From 9c13c2b3b27d0b4ab103a454db5a271dae61d0e3 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 25 Oct 2005 10:46:53 +0000
Subject: [PATCH] fix SQ line
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@3782 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/io/EmblStreamSequence.java | 10 +++++++---
1 file changed, 7 insertions(+), 3 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/EmblStreamSequence.java b/uk/ac/sanger/artemis/io/EmblStreamSequence.java
index 9337ec9ee..45f2f6095 100644
--- a/uk/ac/sanger/artemis/io/EmblStreamSequence.java
+++ b/uk/ac/sanger/artemis/io/EmblStreamSequence.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/EmblStreamSequence.java,v 1.4 2005-07-18 14:31:05 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/EmblStreamSequence.java,v 1.5 2005-10-25 10:46:53 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
@@ -34,7 +34,7 @@ import java.io.Writer;
* This is a subclass of StreamSequence containing EMBL sequence.
*
* @author Kim Rutherford
- * @version $Id: EmblStreamSequence.java,v 1.4 2005-07-18 14:31:05 tjc Exp $
+ * @version $Id: EmblStreamSequence.java,v 1.5 2005-10-25 10:46:53 tjc Exp $
**/
public class EmblStreamSequence extends StreamSequence
@@ -224,13 +224,16 @@ public class EmblStreamSequence extends StreamSequence
if(header_line != null)
writer.write(header_line);
- writer.write("SQ Sequence " +
+ if(header_line == null || !header_line.startsWith("SQ "))
+ writer.write("SQ Sequence " +
length() + " BP; " +
getACount() + " A; " +
getCCount() + " C; " +
getGCount() + " G; " +
getTCount() + " T; " +
getOtherCount() + " other;\n");
+ else
+ writer.write("\n");
int line_length_so_far = 0;
final int BLOCK_LENGTH = 10;
@@ -290,6 +293,7 @@ public class EmblStreamSequence extends StreamSequence
**/
private int getHeaderBaseCount(final String line)
{
+
if(line.startsWith("SQ Sequence "))
{
final String temp_line = line.substring(14);
--
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