From a8e485ec6c8ffd5c6fb44cc30d5420660bfb11f8 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 12 Mar 2008 20:57:24 +0000
Subject: [PATCH] fix for overlapping CDS in to create intergenic features
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@7225 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/components/AddMenu.java | 30 ++++++++++++++++++--
1 file changed, 27 insertions(+), 3 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/AddMenu.java b/uk/ac/sanger/artemis/components/AddMenu.java
index 6df327cd8..4e8da4c5c 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 1.35 2008-02-06 12:17:53 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/AddMenu.java,v 1.36 2008-03-12 20:57:24 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -73,7 +73,7 @@ import javax.swing.KeyStroke;
* should have been called CreateMenu.
*
* @author Kim Rutherford
- * @version $Id: AddMenu.java,v 1.35 2008-02-06 12:17:53 tjc Exp $
+ * @version $Id: AddMenu.java,v 1.36 2008-03-12 20:57:24 tjc Exp $
**/
public class AddMenu extends SelectionMenu
{
@@ -898,6 +898,18 @@ public class AddMenu extends SelectionMenu
if(i==0 && r.getStart()==1)
{
prevEnd = r.getEnd();
+
+ // check for overlapping CDS
+ if(i<cdsRanges.size()-1)
+ {
+ int next = i+1;
+ while(((Range)cdsRanges.get(next)).getStart() <= prevEnd)
+ {
+ prevEnd = ((Range)cdsRanges.get(next)).getEnd();
+ i = next;
+ next++;
+ }
+ }
continue;
}
@@ -917,7 +929,19 @@ public class AddMenu extends SelectionMenu
location, qualifiers);
prevEnd = r.getEnd();
- if(i==cdsRanges.size()-1)
+ // check for overlapping CDS
+ if(i<cdsRanges.size()-1)
+ {
+ int next = i+1;
+ while( next < cdsRanges.size() &&
+ ((Range)cdsRanges.get(next)).getStart() <= prevEnd)
+ {
+ prevEnd = ((Range)cdsRanges.get(next)).getEnd();
+ i = next;
+ next++;
+ }
+ }
+ else if(i==cdsRanges.size()-1)
{
if(entry_group.getSequenceLength() > r.getEnd())
{
--
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