reading Frame");
+ JMenuItem select_orf_item = new JMenuItem("Open Reading Frame");
select_orf_item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent event)
@@ -358,10 +334,9 @@ public class SelectMenu extends SelectionMenu
selectOrf();
}
});
-
add(select_orf_item);
- select_features_in_range_item =
+ final JMenuItem select_features_in_range_item =
new JMenuItem("Features Overlapping Selection");
select_features_in_range_item.addActionListener(new ActionListener()
{
@@ -372,8 +347,21 @@ public class SelectMenu extends SelectionMenu
});
add(select_features_in_range_item);
+
+
+ final JMenuItem select_features_contained_item =
+ new JMenuItem("Features Within Selection");
+ select_features_contained_item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
+ selectContainedFeatures();
+ }
+ });
+
+ add(select_features_contained_item);
- select_base_range_item = new JMenuItem("Base Range ...");
+ JMenuItem select_base_range_item = new JMenuItem("Base Range ...");
select_base_range_item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent event)
@@ -381,10 +369,9 @@ public class SelectMenu extends SelectionMenu
selectBaseRange();
}
});
-
add(select_base_range_item);
- select_aa_range_in_feature_item = new JMenuItem("Feature AA Range ...");
+ JMenuItem select_aa_range_in_feature_item = new JMenuItem("Feature AA Range ...");
select_aa_range_in_feature_item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent event)
@@ -392,12 +379,11 @@ public class SelectMenu extends SelectionMenu
selectFeatureAARange();
}
});
-
add(select_aa_range_in_feature_item);
addSeparator();
- selection_toggle_item = new JMenuItem("Toggle Selection");
+ JMenuItem selection_toggle_item = new JMenuItem("Toggle Selection");
selection_toggle_item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent event)
@@ -405,7 +391,6 @@ public class SelectMenu extends SelectionMenu
toggleSelection();
}
});
-
add(selection_toggle_item);
}
@@ -823,11 +808,8 @@ public class SelectMenu extends SelectionMenu
}
final MarkerRange range = getSelection ().getMarkerRange ();
-
- final Strand strand = getEntryGroup ().getBases ().getForwardStrand ();
-
final MarkerRange start_orf_range =
- strand.getORFAroundMarker (range.getStart (), true);
+ Strand.getORFAroundMarker (range.getStart (), true);
/*final*/ Marker end_marker;
@@ -844,7 +826,7 @@ public class SelectMenu extends SelectionMenu
}
final MarkerRange end_orf_range =
- strand.getORFAroundMarker (end_marker, true);
+ Strand.getORFAroundMarker (end_marker, true);
MarkerRange new_range = range;
@@ -1018,6 +1000,38 @@ public class SelectMenu extends SelectionMenu
}
}
}
+
+
+ /**
+ * If there are some selected bases select the features that are
+ * fully contained within that selection.
+ **/
+ private void selectContainedFeatures () {
+ final MarkerRange selected_marker_range =
+ getSelection ().getMarkerRange ();
+
+ if (selected_marker_range == null) {
+ new MessageDialog (getParentFrame (), "sequence range is not selected");
+ return;
+ } else {
+ try {
+ final FeatureVector featuresInRange =
+ getEntryGroup ().getFeaturesInRange (selected_marker_range.getRawRange ());
+ final FeatureVector featuresContainedByRange = new FeatureVector();
+ for(int i=0; i<featuresInRange.size(); i++)
+ {
+ Feature f = featuresInRange.elementAt(i);
+ Range maxR = f.getMaxRawRange();
+ if(selected_marker_range.getRawStart().getRawPosition() <= maxR.getStart() &&
+ selected_marker_range.getRawEnd().getRawPosition() >= maxR.getEnd())
+ featuresContainedByRange.add(f);
+ }
+ getSelection ().set (featuresContainedByRange);
+ } catch (OutOfRangeException e) {
+ throw new Error ("internal error - unexpected exception: " + e);
+ }
+ }
+ }
/**
* This method sends an GotoEvent to all the GotoEvent listeners that will