From 134ebef1c06bde42608e76ec1a849b2c0e04d26b Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 17 Feb 2009 13:34:45 +0000
Subject: [PATCH] change to make obsolete the default rather than permanently
deleting features
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9817 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/components/EditMenu.java | 85 ++++++++++++++-----
.../genebuilder/gff/PropertiesPanel.java | 11 ++-
2 files changed, 70 insertions(+), 26 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/EditMenu.java b/uk/ac/sanger/artemis/components/EditMenu.java
index 1b4ea7fa6..e8572af23 100644
--- a/uk/ac/sanger/artemis/components/EditMenu.java
+++ b/uk/ac/sanger/artemis/components/EditMenu.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/EditMenu.java,v 1.59 2008-12-09 11:50:25 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/EditMenu.java,v 1.60 2009-02-17 13:34:45 tjc Exp $
**/
package uk.ac.sanger.artemis.components;
@@ -31,6 +31,7 @@ import uk.ac.sanger.artemis.util.*;
import uk.ac.sanger.artemis.components.genebuilder.GeneBuilderFrame;
import uk.ac.sanger.artemis.components.genebuilder.GeneUtils;
import uk.ac.sanger.artemis.components.genebuilder.GeneViewerPanel;
+import uk.ac.sanger.artemis.components.genebuilder.gff.PropertiesPanel;
import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
import uk.ac.sanger.artemis.io.Range;
import uk.ac.sanger.artemis.io.RangeVector;
@@ -60,7 +61,7 @@ import java.util.Vector;
* A menu with editing commands.
*
* @author Kim Rutherford
- * @version $Id: EditMenu.java,v 1.59 2008-12-09 11:50:25 tjc Exp $
+ * @version $Id: EditMenu.java,v 1.60 2009-02-17 13:34:45 tjc Exp $
**/
public class EditMenu extends SelectionMenu
@@ -2147,34 +2148,67 @@ public class EditMenu extends SelectionMenu
**/
protected static void deleteSelectedFeatures (final JFrame frame,
final Selection selection,
- final EntryGroup entry_group) {
- try {
+ final EntryGroup entry_group)
+ {
+ try
+ {
entry_group.getActionController ().startAction ();
final FeatureVector features_to_delete = selection.getAllFeatures ();
-
final String feature_count_string;
-
- if (features_to_delete.size () == 1) {
+ if (features_to_delete.size () == 1)
feature_count_string = "the selected feature";
- } else {
+ else
feature_count_string = features_to_delete.size () + " features";
- }
- if (Options.getOptions ().isNoddyMode ()) {
- // 0 means always popup a YesNoDialog
- if (!checkForSelectionFeatures (frame, selection, 0,
+ if (Options.getOptions ().isNoddyMode ())
+ {
+ if(GeneUtils.isDatabaseEntry(entry_group))
+ {
+ Box boption = Box.createVerticalBox();
+ JCheckBox delete = new JCheckBox("permanently delete", false);
+ 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 + "?")) {
- return;
- }
+ feature_count_string + "?"))
+ {
+ return;
+ }
}
// clear the selection now so that it doesn't need to be updated as each
// feature is deleted
selection.clear ();
- while (features_to_delete.size () > 0) {
+ while (features_to_delete.size () > 0)
+ {
// delete in reverse order for speed
final Feature current_selection_feature =
@@ -2182,19 +2216,24 @@ public class EditMenu extends SelectionMenu
features_to_delete.removeElementAt (features_to_delete.size () - 1);
- try {
+ try
+ {
current_selection_feature.removeFromEntry ();
- } catch (ReadOnlyException e) {
+ }
+ catch (ReadOnlyException e)
+ {
selection.set (current_selection_feature);
- if (features_to_delete.size () == 1) {
+ 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 {
+ }
+ else
+ {
final String message =
"one of the selected features (" +
current_selection_feature.getIDString () +
@@ -2210,7 +2249,9 @@ public class EditMenu extends SelectionMenu
return;
}
}
- } finally {
+ }
+ finally
+ {
entry_group.getActionController ().endAction ();
}
}
diff --git a/uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java b/uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java
index 3673896cb..ef64d9045 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java
@@ -17,7 +17,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java,v 1.6 2008-11-07 12:19:13 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java,v 1.7 2009-02-17 13:34:45 tjc Exp $
*/
package uk.ac.sanger.artemis.components.genebuilder.gff;
@@ -530,8 +530,11 @@ public class PropertiesPanel extends JPanel
return;
obsoleteChanged = false;
-
- GFFStreamFeature gffFeature = (GFFStreamFeature)feature.getEmblFeature();
+ updateObsoleteSettings((GFFStreamFeature)feature.getEmblFeature());
+ }
+
+ public static void updateObsoleteSettings(GFFStreamFeature gffFeature)
+ {
Qualifier isObsoleteQualifier = gffFeature.getQualifierByName("isObsolete");
String isObsoleteNew = (String) isObsoleteQualifier.getValues().get(0);
if(isObsoleteNew.equals("true"))
@@ -547,7 +550,7 @@ public class PropertiesPanel extends JPanel
{
Qualifier idQualifier = gffFeature.getQualifierByName("ID");
- int select = JOptionPane.showConfirmDialog(PropertiesPanel.this,
+ int select = JOptionPane.showConfirmDialog(null,
"Make children of "+idQualifier.getValues().get(0)+"\n"+
(isObsoleteNew.equals("true") ? "obsolete?" : "not obsolete?"),
"Update Children",
--
GitLab