From 4a70475cd2b4aa8bd7014cbe9ae3f0a358350722 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 27 Feb 2007 10:24:32 +0000
Subject: [PATCH] fix for empty columns
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@5523 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/BlastM8ComparisonData.java | 12 +++++++++---
1 file changed, 9 insertions(+), 3 deletions(-)
diff --git a/uk/ac/sanger/artemis/BlastM8ComparisonData.java b/uk/ac/sanger/artemis/BlastM8ComparisonData.java
index fc873758f..9de9e3bc9 100644
--- a/uk/ac/sanger/artemis/BlastM8ComparisonData.java
+++ b/uk/ac/sanger/artemis/BlastM8ComparisonData.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/BlastM8ComparisonData.java,v 1.1 2004-06-09 09:44:10 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/BlastM8ComparisonData.java,v 1.2 2007-02-27 10:24:32 tjc Exp $
*/
package uk.ac.sanger.artemis;
@@ -36,7 +36,7 @@ import java.util.Vector;
* output.
*
* @author Kim Rutherford <kmr@sanger.ac.uk>
- * @version $Id: BlastM8ComparisonData.java,v 1.1 2004-06-09 09:44:10 tjc Exp $
+ * @version $Id: BlastM8ComparisonData.java,v 1.2 2007-02-27 10:24:32 tjc Exp $
**/
public class BlastM8ComparisonData extends SimpleComparisonData {
@@ -67,13 +67,19 @@ public class BlastM8ComparisonData extends SimpleComparisonData {
/**
* Make an AlignMatch object from the given String.
**/
- private static AlignMatch makeMatchFromStringStatic (final String line)
+ private static AlignMatch makeMatchFromStringStatic (String line)
throws IOException {
if (line.trim ().length () == 0 ||
line.startsWith ("#")) {
return null;
}
+ // allow empty columns
+ int index;
+ while((index = line.indexOf("\t\t")) > -1)
+ line = line.substring(0, index) + "\t \t" +
+ line.substring(index+2);
+
final StringTokenizer tokenizer = new StringTokenizer (line, "\t");
if (tokenizer.countTokens () != 12) {
--
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