From 353f11578cb404e8d826b5b8dbae7613d2f01a5c Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Wed, 20 Jun 2012 14:49:06 +0100
Subject: [PATCH] if deleting/obsoleting a CDS then delete/obsolete the entire
gene model
---
uk/ac/sanger/artemis/components/EditMenu.java | 169 ++++++++++--------
1 file changed, 92 insertions(+), 77 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/EditMenu.java b/uk/ac/sanger/artemis/components/EditMenu.java
index 637294bf3..32510c8f7 100644
--- a/uk/ac/sanger/artemis/components/EditMenu.java
+++ b/uk/ac/sanger/artemis/components/EditMenu.java
@@ -2241,100 +2241,78 @@ public class EditMenu extends SelectionMenu
entry_group.getActionController ().startAction ();
final FeatureVector features_to_delete = selection.getAllFeatures ();
- final String feature_count_string;
- if (features_to_delete.size () == 1)
- feature_count_string = "the selected feature";
- else
- feature_count_string = features_to_delete.size () + " features";
+ final String feature_count_str = ( (features_to_delete.size () == 1) ?
+ "the selected feature" : features_to_delete.size () + " features");
+
+ if (!checkForSelectionFeatures (frame, selection, 0,
+ "really delete " + feature_count_str + "?"))
+ return;
+
+ // clear the selection now so it doesn't need updating as each
+ // feature is deleted
+ selection.clear ();
if (Options.getOptions ().isNoddyMode ())
{
if(GeneUtils.isDatabaseEntry(entry_group))
{
- Box boption = Box.createVerticalBox();
- JCheckBox delete = new JCheckBox("permanently delete",
+ Box boption = Box.createVerticalBox();
+ final JCheckBox delete = new JCheckBox("permanently delete",
!Options.getOptions().getPropertyTruthValue("set_obsolete_on_delete"));
- boption.add(new JLabel("Make "+feature_count_string+" obsolete?"));
- boption.add(delete);
- int res = JOptionPane.showConfirmDialog(frame,
- boption, "Make obsolete", JOptionPane.OK_CANCEL_OPTION,
- JOptionPane.QUESTION_MESSAGE);
- if(res == JOptionPane.CANCEL_OPTION)
- return;
-
- // make obsolete rather than permanently delete
- if(!delete.isSelected())
- {
- for(int i=0; i<features_to_delete.size(); i++)
- {
- final Feature currentFeature = features_to_delete.elementAt(i);
- try
- {
- currentFeature.setQualifier(new Qualifier("isObsolete", "true"));
- PropertiesPanel.updateObsoleteSettings(
- (GFFStreamFeature)currentFeature.getEmblFeature());
- }
- catch (Exception e)
- {
- e.printStackTrace();
- }
- }
- return;
- }
- }
- if (!checkForSelectionFeatures (frame, selection, 0,
- "really delete " +
- feature_count_string + "?"))
- {
+ boption.add(new JLabel("Make "+feature_count_str+" obsolete?"));
+ boption.add(delete);
+ final int res = JOptionPane.showConfirmDialog(frame,
+ boption, "Make obsolete", JOptionPane.OK_CANCEL_OPTION,
+ JOptionPane.QUESTION_MESSAGE);
+ if(res == JOptionPane.CANCEL_OPTION)
return;
- }
- }
- // clear the selection now so that it doesn't need to be updated as each
- // feature is deleted
- selection.clear ();
+ for(int i=0; i<features_to_delete.size(); i++)
+ {
+ try
+ {
+ GFFStreamFeature gffFeat =
+ (GFFStreamFeature)features_to_delete.elementAt(i).getEmblFeature();
+
+ // if a CDS the delete / obsolete the entire gene model
+ if(gffFeat.getKey().equals(Key.CDS) &&
+ gffFeat.getChadoGene() != null &&
+ gffFeat.getChadoGene().getGene() != null)
+ gffFeat = (GFFStreamFeature) gffFeat.getChadoGene().getGene();
+ final Feature f = (Feature) gffFeat.getUserData();
+
+ if(!delete.isSelected())
+ {
+ // make obsolete rather than permanently delete
+ f.setQualifier(new Qualifier("isObsolete", "true"));
+ PropertiesPanel.updateObsoleteSettings(gffFeat);
+ }
+ else if(gffFeat.getChadoGene() != null)
+ GeneUtils.deleteAllFeature(f, gffFeat.getChadoGene());
+ else
+ {
+ if(!deleteFeature(frame, f, selection, features_to_delete))
+ return;
+ }
+ }
+ catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+ return;
+ }
+ }
while (features_to_delete.size () > 0)
{
// delete in reverse order for speed
-
final Feature current_selection_feature =
features_to_delete.lastElement ();
-
features_to_delete.removeElementAt (features_to_delete.size () - 1);
- try
- {
- current_selection_feature.removeFromEntry ();
- }
- catch (ReadOnlyException e)
- {
- selection.set (current_selection_feature);
-
- if (features_to_delete.size () == 1)
- {
- final String message =
- "the selected feature (" +
- current_selection_feature.getIDString () +
- ") is read only - cannot continue";
- new MessageDialog (frame, message);
- }
- else
- {
- final String message =
- "one of the selected features (" +
- current_selection_feature.getIDString () +
- ") is read only - cannot continue";
- new MessageDialog (frame, message);
- }
-
- features_to_delete.add (current_selection_feature);
-
- // reset the select so that the user can see what it was
- selection.set (features_to_delete);
-
+ if(!deleteFeature(frame, current_selection_feature, selection, features_to_delete))
return;
- }
}
}
finally
@@ -2342,6 +2320,43 @@ public class EditMenu extends SelectionMenu
entry_group.getActionController ().endAction ();
}
}
+
+ private static boolean deleteFeature(final JFrame frame,
+ final Feature current_selection_feature,
+ final Selection selection,
+ final FeatureVector features_to_delete)
+ {
+ try
+ {
+ current_selection_feature.removeFromEntry ();
+ }
+ catch (ReadOnlyException e)
+ {
+ selection.set (current_selection_feature);
+ if (features_to_delete.size () == 1)
+ {
+ final String message =
+ "the selected feature (" +
+ current_selection_feature.getIDString () +
+ ") is read only - cannot continue";
+ new MessageDialog (frame, message);
+ }
+ else
+ {
+ final String message =
+ "one of the selected features (" +
+ current_selection_feature.getIDString () +
+ ") is read only - cannot continue";
+ new MessageDialog (frame, message);
+ }
+
+ features_to_delete.add (current_selection_feature);
+ // reset the select so that the user can see what it was
+ selection.set (features_to_delete);
+ return false;
+ }
+ return true;
+ }
/**
* Delete the selected feature segments.
--
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