diff --git a/uk/ac/sanger/artemis/components/AddMenu.java b/uk/ac/sanger/artemis/components/AddMenu.java
index dc190584987d726597e115e171024aec7507ce79..c053f637101ff57740b91cc0406c5566591fc554 100644
--- a/uk/ac/sanger/artemis/components/AddMenu.java
+++ b/uk/ac/sanger/artemis/components/AddMenu.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/AddMenu.java,v 1.5 2005-04-05 16:16:54 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/AddMenu.java,v 1.6 2005-04-06 16:07:03 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -54,7 +54,7 @@ import javax.swing.*;
* should have been called CreateMenu.
*
* @author Kim Rutherford
- * @version $Id: AddMenu.java,v 1.5 2005-04-05 16:16:54 tjc Exp $
+ * @version $Id: AddMenu.java,v 1.6 2005-04-06 16:07:03 tjc Exp $
**/
public class AddMenu extends SelectionMenu
{
@@ -153,75 +153,22 @@ public class AddMenu extends SelectionMenu
{
public void actionPerformed (ActionEvent event)
{
- Vector diffs;
- if(alignQueryViewer != null)
- diffs = alignQueryViewer.getDifferenceCoords(false);
- else
- diffs = alignSubjectViewer.getDifferenceCoords(true);
-
- Enumeration eDiffs = diffs.elements();
- while(eDiffs.hasMoreElements())
+ Vector diffs = null;
+ if(alignQueryViewer == null || alignSubjectViewer == null)
{
- Integer coords[] = (Integer[])eDiffs.nextElement();
- int start = coords[0].intValue();
- int end = coords[1].intValue();
-// System.out.println(start+" "+end);
+ if(alignQueryViewer != null)
+ diffs = alignQueryViewer.getDifferenceCoords(false);
+ else
+ diffs = alignSubjectViewer.getDifferenceCoords(true);
+ }
+ else // multi-comparison
+ {
+ Vector diffs1 = alignQueryViewer.getDifferenceCoords(false);
+ Vector diffs2 = alignSubjectViewer.getDifferenceCoords(true);
- final Entry default_entry = entry_group.getDefaultEntry();
- if(default_entry == null)
- {
- new MessageDialog(frame, "There is no default entry");
- return;
- }
-
- Location loc = null;
- Feature temp_feature;
- try
- {
- loc = new Location(start+".."+end);
- temp_feature = default_entry.createFeature(Key.CDS, loc);
- }
- catch(EntryInformationException e)
- {
- // use the default key instead
- final Key default_key =
- default_entry.getEntryInformation().getDefaultKey();
-
- try
- {
- temp_feature =
- default_entry.createFeature(default_key, loc);
- }
- catch(EntryInformationException einfo)
- {
- throw new Error("internal error - unexpected exception: " + einfo);
- }
- catch(ReadOnlyException eRead)
- {
- new MessageDialog(frame, "feature not created: " +
- "the default entry is read only");
- }
- catch(OutOfRangeException eout)
- {
- throw new Error("internal error - unexpected exception: " + eout);
- }
-
- }
- catch(ReadOnlyException e)
- {
- new MessageDialog(frame, "feature not created: " +
- "the default entry is read only");
- }
- catch(OutOfRangeException e)
- {
- throw new Error("internal error - unexpected exception: " + e);
- }
- catch(LocationParseException lpe)
- {
- throw new Error("internal error - unexpected exception: " + lpe);
- }
+ diffs = union(diffs1,diffs2);
}
-
+ createFeatures(diffs, frame);
}
});
@@ -325,6 +272,123 @@ public class AddMenu extends SelectionMenu
add (mark_ambiguities_item);
}
+ /**
+ *
+ * Find the union of coordinates in two Vecor objects.
+ * @param v1 Vector of Integer coordinates
+ * @param v2 Vector of Integer coordinates
+ *
+ */
+ private Vector union(Vector v1, Vector v2)
+ {
+ Vector union = new Vector();
+
+ for(int i=0; i<v1.size(); i++)
+ {
+ Integer[] imatch = (Integer[])v1.get(i);
+ int istart = imatch[0].intValue();
+ int iend = imatch[1].intValue();
+
+ for(int j=0; j<v2.size(); j++)
+ {
+ Integer[] jmatch = (Integer[])v2.get(j);
+ int jstart = jmatch[0].intValue();
+ int jend = jmatch[1].intValue();
+
+ if( (istart >= jstart && istart <= jend) ||
+ (iend >= jstart && iend <= jend) ||
+ (jstart > istart && jend < iend) )
+ {
+ if(jstart > istart)
+ istart = jstart;
+
+ if(iend < jend)
+ jend = iend;
+
+ Integer coords[] = new Integer[2];
+ coords[0] = new Integer(istart);
+ coords[1] = new Integer(jend);
+ union.add(coords);
+ }
+ }
+ }
+
+ return union;
+ }
+
+ /**
+ *
+ * Create features from Vector of coordinates.
+ * @param diffs Vector of coordinates to create feature from.
+ * @param frame The JFrame that owns this JMenu.
+ *
+ */
+ private void createFeatures(Vector diffs, JFrame frame)
+ {
+ Enumeration eDiffs = diffs.elements();
+ while(eDiffs.hasMoreElements())
+ {
+ Integer coords[] = (Integer[])eDiffs.nextElement();
+ int start = coords[0].intValue();
+ int end = coords[1].intValue();
+// System.out.println(start+" "+end);
+
+ final Entry default_entry = entry_group.getDefaultEntry();
+ if(default_entry == null)
+ {
+ new MessageDialog(frame, "There is no default entry");
+ return;
+ }
+
+ Location loc = null;
+ Feature temp_feature;
+ try
+ {
+ loc = new Location(start+".."+end);
+ temp_feature = default_entry.createFeature(Key.CDS, loc);
+ }
+ catch(EntryInformationException e)
+ {
+ // use the default key instead
+ final Key default_key =
+ default_entry.getEntryInformation().getDefaultKey();
+
+ try
+ {
+ temp_feature =
+ default_entry.createFeature(default_key, loc);
+ }
+ catch(EntryInformationException einfo)
+ {
+ throw new Error("internal error - unexpected exception: " + einfo);
+ }
+ catch(ReadOnlyException eRead)
+ {
+ new MessageDialog(frame, "feature not created: " +
+ "the default entry is read only");
+ }
+ catch(OutOfRangeException eout)
+ {
+ throw new Error("internal error - unexpected exception: " + eout);
+ }
+
+ }
+ catch(ReadOnlyException e)
+ {
+ new MessageDialog(frame, "feature not created: " +
+ "the default entry is read only");
+ }
+ catch(OutOfRangeException e)
+ {
+ throw new Error("internal error - unexpected exception: " + e);
+ }
+ catch(LocationParseException lpe)
+ {
+ throw new Error("internal error - unexpected exception: " + lpe);
+ }
+ }
+ }
+
/**
* Create a new AddMenu object.
* @param frame The JFrame that owns this JMenu.