From 4613a682beb08a88ad574069c7df36c5dbc3301a Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 15 Nov 2005 14:02:37 +0000
Subject: [PATCH] tidy & fix
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@3820 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/io/Location.java | 12 +++---------
uk/ac/sanger/artemis/io/LocationParseNode.java | 18 ++++--------------
2 files changed, 7 insertions(+), 23 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/Location.java b/uk/ac/sanger/artemis/io/Location.java
index f7b4df21e..a65e81781 100644
--- a/uk/ac/sanger/artemis/io/Location.java
+++ b/uk/ac/sanger/artemis/io/Location.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/io/Location.java,v 1.6 2005-11-15 12:21:18 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/Location.java,v 1.7 2005-11-15 14:02:37 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
@@ -34,7 +34,7 @@ import uk.ac.sanger.artemis.io.LocationLexer.TokenEnumeration;
* functions for parsing and manipulating the location.
*
* @author Kim Rutherford
- * @version $Id: Location.java,v 1.6 2005-11-15 12:21:18 tjc Exp $
+ * @version $Id: Location.java,v 1.7 2005-11-15 14:02:37 tjc Exp $
*
*/
public class Location
@@ -375,13 +375,7 @@ public class Location
**/
public Location reverseComplement(final int sequence_length)
{
- final Location new_location = new Location(getParsedLocation().copy());
-
- new_location.parse_tree =
- new_location.getParsedLocation().reverseComplement(sequence_length);
-
- new_location.parse_tree = new_location.parse_tree.getCanonical();
- return new_location;
+ return reverseComplement(sequence_length, 1);
}
/**
diff --git a/uk/ac/sanger/artemis/io/LocationParseNode.java b/uk/ac/sanger/artemis/io/LocationParseNode.java
index 15ed80472..b9748398c 100644
--- a/uk/ac/sanger/artemis/io/LocationParseNode.java
+++ b/uk/ac/sanger/artemis/io/LocationParseNode.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/io/LocationParseNode.java,v 1.6 2005-11-15 12:21:18 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/LocationParseNode.java,v 1.7 2005-11-15 14:02:37 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
@@ -33,7 +33,7 @@ import uk.ac.sanger.artemis.util.OutOfRangeException;
* Location. It is a utility class for EMBL.Location.
*
* @author Kim Rutherford
- * @version $Id: LocationParseNode.java,v 1.6 2005-11-15 12:21:18 tjc Exp $
+ * @version $Id: LocationParseNode.java,v 1.7 2005-11-15 14:02:37 tjc Exp $
*
**/
@@ -395,17 +395,6 @@ class LocationParseNode extends EMBLObject
}
}
- /**
- * Return a reversed and complemented copy of this Location.
- * @param sequence_length The length of the sequence that this Location is
- * associated with.
- * @return a reversed and complemented tree.
- **/
- LocationParseNode reverseComplement(final int sequence_length)
- {
- return reverseComplement(sequence_length, 0);
- }
-
/**
* Return a reversed and complemented copy of this Location.
* @param sequence_length The length of the sequence that this Location is
@@ -432,7 +421,8 @@ class LocationParseNode extends EMBLObject
// System.out.println("LocationParseNode.reverseComplement() HERE "+
// start+ ".."+ end +" sequence_length="+sequence_length+
// " range.getEnd()="+range.getEnd()+ " range.getStart()="+range.getStart()+
-// " offset="+offset);
+// " offset="+offset+ " "+
+// start_old+ ".."+end_old);
final Range new_range = new Range(start, end);
final LocationParseNode new_range_node =
--
GitLab