From 9e772c738212d2c8a5cea13d40bfd8d53c15a58d Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Fri, 24 Dec 2004 09:04:20 +0000
Subject: [PATCH] tidy
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2159 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/sequence/Bases.java | 22 +++++++++++-----------
1 file changed, 11 insertions(+), 11 deletions(-)
diff --git a/uk/ac/sanger/artemis/sequence/Bases.java b/uk/ac/sanger/artemis/sequence/Bases.java
index c888e3d5e..80ce229a8 100644
--- a/uk/ac/sanger/artemis/sequence/Bases.java
+++ b/uk/ac/sanger/artemis/sequence/Bases.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/sequence/Bases.java,v 1.8 2004-12-23 17:01:15 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/sequence/Bases.java,v 1.9 2004-12-24 09:04:20 tjc Exp $
*/
package uk.ac.sanger.artemis.sequence;
@@ -45,7 +45,7 @@ import java.util.Iterator;
* non-base letter returns '@'.
*
* @author Kim Rutherford
- * @version $Id: Bases.java,v 1.8 2004-12-23 17:01:15 tjc Exp $ */
+ * @version $Id: Bases.java,v 1.9 2004-12-24 09:04:20 tjc Exp $ */
public class Bases
{
@@ -517,12 +517,12 @@ public class Bases
int range_start_index = real_range.getStart();
int range_end_index = real_range.getEnd();
- final int sequence_string_length = getLength();
+ final int sequence_length = getLength();
if(range_start_index < 1)
range_start_index = 1;
- if(range_end_index > sequence_string_length)
- range_end_index = sequence_string_length;
+ if(range_end_index > sequence_length)
+ range_end_index = sequence_length;
final char sequence_string[] =
getSequence().getCharSubSequence(range_start_index, range_end_index);
@@ -530,14 +530,13 @@ public class Bases
range_start_index--;
range_end_index--;
- final byte[] forward_stop_codon_flags = getForwardStopCodonCache();
- final byte[] reverse_stop_codon_flags = getReverseStopCodonCache();
if(direction == FORWARD)
{
+ final byte[] forward_stop_codon_flags = getForwardStopCodonCache();
for(int i = range_start_index; i < range_end_index - 2; i += 3)
{
- if(i < 0 || i >= sequence_string_length - 2)
+ if(i < 0 || i >= sequence_length - 2)
continue;
final boolean is_stop_codon;
@@ -591,9 +590,10 @@ public class Bases
}
else
{
+ final byte[] reverse_stop_codon_flags = getReverseStopCodonCache();
for (int i = range_end_index ; i > range_start_index + 2 ; i -= 3)
{
- if(i < 2 || i >= sequence_string_length)
+ if(i < 2 || i >= sequence_length)
continue;
final boolean is_stop_codon;
@@ -636,10 +636,10 @@ public class Bases
// return the complemented base position
if(is_stop_codon)
return_positions[current_return_array_index] =
- sequence_string_length - i;
+ sequence_length - i;
else
return_positions[current_return_array_index] =
- - (sequence_string_length - i);
+ - (sequence_length - i);
++current_return_array_index;
}
--
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